bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2025–04–20
77 papers selected by
Catalina Vasilescu, Helmholz Munich
  1. The POLγ Y951N patient mutation disrupts the switch between DNA synthesis and proofreading, triggering mitochondrial DNA instability.
  2. Mitochondrial DNA variant detection in over 6,500 rare disease families by the systematic analysis of exome and genome sequencing data resolves undiagnosed cases.
  3. Integrated analysis of transcriptional and metabolic responses to mitochondrial stress.
  4. Engineering mitochondrial DNA deletions in human cells improves disease modeling.
  5. The mitochondrial unfolded protein response: acting near and far.
  6. In vivo composition of the mitochondrial nucleoid in mice.
  7. Mitochondrial Dynamics: Deciphering the Role of HDL-C in Regulating Mitochondrial Function and Fatty Acid Oxidation in Human Skeletal Muscle.
  8. Mitochondrial mayhem: Disrupting conserved N-terminal motifs in TANGO2 impacts its localization and function.
  9. Mitochondrial complexity is regulated at ER-mitochondria contact sites via PDZD8-FKBP8 tethering.
  10. Coupling of ribosome biogenesis and translation initiation in human mitochondria.
  11. NDUFS8-Related Leigh Syndrome Mimicking a Leukodystrophy.
  12. Emerging mechanisms of human mitochondrial translation regulation.
  13. RRM2B deficiency causes dATP and dGTP depletion through enhanced degradation and slower synthesis.
  14. Optimization of mtDNA-targeted platinum TALENs for bi-directionally modifying heteroplasmy levels in patient-derived m.3243A>G-iPSCs.
  15. Metabolic rewiring caused by mitochondrial dysfunction promotes mTORC1-dependent skeletal aging.
  16. Genetically encoded tool for manipulation of ΔΨm identifies its role as the driver of ISR induced by ATP synthase dysfunction.
  17. Mitochondria-organelle crosstalk in establishing compartmentalized metabolic homeostasis.
  18. MIRO1 mutation leads to metabolic maladaptation resulting in Parkinson's disease-associated dopaminergic neuron loss.
  19. Mechanism of MCUB-Dependent Inhibition of Mitochondrial Calcium Uptake.
  20. Spatial analysis of mitochondrial gene expression reveals dynamic translation hubs and remodeling in stress.
  21. Lipids: emerging actors in mitochondrial protein import.
  22. Mitochondria in focus: From structure and function to their role in human diseases. A review.
  23. STAR/STARD1: a mitochondrial intermembrane space cholesterol shuttle degraded through mitophagy.
  24. Molecular basis of pyruvate transport and inhibition of the human mitochondrial pyruvate carrier.
  25. Approaches to reduce succinate accumulation by restoration of succinate dehydrogenase activity in cultured adrenal cells.
  26. Guidelines for releasing a variant effect predictor.
  27. Active control of mitochondrial network morphology by metabolism-driven redox state.
  28. The recurrent p.Glu3Lys variant in EHHADH is responsible for Fanconi syndrome with early liver dysfunction and mitochondrial abnormalities.
  29. Mitochondrial function regulates cell growth kinetics to actively maintain mitochondrial homeostasis.
  30. Leber Hereditary Optic Neuropathy With Magnetic Resonance Imaging Findings Suggestive of Optic Perineuritis and Optic Neuritis: A Diagnostic Challenge.
  31. Calcium acts as a critical determinant of mitochondria-nuclear networking driven retrograde signaling.
  32. Transcriptome analysis of atad3-null zebrafish embryos elucidates possible disease mechanisms.
  33. The mitochondrial LONP1 protease: molecular targets and role in pathophysiology.
  34. Mipep deficiency in adipocytes impairs mitochondrial protein maturation and leads to systemic inflammation and metabolic dysfunctions.
  35. Mitochondrial quality control in hematopoietic stem cells: mechanisms, implications, and therapeutic opportunities.
  36. Genome Sequencing of Rare Disease Patients Through the Korean Regional Rare Disease Diagnostic Support Program.
  37. Editorial: Metabolic dysregulation in neurodegenerative diseases.
  38. Whole-genome sequencing susses out rare diseases.
  39. Mitochondrial classic metabolism and its often-underappreciated facets.
  40. Perinuclear mitochondrial clustering for mesenchymal-to-epithelial transition in pluripotency induction.
  41. Role of Comprehensive Renal Genetic Testing in Diagnosing a RMND-1 Mitochondrial Disease in Two Adult Cases Exhibiting Variable Disease Phenotypes.
