bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2025–11–23
sixty-six papers selected by
Catalina Vasilescu, Helmholz Munich
  1. Mitochondrial NAD+ gradient sustained by membrane potential and transport.
  2. The mitochondrial protein TMEM177 fine-tunes mammalian cytochrome c oxidase assembly.
  3. Hepatocyte mitochondrial NAD+ content is limiting for liver regeneration.
  4. Accelerate the discovery of genetic variants in mitochondrial diseases with Variant prIOritization using Latent spAce.
  5. Elucidating the Localization and Interactome of Mitochondrial Microproteins.
  6. Retrograde mitochondrial transport regulates mitochondrial biogenesis in zebrafish neurons.
  7. Mitochondrial transplantation restores mitochondrial content and function in SSBP1-related mitochondrial DNA depletion syndrome.
  8. Mitochondria regulate the cell fate decisions of megakaryocyte-erythroid progenitors.
  9. Hypocitrullinemia as an Early Diagnostic Biomarker for MT-ATP6 Mitochondrial Diseases.
  10. A unified mechanism for mitochondrial damage sensing in PINK1-Parkin-mediated mitophagy.
  11. Targeted deletions in human mitochondrial DNA engineered by Type V CRISPR-Cas12a system.
  12. Metformin inhibits mitochondrial complex I in intestinal epithelium to promote glycemic control.
  13. Cholesterol Transport from ER to Outer Mitochondria by ERLIN2 in Steroid Metabolism.
  14. Caloric restriction enhances inheritance of wild-type mitochondrial DNA in Saccharomyces cerevisiae.
  15. Mitophagy in skeletal muscle: Impact of ageing, exercise and disuse.
  16. Fontaine progeroid syndrome with neonatal mitochondrial disease.
  17. Structural basis for ATP-driven double-ring assembly of the human mitochondrial Hsp60 chaperonin.
  18. Mitochondrial variation in Taiwan Biobank reveals ancestry structure and trait associations.
  19. An inherited mitochondrial DNA mutation remodels inflammatory cytokine responses in macrophages and in vivo in mice.
  20. Glutathionylated DNA adducts accumulate in mitochondrial DNA and are regulated by AP endonuclease 1 and tyrosyl-DNA phosphodiesterase 1.
  21. A Scoping Review of POLG-Related Cerebellar Ataxia: Insights and Clinical Perspectives.
  22. Organ-specific rewiring of mitochondrial integrity through COX7A dictates cellular ploidy control.
  23. Mitochondrial Respiratory Supercomplex Assembly Factor COX7RP Contributes to Lifespan Extension in Mice.
  24. Enzymes of the outer mitochondrial membrane regulating cholesterol and fatty acid metabolism in cancer.
  25. CRISPR/Cas9-mediated editing of MIC13 in human induced pluripotent stem cells: A model for mitochondrial hepato-encephalopathy.
  26. Substrate and enzyme determinants for recognition by human mitochondrial RNase P.
  27. Mitochondrial transfer from human embryonic stem cell-derived mature cardiomyocytes to mesenchymal stem cells.
  28. Ecm19 coordinates mitochondrial fission and cellular redox homeostasis.
  29. Anatomical Associations Between Focal Mitochondrial Metabolism and Patterns of Neurodegeneration in Amyotrophic Lateral Sclerosis.
  30. Structures of human organellar SPFH protein complexes.
  31. Genome region aware CADD thresholds for noncoding variant prioritization.
  32. PPA1 Facilitates Thermogenesis in Brown and Beige Fat by Regulating the Mitochondrial Localization of FUS.
  33. Association of cytochrome c oxidase dysfunction with amyloidosis in Alzheimer's disease and patient-derived cerebral organoids.
  34. Mitochondrial dysfunction acts as a modulator of the immunometabolic route for activating the cytosolic DNA sensor pathway in triggering innate immunosurveillance.
  35. Expanding research and care for Leigh syndrome: efforts of a patient-led advocacy organization.
  36. Mitochondrial cristae remodeling: Mechanisms, functions, and pathology.
  37. Nicotinamide adenine dinucleotide fluorescence monitoring as a potential tool for the microvascular and mitochondrial function assessment in heart failure.
  38. Nanomedicines Against Mitochondrial Dysfunction-Induced Metabolic Diseases.
  39. Improving newborn screening accuracy through genome sequencing, targeted metabolomics, and machine learning.
  40. IT TAKES TWO TO TANGO: potential novel therapies for autosomal dominant optic atrophy.
  41. Computational design of a high-precision mitochondrial DNA cytosine base editor.
  42. SLC45A4 encodes a peroxisomal putrescine transporter that promotes GABA de novo synthesis.
  43. Polarized ATP synthase in synaptic mitochondria induced by learning and plasticity signals.
  44. Measuring mitochondrial membrane potential.
  45. Structural changes shifting the redox potential of the outlying cluster N1a in respiratory complex I.
  46. NMPhenogen: a comprehensive database for genotype-phenotype correlation in neuromuscular genetic disorders.
  47. Loss of adenylosuccinate synthetase 1 in mice recapitulates features of ADSS1 myopathy.
  48. Rac1 promotes proximal tubule kidney repair by coupling the actin cytoskeleton to mitochondrial function.
  49. Pathogenic KIF5C mutation disrupts dendritic spine maturation and mitochondrial trafficking in neurodevelopmental disorders.
  50. Scalable and accurate rare variant meta-analysis with Meta-SAIGE.
  51. Succinate puts the brakes on de novo purine synthesis.
  52. Mitochondria in the immune system: Therapeutic potential from mitochondria transfer.
  53. How one nutrient controls cell size.
  54. The dynamic lateral gate of the mitochondrial β-barrel biogenesis machinery is blocked by darobactin A.
  55. Homeostatic control of energy metabolism by monocyte-derived macrophages.
  56. Combinatorial protein engineering identifies potent CRISPR activators with reduced toxicity.
  57. Loss of adenylosuccinate synthetase 1 in mice recapitulates features of ADSS1 myopathy.
  58. Characterizing and controlling CRISPR repair outcomes in nondividing human cells.
  59. Endothelial CYB5R1 is a Coenzyme Q reductase that suppresses ferroptosis and atherosclerosis.
  60. Monitoring Mitochondrial Oxygen Tension: mitoPO2 as Physiologic Transfusion Trigger?
  61. OmniPath: integrated knowledgebase for multi-omics analysis.
  62. Study Designs and Crafting Endpoints for Gene Therapy Development Programs in Rare Disease: A Narrative Review.
  63. ZAK activation at the collided ribosome.
  64. Drp1 in Parkinson's disease: Mechanisms of disease pathology and the promise of targeted therapeutic strategies.
  65. BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants.
  66. Polarity-responsive probe for dual-channel visualization of mitochondrial membrane potential via subcellular immigration.
  1. Sci Adv. 2025 Nov 21. 11(47): eaea7460
    Mitochondrial NAD+ gradient sustained by membrane potential and transport.
    Shivansh Goyal, Scott N Lyons, Xiaolu A Cambronne.
      SLC25A51 is required for the replenishment of free nicotinamide adenine dinucleotide (oxidized form) (NAD+) into mammalian mitochondria. However, it is not known how SLC25A51 imports this anionic molecule to sustain elevated NAD+ concentrations in the matrix. Understanding this would reveal regulatory mechanisms used to maintain critical bioenergetic gradients for cellular respiration, oxidative mitochondrial reactions, and mitochondrial adenosine triphosphate (ATP) production. In this work, mutational analyses and localized NAD+ biosensors revealed that the mitochondrial membrane potential (ΔΨm) works in concert with charged residues in the carrier's inner pore to enable sustained import of NAD+ against its electrochemical gradient into the matrix. Dissipation of the ΔΨm or mutation of select residues in SLC25A51 led to equilibration of NAD+ from the matrix. Corroborating data were obtained with the structurally distinct mitochondrial NAD+ carrier from Saccharomyces cerevisiae (ScNdt1p) and mitochondrial ATP transport suggesting a shared mechanism of charge compensation and electrogenic transport in these mitochondrial carrier family members.
    DOI:  https://doi.org/10.1126/sciadv.aea7460
  2. Mitochondrion. 2025 Nov 16. pii: S1567-7249(25)00096-0. [Epub ahead of print] 102099
    The mitochondrial protein TMEM177 fine-tunes mammalian cytochrome c oxidase assembly.
    Jakob D Busch, Thomas Schöndorf, Dusanka Milenkovic, Xinping Li, Rolf Wibom, Joana F Silva-Rodrigues, Roberta Filograna, Camilla Koolmeister, Nils-Göran Larsson, Diana Rubalcava-Gracia.
      The mitochondrial cytochrome c oxidase (COX, complex IV), a multi-subunit protein complex, plays a crucial role in cellular respiration by reducing oxygen to water and simultaneously pumping protons to enable oxidative phosphorylation (OXPHOS). Thus, defects in its assembly can directly affect cellular energy homeostasis. COX20 is an essential chaperone for the core subunit COX2. In human cultured cells, TMEM177 was found to stabilize COX20 and maintain balanced COX2 levels. In mice, TMEM177 was also identified as an interactor of mitochondrial ribosomes. To understand the function of TMEM177 in vivo, we generated Tmem177 knockout mice. Here, we analyze how TMEM177 loss affects mitochondrial gene expression, as well as the activity and assembly of OXPHOS complexes. We found that a small proportion of the knockout mice died perinatally, while surviving knockout mice tended to gain less weight. TMEM177 depletion moderately reduced COX20 levels, but OXPHOS complexes were preserved. Moreover, Tmem177 and Surf1 double knockout mice were born asymptomatic. In conclusion, TMEM177 fine-tunes complex IV assembly by stabilizing COX20 in vivo. Our findings refine the current model of complex IV assembly in mammals.
    Keywords:  Cytochrome c oxidase; Mitochondria; Mitoribosomes; OXPHOS; mtDNA
    DOI:  https://doi.org/10.1016/j.mito.2025.102099
  3. Nat Metab. 2025 Nov 20.
    Hepatocyte mitochondrial NAD+ content is limiting for liver regeneration.
    Sarmistha Mukherjee, Ricardo A Velázquez Aponte, Caroline E Perry, Won Dong Lee, Kevin A Janssen, Marc Niere, Gabriel K Adzika, Mu-Jie Lu, Hsin-Ru Chan, Xiangyu Zou, Beishan Chen, Nicole Bye, Teresa Xiao, Jin-Seon Yook, Oniel Salik, David W Frederick, Ryan B Gaspar, Khanh V Doan, James G Davis, Joshua D Rabinowitz, Douglas C Wallace, Nathaniel W Snyder, Shingo Kajimura, Xiaolu A Cambronne, Mathias Ziegler, Joseph A Baur.
      Nicotinamide adenine dinucleotide (NAD+) precursor supplementation shows metabolic and functional benefits in rodent models of disease and is being explored as potential therapeutic strategy in humans. However, the wide range of processes that involve NAD+ in every cell and subcellular compartment make it difficult to narrow down the mechanisms of action. Here we show that the rate of liver regeneration is closely associated with the concentration of NAD+ in hepatocyte mitochondria. We find that the mitochondrial NAD+ concentration in hepatocytes of male mice is determined by the expression of the transporter SLC25A51 (MCART1). The heterozygous loss of SLC25A51 modestly decreases mitochondrial NAD+ content in multiple tissues and impairs liver regeneration, whereas the hepatocyte-specific overexpression of SLC25A51 is sufficient to enhance liver regeneration comparably to the effect of systemic NAD+ precursor supplements. This benefit is observed even though NAD+ levels are increased only in mitochondria. Thus, the hepatocyte mitochondrial NAD+ pool is a key determinant of the rate of liver regeneration.
    DOI:  https://doi.org/10.1038/s42255-025-01408-5
  4. Brief Bioinform. 2025 Nov 01. pii: bbaf612. [Epub ahead of print]26(6):
    Accelerate the discovery of genetic variants in mitochondrial diseases with Variant prIOritization using Latent spAce.
    Justine Labory, Youssef Boulaimen, Jasmine Singh, Samira Ait-El-Mkadem Saadi, Véronique Paquis-Flucklinger, Sylvie Bannwarth, Silvia Bottini.
      Interpreting variants from whole-exome sequencing remains a major challenge, particularly for heterogeneous disorders such as mitochondrial diseases (MDs). To address this, we have developed Variant prIoritizatiOn using Latent spAce (VIOLA), a pipeline designed to help find a diagnosis for complex cases. VIOLA uses a variational autoencoder to embed functional annotations into a low-dimensional space, followed by DBSCAN-based outlier detection to identify potential pathogenic variants. Filtering steps and phenotype integration via HPO terms are then applied. The VIOLA score (Vscore) combines variant outlierness, transcriptomic co-expression data, and MD-specific annotations. Two rankings are derived: the VIOLA rank (all variants) and the ARrank (variants compatible with autosomal recessive inheritance). The VIOLA Aggregated score (VAscore) merges Vscore with Exomiser's pathogenicity score. Applied to 20 patients (four diagnosed), VIOLA reduced the variant list by >99% and ranked causal variants within the top 5 using ARrank, outperforming existing methods. Overall, VIOLA is a patient-specific strategy for variant prioritization, helping to resolve challenging MD cases and uncover novel disease mechanisms.
    Keywords:  exome sequencing; machine learning; mitochondrial diseases; multi-omics; variant prioritization
    DOI:  https://doi.org/10.1093/bib/bbaf612
  5. Methods Mol Biol. 2026 ;2992 213-228
    Elucidating the Localization and Interactome of Mitochondrial Microproteins.
    Jiemin Nah, Pooja Sridharan, Lena Ho.
      A large number of novel microproteins discovered to date are nuclear encoded, mitochondrial proteins, pointing to their widespread roles in metabolic regulation. In this chapter, we provide a workflow of how to verify if a candidate microprotein is localized to the mitochondria, its submitochondrial localization (i.e., outer, inner membrane, or matrix) and how to determine its interactome in order to elucidate its molecular function.
