bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2025–02–16
forty-six papers selected by
Catalina Vasilescu, Helmholz Munich
  1. Pharmacologic activation of integrated stress response kinases inhibits pathologic mitochondrial fragmentation.
  2. A microscopy-based screen identifies cellular kinases modulating mitochondrial translation.
  3. Mitochondrial DNA or Genomic DNA Variant(s): Utility of Exhaustive Sequencing in Leigh Syndrome.
  4. Overview of neuroimaging in primary mitochondrial disorders.
  5. Disruption of mitochondrial homeostasis and permeability transition pore opening in OPA1 iPSC-derived retinal ganglion cells.
  6. Mitofusin 2 displays fusion-independent roles in proteostasis surveillance.
  7. Evaluating the efficacy of vatiquinone in preclinical models of Leigh syndrome and GPX4 deficiency.
  8. Advances in human pre-tRNA maturation : TRMT10C and ELAC2 in focus.
  9. From Cell Architecture to Mitochondrial Signaling: Role of Intermediate Filaments in Health, Aging, and Disease.
  10. Mitochondria-targeting siRNA screening identifies mitochondrial calcium uniporter as a factor involved in nucleoid morphology.
  11. Diverse routes to mitophagy governed by ubiquitylation and mitochondrial import.
  12. FBXL4-Related Mitochondrial Depletion Syndrome Underscores the role of Mitophagy in Stem Cell Differentiation during Embryogenesis.
  13. HBimmCue: A Versatile Fluorescent Probe for Multi-Scale Imaging of Lipid Polarity and Membrane Order in Inner Mitochondrial Membrane.
  14. Mitochondrial DNA removal is essential for sperm development and activity.
  15. Clinical spectrum, treatment and outcomes of the m.10197G>A mutation in MT-ND3: a case report, systematic review and meta-analysis.
  16. Mitochondrial potassium channels: New properties and functions.
  17. Mitochondrial Amount Determines Doxorubicin-Induced Cardiotoxicity in Cardiomyocytes.
  18. Impact of physical activity on physical function, mitochondrial energetics, ROS production, and Ca2+ handling across the adult lifespan in men.
  19. Adenylate cyclase 10 promotes brown adipose tissue thermogenesis.
  20. Saccharomyces cerevisiae Dmo2p is required for the stability and maturation of newly translated Cox2p.
  21. TEFM facilitates transition from RNA synthesis to DNA synthesis at H-strand replication origin of mtDNA.
  22. Mitochondrial DNA Damage in the Retinal Pigmented Epithelium (RPE) and Its Role in RPE Pathobiology.
  23. [Focal Segmental Glomerulosclerosis Due to A3243G Point Mutation in the mtDNA Coding for tRNALeu(UUR)].
  24. The apo LETM1 F-EF-hand adopts a closed conformation that underlies a multi-modal sensory role in mitochondria.
  25. Loss of long-chain acyl-CoA dehydrogenase protects against acute kidney injury.
  26. Mitochondrial respiratory analysis of cryopreserved PBMCs isolated from human blood.
  27. Berberine is a Novel Mitochondrial Calcium Uniporter Inhibitor that Disrupts MCU-EMRE Assembly.
  28. Scientists use AI to design life-like enzymes from scratch.
  29. Editorial: Molecular and cellular pathways leading to mitochondrial dysfunction and neurodegeneration: lessons from in vivo models, volume II.
  30. ER-mitochondria contacts mediate lipid radical transfer via RMDN3/PTPIP51 phosphorylation to reduce mitochondrial oxidative stress.
  31. Phenotypic diversity in NAXE mutations.
  32. A non-hydrolysable peptidomimetic for mitochondrial targeting.
  33. Hexokinase-I directly binds to a charged membrane-buried glutamate of mitochondrial VDAC1 and VDAC2.
  34. Niacin ameliorates Charcot-Marie-Tooth 4B1 neuropathy without interfering with nerve regeneration.
  35. Adult Leigh Syndrome Associated with the m.15635T>C Mitochondrial DNA Variant Affecting the Cytochrome b (MT-CYB) Gene.
  36. Optimization of permeabilized brain tissue preparation to improve the analysis of mitochondrial oxidative capacities in specific subregions of the rat brain.
  37. Poldip2 promotes mtDNA elimination during Drosophila spermatogenesis to ensure maternal inheritance.
  38. Extracellular microvesicles/exosomes - magic bullets in horizontal transfer between cells of mitochondria and molecules regulating mitochondria activity.
  39. CRISPuRe-seq: pooled screening of barcoded ribonucleoprotein reporters reveals regulation of RNA polymerase III transcription by the integrated stress response via mTOR.
  40. Acetyl-CoA synthesis in the skin is a key determinant of systemic lipid homeostasis.
  41. Combined genomics and proteomics unveils elusive variants and vast aetiologic heterogeneity in dystonia.
  42. Ribophagy relies on Rpl12.
  43. Instability of high polygenic risk classification and mitigation by integrative scoring.
  44. MRC Centre for Neuromuscular Diseases Biobank London: its role in the advancement of rare and neuromuscular diseases research.
  45. The integrated stress response regulates 18S nonfunctional rRNA decay in mammals.
  46. Massively parallel in vivo Perturb-seq screening.
  1. Elife. 2025 Feb 12. pii: RP100541. [Epub ahead of print]13
    Pharmacologic activation of integrated stress response kinases inhibits pathologic mitochondrial fragmentation.
    Kelsey R Baron, Samantha Oviedo, Sophia Krasny, Mashiat Zaman, Rama Aldakhlallah, Prerona Bora, Prakhyat Mathur, Gerald Pfeffer, Michael J Bollong, Timothy E Shutt, Danielle A Grotjahn, R Luke Wiseman.
      Excessive mitochondrial fragmentation is associated with the pathologic mitochondrial dysfunction implicated in the pathogenesis of etiologically diverse diseases, including many neurodegenerative disorders. The integrated stress response (ISR) - comprising the four eIF2α kinases PERK, GCN2, PKR, and HRI - is a prominent stress-responsive signaling pathway that regulates mitochondrial morphology and function in response to diverse types of pathologic insult. This suggests that pharmacologic activation of the ISR represents a potential strategy to mitigate pathologic mitochondrial fragmentation associated with human disease. Here, we show that pharmacologic activation of the ISR kinases HRI or GCN2 promotes adaptive mitochondrial elongation and prevents mitochondrial fragmentation induced by the calcium ionophore ionomycin. Further, we show that pharmacologic activation of the ISR reduces mitochondrial fragmentation and restores basal mitochondrial morphology in patient fibroblasts expressing the pathogenic D414V variant of the pro-fusion mitochondrial GTPase MFN2 associated with neurological dysfunctions, including ataxia, optic atrophy, and sensorineural hearing loss. These results identify pharmacologic activation of ISR kinases as a potential strategy to prevent pathologic mitochondrial fragmentation induced by disease-relevant chemical and genetic insults, further motivating the pursuit of highly selective ISR kinase-activating compounds as a therapeutic strategy to mitigate mitochondrial dysfunction implicated in diverse human diseases.
    Keywords:  cell biology; human; integrated stress response; mitochondrial fragmentation; mitochondrial morphology; mouse; stress signaling
    DOI:  https://doi.org/10.7554/eLife.100541
  2. Cell Rep. 2025 Jan 28. pii: S2211-1247(24)01494-3. [Epub ahead of print]44(1): 115143
    A microscopy-based screen identifies cellular kinases modulating mitochondrial translation.
    Roya Yousefi, Luis Daniel Cruz-Zaragoza, Anusha Valpadashi, Carina Hansohn, Drishan Dahal, Ricarda Richter-Dennerlein, Silvio Rizzoli, Henning Urlaub, Peter Rehling, David Pacheu-Grau.
      Mitochondrial DNA encodes 13 subunits of the oxidative phosphorylation (OXPHOS) system, which are synthesized inside the organelle and essential for cellular energy supply. How mitochondrial gene expression is regulated and integrated into cellular physiology is little understood. Here, we perform a high-throughput screen combining fluorescent labeling of mitochondrial translation products with small interfering RNA (siRNA)-mediated knockdown to identify cellular kinases regulating translation. As proof of principle, the screen identifies known kinases that affect mitochondrial translation, and it also reveals several kinases not yet linked to this process. Among the latter, we focus on the primarily cytosolic kinase, fructosamine 3 kinase (FN3K), which localizes partially to the mitochondria to support translation. FN3K interacts with the mitochondrial ribosome and modulates its assembly, thereby affecting translation. Overall, our work provides a reliable approach to identify protein functions for mitochondrial gene expression in a high-throughput manner.
    Keywords:  CP: Metabolism; CP: Molecular biology; cellular kinases; click chemistry; mito-FUNCAT; mitochondrial translation; siRNA library
    DOI:  https://doi.org/10.1016/j.celrep.2024.115143
  3. Am J Med Genet A. 2025 Feb 08. e64019
    Mitochondrial DNA or Genomic DNA Variant(s): Utility of Exhaustive Sequencing in Leigh Syndrome.
    Pauline Gaignard, Pierre-Hadrien Becker, Anne-Frederique Dessein, Elise Lebigot, Abdelhamid Slama, Karine Mention, Jamal Ghoumid.
      Pathogenic variants in the nuclear gene NDUFAF8 are a rare cause of mitochondrial complex I deficiency with only three cases described to date. We report here a new case of NDUFAF8 deficiency confirming the phenotype of NDUFAF8-induced complex I biochemical defect, Leigh syndrome and premature death. As a mitochondrial DNA variant in a gene encoding a complex I subunit was also identified in this patient, we discuss the molecular heterogeneity of Leigh syndrome and the need to explore the mitochondrial and nuclear genome to ensure a reliable diagnosis.
    Keywords:  Leigh syndrome; NDUFAF8; complex I; mitochondrial DNA
    DOI:  https://doi.org/10.1002/ajmg.a.64019
  4. Pediatr Radiol. 2025 Feb 12.
    Overview of neuroimaging in primary mitochondrial disorders.
    Sedat Giray Kandemirli, Khalid Al-Dasuqi, Bulent Aslan, Amy Goldstein, Cesar Augusto P F Alves.