  42. An Msp1-Protease Chimera Captures Transient AAA+ Interactions and Unveils Ost4 Mislocalization Errors.
  43. A Comprehensive LOVD Database for Fatty Acid Oxidation Disorders in Chinese Populations.
  44. Cytosolic cytochrome c represses ferroptosis.
  45. A population-based cohort study of mitochondrial disease and mental health conditions in Ontario, Canada.
  46. CAVaLRi: An Algorithm for Rapid Identification of Diagnostic Germline Variation.
  47. Systematic identification of disease-causing promoter and untranslated region variants in 8040 undiagnosed individuals with rare disease.
  48. Effects of mitochondrial O-GlcNAcylation in pericytes after mechanical injury.
  49. Ketone body supported respiration in murine isolated brain mitochondria is augmented by alpha-ketoglutarate and is optimized by neuronal SCOT expression.
  50. Artificial Mitochondrial Nanorobots Deliver Energy In Vivo by Oral Administration.
  51. Sauchinone Ameliorates Senescence Through Reducing Mitochondrial ROS Production.
  52. HDAC11 deficiency regulates age-related muscle decline and sarcopenia.
  53. Broadening the Horizons of Mitochondrial Parkinsonism.
  54. Taurine supplementation improves physical activity level in a hemodialysis patient with mitochondrial disease: a case report.
  55. A red-shifted donor-acceptor hemicyanine-based probe for mitochondrial pH in live cells.
  56. Elevated mitochondrial membrane potential is a therapeutic vulnerability in Dnmt3a-mutant clonal hematopoiesis.
  57. Clinical trials test the safety of stem-cell therapy for Parkinson's disease.
  58. Evolution of genome-wide methylation profiling technologies.
  59. Investigating the genetic association of mitochondrial DNA copy number with neurodegenerative diseases.
  60. Integrator loss leads to dsRNA formation that triggers the integrated stress response.
  61. Structural Basis for Promoter Recognition and Transcription Factor Binding and Release in Human Mitochondria.
  62. Mitochondrial proteins and congenital birth defect risk: a mendelian randomization study.
  63. ALDH7A1 protects against ferroptosis by generating membrane NADH and regulating FSP1.
  64. MitoSNO inhibits mitochondrial hydrogen peroxide (mtH2O2) generation by α-ketoglutarate dehydrogenase (KGDH).
  65. Modeling the different conformations of the human mitochondrial ADP/ATP carrier using AlphaFold and molecular dynamics simulations of the protein-ligand complexes.
  66. Rab11b is necessary for mitochondrial integrity and function in gut epithelial cells.
  67. Mitochondria at the Crossroads: Linking the Mediterranean Diet to Metabolic Health and Non-Pharmacological Approaches to NAFLD.
  68. Nicotinamide N-methyltransferase as a potential therapeutic target for neurodegenerative disorders: Mechanisms, challenges, and future directions.
  69. Clinical characteristics and induced pluripotent stem cells (iPSCs) disease model of Harel-Yoon syndrome caused by compound heterozygous ATAD3A variants.
  70. The impact of long-read sequencing on human population-scale genomics.
  71. Deep Visual Proteomics maps proteotoxicity in a genetic liver disease.
  72. Collective Variables and Facilitated Conformational Opening during Translocation of Human Mitochondrial RNA Polymerase (POLRMT) from Atomic Simulations.
  73. Structural and biochemical mechanism of short-chain enoyl-CoA hydratase (ECHS1) substrate recognition.
  74. Mechanism of allosteric activation in human mitochondrial ClpP protease.
  75. Towards multimodal foundation models in molecular cell biology.
  76. Twenty years of genome-wide association studies.
  77. Transformative advances in modeling brain aging and longevity: Success, challenges and future directions.
  1. Proc Natl Acad Sci U S A. 2025 Apr 22. 122(16): e2417477122
    The POLγ Y951N patient mutation disrupts the switch between DNA synthesis and proofreading, triggering mitochondrial DNA instability.