    Keywords:  Microproteins; Mitochondria; OXPHOS
    DOI:  https://doi.org/10.1007/978-1-0716-5013-4_15
  6. bioRxiv. 2025 Oct 01. pii: 2025.09.29.679307. [Epub ahead of print]
    Retrograde mitochondrial transport regulates mitochondrial biogenesis in zebrafish neurons.
    Angelica E Lang, Chris Stein, Catherine M Drerup.
      To maintain a healthy mitochondrial population in a long-lived cell like a neuron, mitochondria must be continuously replenished through the process of mitochondrial biogenesis. Because the majority of mitochondrial proteins are nuclear encoded, mitochondrial biogenesis requires nuclear sensing of mitochondrial population health and function. This can be a challenge in a large, compartmentalized cell like a neuron in which a large portion of the mitochondrial population is in neuronal compartments far from the nucleus. Using in vivo assessments of mitochondrial biogenesis in zebrafish neurons, we determined that mitochondrial transport between distal axonal compartments and the cell body is required for sustained mitochondrial biogenesis. Estrogen-related receptor transcriptional activation links transport with mitochondrial gene expression. Together, our data support a role for retrograde feedback between axonal mitochondria and the nucleus for regulation of mitochondrial biogenesis in neurons.
    DOI:  https://doi.org/10.1101/2025.09.29.679307
  7. BMB Rep. 2025 Nov 20. pii: 6418. [Epub ahead of print]
    Mitochondrial transplantation restores mitochondrial content and function in SSBP1-related mitochondrial DNA depletion syndrome.
    Dohee Kim, Seo-Eun Lee, JuHyuen Cha, Jun Ho Lee, Young Cheol Kang, Sang-Yeon Lee.
      This study examined therapeutic potential of mitochondrial transplantation using PN-101, a mitochondria preparation derived from human umbilical cord mesenchymal stem cells (UCMSCs), to address SSBP1-related mitochondrial DNA (mtDNA) depletion syndrome. Patient-derived fibroblasts harboring a heterozygous SSBP1 mutation (c.272G＞A:p.Arg91Gln) were treated with PN-101. Its successful uptake and integration into these cells were confirmed. Subsequent analyses revealed that PN-101 treatment significantly increased mtDNA copy numbers in a time- and dose-dependent manner, elevated the expression of key oxidative phosphorylation proteins, and enhanced overall mitochondrial bioenergetics. Taken together, these results provide strong evidence that mitochondrial transplantation holds promise as a therapeutic strategy for primary mitochondrial diseases, including those involving SSBP1 mutations.
  8. Stem Cell Reports. 2025 Nov 20. pii: S2213-6711(25)00324-8. [Epub ahead of print] 102720
    Mitochondria regulate the cell fate decisions of megakaryocyte-erythroid progenitors.
    Eunkyu Sung, Shohei Murakami, Masanobu Morita, Tomoaki Ida, Takaaki Akaike, Hozumi Motohashi.
      Recent studies highlight the critical role of mitochondria in hematopoiesis, especially in stem cell function and erythroid maturation. To explore mitochondrial contributions to cell lineage commitment of hematopoietic progenitors, we utilized Cars2-mutant mice, an ideal model for this purpose. CARS2, a mitochondrial isoform of cysteinyl-tRNA synthetase, has cysteine persulfide synthase (CPERS) activity. Our new mouse model, with reduced CPERS activity, showed that the Cars2 mutation led to mitochondrial inhibition and anemia by suppressing erythroid commitment in megakaryocyte-erythroid progenitors (MEPs). This suppression was reproduced using mitochondrial electron transport chain inhibitors. We identified two distinct MEP populations based on the mitochondrial content: mitochondria-rich MEPs favored erythroid differentiation, while the mitochondria-poor MEPs favored megakaryocyte differentiation. These findings reveal critical contributions of mitochondria to the MEP lineage selection, acting as a "mitochondrial navigation" for lineage commitment.
    Keywords:  CARS2; MEP; differentiation; erythropoesis; megakaryocyte; megakaryocyte-erythroid progenitor; mitochondria; mouse; persulfide; sulfur metabolism
    DOI:  https://doi.org/10.1016/j.stemcr.2025.102720
  9. J Mol Neurosci. 2025 Nov 19. 75(4): 154
    Hypocitrullinemia as an Early Diagnostic Biomarker for MT-ATP6 Mitochondrial Diseases.
    Yingxue Li, Dongjuan Wang, Maobin Zhou, Haoxuan Sun, Siqi Hong, Li Jiang, Yi Guo.
      MT-ATP6 mitochondrial diseases are a group of disorders inherited from the maternal lineage caused by pathogenic variants in the MT-ATP6 gene, which encodes the a subunit of mitochondrial complex V (ATP synthase) in the electron transport chain. In this study, statistical analysis of 69 mitochondrial disease patients with complete blood metabolic screening at our center demonstrated that hypocitrullinemia exhibited 58% sensitivity (7/12) and 100% specificity (57/57) for diagnosing MT-ATP6 mitochondrial diseases. For detecting the m.8993T > G variant, the diagnostic sensitivity reached 78% (7/9) with maintained 100% specificity (60/60). Among the 7 patients with hypocitrullinemia, one had mtDNA large segment deletion syndrome involving MT-ATP6, and the other 6 had MT-ATP6 mitochondrial diseases due to the m.8993T > G variant. Hypocitrullinemia was initially detected in 3 patients during newborn screening and persisted in follow-up evaluations. A literature review identified 42 cases with MT-ATP6 variants exhibiting hypocitrullinemia, of whom 21 were diagnosed with decreased citrulline during newborn screening. We propose that hypocitrullinemia may serve as an early, characteristic serum biomarker for MT-ATP6 mitochondrial diseases, particularly aiding in the early diagnosis of the m.8993T > G variant. It also exhibits high specificity for diagnosing MT-ATP6 mitochondrial diseases and the m.8993T > G variant. Timely interventions, such as proactive diagnosis of pathogenic variants and administration of mitochondrial cofactors and citrulline, can mitigate the risk of decompensation and improve long-term prognosis.
    Keywords:   MT-ATP6 ; Biomarker; Hypocitrullinemia; Leigh syndrome; m.8993T > G
    DOI:  https://doi.org/10.1007/s12031-025-02440-6
  10. EMBO J. 2025 Nov 20.
    A unified mechanism for mitochondrial damage sensing in PINK1-Parkin-mediated mitophagy.
    Julia A Thayer, Jennifer D Petersen, Xiaoping Huang, Luiza M Gruel Budet, James Hawrot, Daniel M Ramos, Shiori Sekine, Yan Li, Michael E Ward, Derek P Narendra.
      Damaged mitochondria can be cleared from the cell by mitophagy, using a pathway formed by the recessive Parkinson's disease genes PINK1 and Parkin. Whether the pathway senses diverse forms of mitochondrial damage via a common mechanism, however, remains uncertain. Here, using a novel Parkin reporter in genome-wide screens, we identified that diverse forms of mitochondrial damage converge on loss of mitochondrial membrane potential (MMP) to activate PINK1. Loss of MMP, but not the presequence translocase-associated import motor (PAM), blocked progression of PINK1 import through the translocase of the inner membrane (TIM23), causing it to remain bound to the translocase of the outer membrane (TOM). Ablation of TIM23 was sufficient to arrest PINK1 within TOM, irrespective of MMP. Meanwhile, TOM (including subunit TOMM5) was required for PINK1 retention on the mitochondrial surface. The energy state outside of the mitochondria further modulated the pathway by controlling the rate of new PINK1 synthesis. Together, our findings point to a convergent mechanism of PINK1-Parkin activation by mitochondrial damage: loss of MMP stalls PINK1 import during its transfer from TOM to TIM23.
    Keywords:  Autophagy; Glycolysis; Parkinson’s Disease; Unfolded Protein Response
    DOI:  https://doi.org/10.1038/s44318-025-00604-z
  11. NAR Mol Med. 2025 Apr;2(2): ugaf021
    Targeted deletions in human mitochondrial DNA engineered by Type V CRISPR-Cas12a system.
    Natalia Nikitchina, Anne-Marie Heckel, Nikita Shebanov, Ilya Mazunin, Ivan Tarassov, Nina Entelis.
      Mutations in mitochondrial DNA (mtDNA) contribute to various neuromuscular diseases, with severity depending on heteroplasmy level when mutant and wild-type mtDNA coexist within the same cell. Developing methods to model mtDNA dysfunction is crucial for experimental therapies. Here, we adapted the Type V CRISPR-AsCas12a system, which recognizes AT-rich PAM sequences, for targeted editing of human mtDNA. We demonstrated that mitochondrial targeting sequence (MTS) from Neurospora crassa ATPase subunit 9 efficiently addressed the AsCas12a effector nuclease into human mitochondria. When programmed with two CRISPR RNAs (crRNAs) targeting distant regions of mtDNA, the mito-AsCas12a can cleave mtDNA, enabling generation of deletions in cultured human cells. Next generation sequencing of the deletions boundaries confirmed mtDNA ligation after the cleavage by the mitoCRISPR-AsCas12a system. Therefore, we provide experimental data proving that a CRISPR system has potential to be used for precise mtDNA manipulation, offering a promising tool for generating predefined deletions in mtDNA and creating cellular models of mitochondrial disorders.
    DOI:  https://doi.org/10.1093/narmme/ugaf021
  12. bioRxiv. 2025 Oct 02. pii: 2025.10.02.678294. [Epub ahead of print]
    Metformin inhibits mitochondrial complex I in intestinal epithelium to promote glycemic control.
    Zachary L Sebo, Ram P Chakrabarty, Rogan A Grant, Karis B D'Alessandro, Alec R Koss, Jenna L E Blum, Shawn M Davidson, Colleen R Reczek, Navdeep S Chandel.
      Metformin is a therapeutically versatile biguanide drug primarily prescribed for type II diabetes. Despite its extensive use, the mechanisms underlying many of its clinical effects, including attenuated postprandial glucose excursions, elevated intestinal glucose uptake, and increased production of lactate, Lac-Phe and GDF15, remain unclear. Here, we map these and other clinical effects of metformin to intestine-specific mitochondrial complex I inhibition. Using human metabolomic data and an orthogonal genetics approach in male mice, we demonstrate that metformin suppresses citrulline synthesis, a metabolite generated exclusively by small intestine mitochondria, and increases GDF15 by inhibiting the mitochondrial respiratory chain at complex I. This inhibition co-opts the intestines to function as a glucose sink, driving uptake of excess glucose and converting it to lactate and Lac-Phe. Notably, the glucose-lowering effect of another biguanide, phenformin, and berberine, a structurally unrelated nutraceutical, similarly depends on intestine-specific mitochondrial complex I inhibition, underscoring a shared therapeutic mechanism.
    DOI:  https://doi.org/10.1101/2025.10.02.678294
  13. Mol Cell Biol. 2025 Nov 18. 1-16
    Cholesterol Transport from ER to Outer Mitochondria by ERLIN2 in Steroid Metabolism.
    Himangshu S Bose, William E Burak, Randy M Whittal.
      Cholesterol trafficking from the endoplasmic reticulum (ER) through the mitochondria-associated ER membrane (MAM) and finally to mitochondria is essential for mammalian survival. ER lipid raft-associated protein 2 (ERLIN2) scaffolds raft-like microdomains in the trans-Golgi network, endosomes, and plasma membrane. We found that ERLIN2 assists in rolling cholesterol trafficking-associated lipid vesicles by facilitating the intermediate folding of cholesterol trafficker steroidogenic acute regulatory protein (StAR) from the ER to MAM prior to delivery to the outer mitochondrial membrane. Each ERLIN2-StAR interaction is short. The absence of ERLIN2 ablates mitochondrial cholesterol transport. Over time, StAR association with ERLIN2 increases from the ER to MAM, thereby enhancing mitochondrial cholesterol transport. Thus, ERLIN2 is central for regulating mitochondrial cholesterol trafficking required for mitochondrial steroid metabolism.
    Keywords:  Steroids; cholesterol; endoplasmic reticulum; mitochondria associated-ER membrane (MAM); pregnenolone; steroidogenic acute regulatory protein (StAR)
    DOI:  https://doi.org/10.1080/10985549.2025.2583172
  14. Sci Rep. 2025 Nov 17. 15(1): 40201
    Caloric restriction enhances inheritance of wild-type mitochondrial DNA in Saccharomyces cerevisiae.
    Wenjuan Zhu, Minoru Yoshida, Feng Ling.
      In Saccharomyces cerevisiae, an asymmetrical division model, mitochondrial (mt) DNA typically exists in a homoplasmic state, but mutations frequently occur. Rolling-circle replication, mediated by the mtDNA recombinase Mhr1p, forms tandem concatemers that are selectively transmitted to budding cells. In crosses between haploids with wild-type (ρ+) and hypersuppressive (HS) ρ- mtDNA, ρ- progeny are predominantly produced due to the replicative advantage of mtDNA with large deletions. We investigated the effects of caloric restriction (CR; 0.5% glucose medium) on mitochondrial distribution and found that ρ+ mtDNA-mitochondria are pre-selected in zygotes and transmitted into buds prior to mitochondrial fusion. This process, termed ρ+ mtDNA-mitochondrial preselection and transmission (ρ+ mtDNA-MPT), was validated by confocal imaging and flow cytometry analyses. The rate of ρ+ progeny increased under CR conditions compared to glucose-abundant media, suggesting that CR enhances ρ+ mtDNA-MPT and promotes the formation of wild-type mtDNA homoplasmy via an Mhr1p-dependent mechanism, which dominates mtDNA inheritance.
    Keywords:  Heteroplasmy; Homoplasmy; Hypersuppresiveness; Mitochondria; Nonmedial budding.; Preselection; mtDNA
    DOI:  https://doi.org/10.1038/s41598-025-23888-x
  15. Exp Physiol. 2025 Nov 19.
    Mitophagy in skeletal muscle: Impact of ageing, exercise and disuse.
    Anastasiya Kuznyetsova, David A Hood.