      Advancements in understanding the clinical, biochemical, and genetic aspects of primary mitochondrial disorders, along with the identification of a broad range of phenotypes frequently involving the central nervous system, have opened a new and crucial area in neuroimaging. This expanding knowledge presents significant challenges for radiologists in clinical settings, as the neuroimaging features and their associated metabolic abnormalities become more complex. This review offers a comprehensive overview of the key neuroimaging features associated with the common primary mitochondrial disorders. It highlights both the classical imaging findings and the emerging diagnostic insights related to several previously identified causative genes for these diseases. The review also provides an in-depth description of the clinicoradiologic presentations and potential underlying mitochondrial defects, aiming to enhance diagnostic abilities of radiologists in identifying primary mitochondrial diseases in their clinical practice.
    Keywords:  Kearns-Sayre syndrome; Leigh syndrome; Mitochondria; Mitochondrial diseases; Neuroimaging
    DOI:  https://doi.org/10.1007/s00247-025-06172-y
  5. Acta Neuropathol Commun. 2025 Feb 13. 13(1): 28
    Disruption of mitochondrial homeostasis and permeability transition pore opening in OPA1 iPSC-derived retinal ganglion cells.
    Michael Whitehead, Joshua P Harvey, Paul E Sladen, Giada Becchi, Kritarth Singh, Yujiao Jennifer Sun, Thomas Burgoyne, Michael R Duchen, Patrick Yu-Wai-Man, Michael E Cheetham.
      Dominant optic atrophy (DOA) is the most common inherited optic neuropathy, characterised by the selective loss of retinal ganglion cells (RGCs). Over 60% of DOA cases are caused by pathogenic variants in the OPA1 gene, which encodes a dynamin-related GTPase protein. OPA1 plays a key role in the maintenance of the mitochondrial network, mitochondrial DNA integrity and bioenergetic function. However, our current understanding of how OPA1 dysfunction contributes to vision loss in DOA patients has been limited by access to patient-derived RGCs. Here, we used induced pluripotent stem cell (iPSC)-RGCs to study how OPA1 dysfunction affects cellular homeostasis in human RGCs. iPSCs derived from a DOA+ patient with the OPA1 R445H variant and isogenic CRISPR-Cas9-corrected iPSCs were differentiated to iPSC-RGCs. Defects in mitochondrial networks and increased levels of reactive oxygen species were observed in iPSC-RGCs carrying OPA1 R445H. Ultrastructural analyses also revealed changes in mitochondrial shape and cristae structure, with decreased endoplasmic reticulum (ER): mitochondrial contact length in DOA iPSC-RGCs. Mitochondrial membrane potential was reduced and its maintenance was also impaired following inhibition of the F1Fo-ATP synthase with oligomycin, suggesting that mitochondrial membrane potential is maintained in DOA iPSC-RGCs through reversal of the ATP synthase and ATP hydrolysis. These impairments in mitochondrial structure and function were associated with defects in cytosolic calcium buffering following ER calcium release and store-operated calcium entry, and following stimulation with the excitatory neurotransmitter glutamate. In response to mitochondrial calcium overload, DOA iPSC-RGCs exhibited increased sensitivity to opening of the mitochondrial permeability transition pore. These data reveal novel aspects of DOA pathogenesis in R445H patient-derived RGCs. The findings suggest a mechanism in which primary defects in mitochondrial network dynamics disrupt core mitochondrial functions, including bioenergetics, calcium homeostasis, and opening of the permeability transition pore, which may contribute to vision loss in DOA patients.
    Keywords:  Calcium homeostasis; Dominant optic atrophy; Mitochondrial networks; Neurodegeneration; OPA1; Retinal ganglion cells; iPSCs
    DOI:  https://doi.org/10.1186/s40478-025-01942-z
  6. Nat Commun. 2025 Feb 10. 16(1): 1501
    Mitofusin 2 displays fusion-independent roles in proteostasis surveillance.
    Mariana Joaquim, Selver Altin, Maria-Bianca Bulimaga, Tânia Simões, Hendrik Nolte, Verian Bader, Camilla Aurora Franchino, Solenn Plouzennec, Karolina Szczepanowska, Elena Marchesan, Kay Hofmann, Marcus Krüger, Elena Ziviani, Aleksandra Trifunovic, Arnaud Chevrollier, Konstanze F Winklhofer, Elisa Motori, Margarete Odenthal, Mafalda Escobar-Henriques.
      Mitochondria are essential organelles and their functional state dictates cellular proteostasis. However, little is known about the molecular gatekeepers involved, especially in absence of external stress. Here we identify a role of MFN2 in quality control independent of its function in organellar shape remodeling. MFN2 ablation alters the cellular proteome, marked for example by decreased levels of the import machinery and accumulation of the kinase PINK1. Moreover, MFN2 interacts with the proteasome and cytosolic chaperones, thereby preventing aggregation of newly translated proteins. Similarly to MFN2-KO cells, patient fibroblasts with MFN2-disease variants recapitulate excessive protein aggregation defects. Restoring MFN2 levels re-establishes proteostasis in MFN2-KO cells and rescues fusion defects of MFN1-KO cells. In contrast, MFN1 loss or mitochondrial shape alterations do not alter protein aggregation, consistent with a fusion-independent role of MFN2 in cellular homeostasis. In sum, our findings open new possibilities for therapeutic strategies by modulation of MFN2 levels.
    DOI:  https://doi.org/10.1038/s41467-025-56673-5
  7. Orphanet J Rare Dis. 2025 Feb 10. 20(1): 65
    Evaluating the efficacy of vatiquinone in preclinical models of Leigh syndrome and GPX4 deficiency.
    Ernst-Bernhard Kayser, Michael Mulholland, Elizaveta A Olkhova, Yihan Chen, Holly Coulson, Owen Cairns, Vivian Truong, Katerina James, Brittany M Johnson, Allison Hanaford, Simon C Johnson.
       BACKGROUND: Genetic mitochondrial diseases are a major challenge in modern medicine. These impact ~ 1:4,000 individuals and there are currently no effective therapies. Leigh syndrome is the most common pediatric presentation of mitochondrial disease. In humans, patients are often treated with antioxidants, vitamins, and strategies targeting energetics. The vitamin-E related compound vatiquinone (EPI-743, α-tocotrienol quinone) has been the subject of at least 19 clinical trials in the US since 2012, but the effects of vatiquinone on an animal model of mitochondrial disease have not yet been reported. Here, assessed the impact of vatiquinone in cellular assays and animal models of mitochondrial disease.
    METHODS: The efficacy of vatiquinone in vitro was assessed using human fibroblasts and HEK293 cells treated with the ferroptosis inducers RSL3 and BSO + Fe(III)Citrate, the mitochondrial oxidative stress inducer paraquat, and the electron transport chain complex I inhibitor rotenone. The therapeutic potential of vatiquinone in vivo was assessed using the tamoxifen-induced mouse model for GPX4 deficiency and the Ndufs4 knockout mouse model of Leigh syndrome.
    RESULTS: Vatiquinone robustly prevented death in cultured cells induced by RSL3 or BSO/iron, but had no effect on paraquat induced cell death. Vatiquinone had no impact on disease onset, progression, or survival in either the tamoxifen-inducible GPX4 deficient model or the Ndufs4(-/-) mouse model, though the drug may have reduced seizure risk.
    CONCLUSIONS: Vatiquinone prevents ferroptosis, but fails to attenuate cell death induced by paraquat or rotenone and provided no significant benefit to survival in two mouse models of disease. Vatiquinone may prevent seizures in the Ndufs4(-/-) model. Our findings are consistent with recent press statements regarding clinical trial results and have implications for drug trial design and reporting in patients with rare diseases.
    Keywords:  Antioxidant; EPI-743; GPX4; Leigh syndrome; Mitochondrial disease; ROS; Vatiquinone
    DOI:  https://doi.org/10.1186/s13023-025-03582-x
  8. J Mol Biol. 2025 Feb 10. pii: S0022-2836(25)00055-5. [Epub ahead of print] 168989
    Advances in human pre-tRNA maturation : TRMT10C and ELAC2 in focus.
    Juhi Sikarwar, Vincent Meynier, Carine Tisné.
      Mitochondrial pre-tRNA maturation is a multi-step process involving the removal of the 5'-leader by PRORP, 3'-trailer processing by ELAC2, 3'-CCA addition by TRNT1, and the incorporation of post-transcriptional modifications. In metazoans, the low structural stability of mitochondrial pre-tRNAs adds significant complexity to these steps, and defects in their maturation have been implicated in various human mitochondrial disorders. In this case, the tRNA methyltransferase complex TRMT10C/SDR5C1 compensates for the pre-tRNA structural alteration to present the pre-tRNA to maturation enzymes. Cryo-electron microscopy structures of human mitochondrial pre-tRNA maturation complexes have provided critical insights into these essential processes. Here we review the current understanding of tRNA maturation within human mitochondria and explore its implications for nuclear pre-tRNA maturation.
    Keywords:  ELAC2; TRMT10C; TRNT1; mitochondria; pre-tRNA maturation; pre-tRNA processing
    DOI:  https://doi.org/10.1016/j.jmb.2025.168989
  9. Int J Mol Sci. 2025 Jan 27. pii: 1100. [Epub ahead of print]26(3):
    From Cell Architecture to Mitochondrial Signaling: Role of Intermediate Filaments in Health, Aging, and Disease.
    Emanuele Marzetti, Rosa Di Lorenzo, Riccardo Calvani, Vito Pesce, Francesco Landi, Hélio José Coelho-Júnior, Anna Picca.
      The coordination of cytoskeletal proteins shapes cell architectures and functions. Age-related changes in cellular mechanical properties have been linked to decreased cellular and tissue dysfunction. Studies have also found a relationship between mitochondrial function and the cytoskeleton. Cytoskeleton inhibitors impact mitochondrial quality and function, including motility and morphology, membrane potential, and respiration. The regulatory properties of the cytoskeleton on mitochondrial functions are involved in the pathogenesis of several diseases. Disassembly of the axon's cytoskeleton and the release of neurofilament fragments have been documented during neurodegeneration. However, these changes can also be related to mitochondrial impairments, spanning from reduced mitochondrial quality to altered bioenergetics. Herein, we discuss recent research highlighting some of the pathophysiological roles of cytoskeleton disassembly in aging, neurodegeneration, and neuromuscular diseases, with a focus on studies that explored the relationship between intermediate filaments and mitochondrial signaling as relevant contributors to cellular health and disease.
    Keywords:  axonal transport; cell architecture; cell quality; cytoskeleton; mitochondrial quality; muscle aging; neurodegeneration; neurofilaments; sarcomere; vimentin
    DOI:  https://doi.org/10.3390/ijms26031100
  10. J Biochem. 2025 Feb 10. pii: mvaf008. [Epub ahead of print]
    Mitochondria-targeting siRNA screening identifies mitochondrial calcium uniporter as a factor involved in nucleoid morphology.