      Skeletal muscle plays an important role in whole-body health, quality of life and regulation of metabolism. The maintenance of a healthy mitochondrial pool is imperative for the preservation of skeletal muscle quality and is mediated through mitochondrial quality control consisting of mitochondrial turnover mediated by a balance between organelle synthesis and degradation. The selective tagging and removal of dysfunctional mitochondria is essential for maintaining mitochondrial quality control and is termed mitophagy. The mechanisms of the initial stages of mitophagy involving the recognition and tagging of mitochondria within skeletal muscle are well established, but our understanding of the terminal step involving organelle degradation mediated via lysosomes is in its infancy. An assessment of the proteolytic functions to facilitate the removal and breakdown of dysfunctional mitochondria is crucial for our understanding of the mechanisms of mitophagy, which is essential for maintaining skeletal muscle health. The aim of this review is to address the current knowledge surrounding mitophagy and lysosomal function, alongside distinct physiological conditions, such as ageing, exercise and disuse, that have varying effects on mitophagy and lysosomal adaptations within skeletal muscle.
    Keywords:  Parkin; adaptation; lysosomes; mitophagy; skeletal muscle; transcription factor EB
    DOI:  https://doi.org/10.1113/EP093041
  16. Hum Genome Var. 2025 Nov 21. 12(1): 26
    Fontaine progeroid syndrome with neonatal mitochondrial disease.
    Mitsuhiko Riko, Daiki Kawamoto, Kentaro Hirayama, Tomoya Tsuchihashi, Takayuki Suzuki, Takuya Sugimoto, Yasushi Okazaki, Kei Murayama, Daisuke Tokuhara.
      Fontaine progeroid syndrome (FPS) is a rare condition characterized by abnormalities in SLC25A24. Some instances of FPS have been reported to be fatal early in life. Here we present the first case of mitochondrial disease diagnosed with FPS in Japan. The diagnosis was based on the presence of the heterozygous known pathogenic variant of SLC25A24, NM_013386.5: c.649C>T and decreased activity of mitochondrial respiratory chain enzyme activity.
    DOI:  https://doi.org/10.1038/s41439-025-00331-1
  17. bioRxiv. 2025 Oct 05. pii: 2025.10.04.680452. [Epub ahead of print]
    Structural basis for ATP-driven double-ring assembly of the human mitochondrial Hsp60 chaperonin.
    Igor Tascón, Jorge P López-Alonso, Yoel Shkolnisky, David Gil-Cartón, Jesús Vilchez-Garcia, Alberto G Berruezo, Yacob Gómez-Llorente, Radhika Malik, Fady Jebara, Malay Patra, Joel A Hirsch, Abdussalam Azem, Iban Ubarretxena-Belandia.
      The ATP-driven mHsp60:mHsp10 chaperonin system assists protein folding within the mitochondrial matrix of human cells. Substrate protein folding has been proposed to occur through interconnected single- and double-ring pathways. In the absence of nucleotide, mHsp60 exists in equilibrium between free protomers and heptameric single rings, while the formation of double rings requires ATP. Here, we present cryo-electron microscopy structures of mHsp60 in the apo state, bound to ATP, and bound to ATP in complex with the cochaperonin mHsp10. ATP binding to single-ring apo mHsp60 7 triggers coordinated conformational changes in the intermediate and apical domains, resulting in a highly dynamic apical region within the ring. Extensive inter-subunit rearrangements flatten the equatorial surface of each ring, thereby enabling inter-ring contacts that stitch the rings together to form double-ring mHsp60 14 . Collectively, these structures define the structural basis of ATP-driven double-ring assembly of a human mitochondrial chaperonin responsible for maintaining mitochondrial protein homeostasis.
    DOI:  https://doi.org/10.1101/2025.10.04.680452
  18. iScience. 2025 Nov 21. 28(11): 113746
    Mitochondrial variation in Taiwan Biobank reveals ancestry structure and trait associations.
    Ting-Hsuan Chou, Pei-Miao Chien, Pin-Xuan Chen, Ni-Chung Lee, Hurng-Yi Wang, Yi-Cheng Chang, Chien-Yu Chen, Pei-Lung Chen, Jacob Shu-Jui Hsu.
      Mitochondrial DNA (mtDNA) variation contributes to human health, but its role in the Taiwanese population remains largely unexplored. Here, we comprehensively analyzed mtDNA variation in the Taiwan Biobank (TWB) by genotyping 1,492 individuals using whole-genome sequencing and imputing variants for 101,473 participants from microarray data. We identified 23 pathogenic mtDNA variants, with approximately 1 in 180 individuals carrying such variants. Analyses of mitochondrial genetic diversity revealed subtle differentiation among maternal ancestry groups. A mitochondrial genome-wide association study across 86 traits identified novel links between MT-ND2 variants and high myopia, as well as 14 variants associated with renal function biomarkers. Notably, renal-associated variants clustered into two groups: ancestral variants of macrohaplogroup M associated with reduced renal function and B4b sub-haplogroup variants linked to improved function. These findings highlight the value of population-specific mtDNA studies in advancing our understanding of mitochondrial genetics and health.
    Keywords:  Biological sciences; Genomic analysis; Genomics; Population
    DOI:  https://doi.org/10.1016/j.isci.2025.113746
  19. Nat Commun. 2025 Nov 20. 16(1): 10222
    An inherited mitochondrial DNA mutation remodels inflammatory cytokine responses in macrophages and in vivo in mice.
    Eloïse Marques, Stephen P Burr, Alva M Casey, Richard J Stopforth, Chak Shun Yu, Keira Turner, Dane M Wolf, Marisa Dilucca, Vincent Paupe, Suvagata Roy Chowdhury, Victoria J Tyrrell, Robbin Kramer, Yamini M Kanse, Chinmayi Pednekar, Chris A Powell, James B Stewart, Julien Prudent, Michael P Murphy, Michal Minczuk, Valerie B O'Donnell, Clare E Bryant, Patrick F Chinnery, Arthur Kaser, Alexander von Kriegsheim, Dylan G Ryan.
      Impaired mitochondrial bioenergetics in macrophages promotes hyperinflammatory cytokine responses, but whether inherited mtDNA mutations drive similar phenotypes is unknown. Here, we profiled macrophages harbouring a heteroplasmic mitochondrial tRNAAla mutation (m.5019A>G) to address this question. These macrophages exhibit combined respiratory chain defects, reduced oxidative phosphorylation, disrupted cristae architecture, and compensatory metabolic adaptations in central carbon metabolism. Upon inflammatory activation, m.5019A>G macrophages produce elevated type I interferon (IFN), while exhibiting reduced pro-inflammatory cytokines and oxylipins. Mechanistically, suppression of pro-IL-1β and COX2 requires autocrine IFN-β signalling. IFN-β induction is biphasic: an early TLR4-IRF3 driven phase, and a later response involving mitochondrial nucleic acids and the cGAS-STING pathway. In vivo, lipopolysaccharide (LPS) challenge of m.5019A>G mice results in elevated type I IFN signalling and exacerbated sickness behaviour. These findings reveal that a pathogenic mtDNA mutation promotes an imbalanced innate immune response, which has potential implications for the progression of pathology in mtDNA disease patients.
    DOI:  https://doi.org/10.1038/s41467-025-65023-4
  20. Proc Natl Acad Sci U S A. 2025 Nov 25. 122(47): e2509312122
    Glutathionylated DNA adducts accumulate in mitochondrial DNA and are regulated by AP endonuclease 1 and tyrosyl-DNA phosphodiesterase 1.
    Yu Hsuan Chen, Martin Esparza Sanchez, Ta I Hung, Jin Tang, Wenyan Xu, Jiekai Yin, Yinsheng Wang, Chia-En A Chang, Huimin Zhang, Junjie Chen, Linlin Zhao.
      Mitochondrial DNA (mtDNA) is crucial for cellular energy production, metabolism, and signaling. Its dysfunction is implicated in various diseases, including mitochondrial disorders, neurodegeneration, and diabetes. mtDNA is susceptible to damage by endogenous and environmental factors; however, unlike nuclear DNA (nDNA), mtDNA lesions do not necessarily lead to an increased mutation load in mtDNA. Instead, mtDNA lesions have been implicated in innate immunity and inflammation. Here, we report a type of mtDNA damage: glutathionylated DNA (GSH-DNA) adducts. These adducts are formed from abasic (AP) sites, key intermediates in base excision repair, or from alkylation DNA damage. Using mass spectrometry, we quantified the GSH-DNA lesion in both nDNA and mtDNA and found its significant accumulation in mtDNA of two different human cell lines, with levels one or two orders of magnitude higher than in nDNA. The formation of GSH-DNA adducts is influenced by TFAM and polyamines, and their levels are regulated by repair enzymes AP endonuclease 1 (APE1) and tyrosyl-DNA phosphodiesterase 1 (TDP1). The accumulation of GSH-DNA adducts is associated with the downregulation of several ribosomal and complex I subunit proteins and the upregulation of proteins related to redox balance and mitochondrial dynamics. Molecular dynamics (MD) simulations revealed that the GSH-DNA lesion stabilizes the TFAM-DNA binding, suggesting shielding effects from mtDNA transactions. Collectively, this study provides critical insights into the formation, regulation, and biological effects of GSH-DNA adducts in mtDNA. Our findings underscore the importance of understanding how these lesions may contribute to innate immunity and inflammation.
    Keywords:  DNA damage; DNA repair; GSH; PRDX6; TFAM
    DOI:  https://doi.org/10.1073/pnas.2509312122
  21. Tremor Other Hyperkinet Mov (N Y). 2025 ;15 55
    A Scoping Review of POLG-Related Cerebellar Ataxia: Insights and Clinical Perspectives.
    Stefania Kalampokini, Iraklis Keramidiotis, Stylianos Ravanidis, Piergiorgio Lochner, Vasilios K Kimiskidis, Georgios M Hadjigeorgiou.
       Background: Cerebellar ataxia is one of the most common movement disorders in mitochondrial disease, with POLG mutations being a frequent cause. This scoping review aimed to summarize current knowledge regarding cerebellar ataxia due to POLG mutations, focusing on epidemiological, clinical, radiological features and genotype-phenotype correlations.
    Methods: We searched PubMed and Web of Science databases for all articles published in English till September 2025 describing cases of POLG-related cerebellar ataxia.
    Results: In homozygous or compound heterozygous POLG mutation carriers, cerebellar ataxia seems to be progressive, and can initiate from either the bulbar muscles, trunk, or limbs. Age at onset varies greatly, ranging from birth to the early 70s. The most common variants in POLG-related cerebellar ataxia are W748S and A476T, localized in the linker region of POLG gene. Cerebellar ataxia due to POLG mutations can present in combination with progressive external ophthalmoplegia, sensory neuropathy, epilepsy (including status epilepticus), headache, other hyperkinetic movement disorders such as myoclonus and tremor, cognitive or affective disorders. Brain imaging commonly reveals atrophy of the vermis or cerebellar hemispheres, cortical atrophy, and/or bilateral T2/FLAIR lesions in both white matter and deep brain nuclei, including inferior olivary nuclei.
    Conclusion: POLG-related ataxia should be included in the differential diagnosis of slowly progressive cerebellar ataxias. POLG-related disease comprises a continuum of clinical features; the combination with progressive external ophthalmoplegia, sensory neuropathy, epilepsy, hyperkinetic movement disorders, as well as characteristic imaging findings, can aid the diagnosis of this underdiagnosed entity. These findings contribute to a better characterization of the phenotype-genotype relationship in the extended pool of POLG-related mitochondrial diseases.
    Highlights: This review summarizes current knowledge regarding cerebellar ataxia due to POLG mutations. A slowly progressive cerebellar ataxia in combination with sensory neuropathy, progressive external ophthalmoplegia, epilepsy, myoclonus, and characteristic imaging findings, including cerebellar atrophy, bilateral lesions in deep brain nuclei (thalami, olivary nuclei) should raise suspicion for POLG-related disease.
    Keywords:  POLG mutation; POLG-related ataxia; cerebellar ataxia; movement disorders; phenotype-genotype
    DOI:  https://doi.org/10.5334/tohm.1027
  22. bioRxiv. 2025 Sep 30. pii: 2025.09.29.678879. [Epub ahead of print]
    Organ-specific rewiring of mitochondrial integrity through COX7A dictates cellular ploidy control.
    Archan Chakraborty, Sophia DeLuca, Meera Gangasani, Stephen Rogers, Nenad Bursac, Donald T Fox.
      To achieve proper cell and tissue size, cytoplasmic and nuclear growth must be coordinated. Disrupting this coordination causes birth defects and disease. In nature's largest cells, nuclear growth occurs through polyploidization (whole-genome-duplication). How the massive nuclear growth of polyploid cells is coordinated with cytoplasmic growth processes such as mitochondrial biogenesis is relatively unclear. Here, focusing on one of nature's most commonly polyploid organs-the heart-we uncover cross-talk between cytoplasmic mitochondrial biogenesis/integrity and nuclear growth/polyploidy. From a human-to-fly screen, we uncover novel regulators of cardiomyocyte ploidy, including mitochondrial integrity regulators. In comparing these cardiac hits with a parallel screen in another polyploid tissue, the salivary gland, we discovered two opposing roles for Cytochrome-c-oxidase-subunit-7A (COX7A). While salivary gland COX7A preserves mitochondrial integrity to promote polyploidy and optimal organ growth, cardiac COX7A instead suppresses mitochondrial biogenesis to repress polyploidy and prevent hypertrophic organ growth. Among all electron transport chain genes, only COX7A functions as a cardiac growth repressor. Fly hearts with compromised COX7A show abnormally high cardiac output. Human COX7A1, a mitochondrial-localized protein, similarly represses polyploidy of human iPSC-derived cardiomyocytes. In summary, our human-fly-human approach reveals conserved rewiring of mitochondrial integrity in heart tissue that switches COX7A's role from ploidy promotion to repression. Our findings reveal fundamental cross-talk between mitochondrial biogenesis and genome duplication that are critical in growing metazoan tissues.
    DOI:  https://doi.org/10.1101/2025.09.29.678879
  23. Aging Cell. 2025 Nov 18. e70294
    Mitochondrial Respiratory Supercomplex Assembly Factor COX7RP Contributes to Lifespan Extension in Mice.
    Kazuhiro Ikeda, Sachiko Shiba, Masataka Yokoyama, Masanori Fujimoto, Kuniko Horie, Tomoaki Tanaka, Satoshi Inoue.
      COX7RP is a critical factor that assembles mitochondrial respiratory chain complexes into supercomplexes, which is considered to modulate energy production efficiency. Whether COX7RP contributes to metabolic homeostasis and lifespan remains elusive. We here observed that COX7RP-transgenic (COX7RP-Tg) mice exhibit a phenotype characterized by a significant extension of lifespan. In addition, metabolic alterations were observed in COX7RP-Tg mice, including lower blood glucose levels at 120 min during the glucose tolerance test (GTT) without a significant difference in the area under the curve (AUC), as well as reduced serum triglyceride (TG) and total cholesterol (TC) levels. Moreover, COX7RP-Tg mice exhibited elevated ATP and nicotinamide adenine dinucleotide levels, reduced ROS production, and decreased senescence-associated β-galactosidase levels. Single-nucleus RNA-sequencing (snRNA-seq) revealed that senescence-associated secretory phenotype genes were downregulated in old COX7RP-Tg white adipose tissue (WAT) compared with old WT WAT, particularly in adipocytes. This study provides a clue to the role of mitochondrial respiratory supercomplex assembly factor COX7RP in resistance to aging and longevity extension.
    Keywords:  lifespan; metabolism; mitochondria; supercomplex; white adipose tissue
    DOI:  https://doi.org/10.1111/acel.70294
  24. Adv Cancer Res. 2025 ;pii: S0065-230X(25)00017-X. [Epub ahead of print]168 63-97
    Enzymes of the outer mitochondrial membrane regulating cholesterol and fatty acid metabolism in cancer.
    Leilei Zhang, Milagros Junco, Danyelle M Townsend, Eduardo N Maldonado.
      Mitochondria are major sites of ATP production, also serving as metabolic and biosynthetic hubs. The structure of mitochondria comprises a matrix enclosed by an inner membrane which is separated from the outer mitochondrial membrane (OMM) by the intermembrane space. The OMM is a lipid bilayer that forms an interphase between mitochondria and the surrounding cytosol. While its primary function is to act as a selective barrier, controlling the exchange of molecules between these two cellular compartments, the OMM also plays a crucial role in various metabolic and regulatory processes. It is home to 114 distinct proteins, including transporters, signaling molecules, and structural components. Among these, approximately 30 are enzymes that actively participate in the regulation of lipid metabolism, amino acid processing, calcium homeostasis, and heme biosynthesis. These enzymatic functions highlight the OMM's significance beyond its structural role, positioning it as a key player in cellular energy balance, apoptosis, and intracellular signaling pathways. Here, we focus on OMM proteins involved in the synthesis and utilization of cholesterol and fatty acids. We describe the mechanisms of action, effects, regulation, association with cancer progression, and their potential as pharmacological targets of the steroid acute regulatory protein (StAR), translocator protein (TSPO), acetyl-CoA carboxylase β (ACCβ), acyl-CoA synthetases long chain family member 1 and 6 (ACSL1 and ACSL6), and carnitine palmitoyl transferases 1A and 1B (CPT1A and CPT1B). Overall, we provide a comprehensive view of these OMM enzymes in non-cancerous and cancer cells as well as their potential as targets for developing novel chemotherapies.
    Keywords:  Acetyl-CoA carboxylase β; Acyl-CoA synthetases long chain family members 1 and 6; Carnitine palmitoyl transferases 1A and 1B; Cholesterol; Fatty acids; Mitochondria; Outer mitochondrial membrane; Steroid acute regulatory proteins; Translocator protein
    DOI:  https://doi.org/10.1016/bs.acr.2025.06.002
  25. Stem Cell Res. 2025 Nov 10. pii: S1873-5061(25)00220-X. [Epub ahead of print]89 103870
    CRISPR/Cas9-mediated editing of MIC13 in human induced pluripotent stem cells: A model for mitochondrial hepato-encephalopathy.
    Haribaskar Ramachandran, Alexander Becker, Jochen Dobner, Barbara Hildebrandt, Felix Distelmaier, Andrea Rossi, Ruchika Anand.
      MIC13 is essential for cristae formation and functions as a key component of the large mitochondrial multi subunit MICOS complex. Mutations in MIC13 causes severe mitochondrial disease called mitochondrial hepato-encephalopathy. In this study, we describe the generation of a human induced pluripotent stem cell (iPSC) line carrying a patient-specific MIC13 mutation, introduced using a CRISPR/Cas knock-in approach. The resulting iPSC line will provide a valuable model to study the pediatric severe mitochondrial disease and to determine the pathological mechanisms as well as to facilitate the identification of potential therapeutic targets in the future.
    DOI:  https://doi.org/10.1016/j.scr.2025.103870
  26. Nucleic Acids Res. 2025 Nov 13. pii: gkaf1145. [Epub ahead of print]53(21):
    Substrate and enzyme determinants for recognition by human mitochondrial RNase P.
    Enxhi Hazisllari, Danijela Radovanović, Ursula Toth, Elisa Vilardo, Roland K Hartmann, Walter Rossmanith.
      RNase P enzymes of widely varying architectures recognize the 5'-leader/acceptor-stem junction and the D/T loop-interaction region of precursor tRNAs to direct cleavage to the 5' end of tRNAs. In contrast, human mitochondrial RNase P (mtRNase P) encases the entire tRNA with the aid of the methyltransferase subcomplex TRMT10C-SDR5C1. Here, we performed a kinetic analysis of substrate recognition by mtRNase P using substrate and protein variants. Surprisingly, processing by mtRNase P was found to be more efficient for tRNA precursors with longer 5' extensions and decreased sharply at a leader length of 1 nt. MtRNase P also employs a more rigid "measuring mechanism" for cleavage-site selection than the related single-subunit enzymes, so that even substrates with a G:C base-pair extension of the acceptor stem are cleaved predominantly at the canonical site. The specific contacts of TRMT10C-SDR5C1 with the anticodon loop are not crucial for efficient processing, but without interactions with the pre-tRNA, TRMT10C-SDR5C1 is unable to stimulate cleavage by the nuclease subunit PRORP, also explaining why mtRNase P reaches its limits with the D-armless mitochondrial tRNASer(AGY). Our findings set human mtRNase P apart in terms of substrate recognition from all other known forms of RNase P, including the related single-polypeptide PRORPs.
    DOI:  https://doi.org/10.1093/nar/gkaf1145
  27. BMB Rep. 2025 Nov 20. pii: 6458. [Epub ahead of print]
    Mitochondrial transfer from human embryonic stem cell-derived mature cardiomyocytes to mesenchymal stem cells.
    Ye Seul Jeong, Dasol Kim, Yoon Ji Jung, Jung Won Yoon, Yong Seong Kwon, Seong-Jang Kim, Jae Ho Kim.
      Mitochondria are crucial for energy metabolism and their dysfunction is implicated in the development of various human diseases. Direct mitochondrial transplantation has shown potential in reversing mitochondrial dysfunction in recipient cells. Mesenchymal stem cells (MSCs) present a promising approach as donor cells for such transplantation. We have previously demonstrated that tomatidine, a natural steroidal alkaloid, promotes the differentiation of human embryonic stem cells (hESCs) into mature cardiomyocytes by enhancing mitochondrial quantity and function. In this study, we assessed the capacity of hESCderived cardiomyocytes (hESC-CMs) and MSCs as donor cells for mitochondrial transplantation. Mitochondria were extracted from MSCs, immature hESC-CMs, and tomatidine-treated mature hESC-CMs. Treating MSCs with mitochondria derived from mature hESC-CMs led to a marked increase in mitochondrial protein levels, such as COX IV and MIC60, in the recipient MSCs, in comparison to those receiving mitochondria from immature hESC-CMs or MSCs. Transplantation of mature hESC-CM-derived mitochondria significantly enhanced the proliferation of recipient MSCs. These findings indicate that mature hESC-CMs are highly effective as donor cells for mitochondrial transplantation in addressing mitochondrial dysfunction.
  28. Redox Rep. 2025 Dec;30(1): 2589569
    Ecm19 coordinates mitochondrial fission and cellular redox homeostasis.
    Tiantian Chen, Sisi Lei, Haomin Qiu, Dan Zhao, Cuimei Hu, Yi Li, Xueya Zhao, Tiantian Tang, Jiaxin Deng, Zengyi Huang, Xianwen Dong, Yu Hou, Xudong Duan.
       BACKGROUND: Mitochondrial dynamics are tightly coupled with cellular redox homeostasis; however, the underlying regulatory mechanisms remain poorly defined.
    METHODS: We constructed yeast mutants and evaluated mitochondrial function, morphology, and redox states using growth assays, fluorescence imaging, and flow cytometry. RNA sequencing, RIP assays, and RT-qPCR were applied to identify Ecm19p target genes.
    RESULTS: Deletion of ECM19 alone had no evident impact on mitochondrial morphology or respiratory function. In contrast, double deletion of ECM19 with the fusion gene FZO1 (ecm19D fzo1D) rescued mitochondrial function and morphology and reduced ROS and malondialdehyde levels relative to fzo1D. Conversely, combining ecm19D with fission genes MDV1 or CAF4 resulted in hyperfused mitochondria, dependent on the division factor Dnm1p. RNA-seq revealed that ecm19D upregulates redox processes, including catalase (CTA1) and thiol peroxidase (TSA2). RIP-PCR confirmed Ecm19p binds directly to CTA1 and TSA2 transcripts and reduces their mRNA stability. Under H₂O₂ stress, ecm19D cta1D and ecm19D tsa2D double mutants exhibited improved growth, elevated antioxidant capacity, and lower ROS and malondialdehyde than single mutants.
    CONCLUSION: Ecm19 collaborates with Mdv1 and Caf4 to promote mitochondrial fission and post-transcriptionally represses CTA1 and TSA2 expression to regulate cellular redox, thereby coordinating mitochondrial fission with redox homeostasis.
    Keywords:  CAF4; CTA1; ECM19; MDV1; Mitochondrial fission; Mitochondrial fusion; TSA2; cellular redox
    DOI:  https://doi.org/10.1080/13510002.2025.2589569
  29. Ann Neurol. 2025 Nov 21.
    Anatomical Associations Between Focal Mitochondrial Metabolism and Patterns of Neurodegeneration in Amyotrophic Lateral Sclerosis.
    Marlene Tahedl, We Fong Siah, Efstratios Karavasilis, Jennifer C Hengeveld, Mark A Doherty, Russell L McLaughlin, Orla Hardiman, Ee Ling Tan, Foteini Christidi, Jana Kleinerova, Peter Bede.
       OBJECTIVE: Amyotrophic lateral sclerosis (ALS) has a very specific neuroimaging signature, but the molecular underpinnings of the strikingly selective anatomic involvement have not elucidated to date. Accordingly, a large neuroimaging study was conducted with 258 participants to evaluate associations between patterns of neurodegeneration and focal metabolic metrics.
    METHODS: Structural and diffusivity alterations were systematically evaluated in a genetically stratified cohort. Voxelwise associations between neurodegeneration and physiological mitochondrial indices were systematically evaluated over the entire brain and also examined in specific regions.
    RESULTS: Significant topological associations were identified between physiological mitochondria tissue density, nicotinamide adenine dinucleotide (NADH)-ubiquinone oxidoreductase, succinate dehydrogenase, cytochrome c oxidase (COX), mitochondrial respiratory capacity (MRC), tissue respiratory capacity (TRC), and propensity to focal atrophy in ALS. Anatomic correlations between mitochondrial metrics and morphometric change were particularly strong in GGGGCC hexanucleotide repeat carriers in C9orf72. Diffusivity analyses also confirmed associations between brain metabolism and microstructural degeneration. Higher focal mitochondria tissue density was associated with higher likelihood of frontal, temporal, cerebellar, opercular, thalamic, cingulum, putamen, corpus callosum, and corona radiata degeneration. Uncinate fasciculus degeneration was associated with higher Complex I, II, COX, and TRC activity. Topological associations were readily replicated in an external validation cohort.
    INTERPRETATION: Our data indicate that brain regions with high metabolic activity are particularly vulnerable to neurodegeneration in ALS. Anatomic associations between physiological cerebral metabolism and patterns of neurodegeneration implicate mitochondrial dysfunction in the pathophysiology of ALS. Although mitochondrial dysfunction may not be the primary etiological factor, it may represent a shared bottleneck of multiple converging molecular and genetic pathways, offering a potential opportunity for meaningful pharmacological intervention. ANN NEUROL 2025.
    DOI:  https://doi.org/10.1002/ana.78099
  30. Nat Commun. 2025 Nov 17. 16(1): 10064
    Structures of human organellar SPFH protein complexes.
    Jingjing Gao, Dawafuti Sherpa, Nikita Kupko, Haruka Chino, Jianwei Zeng, Sichen Shao.
      Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) family proteins are found in all kingdoms of life and in multiple eukaryotic organelles. SPFH proteins assemble into homo- or hetero-oligomeric rings that form domed structures. Most SPFH assemblies also abut a cellular membrane, where they are implicated in diverse functions ranging from membrane organization to protein quality control. However, the precise architectures of different SPFH complexes remain unclear. Here, we report single-particle cryo-EM structures of the endoplasmic reticulum (ER)-resident Erlin1/2 complex and the mitochondrial prohibitin (PHB1/2) complex, revealing assemblies of 13 heterodimers of Erlin1 and Erlin2 and 11 heterodimers of PHB1 and PHB2, respectively. We also describe key interactions underlying the architecture of each complex and conformational heterogeneity of the PHB1/2 complex. Our findings elucidate the distinct stoichiometries and properties of human organellar SPFH complexes and highlight common principles of SPFH complex organization.
    DOI:  https://doi.org/10.1038/s41467-025-65078-3
  31. NAR Genom Bioinform. 2025 Dec;7(4): lqaf157
    Genome region aware CADD thresholds for noncoding variant prioritization.