    Hirotaka Kanon, Takaya Ishihara, Reiko Ban-Ishihara, Azusa Ota, Tatsuki Yasuda, Aoi Ichikawa, Ruo Ueyama, Taiki Baba, Kohsuke Takeda, Emi Ogasawara, Naotada Ishihara.
      Mitochondria are believed to have originated from the endosymbiosis of bacteria and they still contain their own genome, which is called mitochondrial DNA (mtDNA). Under fluorescence microscopy of cultured mammalian cells, mtDNA is observed as numerous tiny dot-like structures called mitochondrial nucleoids. In live-imaging, the morphology and distribution of nucleoids are change dynamically, but the molecular details remain poorly understood. In this study, we constructed a custom siRNA library targeting 1,164 human mitochondria-related genes, and from live-imaging-based screening of HeLa cells, we identified that mitochondria calcium uniporter (MCU), a pore-forming subunit of the mitochondrial Ca2+ channel, is involved in nucleoid morphology. We found that suppression of MCU by RNAi induced the formation of highly enlarged nucleoids as well as respiratory dysfunction and that the re-introduction of MCU or treatment with Ca2+ ionophore recovered the enlarged nucleoid morphology. These results suggest that mitochondrial Ca2+ uptake via MCU is associated with nucleoid morphology. The constructed siRNA library might be widely applied to analyze the roles of mitochondrial proteins in various cellular events, making it useful to understand the multifaceted functions of mitochondria in human cells.
    Keywords:  Mitochondria; mitochondrial calcium ion; mitochondrial calcium uniporter; mitochondrial nucleoid; siRNA screening
    DOI:  https://doi.org/10.1093/jb/mvaf008
  11. Trends Cell Biol. 2025 Feb 07. pii: S0962-8924(25)00003-0. [Epub ahead of print]
    Diverse routes to mitophagy governed by ubiquitylation and mitochondrial import.
    Michael J Clague, Sylvie Urbé.
      The selective removal of mitochondria by mitophagy proceeds via multiple mechanisms and is essential for human well-being. The PINK1/Parkin and NIX/BNIP3 pathways are strongly linked to mitochondrial dysfunction and hypoxia, respectively. Both are regulated by ubiquitylation and mitochondrial import. Recent studies have elucidated how the ubiquitin kinase PINK1 acts as a sensor of mitochondrial import stress through stable interaction with a mitochondrial import supercomplex. The stability of BNIP3 and NIX is regulated by the SCFFBXL4 ubiquitin ligase complex. Substrate recognition requires an adaptor molecule, PPTC7, whose availability is limited by mitochondrial import. Unravelling the functional implications of each mode of mitophagy remains a critical challenge. We propose that mitochondrial import stress prompts a switch between these two pathways.
    Keywords:  BNIP3; FBXL4; PINK1; PPTC7; mitophagy; ubiquitin
    DOI:  https://doi.org/10.1016/j.tcb.2025.01.003
  12. Stem Cell Rev Rep. 2025 Feb 12.
    FBXL4-Related Mitochondrial Depletion Syndrome Underscores the role of Mitophagy in Stem Cell Differentiation during Embryogenesis.
    Pankaj Prasun.
      FBXL4- related mitochondrial depletion syndrome is a very rare inherited disorder characterized by global developmental delays, hypotonia, seizures, growth failure, and early onset lactic acidosis. Often, it is associated with structural brain and heart defects, and facial dysmorphism suggesting an embryogenesis defect. FBXL4 encodes F-box and leucine-rich repeat protein 4 (FBXL4) which is involved in mitochondrial quality control and maintenance by regulating mitophagy. A recent study suggests that FBXL4 deficiency leads to increased mitophagy. Fine tuning of mitophagy is essential for stem cell differentiation during embryogenesis. The disruption of this process is the likely explanation of developmental defects in FBXL4- related mitochondrial depletion syndrome.
    Keywords:  Embryogenesis; FBXL4; Mitochondria; Mitophagy; Stem cell Differentiation
    DOI:  https://doi.org/10.1007/s12015-025-10854-3
  13. Adv Sci (Weinh). 2025 Feb 09. e2414343
    HBimmCue: A Versatile Fluorescent Probe for Multi-Scale Imaging of Lipid Polarity and Membrane Order in Inner Mitochondrial Membrane.
    Shu Gao, Jing Sun, Yiwei Hou, Xichuan Ge, Ming Shi, Hongxi Zheng, Yan Zhang, Meiqi Li, Baoxiang Gao, Peng Xi.
      Mitochondrial membrane environmental dynamics are crucial for understanding function, yet high-resolution observation remains challenging. Here, HBimmCue is introduced as a fluorescent probe localized to inner mitochondrial membrane (IMM) that reports lipid polarity and membrane order changes, which correlate with cellular respiration levels. Using HBimmCue and fluorescence lifetime imaging microscopy (FLIM), IMM lipid heterogeneity is uncovered across scales, from nanoscale structures within individual mitochondria to mouse pre-implantation embryos. At the sub-organelle level, stimulated emission depletion (STED)-FLIM imaging highlights nanoscale polarity variations within the IMM. At the sub-cellular and cellular level, reduced IMM lipid polarity is observed in damaged mitochondria marked for lysosomal degradation and distinct IMM lipid distributions are identified in neurons and disease models. Additionally, metabolic dysfunction associated with oocytes aging and metabolic reprogramming from zygote to blastocyst is detected. Together, the work demonstrates the broad applicability of HBimmCue, offering a new paradigm for investigating lipid polarity and respiration level at multiple scales.
    Keywords:  HBimmCue; fluorescence lifetime imaging microscopy; inner mitochondrial membrane; lipid polarity
    DOI:  https://doi.org/10.1002/advs.202414343
  14. EMBO J. 2025 Feb 11.
    Mitochondrial DNA removal is essential for sperm development and activity.
    Zhe Chen, Fan Zhang, Annie Lee, Michaela Yamine, Zong-Heng Wang, Guofeng Zhang, Christian Combs, Hong Xu.
      Active mitochondrial DNA (mtDNA) elimination during spermatogenesis has emerged as a conserved mechanism ensuring the uniparental mitochondrial inheritance in animals. However, given the existence of post-fertilization processes degrading sperm mitochondria, the physiological significance of mtDNA removal during spermatogenesis is not clear. Here we show that mtDNA clearance is indispensable for sperm development and activity. We uncover a previously unappreciated role of Poldip2 as a mitochondrial exonuclease that is specifically expressed in late spermatogenesis and required for sperm mtDNA elimination in Drosophila. Loss of Poldip2 impairs mtDNA clearance in elongated spermatids and impedes the progression of individualization complexes that strip away cytoplasmic materials and organelles. Over time, poldip2 mutant sperm exhibit marked nuclear genome fragmentation, and the flies become completely sterile. Notably, these phenotypes were rescued by expressing a mitochondrially targeted bacterial exonuclease, which ectopically removes mtDNA. Our work illustrates the developmental necessity of mtDNA clearance for effective cytoplasm removal at the end of spermatid morphogenesis, and for preventing potential nuclear-mitochondrial genome imbalance in mature sperm, in which nuclear genome activity is shut down.
    Keywords:   Drosophila spermatogenesis; EndoG; Exonuclease; Male Sterile; Maternal Inheritance
    DOI:  https://doi.org/10.1038/s44318-025-00377-5
  15. Orphanet J Rare Dis. 2025 Feb 08. 20(1): 59
    Clinical spectrum, treatment and outcomes of the m.10197G>A mutation in MT-ND3: a case report, systematic review and meta-analysis.
    YuZhi Shi, Bin Chen, SongTao Niu, XinGao Wang, ZaiQiang Zhang.
       BACKGROUND: A correlation between various sites or types of mutations in mitochondrial DNA ND3 and the development of a specific mitochondrial disease or phenotype has yet to be fully established.
    METHODS: This study reports a rare case of adult-onset Leigh syndrome (LS) and Leber hereditary optic neuropathy and dystonia (LDYT) overlap syndrome caused by the m.10197G>A mutation in ND3. A review of the literature was conducted to investigate the clinical spectrum, treatment and outcome resulting from the m.10197G>A mutation. Phenotypes associated with the m.10197G>A mutation were classified into three categories: LS/LS+ (LS-involved overlap syndrome), Leber hereditary optic neuropathy (LHON)/LHON+ (LHON-involved overlap syndrome) and other mitochondrial encephalopathies or presentations.
    RESULTS: A total of 84 participants (78 patients and 6 asymptomatic carriers) with the m.10197G>A mutation retrieved from 33 articles and the patient whose case we reported were included in the review and meta-analysis. Among all the participants, 55.3% (47/85) and 28.2% (24/85) presented with LS/LS+ and LHON/LHON+, respectively. The median age at onset for LS/LS+ was significantly younger than that for LHON/LHON+ [median, (Q1-Q3), 3.0 (0.58-9.5) vs. 13.5 (5.75-41.75), P = 0.001]. A negative linear correlation was observed between mutation load and age of onset in patients who presented with LS/LS+ (R2 = 0.592, P < 0.001), with the age of onset ranging from infancy to adulthood. Patients with an older age at onset [OR (95% CI), 1.46 (1.12-1.91), P = 0.005] or higher mutation loads [OR (95% CI), 1.14 (1.03-1.26), P = 0.011] were more likely to present with LHON/LHON+ than with LS/LS+. A total of 17 patients were documented as having received a combination of mitochondrial cofactor treatments. Compared with patients with LHON/LHON+, patients with LS/LS+ exhibited an exceedingly high probability of a stable or worsen outcome (93.8% vs. 33.3%, P = 0.006).
    CONCLUSIONS: LS/LS+ and LHON/LHON+ are the predominant presentations of the m.10197G>A mutation. An older age at onset and greater mutation load increases the probability of an LHON/LHON+ presentation. Patients presenting with LS/LS+ have an exceedingly high possibility of an unfavorable outcome. The identification of factors and outcomes associated with phenotypes in patients with the m.10197G>A mutation facilitates the provision of improved prognostic counseling for patients and their family members who are carriers of this mutation.
    Keywords:   ND3 ; Dystonia; Leber hereditary optic neuropathy; Leigh syndrome; Mitochondrial disease
    DOI:  https://doi.org/10.1186/s13023-025-03588-5
  16. Biochim Biophys Acta Bioenerg. 2025 Feb 09. pii: S0005-2728(25)00012-X. [Epub ahead of print] 149546
    Mitochondrial potassium channels: New properties and functions.
    Adam Szewczyk, Piotr Bednarczyk, Bogusz Kulawiak, Monika Żochowska, Barbara Kalenik, Joanna Lewandowska, Karolina Pytlak, Shur Gałecka, Antoni Wrzosek, Piotr Koprowski.
      Mitochondria are recently implicated in phenomena such as cytoprotection, cellular senescence, tumor metabolism, and inflammation. The basis of these processes relies on biochemical functions of mitochondria such as the synthesis of reactive oxygen species or biophysical properties such as the integrity of the inner mitochondrial membrane. The transport of potassium cations plays an important role in all these events. The K+ influx is mediated by potassium channels present in the inner mitochondrial membrane. In this article, we present an overview of our new findings on the properties of mitochondrial large-conductance calcium-activated and mitochondrial ATP-regulated potassium channels. This concerns the role of mitochondrial potassium channels in cellular senescence, and interactions with other mitochondrial proteins or small molecules such as quercetin, hemin, and hydrogen sulfide. We also discuss the prospects of research on potassium channels present in mitochondria.
    Keywords:  Hemin; Hydrogen sulfide; Kinases; Mitochondria; Potassium channels; Quercetin; ROS; Senescence
    DOI:  https://doi.org/10.1016/j.bbabio.2025.149546
  17. Adv Sci (Weinh). 2025 Feb 07. e2412017
    Mitochondrial Amount Determines Doxorubicin-Induced Cardiotoxicity in Cardiomyocytes.
    Weiyao Xiong, Bin Li, Jianan Pan, Dongjiu Li, Haihua Yuan, Xin Wan, Yanjie Zhang, Lijun Fu, Junfeng Zhang, Ming Lei, Alex Chia Yu Chang.
      Doxorubicin, an anthracycline commonly used for treating cancer patients, is known for its cardiotoxic side-effects. Although dose-dependent, but susceptibility remains variable among patients, and childhood-exposure-adult-onset remains challenging. Besides topoisomerase toxicity, Doxorubicin is also toxic to the mitochondria yet the underlying late onset mechanism remains elusive. Here, it is observed that the mitochondrial copy number in PBMCs of patients treated with anthracycline chemotherapy is negatively correlated with the change in plasma BNP levels after treatment. Isogenic hiPSC-CMs are generated with high, norm, and low mitochondrial copy numbers using mitochondrial transplantation and the YFP-Parkin system. Remarkably, lower mitochondria copy number translates to lower IC50, suggesting increased susceptibility. Mitochondria supplementation by intramyocardial injection prevents doxorubicin induced heart failure. Mechanistically, doxorubicin treatment leads to mPTP opening and mitochondrial DNA (mtDNA) leakage. This mtDNA leakage event activates the cGAS-STING pathway and drives inflammation and myocardial senescence. Cardiomyocyte-specific knockout of Sting (Myh6-Cre/Stingflox/flox; StingCKO) and over expression of mitochondrial tagged DNase1 in mice partially rescue doxorubicin-induced cardiac dysfunction. In conclusion, the work establishes a negative correlation between cardiomyocyte mitochondrial copy number and doxorubicin toxicity. Molecularly, it is demonstrated that mtDNA leakage activates cGAS-STING pathway and accelerates myocardial dysfunction. These insights offer new co-administration strategies for cancer patients.
    Keywords:  cGAS‐STING; doxorubicin induced cardiotoxicity; mitochondrial amount; mitochondrial transplantation; senescence
    DOI:  https://doi.org/10.1002/advs.202412017
  18. Cell Rep Med. 2025 Feb 06. pii: S2666-3791(25)00041-2. [Epub ahead of print] 101968
    Impact of physical activity on physical function, mitochondrial energetics, ROS production, and Ca2+ handling across the adult lifespan in men.
    Marina Cefis, Vincent Marcangeli, Rami Hammad, Jordan Granet, Jean-Philippe Leduc-Gaudet, Pierrette Gaudreau, Caroline Trumpff, Qiuhan Huang, Martin Picard, Mylène Aubertin-Leheudre, Marc Bélanger, Richard Robitaille, José A Morais, Gilles Gouspillou.
      Aging-related muscle atrophy and weakness contribute to loss of mobility, falls, and disability. Mitochondrial dysfunction is widely considered a key contributing mechanism to muscle aging. However, mounting evidence positions physical activity as a confounding factor, making unclear whether muscle mitochondria accumulate bona fide defects with aging. To disentangle aging from physical activity-related mitochondrial adaptations, we functionally profiled skeletal muscle mitochondria in 51 inactive and 88 active men aged 20-93. Physical activity status confers partial protection against age-related decline in physical performance. Mitochondrial respiration remains unaltered in active participants, indicating that aging per se does not alter mitochondrial respiratory capacity. Mitochondrial reactive oxygen species (ROS) production is unaffected by aging and higher in active participants. In contrast, mitochondrial calcium retention capacity decreases with aging regardless of physical activity and correlates with muscle mass, performance, and the stress-responsive metabokine/mitokine growth differentiation factor 15 (GDF15). Targeting mitochondrial calcium handling may hold promise for treating aging-related muscle impairments.
    Keywords:  calcium retention capacity; functional capacities; intermuscular fat accumulation; mitochondria; mitochondrial permeability transition pore; muscle atrophy and weakness; physical performance; reactive oxygen species; sarcopenia; skeletal muscle aging
    DOI:  https://doi.org/10.1016/j.xcrm.2025.101968
  19. iScience. 2025 Feb 21. 28(2): 111833
    Adenylate cyclase 10 promotes brown adipose tissue thermogenesis.
    Anupam Das, Christine Mund, Eman Hagag, Ruben Garcia-Martin, Eleftheria Karadima, Anke Witt, Mirko Peitzsch, Andreas Deussen, Triantafyllos Chavakis, Thomas Noll, Vasileia Ismini Alexaki.
      Brown adipose tissue (BAT) thermogenesis dissipates energy through heat production and thereby it opposes metabolic disease. It is mediated by mitochondrial membrane uncoupling, yet the mechanisms sustaining the mitochondrial membrane potential (ΔΨm) in brown adipocytes are poorly understood. Here we show that isocitrate dehydrogenase (IDH) activity and the expression of the soluble adenylate cyclase 10 (ADCY10), a CO2/bicarbonate sensor residing in mitochondria, are upregulated in BAT of cold-exposed mice. IDH inhibition or ADCY10 deficiency reduces cold resistance of mice. Mechanistically, IDH increases the ΔΨm in brown adipocytes via ADCY10. ADCY10 sustains complex I activity and the ΔΨm via exchange protein activated by cAMP1 (EPAC1). However, neither IDH nor ADCY10 inhibition affect uncoupling protein 1 (UCP1) expression. Hence, we suggest that ADCY10, acting as a CO2/bicarbonate sensor, mediates the effect of IDH on complex I activity through cAMP-EPAC1 signaling, thereby maintaining the ΔΨm and enabling thermogenesis in brown adipocytes.
    Keywords:  Cell biology; Molecular biology; Physiology
    DOI:  https://doi.org/10.1016/j.isci.2025.111833
  20. FEBS J. 2025 Feb 11.
    Saccharomyces cerevisiae Dmo2p is required for the stability and maturation of newly translated Cox2p.
    Maria Antônia Kfouri Martins Soares, Letícia Veloso Ribeiro Franco, Jhulia Almeida Clarck Chagas, Fernando Gomes, Mário H Barros.
      Based on available platforms detailing the Saccharomyces cerevisiae mitochondrial proteome and other high-throughput studies, we identified the yeast gene DMO2 as having a profile of genetic and physical interactions that indicate a putative role in mitochondrial respiration. Dmo2p is a homologue to human distal membrane-arm assembly complex protein 1 (DMAC1); both proteins have two conserved cysteines in a Cx2C motif. Here, we localised Dmo2p in the mitochondrial inner membrane with the conserved cysteines facing the intermembrane space. The respiratory deficiency of dmo2 mutants at 37°C led to a reduction in cytochrome c oxidase (COX) activity (COX) and in the formation of cytochrome bc1 complex-COX supercomplexes; dmo2 also has a rapid turnover of Cox2p, the second subunit of the COX complex that harbours the binuclear CuA centre. Moreover, Dmo2p co-immunoprecipitates with Cox2p and components required for maturation of the CuA centre, such as Sco1p and Sco2p. Finally, DMO2 overexpression can suppress cox23 respiratory deficiency, a mutant that has impaired mitochondrial copper homeostasis. Mass spectrometry data unveiled the interaction of Dmo2p with different large molecular complexes, including bc1-COX supercomplexes, the TIM23 machinery and the ADP/ATP nucleotide translocator. Overall, our data suggest that Dmo2p is required for Cox2p maturation, potentially by aiding proteins involved in copper transport and incorporation into Cox2p.
    Keywords:  COX assembly; CuA site formation; DMAC1 homologue
    DOI:  https://doi.org/10.1111/febs.70009
  21. Commun Biol. 2025 Feb 08. 8(1): 202
    TEFM facilitates transition from RNA synthesis to DNA synthesis at H-strand replication origin of mtDNA.
    Shigeru Matsuda, Masunari Nakayama, Yura Do, Takashi Ishiuchi, Mikako Yagi, Sjoerd Wanrooij, Kazuto Nakada, Fan-Yan Wei, Kenji Ichiyanagi, Hiroyuki Sasaki, Dongchon Kang, Takehiro Yasukawa.
      Transcription of human mitochondrial DNA (mtDNA) begins from specific transcription promoters. In strand-asynchronous mtDNA replication, transcripts from the light-strand promoter serve as primers for leading-strand synthesis at the origin of the H-strand replication (OH). A 7S DNA strand, a presumed aborted replication product, is also synthesized from OH. Transition from RNA synthesis to DNA synthesis at OH is crucial for balancing replication with transcription, yet the mechanism remains unclear. Herein, we examine the role of mitochondrial transcription elongation factor (TEFM) in this process. TEFM knockout results in decreased 7S DNA, strand-asynchronous replication intermediates, and mtDNA copy number, all of which are concordant with downregulation of RNA-to-DNA transition at OH. Conversely, levels of tRNAs encoded near transcription promoters increase, indicating enhanced transcription initiation frequency. Taken together, we propose that, in addition to conferring processivity to the mitochondrial RNA polymerase, TEFM plays a crucial role in maintaining the balance between mitochondrial transcription and replication.