    Jude-Félix Tenywa, Jean-Baptiste Lamouche, Sarah Baer, Samuel Nicaise, Antony Le Béchec, Amélie Piton, Jean Muller.
      The democratization of genome sequencing for genetic diseases is leading to the identification of a large amount of variants in noncoding regions. Unless supported by a strong clinically oriented diagnostic hypothesis, these variants remain largely under-analyzed due to the limited availability of in silico prediction tools for prioritization and the lack of functional assays for validation. We discuss here the current state of whole-genome analysis using the combined annotation-dependent depletion (CADD) score, one of the most efficient genome-wide prediction and most popular prioritization tool for genetic variants. In light of the worldwide participative ClinVar database that stores the disease classification of millions of human genetic variants, we evaluated the use of genomic region-specific thresholds to guide the geneticists in prioritizing noncoding region variants using the CADD score.
    DOI:  https://doi.org/10.1093/nargab/lqaf157
  32. Curr Med Sci. 2025 Nov 19.
    PPA1 Facilitates Thermogenesis in Brown and Beige Fat by Regulating the Mitochondrial Localization of FUS.
    Yue Sun, Heng-le Ding, Jin-Fu Zhang, Yuan-Yuan Su, Nan Yang, Ye Yin, Hai-Yan Lin, Xiao-Rong Zhu.
       OBJECTIVE: Brown and beige adipocytes dissipate energy through thermogenesis, and the impaired thermogenic function of these adipocytes is a key driver of obesity and related metabolic disorders. However, the molecular mechanisms governing adipocyte thermogenesis are not fully understood. This study investigated the role of inorganic pyrophosphatase 1 (PPA1) in regulating adipocyte thermogenesis and assessed its potential as a therapeutic target for obesity and metabolic disorders.
    METHODS: To investigate the function of PPA1 in adipose tissue thermogenesis, we generated adipose-specific heterozygous PPA1 knockout mice via the Cre-loxP system and established cold exposure models. PPA1 deletion effects were assessed by hematoxylin and eosin (H&E) staining, immunofluorescence, quantitative polymerase chain reaction (qPCR), and immunoblotting. Mitochondrial changes during browning were further characterized via transmission electron microscopy (TEM), mitochondrial DNA (mtDNA) quantification, qPCR, and Western blotting. The molecular mechanisms involved were subsequently dissected via mass spectrometry, coimmunoprecipitation (Co-IP), and immunofluorescence colocalization.
    RESULTS: Adi-PPA1fl/+ mice presented impaired adipose tissue thermogenesis upon cold exposure. Mechanistically, PPA1 deficiency impaired adipose browning in an enzyme activity-independent manner. PPA1 knockdown promoted the aberrant translocation and accumulation of fused in sarcoma (FUS) to mitochondria, which triggered mitochondrial dysfunction and suppressed browning. Crucially, silencing FUS effectively rescued the mitochondrial defects caused by PPA1 depletion.
    CONCLUSION: PPA1 functions as a nonenzymatic positive regulator of adipocyte thermogenesis by interacting with FUS to prevent its mitochondrial mislocalization, thereby maintaining mitochondrial function and promoting adipose browning. These findings highlight PPA1 as a potential therapeutic avenue for obesity and metabolic disorders.
    Keywords:  Adipose browning; FUS; Mitochondria; Obesity; PPA1; Thermogenesis
    DOI:  https://doi.org/10.1007/s11596-025-00143-y
  33. bioRxiv. 2025 Oct 02. pii: 2025.10.01.679889. [Epub ahead of print]
    Association of cytochrome c oxidase dysfunction with amyloidosis in Alzheimer's disease and patient-derived cerebral organoids.
    Tienju Wang, Yanting Chen, Jing Tian, Khloud Emam, Lan Guo, Tao Ma, Heng Du.
      Patients with Alzheimer's disease (AD) demonstrate brain mitochondrial dysfunction and energy deficiency that are closely associated with cognitive impairment. Cytochrome c oxidase (CCO), also known as mitochondrial complex IV, is the terminal enzyme in mitochondrial electron transport chain (ETC). Consistent with the pivotal role of CCO in mitochondrial bioenergetics and high demand for energy to sustain neuronal function, CCO dysfunction has been linked to neurological disorders including AD. However, it remains unclear whether mitochondrial CCO dysfunction represents an adaptive response to AD-associated toxic molecules versus a bona fide pathology to promote AD development. In this study, by meta-analysis of publicly available proteomics analysis of post-mortem frontal lobe tissues from four large cohorts of patients with AD we identified loss of key CCO subunits including mitochondrial DNA (mtDNA)-encoded COX1 and COX3 as well as nuclear DNA (nDNA)-encoded COX5A, COX6B1, COX7C, COX8A, and NDUFA4 in patients with AD. Further biochemical analysis using post-mortem frontal lobe tissues showed lowered CCO activity of neuronal mitochondria from patients with AD, suggesting CCO vulnerability and its potential association with amyloidosis in AD. Lastly, in addition to the inverse relationship between neuronal CCO activity and brain amyloidosis in the tested AD cohort, pharmacological inhibition of CCO promoted amyloid production and elevated beta-secretase 1 (BACE1) activity in cerebral organoids derived from human induced pluripotent stem cells (hiPSCs) from one nonAD and one AD subject. The simplest interpretation of the results is that CCO dysfunction in the frontal lobe is a phenotypic mitochondrial change accompanying AD, which may contribute to the development of brain amyloidosis.
    DOI:  https://doi.org/10.1101/2025.10.01.679889
  34. J Transl Med. 2025 Nov 19. 23(1): 1321
    Mitochondrial dysfunction acts as a modulator of the immunometabolic route for activating the cytosolic DNA sensor pathway in triggering innate immunosurveillance.
    Cristina Algieri, Salvatore Nesci, Francesca Oppedisano.
      Mitochondria, in addition to their classic role in energy production, have emerged as central hubs in the regulation of innate immunity. Under conditions of cellular stress, mitochondrial dysfunction triggers the release of mitochondrial DNA (mtDNA) into the cytosol or extracellular space, activating potent inflammatory pathways such as cGAS-STING, NLRP3 and TLR9. mtDNA release, driven by factors such as oxidative damage, membrane permeabilization, and various cell death pathways, is involved in immune surveillance and the pathogenesis of various diseases. At the same time, this downstream event leads to profound reorganization of immune cell metabolism, influencing functional polarization and inflammatory outcomes. This review presents the mitochondrion as an interface between metabolism, immunity, immunometabolites, and danger signalling. We explore the molecular mechanisms of mtDNA release, its conversion into immune signals, and its impact on metabolism in immune cells. Translational implications for pathologies such as neurodegenerative, autoimmune, and neoplastic diseases are also discussed. Deciphering the interconnection between mitochondrial stress, mtDNA release, and immunometabolic rewiring could open new avenues for the treatment of complex diseases and drive innovation in immunotherapy and regenerative medicine.
    Keywords:  Complex diseases; Immunity; Inflammation; Metabolism; Mitochondria
    DOI:  https://doi.org/10.1186/s12967-025-07392-4
  35. Res Involv Engagem. 2025 Nov 20. 11(1): 137
    Expanding research and care for Leigh syndrome: efforts of a patient-led advocacy organization.
    Sophia Zilber, Melinda Burnworth, Titilola Afolabi, Jonathan R Brestoff, Michal Minczuk, Alejandro Rodriguez Luis, Qinglan Ling, Alessandro Prigione, Isabella Tolle, Ibrahim Elsharkawi, Ethan Perlstein, Danielle Boyce, Simon Johnson, Kasey Woleben.
      
    Keywords:  Gene therapy; Leigh syndrome; Mitochondrial disease; Patient advocacy; Rare disease
    DOI:  https://doi.org/10.1186/s40900-025-00808-x
  36. Cell Insight. 2025 Dec;4(6): 100285
    Mitochondrial cristae remodeling: Mechanisms, functions, and pathology.
    Jianglong Yu, Yuanchun Luo, Jiacheng Lin, Zhuofan Li, Zheng Fang, He He, Chaojun Yan, Zhiyin Song.
      Mitochondrial cristae are the principal sites of oxidative phosphorylation and are central to mitochondria-dependent energy metabolism. Rather than static folds, cristae are dynamic bioenergetic compartments that remodel in response to physiological and stress cues. During remodeling, their number, length, width, lateral alignment, curvature/stiffness, and the geometry of crista junctions (CJs) can change. Depending on cellular context, cristae may increase in abundance, tighten or widen, and exhibit opening or closure of CJs, with corresponding effects on respiratory-chain organization and supercomplex assembly. Key regulators include OPA1 (and its proteolytic processing), the MICOS complex that scaffolds CJs, F1Fo-ATP synthase dimerization/oligomerization that shapes high-curvature ridges, and cardiolipin, which stabilizes inner-membrane architecture. Abnormal cristae compromise electron transport, ATP production, and mitochondrial metabolism, contributing to neurodegeneration and metabolic disease etc. In this review, we synthesize current insights into the molecular control of cristae ultrastructure and its impact on mitochondrial metabolism, delineate structural features and quantitative readouts, and highlight mechanisms that govern cristae remodeling under physiological and stress conditions, with an emphasis on diseases arising from aberrant crista architecture.
    Keywords:  Cardiolipin; Cristae remodeling; F1Fo-ATP synthase; MICOS complex; OPA1; Oxidative phosphorylation
    DOI:  https://doi.org/10.1016/j.cellin.2025.100285
  37. Cardiol J. 2025 Nov 19.
    Nicotinamide adenine dinucleotide fluorescence monitoring as a potential tool for the microvascular and mitochondrial function assessment in heart failure.
    Aleksandra Parzuchowska, Maria Tarnawska, Dorota Smolarek, Barbara Kutryb-Zając, Marcin Hellmann.
      
    Keywords:  endothelium; flow-mediated skin fluorescence; heart failure; microcirculation; mitochondria
    DOI:  https://doi.org/10.5603/cj.106572
  38. Adv Sci (Weinh). 2025 Nov 21. e14522
    Nanomedicines Against Mitochondrial Dysfunction-Induced Metabolic Diseases.
    Ke Xu, Leyi Wang, Tao Lv, Chen Jin, Qiong Wu, Yongjie Zhou, Gang Xu, Zhenyu Duan, Kui Luo, Jiayin Yang.
      Mitochondrial dysfunction is a common pathology for metabolic diseases such as obesity, diabetes, non-alcoholic fatty liver disease, atherosclerosis, Alzheimer's disease (AD), and Parkinson's disease (PD). Nanomedicines provide a revolutionary strategy for mitochondrial function repair. They can realize targeted delivery, responsive release, and integration of multimodal therapies through nanotechnology and engineering and overcome limitations of traditional therapeutic methods, such as insufficient targeting, low bioavailability, and toxic side effects. In this article, the pathological characteristics of mitochondria are first introduced, and the relationship between mitochondrial dysfunction and metabolic diseases are illustrated. Structural features and design strategies of nanomedicines targeting mitochondrial dysfunction are summarized, with particular elaboration on targeting strategies and response mechanisms for diseased organs and subcellular organelles such as the liver, adipose tissue, atherosclerotic plaques, the brain, and mitochondria. The application and clinical translation of nanomedicines in obesity, atherosclerosis, diabetes, non-alcoholic fatty liver disease (NAFLD), and brain metabolic disorders are detailed. This article is concluded with a summary and outlook of the current research status, challenges, and future development directions.
    Keywords:  metabolic diseases; mitochondrial dysfunction; nanomedicine; targeted delivery
    DOI:  https://doi.org/10.1002/advs.202514522
  39. BMC Med Genomics. 2025 Nov 19. 18(1): 187
    Improving newborn screening accuracy through genome sequencing, targeted metabolomics, and machine learning.
    Yuhan Xie, Gang Peng, Irina Tikhonova, Gregory Enns, Hongyu Zhao, Tina Cowan, Curt Scharfe.
       BACKGROUND: Newborn screening (NBS) enables early detection of metabolic disorders, but current tandem mass spectrometry (MS/MS) methods often lead to false positives and require confirmatory testing, causing diagnostic delays. We evaluated whether integrating genome sequencing, expanded metabolite profiling, and artificial intelligence/machine learning (AI/ML) could improve the accuracy of NBS.
    METHODS: We analyzed dried blood spots (DBS) from 119 screen-positive cases identified by the California NBS program across four disorders: GA-I, PA/MMA, OTCD, and VLCADD. Genome sequencing was performed to identify variants in condition-related genes using ACMG guidelines, and an AI/ML classifier trained on previously generated metabolomic data was applied to differentiate true and false positives.
    RESULTS: Genome sequencing confirmed 89% (31/35) of true positives based on the presence of two reportable variants. Among 84 false positives, 74% (62) had no variant, while 26% (22) carried a pathogenic/likely pathogenic variant or rare VUS in a condition-related gene. For VLCADD, half of false positives (15/29) were ACADVL variant carriers (P = 4.66 × 10⁻⁷). VLCADD biomarker levels were highest in patients, intermediate in carriers, and lowest in non-carriers, indicating that ACADVL variants elevate biomarker levels and increase false-positive rates. Metabolomics with AI/ML detected all true positives (100% sensitivity), while genome sequencing reduced false positives by 98.8%.
    CONCLUSION: Targeted metabolomics with AI/ML showed high sensitivity for identifying true positives, though its ability to reduce false positives varied by condition. Genome sequencing effectively reduced false positives but lacked sufficient sensitivity as a standalone test. The elevated false-positive rate among pathogenic variant carriers underscores the potential value of parental or prenatal carrier screening to improve NBS accuracy. Integrating genomic and metabolomic data may enhance NBS precision and enable earlier diagnosis and intervention for rare diseases.
    Keywords:  Dried blood spot; Machine learning; Metabolic disorder; Metabolomics profiling; Molecular diagnostics; Newborn screening; Next-generation sequencing; Rare diseases
    DOI:  https://doi.org/10.1186/s12920-025-02261-x
  40. Front Ophthalmol (Lausanne). 2025 ;5 1688232
    IT TAKES TWO TO TANGO: potential novel therapies for autosomal dominant optic atrophy.
    Ritu Sampige, Lyra E A Seaborn, Molly Pluenneke, Annika Jyothi, Sophie Saland, Chisom M Chinedu-Obi, Caroline Keehn, Andrew G Lee.
      Autosomal dominant optic atrophy (ADOA) is among the most prevalent inherited optic neuropathies with hallmark symptoms of bilateral, painless, progressive, and typically permanent vision loss over time. ADOA can affect patients' quality of life with debilitating visual symptoms, and there is a pressing need for effective therapeutics. In this paper, we review the current and future investigational therapies for ADOA, including the use of intravitreal injections of antisense oligonucleotides through Targeted Augmentation of Nuclear Gene Output (TANGO), CRISPR-based therapy, genetic editing, gene replacement approaches, and idebenone, a small-molecule mitochondrial modulator. Additionally, we review clinical trials for ADOA treatment and opportunities for future research on ADOA therapeutics, including the utilization of mitochondria-targeted peptides and antioxidants, NAD+ boosters/metabolic support, mitophagy and fission-fusion modulators, and cell-based regenerative therapy. The use of emerging technology to compensate for OPA1 protein haploinsufficiency provides new and vast avenues for the management of this otherwise vision-altering disease. Increased awareness of therapeutics for ADOA will allow for patient counseling regarding treatment access via clinical trials and for underscoring the importance of genetically testing family members, who may be incidentally identified with ADOA in a timely manner for newly available therapies. While patients with ADOA typically have poor visual prognoses, there are increasing promising therapies with the potential for preserving and improving visual function.
    Keywords:  OPA1; Targeted Augmentation of Nuclear Gene Output (TANGO); autosomal dominant optic atrophy; idebenone; review
    DOI:  https://doi.org/10.3389/fopht.2025.1688232
  41. Nat Struct Mol Biol. 2025 Nov 17.
    Computational design of a high-precision mitochondrial DNA cytosine base editor.
    Li Mi, Yu-Xuan Li, Xinchen Lv, Zi-Li Wan, Xu Liu, Kairan Zhang, Huican Li, Yue Yao, Leping Zhang, Zhe Xu, Xingyu Zhuang, Kunqian Ji, Min Jiang, Yangming Wang, Peilong Lu.
      Bystander editing remains a major limitation of current base editors, hindering their precision and therapeutic potential. Here, we present a de novo protein design strategy that creates a structurally rigid interface between a DNA-binding TALE domain and a cytosine deaminase, forming a unified editing module termed TALE-oriented deaminase (TOD). Cryo-EM analysis of TOD-DNA complexes confirms that this precise spatial architecture tightly restricts the deaminase activity window, thereby minimizing unwanted deamination. To further enhance editing specificity, we develop a split version, termed DdCBE-TOD, which virtually eliminates off-target editing. As a proof of concept, we apply DdCBE-TOD to generate a mitochondrial disease mouse model and to correct a pathogenic mutation associated with MERRF syndrome in patient-derived cells, achieving single-nucleotide precision. This work introduces a generalizable and computationally guided approach for ultra-precise base editing, offering a promising platform for both mechanistic studies and therapeutic correction of single-nucleotide mutations.
    DOI:  https://doi.org/10.1038/s41594-025-01714-2
  42. Nat Commun. 2025 Nov 20. 16(1): 10198
    SLC45A4 encodes a peroxisomal putrescine transporter that promotes GABA de novo synthesis.
    Cecilia Colson, Yujue Wang, James Atherton, Nisha Rani Dahiya, Davood Kharaghani, Xiaoyang Su.
      Solute carriers (SLC) are membrane proteins that facilitate the transportation of ions and metabolites across either the plasma membrane or the membrane of intracellular organelles. With more than 450 human genes annotated as SLCs, many of them are still orphan transporters without known biochemical functions. We develop a metabolomic-transcriptomic association analysis, and we find that the expression of SLC45A4 has a strong positive correlation with the cellular level of γ-aminobutyric acid (GABA). Using mass spectrometry and the stable isotope tracing approach, we demonstrate that SLC45A4 promotes GABA de novo synthesis through the Arginine/Ornithine/Putrescine (AOP) pathway. SLC45A4 functions as a putrescine transporter localized to the peroxisome membrane to facilitate GABA production. Taken together, our results reveal a biochemical mechanism where SLC45A4 controls GABA production.
    DOI:  https://doi.org/10.1038/s41467-025-62721-x
  43. Commun Biol. 2025 Nov 20. 8(1): 1618
    Polarized ATP synthase in synaptic mitochondria induced by learning and plasticity signals.
    Yi Hu, Xi Wang, Kaiyuan Liu, Songhai Xiong, Bing Cai, Ji-Song Guan, Min Gu, Hong Xie.
      MINFLUX is a cutting-edge single-molecule localization microscopy technology that surpasses the conventional diffraction limit, enabling nanostructure visualization with exceptional precision. However, its application has largely been limited to cultured cells. In this research, we refined sample preparation protocols for 3D MINFLUX imaging in fixed brain tissue, focusing on mitochondrial distribution within dendritic spines and engram cells of the dentate gyrus. Probing single molecules reveals that mitochondrial inner membrane proteins reorganize during synaptic plasticity in dendritic spines of engram cells. Using 3D MINFLUX nanoscopy, we identified a significant redistribution of α-F1-ATP synthase, correlating with learning-related activities. This redistribution suggests a pivotal role for polarized ATP synthesis near the postsynaptic zone in modulating synaptic plasticity and memory consolidation. Dual-color 3D MINFLUX imaging uncovered distinct mitochondrial reorganization patterns involving both inner and outer membranes in dendritic spines. These patterns, induced by plasticity signals, persist for up to 12 h in neuronal cultures, highlighting distinct regulatory mechanisms governing mitochondrial proteins during plasticity. These findings provide new insights into the molecular mechanisms underlying synaptic plasticity and demonstrate the transformative potential of 3D MINFLUX imaging for studying neuronal processes in the brain.
    DOI:  https://doi.org/10.1038/s42003-025-08963-3
  44. EMBO J. 2025 Nov 17.
    Measuring mitochondrial membrane potential.
    Oscar Tovar-Ferrero, Javier Rubio, Antonio Zorzano, Guillermo Martínez-Corrales, Marc Liesa.
      
    DOI:  https://doi.org/10.1038/s44318-025-00632-9
  45. Structure. 2025 Nov 19. pii: S0969-2126(25)00403-4. [Epub ahead of print]
    Structural changes shifting the redox potential of the outlying cluster N1a in respiratory complex I.
    Daniel Wohlwend, Thilo Seifermann, Emmanuel Gnandt, Marta Vranas, Stefan Gerhardt, Thorsten Friedrich.
      Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is central to energy metabolism by coupling NADH oxidation and quinone reduction with proton translocation across the membrane. Electrons are transferred from the primary acceptor flavin mononucleotide via a chain of iron-sulfur clusters to quinone. The enigmatic cluster N1a is conserved, but not part of this electron transfer chain. We reported on variants of the complex in which N1a is not detectable by EPR spectroscopy. This was tentatively attributed to the lower redox potential of the variant N1a. However, it remained an open question, whether the variants contain this cluster at all. Here, we determined the structures of these variants by X-ray crystallography and cryogenic-electron microscopy. Cluster N1a is present in all variants and the shift of its redox potential is explained by nearby structural changes. A role of the cluster for the mechanism of the complex is discussed.
    Keywords:  EPR spectroscopy; NADH dehydrogenase; X-ray crystallography; bioenergetics; biological electron transfer; cryo-electron microscopy; iron-sulfur cluster; redox potential; respiratory complex I
    DOI:  https://doi.org/10.1016/j.str.2025.10.016
  46. Front Neurosci. 2025 ;19 1696899
    NMPhenogen: a comprehensive database for genotype-phenotype correlation in neuromuscular genetic disorders.
    Usha Manjunath, Venkatesh R, Sacheta Sudhendra Kulkarni, Harshatha N Reddy, Anupama Anil, Rakesh Kumar Mishra, Gayatri Rangarajan Iyer.
      Neuromuscular genetic disorders (NMGDs) are genetically and clinically diverse group of inherited diseases that affect approximately 1 in 1,000 people worldwide with a calculated prevalence of 37 per 10,000 in the general population. These disorders arise from a variety of genetic changes such as insertions, deletions, duplications and expansions of repeats in more than 747 nuclear and mitochondrial genes critical for the function of peripheral nerves, motor neurons, neuromuscular junctions or skeletal muscles, leading to progressive weakness and degeneration of muscles. Major subtypes include muscular dystrophies, congenital myopathies, motor neuron diseases, peripheral neuropathies, and mitochondrial myopathies. Clinical presentation of NMGDs is highly variable in the age of onset, severity and pattern of muscle involvement, often leading to prolonged and complex diagnostic process. Conventional diagnostic methods have relied on clinical history, physical examination and invasive procedures like muscle biopsy. But the development of next-generation sequencing (NGS) has transformed diagnostics by enabling comprehensive analysis of NMGD-related genes. Despite this advancement, interpreting the numerous variants identified by NGS remains challenging. The guidelines of the American College of Medical Genetics and Genomics (ACMG) offer a standardized approach to variant classification as pathogenic, likely pathogenic, variant of uncertain significance, likely benign and benign. However, this requires the integration of complex evidence from population data, computational predictions, and functional assays. The major challenge is the robust correlation of genotypic information with the huge phenotypic range of NMGDs which is a task complicated by the unavailability of population-specific genetic databases. To address these issues, we have developed NMPhenogen (https://gi-lab-tigs.github.io/Homepage/), a new database designed to enhance the diagnosis and understanding of NMGDs. NMPhenogen is a centralized repository for data related to NMGD-associated genes and variants along with their clinical presentations. It includes two primary modules: NMPhenoscore, which enhances disease-phenotype correlations, and a Variant classifier, which facilitates standardized variant classification based on published guidelines. This combined resource aims to streamline the diagnostic process, support clinical decision-making, and eventually contribute to improving patient care and genetic counseling.
    Keywords:  ACMG; NMGD; NMPhenoscore; disease prioritization; neuromuscular disorders; variant classification; variant classifier; variant interpretation tool
    DOI:  https://doi.org/10.3389/fnins.2025.1696899
  47. bioRxiv. 2025 Oct 02. pii: 2025.10.01.679796. [Epub ahead of print]
    Loss of adenylosuccinate synthetase 1 in mice recapitulates features of ADSS1 myopathy.
    Morgan E Kim, Kathryn M Yammine, Emily T Hickey, Catalina Matias, Lou C Dubosclard, Jeffrey J Widrick, Jeffrey J Brault, Behzad Moghadaszadeh, Alan H Beggs.
      ADSS1 myopathy is an ultra-rare congenital myopathy characterized by progressive cardiac and skeletal muscle degeneration with childhood to adolescent onset. This autosomal recessive disease is caused by mutations in the ADSS1 gene, encoding the enzyme adenylosuccinate synthetase (AdSS1). AdSS1 plays a critical role in the adenine nucleotide cycle, which is important for energy metabolism in muscle cells. Enzymatic defects, engendered by loss-of-function mutations in ADSS1 , lead to a bottleneck in the adenine nucleotide cycle, causing metabolic dysfunction which ultimately results in progressive muscle weakness, mobility impairment, and respiratory and cardiac dysfunction, often requiring the use of a ventilator. Despite its debilitating nature, there are currently no cures or targeted treatments available, and little research into possible therapeutic strategies has been done. With a limited patient profile encompassing fewer than 200 known patients worldwide, establishing a mouse model for ADSS1 myopathy is critical to understanding its pathogenesis and for developing future therapies. Here, we present and characterize the first mouse model of ADSS1 myopathy - a constitutive Adss1 knockout model - by (1) defining its natural history, (2) exploring its metabolic pathomechanisms, and (3) characterizing its histopathological features. We find that Adss1 KO/KO mice have subtle motor deficits and present with histopathological features consistent with patient phenotypes. Overall, we show that despite a relatively mild phenotype, this novel mouse model has quantifiable pathological features that can be used to develop therapies for, and further probe pathophysiology of, ADSS1 myopathy.
    DOI:  https://doi.org/10.1101/2025.10.01.679796
  48. Proc Natl Acad Sci U S A. 2025 Nov 25. 122(47): e2504565122
    Rac1 promotes proximal tubule kidney repair by coupling the actin cytoskeleton to mitochondrial function.
    Olga M Viquez, Meiling Melzer, Shensen Li, Matthew Tantengco, Xinyu Dong, Eric Sha, Jeffery Huang, Evan S Krystofiak, Rachel C Hart, Wentian Luo, Christian Warren, Al-Borhan Bayazid, Richard Zhang, Ryoichi Bessho, Volker H Haase, Cord Brakebusch, Takanari Inoue, Craig Brooks, Matthew H Wilson, Andrew S Terker, Juan P Arroyo, Ambra Pozzi, Roy Zent, Fabian Bock.
      The kidney proximal tubule (PT) is a specialized polarized epithelium that functions as a high capacity resorptive machine. PT cells are exquisitely sensitive to ischemia due to their high metabolic rate. The small GTPase Rac1 regulates epithelial function by promoting polarity through its effects on the actin cytoskeleton. We show that Rac1, in the setting of the recovery of the PT from ischemic injury, plays a critical role in reconstituting cellular bioenergetics by promoting actin cytoskeleton formation around damaged mitochondria. This mechanism removes damaged mitochondria through mitophagy and preserves PT metabolic capacity and reabsorption function. Loss of Rac1 causes intracellular lipid accumulation, energy depletion, and PT cell atrophy. Thus, Rac1 promotes the repair of PT cells by enhancing mitochondrial bioenergetics, rather than by regulating cell polarity via a mechanism that links the actin cytoskeleton to metabolic demands and cell morphology.
    Keywords:  actin cytoskeleton; kidney repair; mitochondria
    DOI:  https://doi.org/10.1073/pnas.2504565122
  49. Neurobiol Dis. 2025 Nov 17. pii: S0969-9961(25)00413-9. [Epub ahead of print] 107196
    Pathogenic KIF5C mutation disrupts dendritic spine maturation and mitochondrial trafficking in neurodevelopmental disorders.