    DOI:  https://doi.org/10.1038/s42003-025-07645-4
  22. Adv Exp Med Biol. 2025 ;1468 375-379
    Mitochondrial DNA Damage in the Retinal Pigmented Epithelium (RPE) and Its Role in RPE Pathobiology.
    Raela B Ridley, Ashley C Amontree, Alfred S Lewin, Cristhian J Ildefonso.
      Retinal pigmented epithelial (RPE) cells have critical functions in the retina. These cells rely heavily on their mitochondria to generate energy, offer metabolites for biosynthesis through the TCA cycle, regulate apoptosis, and process lipids from photoreceptors. Therefore, mitochondrial damage has significant consequences for the RPE and, by proxy, photoreceptors. Researchers have identified damaged mitochondrial DNA (mtDNA) accumulation in patient samples from aged and diseased individuals. These damages include point mutations and complete deletions of mtDNA segments. The most significant observation in these studies is a positive correlation between the accumulation of damaged mtDNA with the stage of AMD rather than aging. This chapter will discuss how mitochondrial dysfunction in the RPE can drive disease pathobiology by altering their physiological functions.
    Keywords:  Age-related macular degeneration; DNA repair; Mitochondria; Retina pigmented epithelium; Senescence
    DOI:  https://doi.org/10.1007/978-3-031-76550-6_62
  23. G Ital Nefrol. 2024 Dec 23. pii: 2024-vol6. [Epub ahead of print]41(6):
    [Focal Segmental Glomerulosclerosis Due to A3243G Point Mutation in the mtDNA Coding for tRNALeu(UUR)].
    Michele Marchini, Valentina Bianco, Matteo Trezzi, Sonila Mocka, Lucio Manenti.
      Mithocondropathies are inherited disorders that can result from abnormalities in the mitochondrial or nuclear DNA. Genetic abnormalities impacting the mitochondrial DNA (mtDNA) are consequently passed down through the maternal line. Renal manifestations of mtDNA disorders are often poorly recognized or misdiagnosed for the widely diverse phenotypic expression of this condition. Here we describe the case of a 34-year-old man with a history of chronic kidney disease, proteinuria, diabetes mellitus and sensorineural hearing loss, with worsening renal function and proteinuria with positive family history. Kidney biopsy showed focal segmental glomerulosclerosis (FSGS) and whole exome sequencing revealed a mtDNA point mutation (A→G) at position 3243 which code for a transfer RNA (tRNALeu(UUR)). Different point mutations in mitochondrial DNA have now been associated with focal segmental glomerulosclerosis but genetic screening for mtDNA mutations is often neglected and this condition overlooked. Consideration of an underlying mitochondrial disease should be made in patients presenting with deafness, diabetes, renal failure and a positive family history of kidney disease.
    Keywords:  Focal segmental glomerulosclerosis; Genetics of Kidney Disease; Mitochondrial disease; Nephrotic Syndrome
    DOI:  https://doi.org/10.69097/41-06-2024-07
  24. FEBS Lett. 2025 Feb 10.
    The apo LETM1 F-EF-hand adopts a closed conformation that underlies a multi-modal sensory role in mitochondria.
    Qi-Tong Lin, Danielle M Colussi, Peter B Stathopulos.
      Leucine zipper EF-hand containing transmembrane protein-1 (LETM1) plays a critical role in mitochondrial function, with haploinsufficiency linked to Wolf-Hirschhorn syndrome. Here, we present the solution NMR structure of the calcium (Ca2+)-depleted LETM1 EF-hand domain, revealing a closed conformation facilitated by a distinct F1-helix pivot rather than decreased interhelical angle. Further, we observe regiospecific unfolding in response to hot and cold denaturation and show H662 has a pKa in-line with physiological pH fluctuations. Finally, we demonstrate Ca2+-dependent transient interactions between the EF-hand and other LETM1 or GHITM protein domains. Collectively, our data reveal the apo-to-holo structural dynamics and mechanisms underlying the multi-modal sensing by the LETM1 EF-hand domain, highlighting its role as an adaptable regulatory element within the mitochondrial matrix.
    Keywords:  F‐EF‐hand domain; LETM1; apo; calcium sensor; leucine zipper EF‐hand containing transmembrane protein‐1; pH sensor; solution NMR structure; temperature sensor
    DOI:  https://doi.org/10.1002/1873-3468.70006
  25. JCI Insight. 2025 Feb 11. pii: e186073. [Epub ahead of print]
    Loss of long-chain acyl-CoA dehydrogenase protects against acute kidney injury.
    Takuto Chiba, Akira Oda, Yuxun Zhang, Katherine E Pfister, Joanna Bons, Sivakama S Bharathi, Ayako Kinoshita, Bob B Zhang, Adam C Richert, Birgit Schilling, Eric S Goetzman, Sunder Sims-Lucas.
      The renal tubular epithelial cells (RTECs) are particularly vulnerable to acute kidney injury (AKI). While fatty acids are the preferred energy source for RTECs via fatty acid oxidation (FAO), FAO-mediated H2O2 production in mitochondria has been shown to be a major source of oxidative stress. We have previously shown that a mitochondrial flavoprotein, long-chain acyl-CoA dehydrogenase (LCAD), which catalyzes a key step in mitochondrial FAO, directly produces H2O2 in vitro. Further, we showed that renal LCAD becomes hyposuccinylated during AKI. Here, we demonstrated that succinylation of recombinant LCAD protein suppresses the production of H2O2. Following two distinct models of AKI, cisplatin treatment or renal ischemia/reperfusion injury (IRI), LCAD-/- mice demonstrated renoprotection. Specifically, LCAD-/- kidneys displayed mitigated renal tubular injury, decreased oxidative stress, preserved mitochondrial function, enhanced peroxisomal FAO, and decreased ferroptotic cell death. LCAD deficiency confers protection against two distinct models of AKI. This suggests a therapeutically attractive mechanism whereby preserved mitochondrial respiration as well as enhanced peroxisomal FAO by loss of LCAD mediates renoprotection against AKI.
    Keywords:  Cell stress; Fatty acid oxidation; Metabolism; Nephrology
    DOI:  https://doi.org/10.1172/jci.insight.186073
  26. Cryobiology. 2025 Feb 13. pii: S0011-2240(25)00018-5. [Epub ahead of print]118 105212
    Mitochondrial respiratory analysis of cryopreserved PBMCs isolated from human blood.
    C Payne, E Louw, N Baines, B Botha, C Lombard, B Allwood, G Maarman.
      Mitochondrial bioenergetics of PBMCs have been linked with several factors that contribute to a better understanding of several human diseases. Due to the complex logistics of clinical studies, samples are often cryopreserved for later analysis. Current data on whether cryopreservation negatively affects the mitochondrial function of PBMCs is discrepant. We isolated and cryopreserved peripheral blood mononuclear cells (PBMCs) from human whole blood and tested mitochondrial function using a substrate-uncoupler-inhibitor-titration protocol on the Oroboros instrument. After three months of storage in a cryopreservation medium (at -80 °C), several aspects of mitochondrial bioenergetics were measured. We demonstrate that cryopreservation did not adversely affect mitochondrial parameters (routine, leak, complex-I linked OXPHOS, cytochrome-c response, ETS capacity, the contributions of the N and S-pathways to ETS, ROX, complex-IV activity and mitochondrial coupling). Therefore, after three months of cryopreservation at -80 °C, human PBMC-mitochondria were fully coupled and functional. Therefore, clinical studies may cryopreserve PBMCs for later mitochondrial analyses.
    Keywords:  Cryopreserved PBMCs; Mitochondrial respiration; Oroboros
    DOI:  https://doi.org/10.1016/j.cryobiol.2025.105212
  27. Adv Sci (Weinh). 2025 Feb 07. e2412311
    Berberine is a Novel Mitochondrial Calcium Uniporter Inhibitor that Disrupts MCU-EMRE Assembly.
    Haixin Zhao, Siqi Chen, Nian Cao, Wenjun Wu, Guangqin Liu, Jun Gao, Jiayi Chen, Ting Li, Dingyi Lu, Lingmin Zeng, Haizhen Zhu, Weina Zhang, Qing Xia, Teng Li, Tao Zhou, Xue-Min Zhang, Ai-Ling Li, Xin Pan.
      The mitochondrial calcium uniporter (MCU) complex mediates Ca2+ entry into mitochondria, which plays a crucial role in regulating cellular energy metabolism and apoptosis. Dysregulation of MCU is implicated in various diseases, such as neurodegenerative disorders, cardiac diseases, and cancer. Despite its importance, developing specific and clinically viable MCU inhibitors is challenging. Here, Berberine, a well-established drug with a documented safety profile, is identified as a potent MCU inhibitor through a virtual screening of an FDA-approved drug library. Berberine localizes within mitochondria and directly binds to the juxtamembrane loop domain of MCU. This binding disrupts the interaction of MCU with its essential regulator, EMRE, thereby inhibiting rapid Ca2+ entry into the mitochondria. Notably, Berberine pretreatment reduces mitochondrial Ca2+ overload and mitigates ischemia/reperfusion-induced myocardial injury in mice. These findings establish Berberine as a potent MCU inhibitor, offering a safe therapeutic strategy for diseases associated with dysregulated mitochondrial calcium homeostasis.
    Keywords:  EMRE; MCU (mitochondrial calcium uniporter); berberine; mitochondrial calcium signaling; myocardial injury; small molecules
    DOI:  https://doi.org/10.1002/advs.202412311
  28. Nature. 2025 Feb 13.
    Scientists use AI to design life-like enzymes from scratch.
    Miryam Naddaf.
      
    Keywords:  Machine learning; Molecular biology
    DOI:  https://doi.org/10.1038/d41586-025-00488-3
  29. Front Neurosci. 2025 ;19 1557013
    Editorial: Molecular and cellular pathways leading to mitochondrial dysfunction and neurodegeneration: lessons from in vivo models, volume II.
    Shabab B Hannan, Federica De Lazzari, Aurora Gomez-Duran, Juan A Navarro, Gloria Brea-Calvo, Alvaro Sanchez-Martinez.
      
    Keywords:  ATAD3; Drosophila; Parkinson's disease; Pink1; SARS-CoV-2; Usp14; metformin; mitochondria
    DOI:  https://doi.org/10.3389/fnins.2025.1557013
  30. Nat Commun. 2025 Feb 10. 16(1): 1508
    ER-mitochondria contacts mediate lipid radical transfer via RMDN3/PTPIP51 phosphorylation to reduce mitochondrial oxidative stress.