    Xiaojun Wang, Luyu Ye, Santasree Banerjee, Jiabin Feng, Tailin Liao, Ziyi Wang, Jiale Qin, Jianhong Luo, Wei Yang, Junyu Xu, Chen Li.
      KIF5C, a kinesin-1 motor protein critical for neuronal cargo transport, has been clinically associated with developmental delay and intellectual disability (DD/ID), although its pathogenic mechanisms are yet to be elucidated. Building on our prior identification of a de novo heterozygous KIF5C variant in a patient with DD/ID, a conditional knock-in mouse model was constructed to determine disease pathogenesis. The mutant mice exhibited core clinical phenotypes, including growth retardation, microcephaly, and deficits in social and spatial memory. Electrophysiological recordings revealed a decreased frequency of miniature excitatory postsynaptic currents, impaired long-term potentiation, and altered presynaptic vesicle release probability. Mechanistically, hippocampal neurons displayed decreased mature dendritic spines and impaired axonal mitochondrial transport, collectively contributing to diminished excitatory neurotransmission. Nonetheless, the overexpression of KIF5C in hippocampal CA1 neurons enhanced memory performance and excitatory synaptic transmission in the mutant mice. Overall, these findings establish that KIF5C dysfunction disrupts dendritic spine maturation at the postsynaptic terminal, axonal mitochondrial transport, and presynaptic vesicle release. Thus, a critical cellular mechanism underlying DD/ID pathogenesis has been identified in this research, opening novel therapeutic avenues.
    Keywords:  Global developmental delay; Intellectual disability; KIF5C; Mitochondrial transport
    DOI:  https://doi.org/10.1016/j.nbd.2025.107196
  50. Nat Genet. 2025 Nov 20.
    Scalable and accurate rare variant meta-analysis with Meta-SAIGE.
    Eunjae Park, Kisung Nam, Seokho Jeong, Karl Keat, Dokyoon Kim, Vikas Bansal, Wei Zhou, Seunggeun Lee.
      Meta-analysis enhances the power of rare variant association tests by combining summary statistics across several cohorts. However, existing methods often fail to control type I error for low-prevalence binary traits and are computationally intensive. Here we introduce Meta-SAIGE-a scalable method for rare variant meta-analysis that accurately estimates the null distribution to control type I error and reuses the linkage disequilibrium matrix across phenotypes to boost computational efficiency in phenome-wide analyses. Simulations using UK Biobank whole-exome sequencing data show that Meta-SAIGE effectively controls type I error and achieves power comparable to pooled individual-level analysis with SAIGE-GENE+. Applying Meta-SAIGE to 83 low-prevalence phenotypes in UK Biobank and All of Us whole-exome sequencing data identified 237 gene-trait associations. Notably, 80 of these associations were not significant in either dataset alone, underscoring the power of our meta-analysis.
    DOI:  https://doi.org/10.1038/s41588-025-02403-y
  51. Mol Cell. 2025 Nov 20. pii: S1097-2765(25)00861-5. [Epub ahead of print]85(22): 4109-4110
    Succinate puts the brakes on de novo purine synthesis.
    Timothy C Kenny, Kıvanç Birsoy.
      In this issue of Molecular Cell, Nengroo et al.1 report that the tricarboxylic acid (TCA) cycle enzyme succinate dehydrogenase (SDH) is essential for de novo purine synthesis, revealing a previously unrecognized metabolic dependency in cancer that can be leveraged therapeutically.
    DOI:  https://doi.org/10.1016/j.molcel.2025.10.020
  52. Int Rev Immunol. 2025 Nov 17. 1-30
    Mitochondria in the immune system: Therapeutic potential from mitochondria transfer.
    Thao Hoang Nhu Le, Van Thi Tuong Nguyen.
      Mitochondria serve as the powerhouses of living cells, supplying energy and essential building blocks for cellular activities. The immune system exhibits a dynamic and active characteristic within the body, wherein immune cells are constantly activated and primed for pathogens without causing harmful effects on the self-body. These characteristics necessitate that immune cells function effectively and correctly, supported by a sufficient energy supply and metabolism from the mitochondria. Mitochondrial dysfunction leads to immune dysregulation, resulting in inappropriate inflammation, autoimmunity, immunodeficiency, and hypersensitive responses, all of which contribute to the development of illness and disease. Recent studies on mitochondrial transfer in immune cells indicate that mitochondrial replacement could emerge as a promising tool for rectifying immune cell function. This review will emphasize the role of mitochondria in various immune cell types and explore how mitochondrial dysfunction can result in pathogenesis in different conditions. We also discuss the potential application of mitochondrial transfer and transplantation to- and from immune cells in the context of health and disease.
    Keywords:  Immunology; immunometabolism; mesenchymal stem cells; metabolism; mitochondria transfer
    DOI:  https://doi.org/10.1080/08830185.2025.2577986
  53. Elife. 2025 Nov 19. pii: e109482. [Epub ahead of print]14
    How one nutrient controls cell size.
    Angela Montero, Lydia W S Finley.
      The metabolic fate of a nutrient called pyruvate determines how big cells become.
    Keywords:  D. melanogaster; biochemistry; cell biology; cell growth; chemical biology; genetics; hepatocytes; human; pyruvate metabolism; redox state; translation
    DOI:  https://doi.org/10.7554/eLife.109482
  54. Nat Commun. 2025 Nov 20.
    The dynamic lateral gate of the mitochondrial β-barrel biogenesis machinery is blocked by darobactin A.
    Kathryn A Diederichs, Istvan Botos, Scout Hayashi, Gvantsa Gutishvili, Vadim Kotov, Katie Kuo, Akira Iinishi, Gwendolyn Cooper, Benjamin Schwarz, Herve Celia, Thomas C Marlovits, Kim Lewis, James C Gumbart, Joseph A Mindell, Susan K Buchanan.
      The folding and insertion of β-barrel proteins into the mitochondrial outer membrane is facilitated by the sorting and assembly machinery (SAM) complex. Here we report two 2.8 Å cryo-EM structures of the Thermothelomyces thermophilus SAM complex in the absence of substrate in which the Sam50 lateral gate adopts two different conformations: the first is a closed lateral gate as observed in previously published structures, while the second contains a Sam50 with the first four β-strands rotated outwards by approximately 45°, resulting in an open lateral gate. The observed monomeric open conformation contrasts our previous work where the open conformation was adopted by non-physiological up-down dimers. To understand how these lateral gate dynamics are influenced by substrate, we studied the interaction of the SAM complex with a β-signal peptide mimic, darobactin A. Darobactin A binds to the SAM complex with nanomolar affinity and inhibits the import and assembly of mitochondrial β-barrel proteins in vitro. Lastly, we solved a 3.0 Å cryo-EM structure of the Thermothelomyces thermophilus SAM complex bound to darobactin A, which reveals that darobactin A stabilizes the Sam50 lateral gate similar to the open conformation by binding to strand β1, therefore blocking β-barrel biogenesis.
    DOI:  https://doi.org/10.1038/s41467-025-66417-0
  55. EMBO J. 2025 Nov 17.
    Homeostatic control of energy metabolism by monocyte-derived macrophages.
    Rui Martins, Birte Blankehaus, Faouzi Braza, Miguel Mesquita, Pedro Ventura, Sumnima Singh, Sebastian Weis, Maria Pires, Sara Pagnotta, Qian Wu, Sílvia Cardoso, Elisa Jentho, Ana Figueiredo, Pedro Faísca, Ana Nóvoa, Vanessa Alexandra Morais, Stefanie K Wculek, David Sancho, Moises Mallo, Miguel P Soares.
      Multicellular organisms rely on inter-organ communication networks to maintain vital parameters within a dynamic physiological range. Macrophages are central to this homeostatic control system, sensing and responding to deviations of those parameters to sustain organismal homeostasis. Here, we demonstrate that dysregulation of iron (Fe) metabolism, imposed by the deletion of ferritin H chain (FTH) in mouse parenchymal cells, is sensed by monocyte-derived macrophages. In response, monocyte-derived macrophages support tissue function, energy metabolism, and thermoregulation via a mechanism that sustains the mitochondria of parenchymal cells. Mechanistically, FTH supports a transcriptional program promoting mitochondrial biogenesis in macrophages, involving mitochondrial transcription factor A (TFAM). Moreover, FTH sustains macrophage viability and supports intercellular mitochondrial transfer from donor parenchymal cells. In conclusion, monocyte-derived macrophages cross-regulate iron and energy metabolism to support tissue function and organismal homeostasis.
    Keywords:  Ferritin; Homeostasis; Macrophages; Metabolism; Mitochondria
    DOI:  https://doi.org/10.1038/s44318-025-00622-x
  56. Nat Commun. 2025 Nov 20.
    Combinatorial protein engineering identifies potent CRISPR activators with reduced toxicity.
    Marla Giddins, Alexander F Kratz, Mark B De Los Santos, Antoine Forget, Richa Tiwari, Gwendolyn Jang, Tomasz Blazejewski, Chuyan Qin, Yiming Huang, Yeh-Hsing Lao, Thomas Falconer, Kam W Leong, Nevan Krogan, Max Staller, Harris Wang, Lai Wei, Alejandro Chavez.
      Current protein engineering methods are inadequate to explore the combinatorial potential offered by nature's vast repertoire of protein domains-limiting our ability to create optimal synthetic tools. To overcome this barrier, we develop an approach to create and test thousands of chimeric proteins and employ it to probe an expansive combinatorial landscape of over 15,000 multi-domain CRISPR activators. Our findings indicate that many activators produce substantial cellular toxicity, often unrelated to their capacity to regulate gene expression. We also explore the biochemical features of activation domains and determine how their combinatorial interactions shape activator behavior. Finally, we identify two potent CRISPR activators, MHV and MMH, and demonstrate their enhanced activity across diverse targets and cell types compared to the gold-standard MCP activator, synergistic activation mediator (SAM).
    DOI:  https://doi.org/10.1038/s41467-025-65986-4
  57. Hum Mol Genet. 2025 Nov 20. pii: ddaf167. [Epub ahead of print]
    Loss of adenylosuccinate synthetase 1 in mice recapitulates features of ADSS1 myopathy.
    Morgan E Kim, Kathryn M Yammine, Emily T Hickey, Catalina Matias, Lou C Dubosclard, Jeffrey J Widrick, Jeffrey J Brault, Behzad Moghadaszadeh, Alan H Beggs.
      ADSS1 myopathy is an ultrarare congenital myopathy characterized by progressive cardiac and skeletal muscle degeneration with childhood to adolescent onset. This autosomal recessive disease is caused by mutations in the ADSS1 gene, encoding the enzyme adenylosuccinate synthetase (AdSS1). AdSS1 plays a critical role in the adenine nucleotide cycle, which is important for energy metabolism in muscle cells. Enzymatic defects, engendered by loss-of-function mutations in ADSS1, lead to a bottleneck in the adenine nucleotide cycle, causing metabolic dysfunction that ultimately results in progressive muscle weakness, mobility impairment, and respiratory and cardiac dysfunction, often requiring the use of a ventilator. Despite its debilitating nature, there are currently no cures or targeted treatments available, and little research into possible therapeutic strategies has been done. With a limited patient profile encompassing fewer than 200 known patients worldwide, establishing a mouse model for ADSS1 myopathy is critical to understanding its pathogenesis and for developing future therapies. Here, we present and characterize the first mouse model of ADSS1 myopathy-a constitutive Adss1 knockout model-by (1) defining its natural history, (2) exploring its metabolic pathomechanisms, and (3) characterizing its histopathological features. We find that Adss1KO/KO mice have subtle motor deficits and present with histopathological features consistent with patient phenotypes. Overall, we show that despite a relatively mild phenotype, this novel mouse model has quantifiable pathological features that can be used to develop therapies for, and further probe pathophysiology of, ADSS1 myopathy.
    Keywords:  ADSS1; adenylosuccinate synthetase; metabolic myopathy; mouse model; purine metabolism
    DOI:  https://doi.org/10.1093/hmg/ddaf167
  58. Nat Commun. 2025 Nov 17. 16(1): 9883
    Characterizing and controlling CRISPR repair outcomes in nondividing human cells.
    Gokul N Ramadoss, Samali J Namaganda, Manasi M Kumar, Jennifer R Hamilton, Rohit Sharma, Karena G Chow, Luke A Workley, Bria L Macklin, Mengyuan Sun, Alvin S Ha, Jia-Cheng Liu, Christof Fellmann, Hannah L Watry, Philip H Dierks, Rudra S Bose, Julianne Jin, Barbara S Perez, Cindy R Sandoval Espinoza, Madeline P Matia, Serena H Lu, Luke M Judge, Brian R Shy, Andre Nussenzweig, Britt Adamson, Niren Murthy, Jennifer A Doudna, Martin Kampmann, Bruce R Conklin.
      Genome editing is poised to revolutionize treatment of genetic diseases, but poor understanding and control of DNA repair outcomes hinders its therapeutic potential. DNA repair is especially understudied in nondividing cells like neurons, limiting the efficiency and precision of genome editing in many clinically relevant tissues. Here, we address this barrier by using induced pluripotent stem cells (iPSCs) and iPSC-derived neurons to examine how postmitotic human neurons repair Cas9-induced DNA damage. CRISPR editing outcomes differ dramatically in neurons compared to genetically identical dividing cells: neurons take longer to fully resolve this damage, and upregulate non-canonical DNA repair factors in the process. Manipulating this response with chemical or genetic perturbations allows us to direct DNA repair toward desired editing outcomes in nondividing human neurons, cardiomyocytes, and primary T cells. By studying DNA repair in clinically relevant cells, we reveal unforeseen challenges and opportunities for precise therapeutic editing.
    DOI:  https://doi.org/10.1038/s41467-025-66058-3
  59. Res Sq. 2025 Sep 29. pii: rs.3.rs-7603489. [Epub ahead of print]
    Endothelial CYB5R1 is a Coenzyme Q reductase that suppresses ferroptosis and atherosclerosis.