    Isshin Shiiba, Naoki Ito, Hijiri Oshio, Yuto Ishikawa, Takahiro Nagao, Hiroki Shimura, Kyu-Wan Oh, Eiki Takasaki, Fuya Yamaguchi, Ryoan Konagaya, Hisae Kadowaki, Hideki Nishitoh, Takehito Tanzawa, Shun Nagashima, Ayumu Sugiura, Yuuta Fujikawa, Keitaro Umezawa, Yasushi Tamura, Byung Il Lee, Yusuke Hirabayashi, Yasushi Okazaki, Tomohiro Sawa, Ryoko Inatome, Shigeru Yanagi.
      The proximal domains of mitochondria and the endoplasmic reticulum (ER) are linked by tethering factors on each membrane, allowing the efficient transport of substances, including lipids and calcium, between them. However, little is known about the regulation and function of mitochondria-ER contacts (MERCs) dynamics under mitochondrial damage. In this study, we apply NanoBiT technology to develop the MERBiT system, which enables the measurement of reversible MERCs formation in living cells. Analysis using this system suggests that induction of mitochondrial ROS increases MERCs formation via RMDN3 (also known as PTPIP51)-VAPB tethering driven by RMDN3 phosphorylation. Disruption of this tethering caused lipid radical accumulation in mitochondria, leading to cell death. The lipid radical transfer activity of the TPR domain in RMDN3, as revealed by an in vitro liposome assay, suggests that RMDN3 transfers lipid radicals from mitochondria to the ER. Our findings suggest a potential role for MERCs in cell survival strategy by facilitating the removal of mitochondrial lipid radicals under mitochondrial damage.
    DOI:  https://doi.org/10.1038/s41467-025-56666-4
  31. Neurol Sci. 2025 Feb 12.
    Phenotypic diversity in NAXE mutations.
    Ismail Solmaz, Dilek Yalnızoğlu, Ali Dursun, Kısmet Çıkı, Halil Tuna Akar, Rıza Köksal Özgül, Can Koşukçu, Abdullah Sezer, Deniz Çağdaş, Saliha Esenboğa, Begüm Özbek, Damla Aygün, Didem Yücel Yılmaz, Şafak Parlak, Rahşan Göçmen, Kader Karlı Oğuz, Banu Anlar.
       BACKGROUND/AIM: NAD(P)HX epimerase (NAXE) gene mutations have been associated with early onset progressive encephalopathy. We present three patients with NAXE gene mutations and different initial manifestations.
    CASES: Patient(P)1 was a 30 month-old boy whose neurological regression started after an infection and progressed, ultimately leading to death one year later. His brain magnetic resonance imaging (MRI) findings were suggesting metabolic stroke. P2, nine year-old sister of P1, had mild developmental delay since birth, seizures after age 5 years and pellagra-like skin lesions. P3 was a 15 year old female presenting multifocal neurological signs progressing over months and leading to respiratory insufficiency. Her initial MRI was normal but inflammatory lesions appeared three months after the onset of symptoms. Laboratory investigations including biochemical, serological and metabolic tests, and brain biopsy were unrevealing. Clinical presentation of P1 and P3 initially suggested autoimmune neurological disease, but no response to immunotherapy was obtained. Two different types of variants c.641T > G; p.Ile214Ser and c.128 C > A, p.Ser43* were detected in NAXE in these patients' two unrelated families. All patients were given mitochondrial cocktail including niacin.
    DISCUSSION: NAXE plays an important role in the electron donors for the mitochondrial respiratory chain. Mutations result in accumulation of toxic metabolites, disruption of energy production, and possibly cell death. P1-3 displayed different ages of onset, different clinical courses and MRI findings unreported previously, suggesting immune-mediated encephalitis and metabolic stroke in P1, and an inflammatory process in P3. NAXE mutations should be considered in progressive central nervous system symptoms.
    Keywords:   NAXE ; Mitochondrial; Pellagra; Respiratory failure; Stroke
    DOI:  https://doi.org/10.1007/s10072-025-08006-z
  32. J Mater Chem B. 2025 Feb 10.
    A non-hydrolysable peptidomimetic for mitochondrial targeting.
    Yeray Folgar-Cameán, Daniel Torralba-Maldonado, Patricia Fulias-Guzmán, Marta Pazo, Irene Máximo-Moreno, Miriam Royo, Ona Illa, Javier Montenegro.
      Peptidomimetics, molecules that mimic the activity of natural peptides with improved stability or bioavailability, have emerged as interesting materials with applications in biomedicine. In this study, we describe a hybrid γ,γ-peptidomimetic that efficiently aims at mitochondria, a key therapeutic target associated with several disorders, in living cells. Peptide backbones with a component of cationic and hydrophobic amino acids have been shown to preferentially target mitochondria due to their high negative membrane potential and hydrophobic character of the membranous invaginations of these key organelles. We here exploit the advantageous bioorthogonal properties of a peptidomimetic scaffold that consists of an alternation of (1S,3R)-3-amino-2,2-dimethylcyclobutane-1-carboxylic acid and an Nα-functionalised cis-γ-amino-L-proline derivative. This peptidomimetic exhibited excellent membrane translocation efficiency, mitochondrial targeting ability, and biocompatibility. Mitochondrial targeting was confirmed to be dependent on the electrochemical potential generated by the electron transport chain. The presence of non-natural amino acids rendered the compound exceptionally stable in the presence of proteases, maintaining its integrity and functionality for targeting the organelle even after 1 week of incubation in serum. This stability, coupled with its targeting abilities and the low cytosolic/endosomal residual signal, facilitated the tracking of relevant mitochondrial dynamics, including fission events and intracellular movement. Additionally, this peptidomimetic scaffold allowed the sustained and precise mitochondrial targeting of a pH sensitive ratiometric probe, 5(6)-carboxy-SNARF-1, which enabled mitochondrial pH monitoring. In summary, our study introduces a biomimetic peptide with exceptional mitochondria-targeting properties, ensuring stability in biological media and offering insights into crucial mitochondrial processes.
    DOI:  https://doi.org/10.1039/d4tb01626b
  33. Commun Biol. 2025 Feb 10. 8(1): 212
    Hexokinase-I directly binds to a charged membrane-buried glutamate of mitochondrial VDAC1 and VDAC2.
    Sebastian Bieker, Michael Timme, Nils Woge, Dina G Hassan, Chelsea M Brown, Siewert J Marrink, Manuel N Melo, Joost C M Holthuis.
      Binding of hexokinase HKI to mitochondrial voltage-dependent anion channels (VDACs) has far-reaching physiological implications. However, the structural basis of this interaction is unclear. Combining computer simulations with experiments in cells, we here show that complex assembly relies on intimate contacts between the N-terminal α-helix of HKI and a charged membrane-buried glutamate on the outer wall of VDAC1 and VDAC2. Protonation of this residue blocks complex formation in silico while acidification of the cytosol causes a reversable release of HKI from mitochondria. Membrane insertion of HKI occurs adjacent to the bilayer-facing glutamate where a pair of polar channel residues mediates a marked thinning of the cytosolic leaflet. Disrupting the membrane thinning capacity of VDAC1 dramatically impairs its ability to bind HKI in silico and in cells. Our data reveal key topological and mechanistic insights into HKI-VDAC complex assembly that may benefit the development of therapeutics to counter pathogenic imbalances in this process.
    DOI:  https://doi.org/10.1038/s42003-025-07551-9
  34. Brain Commun. 2025 ;7(1): fcaf039
    Niacin ameliorates Charcot-Marie-Tooth 4B1 neuropathy without interfering with nerve regeneration.
    Silvia Cipriani, Emanuela Porrello, Matteo Cerea, Andrea Gazzaniga, Roberta Di Guardo, Amanda Heslegrave, Serena Valenzano, Ubaldo Del Carro, Phu Duong, John Svaren, Stefano Carlo Previtali, Alessandra Bolino.
      Charcot-Marie-Tooth (CMT) neuropathies represent a broad and very heterogeneous group of disorders for which no therapies are yet available. Due to the huge genetic heterogeneity, therapeutical approaches that can benefit several forms independently of the unique pathogenetic mechanism have been sought. Niacin, nicotinic acid, is a vitamin used for many decades as anti-dyslipidaemic and anti-cholesterol drug product under the commercial name of Niaspan®, the extended-release formulation of niacin. Of note, niacin can have other effects depending on the dose, formulation and physiology and it has been used to reduce inflammation, to promote angiogenesis and to protect neurons, muscle and axons by boosting nicotinamide adenine dinucleotide (NAD+) levels. Niacin also activates TNF-alpha convertase enzyme (TACE) secretase, which negatively regulates Neuregulin type I-mediated signalling in the peripheral nervous system and myelination. We previously postulated that niacin-mediated TACE activation can be effective in reducing aberrant excessive myelin associated with different CMT forms. Here, we explored efficacy of this strategy by performing a long-term preclinical trial and we provided evidence that a novel niacin-based long-lasting formulation ameliorates neurophysiology and reduces fibre degeneration in a model of Charcot-Marie-Tooth type 4B1 (CMT4B1) neuropathy, characterized by aberrant myelin. We also sought to determine whether this strategy might interfere with nerve regeneration, which is dependent on Neuregulin type I signalling. Surprisingly, we found that the Mtmr2 knockout mice, a model of CMT4B1, have a defect in nerve regeneration and that niacin-based treatment is not detrimental to nerve regeneration.
    Keywords:  Charcot-Marie-Tooth; myelin; nerve regeneration; neuropathy; nicotinic acid
    DOI:  https://doi.org/10.1093/braincomms/fcaf039
  35. Int J Mol Sci. 2025 Jan 27. pii: 1116. [Epub ahead of print]26(3):
    Adult Leigh Syndrome Associated with the m.15635T>C Mitochondrial DNA Variant Affecting the Cytochrome b (MT-CYB) Gene.
    Concetta Valentina Tropeano, Chiara La Morgia, Alessandro Achilli, Luisa Iommarini, Gaia Tioli, Leonardo Caporali, Anna Olivieri, Maria Lucia Valentino, Rocco Liguori, Piero Barboni, Andrea Martinuzzi, Caterina Tonon, Raffaele Lodi, Antonio Torroni, Valerio Carelli, Anna Maria Ghelli.
      We report on a sporadic patient suffering Leigh syndrome characterized by bilateral lesions in the lenticular nuclei and spastic dystonia, intellectual disability, sensorineural deafness, hypertrophic cardiomyopathy, exercise intolerance, and retinitis pigmentosa. Complete sequencing of mitochondrial DNA revealed the heteroplasmic nucleotide change m.15635T>C affecting a highly conserved amino acid position (p.Ser297Pro) in the cytochrome b (MT-CYB) gene on a haplogroup K1c1a background, which includes a set of four non-synonymous polymorphisms also present in the same gene. Biochemical studies documented respiratory chain impairment due to complex III defect. This variant fulfils the criteria for being pathogenic and was previously reported in a sporadic case of fatal neonatal polyvisceral failure.
    Keywords:  Leigh syndrome; MT-CYB; Respiratory complex III; mtDNA
    DOI:  https://doi.org/10.3390/ijms26031116
  36. J Neurosci Methods. 2025 Feb 05. pii: S0165-0270(25)00028-7. [Epub ahead of print] 110387
    Optimization of permeabilized brain tissue preparation to improve the analysis of mitochondrial oxidative capacities in specific subregions of the rat brain.
    Léa Dorémus, Emilie Dugast, Arnaud Delafenêtre, Morgane Delouche, Thomas Aupy, Olivier Bernard, Stéphane Sebille, Nathalie Thiriet, Jérôme Piquereau.
       BACKGROUND: As the major energy producer of cerebral tissue, mitochondria play key roles in brain physiology and physiopathology. Yet, the fine details of the functioning of mitochondrial oxidative phosphorylation in this organ are still scattered with grey area. This is partly due to the heterogeneity of this tissue that challenges our abilities to study specific cerebral subregions. In the last decades, cerebral mitochondria have largely been studied as a single entity by isolating mitochondria from large sections of brain. Given the evidence that these organelles must adapt to brain areas functions, it seems crucial to develop technologies enabling study of the mitochondria in given subregions.
    NEW METHOD: A few years ago, a method allowing the investigation of mitochondrial functions in permeabilized brain subregions have been proposed by Holloway's team. Although this protocol represented a significant advance, we propose improvements in the tissue permeabilization procedure and in the conditions for measuring oxidative capacity.
    RESULTS AND COMPARISON WITH EXISTING METHODS: The present study demonstrates that adjustments enabled obtention of higher respiration values than Holloway's protocol and might allow the detection of slight mitochondrial alterations. In a second part of this study, we showed that cortex, striatum, hippocampus and cerebellum displayed similar maximal oxidative capacities (under pyruvate, malate and succinate) while complex IV-driven respiration is significantly lower in cerebellum compared to cortex. These observations were supported by the measurement of citrate synthase and cytochrome oxidase activities.
    CONCLUSION: The developed procedure improves the investigations of mitochondrial electron transfer chain in specific cerebral regions.
    Keywords:  cerebral subregions; mitochondrial functions; mitochondrial oxidative capacities; permeabilized tissue
    DOI:  https://doi.org/10.1016/j.jneumeth.2025.110387
  37. EMBO J. 2025 Feb 11.
    Poldip2 promotes mtDNA elimination during Drosophila spermatogenesis to ensure maternal inheritance.
    Ziming Wang, Tirawit Meerod, Nuria Cortes-Silva, Ason C-Y Chiang, Ziyan Nie, Ying Di, Peiqiang Mu, Ankit Verma, Adam James Reid, Hansong Ma.
      Maternal inheritance of mitochondrial DNA (mtDNA) is highly conserved in metazoans. While many species eliminate paternal mtDNA during late sperm development to foster maternal inheritance, the regulatory mechanisms governing this process remain elusive. Through a forward genetic screen in Drosophila, we identified 47 mutant lines exhibiting substantial retention of mtDNA in mature sperm. We mapped one line to poldip2, a gene predominantly expressed in the testis. Disruption of poldip2 led to substantial mtDNA retention in mature sperm and subsequent paternal transmission to progeny. Further investigation via imaging, biochemical analyses and ChIP assays revealed that Poldip2 is a mitochondrial matrix protein capable of binding mtDNA. Moreover, we showed that ClpX, the key component of a major mitochondrial protease, interacts with Poldip2 to co-regulate mtDNA elimination in Drosophila spermatids. This study sheds light on the mechanisms underlying mtDNA removal during spermatogenesis and underscores the pivotal role of this process in safeguarding maternal inheritance.
    Keywords:  ClpXP; Paternal Leakage; Paternal mtDNA Elimination; Poldip2; mtDNA Maternal Inheritance
    DOI:  https://doi.org/10.1038/s44318-025-00378-4
  38. Stem Cells. 2025 Feb 14. pii: sxae086. [Epub ahead of print]
    Extracellular microvesicles/exosomes - magic bullets in horizontal transfer between cells of mitochondria and molecules regulating mitochondria activity.
    Mariusz Z Ratajczak, Kannathasan Thetchinamoorthy, Diana Wierzbicka, Adrian Konopko, Janina Ratajczak, Magdalena Kucia.
      Extracellular microvesicles (ExMVs) were one of the first communication platforms between cells that emerged early in evolution. Evidence indicates that all types of cells secrete these small circular structures surrounded by a lipid membrane that plays an important role in cellular physiology and some pathological processes. ExMVs interact with target cells and may stimulate them by ligands expressed on their surface and/or transfer to the target cells their cargo comprising various RNA species, proteins, bioactive lipids, and signaling nucleotides. These small vesicles can also hijack some organelles from the cells and, in particular, transfer mitochondria, which are currently the focus of scientific interest for their potential application in clinical settings. Different mechanisms exist for transferring mitochondria between cells, including their encapsulation in ExMVs or their uptake in a "naked" form. It has also been demonstrated that mitochondria transfer may involve direct cell-cell connections by signaling nanotubules. In addition, evidence accumulated that ExMVs could be enriched for regulatory molecules, including some miRNA species and proteins that regulate the function of mitochondria in the target cells. Recently, a new beneficial effect of mitochondrial transfer has been reported based on inducing the mitophagy process, removing damaged mitochondria in the recipient cells to improve their energetic state. Based on this novel role of ExMVs in powering the energetic state of target cells, we present a current point of view on this topic and review some selected most recent discoveries and recently published most relevant papers.
    Keywords:  Extracellular microvesicles; exosomes; mitophagy; signaling nanotubules; transfer of mitochondria
    DOI:  https://doi.org/10.1093/stmcls/sxae086
  39. Nucleic Acids Res. 2025 Feb 08. pii: gkaf062. [Epub ahead of print]53(4):
    CRISPuRe-seq: pooled screening of barcoded ribonucleoprotein reporters reveals regulation of RNA polymerase III transcription by the integrated stress response via mTOR.
    David T Harris, Calvin H Jan.
      Genetic screens using CRISPR (Clustered Regularly Interspaced Palindromic Repeats) provide valuable information about gene function. Nearly all pooled screening technologies rely on the cell to link genotype to phenotype, making it challenging to assay mechanistically informative, biochemically defined phenotypes. Here, we present CRISPuRe-seq (CRISPR PuRification), a novel pooled screening strategy that expands the universe of accessible phenotypes through the purification of ribonucleoprotein complexes that link genotypes to expressed RNA barcodes. While screening for regulators of the integrated stress response (ISR), we serendipitously discovered that the ISR represses transfer RNA (tRNA) production under conditions of reduced protein synthesis. This regulation is mediated through inhibition of mTORC1 and corresponding activation of the RNA polymerase III inhibitor MAF1. These data demonstrate that coherent downregulation of tRNA expression and protein synthesis is achieved through cross-talk between the ISR and mTOR, two master integrators of cell state.
    DOI:  https://doi.org/10.1093/nar/gkaf062
  40. Cell Rep. 2025 Feb 10. pii: S2211-1247(25)00055-5. [Epub ahead of print]44(2): 115284
    Acetyl-CoA synthesis in the skin is a key determinant of systemic lipid homeostasis.
    Phuong T T Nguyen, Mia Shiue, Nina Kuprasertkul, Pedro Costa-Pinheiro, Luke T Izzo, Laura V Pinheiro, Hayley A Affronti, Gabriel Gugiu, Shivani Ghaisas, Joyce Y Liu, Jordan C Harris, Charles W Bradley, John T Seykora, Xiaolu Yang, Taku Kambayashi, Clementina Mesaros, Brian C Capell, Kathryn E Wellen.
      ATP-citrate lyase (ACLY) generates cytosolic acetyl-coenzyme A (acetyl-CoA) for lipid synthesis and is a promising therapeutic target in diseases with altered lipid metabolism. Here, we developed inducible whole-body Acly-knockout mice to determine the requirement for ACLY in normal tissue functions, uncovering its crucial role in skin homeostasis. ACLY-deficient skin upregulates the acetyl-CoA synthetase ACSS2; deletion of both Acly and Acss2 from the skin exacerbates skin abnormalities, with differential effects on two major lipid-producing skin compartments. While the epidermis is depleted of barrier lipids, the sebaceous glands increase production of sebum, supplied at least in part by circulating fatty acids and coinciding with adipose lipolysis and fat depletion. Dietary fat supplementation further boosts sebum production and partially rescues both the lipoatrophy and the aberrant skin phenotypes. The data establish a critical role for cytosolic acetyl-CoA synthesis in maintaining skin barrier integrity and highlight the skin as a key organ in systemic lipid regulation.
    Keywords:  ACLY; ACSS2; CP: Metabolism; acetyl-CoA; adipose; epidermis; lipid metabolism; sebaceous glands; skin; skin barrier
    DOI:  https://doi.org/10.1016/j.celrep.2025.115284
  41. Brain. 2025 Feb 12. pii: awaf059. [Epub ahead of print]
    Combined genomics and proteomics unveils elusive variants and vast aetiologic heterogeneity in dystonia.