    Adam Straub, Robert Hall, Svetlana Samovich, Mate Katona, Shuai Yuan, Megan Miller, Scott Hahn, Rolondo Cuevas, Fei Cheng, Sonia Salvatore, Maximiliano Vazquez, Ahssan Sekandari, Cynthia St Hilaire, Marco Fazzari, Bruce Freeman, Francisco Schopfer, Valerian Kagan, Hülya Bayir.
      Spatial-temporal coordination of oxidoreductase substrate specificity and turnover regulates redox-mediated signaling, shaping physiological and pathological outcomes. Here, we reveal novel actions of cytochrome b5 reductase 1 (CYB5R1) when localized to the outer mitochondrial membrane of endothelial cells. Specifically, CYB5R1 functions as a Coenzyme Q (CoQ)-dependent redox cycler, protecting against iron-dependent lipid oxidation or ferroptosis. CYB5R1 catalyzes CoQ redox cycling via electron transfer reactions that suppresses both lipid hydroperoxide accumulation and ferroptosis. CoQ-insufficiency or disruption of CYB5R1-CoQ coupling impairs these reactions, leading to elevated hydrogen peroxide production and initiating a ferroptotic cascade. Ferroptosis plays a pathogenic role in atherogenesis, and we report that both global and endothelial-specific CYB5R1 knockout significantly exacerbate plaque formation. Through a rational chemical library design and screening, we synthesized and tested CP50, a quinone-nitroalkene hybrid that upregulates CYB5R1, prevents glutathione peroxidase-4 (GPX4) degradation, limits lipid oxidation, confers potent anti-ferroptotic activity and in a murine model, profoundly inhibit atherogenesis. These findings a) establish CYB5R1 as a novel mitochondrial "redox rheostat" that governs endothelial ferroptotic susceptibility through substrate redox regulation and b) reveals a safe small molecule therapeutic strategy that can impact a broad range of diseases.
    DOI:  https://doi.org/10.21203/rs.3.rs-7603489/v1
  60. Transfus Med Rev. 2025 Oct 26. pii: S0887-7963(25)00057-4. [Epub ahead of print]39(4): 150932
    Monitoring Mitochondrial Oxygen Tension: mitoPO2 as Physiologic Transfusion Trigger?
    Lucia W J M Streng, Floor A Harms, Egbert G Mik.
      Hemoglobin-based red blood cell transfusion (RBC) triggers are inadequate for personalized transfusion decisions because they are population-based and therefore unable to identify individual patients that will benefit from RBC transfusion. Therefore, physiological transfusion triggers are sought after to provide tools for a more individualize approach. Since mitochondria are the ultimate destination of oxygen it seems reasonable to suggest that measuring oxygen at the mitochondrial level might provide insight in the need for RBC transfusion. Mitochondrial oxygen tension (mitoPO2) is a novel clinical parameter that can be measured by an optical technology. This narrative review provides a brief introduction on mitoPO2 monitoring and uses 5 recent studies to explore the potential of mitoPO2 as tool for assessing need for transfusion and/or monitoring the effect of transfusion. A mathematical model shows an ideal behavior of mitoPO2 on critical hematocrit and from 4 recent clinical studies we learn that mitoPO2 is an independent parameter that can be used in transfusion-related studies. Further investigation into the potential role of mitoPO2 in transfusion medicine is needed.
    Keywords:  Delayed fluorescence; Mitochondrial oxygen tension; Protoporphyrin IX; Red blood cell transfusion; Transfusion trigger; mitoPO(2)
    DOI:  https://doi.org/10.1016/j.tmrv.2025.150932
  61. Nucleic Acids Res. 2025 Nov 18. pii: gkaf1126. [Epub ahead of print]
    OmniPath: integrated knowledgebase for multi-omics analysis.
    Dénes Türei, Jonathan Schaul, Nicolàs Palacio-Escat, Balázs Bohár, Yunfan Bai, Francesco Ceccarelli, Elif Çevrim, Macabe Daley, Melih Darcan, Daniel Dimitrov, Tunca Doğan, Daniel Domingo-Fernández, Aurelien Dugourd, Attila Gábor, Lejla Gul, Benjamin A Hall, Charles Tapley Hoyt, Olga Ivanova, Michal Klein, Toby Lawrence, Diego Mañanes, Dezső Módos, Sophia Müller-Dott, Márton Ölbei, Christina Schmidt, Bünyamin Şen, Fabian J Theis, Atabey Ünlü, Erva Ulusoy, Alberto Valdeolivas, Tamás Korcsmáros, Julio Saez-Rodriguez.
      Analysis and interpretation of omics data largely benefit from the use of prior knowledge. However, this knowledge is fragmented across resources and often is not directly accessible for analytical methods. We developed OmniPath (https://omnipathdb.org/), a database combining diverse molecular knowledge from 168 resources. It covers causal protein-protein, gene regulatory, microRNA, and enzyme-post-translational modification interactions, cell-cell communication, protein complexes, and information about the function, localization, structure, and many other aspects of biomolecules. It prioritizes literature curated data, and complements it with predictions and large scale databases. To enable interactive browsing of this large corpus of knowledge, we developed OmniPath Explorer, which also includes a large language model agent that has direct access to the database. Python and R/Bioconductor client packages and a Cytoscape plugin create easy access to customized prior knowledge for omics analysis environments, such as scverse. OmniPath can be broadly used for the analysis of bulk, single-cell, and spatial multi-omics data, especially for mechanistic and causal modeling.
    DOI:  https://doi.org/10.1093/nar/gkaf1126
  62. Adv Ther. 2025 Nov 21.
    Study Designs and Crafting Endpoints for Gene Therapy Development Programs in Rare Disease: A Narrative Review.
    on behalf of the Rare Disease Clinical Outcome Assessment Consortium
      Gene therapies are emerging as a promising strategy for the treatment of rare genetic diseases, for which treatment options are often limited and do not address the underlying disease mechanisms. However, there are significant challenges for gene therapy programs, including defining a suitable first-in-human cohort and selecting endpoints with appropriate variability, sensitivity, reliability, and clinical meaningfulness; a systematic framework for the assessment and approval of these treatments is lacking. In this review, we share insights from 12 clinical development programs that culminated in recent approvals of gene therapies for rare genetic diseases (2016-2023). These approvals highlight useful strategies for navigating the unique challenges of gene therapy trials, including early and frequent engagement with regulatory bodies, incorporating the patient voice, selecting meaningful clinical outcome assessments and suitable controls, and leveraging well-matched real-world data to understand long-term efficacy, durability, and safety. By systematically documenting and analyzing detailed examples in this review, it becomes possible to derive data-driven solutions that can inform the design of future studies. Such solutions may diverge from prior assumptions or preconceptions but can provide a more evidence-based foundation for improving trial efficiency, and ultimately accelerate the development of urgently needed therapies for patients with rare genetic diseases.
    Keywords:  Clinical development; Clinical outcome assessments; Clinical trials; Endpoints; Gene therapy; Genetic disorders; Marketing authorization; Rare diseases; Regulatory approval; Study design
    DOI:  https://doi.org/10.1007/s12325-025-03385-3
  63. Nature. 2025 Nov 19.
    ZAK activation at the collided ribosome.
    Vienna L Huso, Shuangshuang Niu, Marco A Catipovic, James A Saba, Timo Denk, Eugene Park, Jingdong Cheng, Otto Berninghausen, Thomas Becker, Rachel Green, Roland Beckmann.
      Ribosome collisions activate the ribotoxic stress response mediated by the MAP3K ZAK, which in turn regulates cell-fate consequences through downstream phosphorylation of the MAPKs p38 and JNK1. Despite the critical role of ZAK during cellular stress, a mechanistic and structural understanding of ZAK-ribosome interactions and how these lead to activation remain elusive. Here we combine biochemistry and cryo-electron microscopy to discover distinct ZAK-ribosome interactions required for constitutive recruitment and for activation. We find that upon induction of ribosome collisions, interactions between ZAK and the ribosomal protein RACK1 enable its activation by dimerization of its SAM domains at the collision interface. Furthermore, we discover how this process is negatively regulated by the ribosome-binding protein SERBP1 to prevent constitutive ZAK activation. Characterization of novel SAM variants as well as a known pathogenic variant of the SAM domain of ZAK supports a key role of the SAM domain in regulating kinase activity on and off the ribosome, with some mutants bypassing the ribosome requirement for ZAK activation. Collectively, our data provide a mechanistic blueprint of the kinase activity of ZAK at the collided ribosome interface.
    DOI:  https://doi.org/10.1038/s41586-025-09772-8
  64. Life Sci. 2025 Nov 15. pii: S0024-3205(25)00722-2. [Epub ahead of print] 124086
    Drp1 in Parkinson's disease: Mechanisms of disease pathology and the promise of targeted therapeutic strategies.
    Shan Liu, Zhipeng Huang, Zhixue Yin, Li Chen, Lisha Ye, Dechou Zhang, Xue Bai.
      Parkinson's Disease (PD) is a progressive neurodegenerative disorder marked by dopaminergic neuron degeneration, mitochondrial dysfunction, and Alpha-synuclein (α-synuclein) aggregation. Dynamin-related protein 1 (Drp1), a key regulator of mitochondrial fission, plays a critical role in PD. Overactivation of Drp1 causes excessive mitochondrial fragmentation, impairing mitochondrial function, increasing Reactive oxygen species (ROS) production, and exacerbating oxidative stress, neuroinflammation, and protein misfolding, all of which contribute to PD pathology. Targeting Drp1 with small molecule inhibitors and gene interventions has shown promise in preclinical models by reducing mitochondrial dysfunction, oxidative damage, and neuronal death. Combination therapies, integrating Drp1 inhibitors with antioxidants and anti-inflammatory agents, have demonstrated synergistic effects. Despite promising preclinical findings, clinical studies on Drp1-targeted therapies are still in early stages, with challenges like specificity and off-target effects. Future research will focus on refining Drp1-targeted therapies, including precision medicine, multi-target strategies, and clinical trials to assess efficacy, safety, and pharmacokinetics. This review highlights Drp1 as a promising therapeutic target for PD and discusses future clinical translation challenges.
    DOI:  https://doi.org/10.1016/j.lfs.2025.124086
  65. Cell. 2025 Nov 19. pii: S0092-8674(25)01234-6. [Epub ahead of print]
    BRAIN-MAGNET: A functional genomics atlas for interpretation of non-coding variants.
    Ruizhi Deng, Elena Perenthaler, Anita Nikoncuk, Soheil Yousefi, Kristina Lanko, Rachel Schot, Michela Maresca, Eva Medico-Salsench, Leslie E Sanderson, Michael J Parker, Wilfred F J van Ijcken, Joohyun Park, Marc Sturm, Tobias B Haack, Gennady V Roshchupkin, Eskeatnaf Mulugeta, Tahsin Stefan Barakat.
      Genome-wide assessment of genetic variation is becoming routine in genetics, yet functional interpretation of non-coding single nucleotide variants in both common and rare diseases remains a major challenge. Here, we used chromatin immunoprecipitation coupled to self-transcribing active regulatory region sequencing (ChIP-STARR-seq) to functionally annotate non-coding regulatory elements (NCREs) in cellular models of human brain development. This provides gene regulatory insights into neural stem cells and evidence of NCRE priming already in embryonic stem cells for later neural activity. Based on this functional genomics atlas, we developed BRAIN-MAGNET (brain-focused artificial intelligence method to analyze genomes for non-coding regulatory element mutation targets), a functionally validated convolutional neural network that predicts NCRE activity from DNA sequence composition and identifies nucleotides required for NCRE function. BRAIN-MAGNET allows fine-mapping of genome-wide association study (GWAS) loci for common neurological traits and prioritizing candidate disease-causing rare non-coding variants in genetically unexplained individuals with neurogenetic disorders. Together, this NCRE atlas and BRAIN-MAGNET represent a powerful resource for the interpretation of non-coding genetic variation, possibly aiding the identification of previously unrecognized enhanceropathies.
    Keywords:  Genomics England 100,000 Genomes project; RAB7A; artificial intelligence; diagnostics; enhancer; gene regulation; massively parallel reporter assay; neurodevelopmental disorders; neurogenetics; non-coding genome; whole-genome sequencing
    DOI:  https://doi.org/10.1016/j.cell.2025.10.029
  66. Spectrochim Acta A Mol Biomol Spectrosc. 2025 Nov 13. pii: S1386-1425(25)01501-X. [Epub ahead of print]348(Pt 1): 127193
    Polarity-responsive probe for dual-channel visualization of mitochondrial membrane potential via subcellular immigration.
    Qilong Zhang, Bingbing Pan, Ranxu Zhou, Mingze Wu, Gengxiu Zheng, Minggang Tian, Zhongqian Cui.
      Mitochondrial membrane potential (∆Ψm) plays central roles in cell apoptosis, signalling, metabolism, and other crucial bioevents. However, most of the current dual-emissive fluorescent probes for ∆Ψm works on aggregation mechanism, rendering possible interferences from inhomogeneous staining, cell numbers, and other factors. To resolve this knot, in this work we have developed a dual-emissive fluorescent probe detecting ∆Ψm based on polarity-response mechanism. The probe was designed to display different emission wavelength under different polarity, and simultaneously high affinity to both mitochondria and RNA. In live cells, mitochondria maintain a high negative transmembrane potential. Under this condition, the probe specifically targeted mitochondria because of its cationic structure. After the depolarization of ∆Ψm, the probe lost its mitochondrial targeting capability and shifted the target to RNA owing to its high RNA affinity. The distinct polar environments between the mitochondrial inner membrane and RNA result in a significant red shift in the fluorescence wavelength of the probe after its relocation from mitochondria to RNA. In this manner, the probe enabled the dual-emissive evaluation of the ∆Ψm. The probe was successfully applied to visualize the reversible change of ∆Ψm in real-time and in-situ manner. With the probe, the decrease of ∆Ψm in apoptosis procedure induced by toxins and anti-tumor drugs was also detected.
    Keywords:  Cell apoptosis; Dual-emissive visualization; Fluorescent probe; Mitochondrial membrane potential; Reversible detection
    DOI:  https://doi.org/10.1016/j.saa.2025.127193
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