    Michael Zech, Ivana Dzinovic, Matej Skorvanek, Philip Harrer, Jan Necpal, Robert Kopajtich, Volker Kittke, Erik Tilch, Chen Zhao, Eugenia Tsoma, Ugo Sorrentino, Elisabetta Indelicato, Antonia Stehr, Alice Saparov, Lucia Abela, Miriam Adamovicova, Alexandra Afenjar, Birgit Assmann, Janette Baloghova, Matthias Baumann, Riccardo Berutti, Zuzana Brezna, Melanie Brugger, Theresa Brunet, Benjamin Cogne, Isabel Colangelo, Erin Conboy, Felix Distelmaier, Matthias Eckenweiler, Barbara Garavaglia, Arie Geerlof, Elisabeth Graf, Annette Hackenberg, Denisa Harvanova, Bernhard Haslinger, Petra Havrankova, Georg F Hoffmann, Wibke G Janzarik, Boris Keren, Miriam Kolnikova, Konstantinos Kolokotronis, Zuzana Kosutzka, Anne Koy, Martin Krenn, Magdalena Krygier, Katarina Kusikova, Oliver Maier, Thomas Meitinger, Christian Mertes, Ivan Milenkovic, Edoardo Monfrini, Andre Santos Dias Mourao, Thomas Musacchio, Mathilde Nizon, Miriam Ostrozovicova, Martin Pavlov, Iva Prihodova, Irena Rektorova, Luigi M Romito, Barbora Rybanska, Ariane Sadr-Nabavi, Susanne Schwenger, Ali Shoeibi, Alexandra Sitzberger, Dmitrii Smirnov, Jana Svantnerova, Raushana Tautanova, Sandra P Toelle, Olga Ulmanova, Francesco Vetrini, Katharina Vill, Matias Wagner, David Weise, Giovanna Zorzi, Alessio Di Fonzo, Konrad Oexle, Steffen Berweck, Volker Mall, Sylvia Boesch, Barbara Schormair, Holger Prokisch, Robert Jech, Juliane Winkelmann.
      Dystonia is a rare-disease trait for which large-scale genomic investigations are still underrepresented. Genetic heterogeneity among patients with unexplained dystonia warrants interrogation of entire genome sequences, but this has not yet been systematically evaluated. To significantly enhance our understanding of the genetic contribution to dystonia, we (re)analyzed 2,874 whole-exome sequencing (WES), 564 whole-genome sequencing (WGS), as well as 80 fibroblast-derived proteomics datasets, representing the output of high-throughput analyses in 1,990 patients and 973 unaffected relatives from 1,877 families. Recruitment and precision-phenotyping procedures were driven by long-term collaborations of international experts with access to overlooked populations. By exploring WES data, we found that continuous scaling of sample sizes resulted in steady gains in the number of associated disease genes without plateauing. On average, every second diagnosis involved a gene not previously implicated in our cohort. Second-line WGS focused on a subcohort of undiagnosed individuals with high likelihood of having monogenic forms of dystonia, comprising large proportions of patients with early onset (81.3%), generalized symptom distribution (50.8%) and/or coexisting features (68.9%). We undertook extensive searches for variants in nuclear and mitochondrial genomes to uncover 38 (ultra)rare diagnostic-grade findings in 37 of 305 index patients (12.1%), many of which had remained undetected due to methodological inferiority of WES or pipeline limitations. WGS-identified elusive variations included alterations in exons poorly covered by WES, RNA-gene variants, mitochondrial-DNA mutations, small copy-number variants, complex rearranged genome structure, and short tandem repeats. For improved variant interpretation in WGS-inconclusive cases, we employed systematic integration of quantitative proteomics. This aided in verifying diagnoses related to technically challenging variants and in upgrading a variant of uncertain significance (3 of 70 WGS-inconclusive index patients, 4.3%). Further, unsupervised proteomic outlier-analysis supplemented with transcriptome sequencing revealed pathological gene underexpression induced by transcript disruptions in three more index patients with underlying (deep) intronic variants (3/70, 4.3%), highlighting the potential for targeted antisense-oligonucleotide therapy development. Finally, trio-WGS prioritized a de-novo missense change in the candidate PRMT1, encoding a histone-methyltransferase. Data-sharing strategies supported the discovery of three distinct PRMT1 de-novo variants in four phenotypically similar patients, associated with loss-of-function effects in in-vitro assays. This work underscores the importance of continually expanding sequencing cohorts to characterize the extensive spectrum of gene aberrations in dystonia. We show that a pool of unresolved cases is amenable to WGS and complementary multi-omic studies, directing advanced etiopathological concepts and future diagnostic-practice workflows for dystonia.
    Keywords:  dystonia; genomics; multi-omics; proteomics; transcriptomics; whole-genome sequencing
    DOI:  https://doi.org/10.1093/brain/awaf059
  42. Nat Cell Biol. 2025 Feb 11.
    Ribophagy relies on Rpl12.
    Katarzyna Tutak, Katrin Karbstein.
      
    DOI:  https://doi.org/10.1038/s41556-024-01594-6
  43. Nat Commun. 2025 Feb 12. 16(1): 1584
    Instability of high polygenic risk classification and mitigation by integrative scoring.
    Anika Misra, Buu Truong, Sarah M Urbut, Yang Sui, Akl C Fahed, Jordan W Smoller, Aniruddh P Patel, Pradeep Natarajan.
      Polygenic risk scores (PRS) continue to improve with novel methods and expanding genome-wide association studies. Healthcare and commercial laboratories are increasingly deploying PRS reports to patients, but it is unknown how the classification of high polygenic risk changes across individual PRS. Here, we assess the association and classification performance of cataloged PRS for three complex traits. We chronologically order all trait-related publications (Pubn) and identify the single PRS Best(Pubn) for each Pubn that has the strongest association with the target outcome. While each Best(Pubn) demonstrates generally consistent population-level strengths of associations, the classification of individuals in the top 10% of each Best(Pubn) distribution varies widely. Using the PRSmix framework, which integrates information across several PRS to improve prediction, we generate corresponding ChronoAdd(Pubn) scores for each Pubn that combine all polygenic scores from all publications up to and including Pubn. When compared with Best(Pubn), ChronoAdd(Pubn) scores demonstrate more consistent high-risk classification amongst themselves. This integrative scoring approach provides stable and reliable classification of high-risk individuals and is an adaptable framework into which new scores can be incorporated as they are introduced, integrating easily with current PRS implementation strategies.
    DOI:  https://doi.org/10.1038/s41467-025-56945-0
  44. Neuromuscul Disord. 2025 Jan 28. pii: S0960-8966(25)00007-0. [Epub ahead of print]48 105280
    MRC Centre for Neuromuscular Diseases Biobank London: its role in the advancement of rare and neuromuscular diseases research.
    Pierpaolo Ala, Silvia Torelli, Aisha Ahmed, Mary M Reilly, Michael G Hanna, Francesco Muntoni, Jennifer Morgan.
      Neuromuscular diseases are either inherited or acquired conditions that cause muscle wasting and weakness and sensory loss in some forms, which result in disability and in some cases reduced survival. Although much progress has been made in diagnosing these relatively rare conditions, the genetic cause of many remain to be elucidated. Few neuromuscular diseases currently have a cure and there is a need for reliable biomarkers to monitor disease progression and response to treatment. As they are rare and often heterogeneous conditions, it is difficult for researchers to obtain human material crucial for biomedical research. Since its inception in 2008, the MRC Centre for Neuromuscular Diseases Biobank has provided samples that have been vital in facilitating translational research ranging from molecular pathophysiology, drug discovery, clinical trials and evaluation of biomarkers. This has resulted in many high-profile research publications that clearly demonstrate the impact of neuromuscular biobanking for diagnostics, basic and translational research, drug development, and therapy.
    Keywords:  Biobanking; Neuromuscular diseases; Pathogenesis; Translational research
    DOI:  https://doi.org/10.1016/j.nmd.2025.105280
  45. Mol Cell. 2025 Feb 07. pii: S1097-2765(25)00047-4. [Epub ahead of print]
    The integrated stress response regulates 18S nonfunctional rRNA decay in mammals.
    Aaztli R Coria, Akruti Shah, Mohammad Shafieinouri, Sarah J Taylor, Emilien Orgebin, Wilfried Guiblet, Jennifer T Miller, Indra Mani Sharma, Colin Chih-Chien Wu.
      18S nonfunctional rRNA decay (NRD) detects and eliminates translationally nonfunctional 18S rRNA. Although this process is critical for ribosome quality control, the mechanisms underlying nonfunctional 18S rRNA turnover remain elusive, particularly in mammals. Here, we show that mammalian 18S NRD initiates through the integrated stress response (ISR) via GCN2. Nonfunctional 18S rRNA induces translational arrest at start sites. Biochemical analyses demonstrate that ISR activation limits translation initiation and attenuates collisions between scanning 43S preinitiation complexes and stalled nonfunctional ribosomes. The ISR promotes 18S NRD and 40S ribosomal protein turnover by RNF10-mediated ubiquitination. Ultimately, RIOK3 binds the resulting ubiquitinated 40S subunits and facilitates 18S rRNA decay. Overall, mammalian 18S NRD acts through GCN2, followed by ubiquitin-dependent 18S rRNA degradation involving the ubiquitin E3 ligase RNF10 and the atypical protein kinase RIOK3. These findings establish a dynamic feedback mechanism by which the GCN2-RNF10-RIOK3 axis surveils ribosome functionality at the translation initiation step.
    Keywords:  GCN2; RIOK3; integrated stress response; nonfunctional 18S rRNA; ribosome stalling
    DOI:  https://doi.org/10.1016/j.molcel.2025.01.017
  46. Nat Protoc. 2025 Feb 12.
    Massively parallel in vivo Perturb-seq screening.
    Xinhe Zheng, Patrick C Thompson, Cassandra M White, Xin Jin.
      Advances in genomics have identified thousands of risk genes impacting human health and diseases, but the functions of these genes and their mechanistic contribution to disease are often unclear. Moving beyond identification to actionable biological pathways requires dissecting risk gene function and cell type-specific action in intact tissues. This gap can in part be addressed by in vivo Perturb-seq, a method that combines state-of-the-art gene editing tools for programmable perturbation of genes with high-content, high-resolution single-cell genomic assays as phenotypic readouts. Here we describe a detailed protocol to perform massively parallel in vivo Perturb-seq using several versatile adeno-associated virus (AAV) vectors and provide guidance for conducting successful downstream analyses. Expertise in mouse work, AAV production and single-cell genomics is required. We discuss key parameters for designing in vivo Perturb-seq experiments across diverse biological questions and contexts. We further detail the step-by-step procedure, from designing a perturbation library to producing and administering AAV, highlighting where quality control checks can offer critical go-no-go points for this time- and cost-expensive method. Finally, we discuss data analysis options and available software. In vivo Perturb-seq has the potential to greatly accelerate functional genomics studies in mammalian systems, and this protocol will help others adopt it to answer a broad array of biological questions. From guide RNA design to tissue collection and data collection, this protocol is expected to take 9-15 weeks to complete, followed by data analysis.
    DOI:  https://doi.org/10.1038/s41596-024-01119-3
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