    Josefin M E Forslund, Tran V H Nguyen, Vimal Parkash, Andreas Berner, Steffi Goffart, Jaakko L O Pohjoismäki, Paulina H Wanrooij, Erik Johansson, Sjoerd Wanrooij.
      Mitochondrial DNA (mtDNA) stability, essential for cellular energy production, relies on DNA polymerase gamma (POLγ). Here, we show that the POLγ Y951N disease-causing mutation induces replication stalling and severe mtDNA depletion. However, unlike other POLγ disease-causing mutations, Y951N does not directly impair exonuclease activity and only mildly affects polymerase activity. Instead, we found that Y951N compromises the enzyme's ability to efficiently toggle between DNA synthesis and degradation, and is thus a patient-derived mutation with impaired polymerase-exonuclease switching. These findings provide insights into the intramolecular switch when POLγ proofreads the newly synthesized DNA strand and reveal a new mechanism for causing mitochondrial DNA instability.
    Keywords:  DNA polymerases; mitochondria; mitochondrial disease; mtDNA; mtDNA replication
    DOI:  https://doi.org/10.1073/pnas.2417477122
  2. HGG Adv. 2025 Apr 15. pii: S2666-2477(25)00044-2. [Epub ahead of print] 100441
    Mitochondrial DNA variant detection in over 6,500 rare disease families by the systematic analysis of exome and genome sequencing data resolves undiagnosed cases.
    Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium
      Variants in the mitochondrial genome (mtDNA) cause a diverse collection of mitochondrial diseases and have extensive phenotypic overlap with Mendelian diseases encoded on the nuclear genome. The mtDNA is not always specifically evaluated in patients with suspected Mendelian disease, resulting in overlooked diagnostic variants. Here, we analyzed a cohort of 6,660 rare disease families (5,625 genetically undiagnosed, 84%) from the Genomics Research to Elucidate the Genetics of Rare diseases (GREGoR) Consortium as well as other rare disease cohorts. Using dedicated pipelines to address the technical challenges posed by the mtDNA-circular genome, variant heteroplasmy, and nuclear misalignment-we called single nucleotide variants, small indels, and large mtDNA deletions from exome and/or genome sequencing data, in addition to RNA-sequencing data when available. Diagnostic mtDNA variants were identified in 10 previously genetically undiagnosed families (one large deletion, eight reported pathogenic variants, one previously unreported likely pathogenic variant), as well as candidate diagnostic variants in a further 11 undiagnosed families. In one additional undiagnosed proband, detection of >900 heteroplasmic variants provided functional evidence of pathogenicity to a de novo variant in the nuclear gene POLG (DNA polymerase gamma), responsible for mtDNA replication and repair. Overall, mtDNA variant calling from data generated by exome and genome sequencing-primarily for nuclear variant analysis-resulted in a genetic diagnosis for 0.2% of undiagnosed families affected by a broad range of rare diseases, as well as identification of additional promising candidates.
    DOI:  https://doi.org/10.1016/j.xhgg.2025.100441
  3. Cell Rep Methods. 2025 Apr 08. pii: S2667-2375(25)00063-3. [Epub ahead of print] 101027
    Integrated analysis of transcriptional and metabolic responses to mitochondrial stress.
    Liam P Kelley, Song-Hua Hu, Sarah A Boswell, Peter K Sorger, Alison E Ringel, Marcia C Haigis.
      Mitochondrial stress arises from a variety of sources, including mutations to mitochondrial DNA, the generation of reactive oxygen species, and an insufficient supply of oxygen or fuel. Mitochondrial stress induces a range of dedicated responses that repair damage and restore mitochondrial health. However, a systematic characterization of transcriptional and metabolic signatures induced by distinct types of mitochondrial stress is lacking. Here, we defined how primary human fibroblasts respond to a panel of mitochondrial inhibitors to trigger adaptive stress responses. Using metabolomic and transcriptomic analyses, we established integrated signatures of mitochondrial stress. We developed a tool, stress quantification using integrated datasets (SQUID), to deconvolute mitochondrial stress signatures from existing datasets. Using SQUID, we profiled mitochondrial stress in The Cancer Genome Atlas (TCGA) PanCancer Atlas, identifying a signature of pyruvate import deficiency in IDH1-mutant glioma. Thus, this study defines a tool to identify specific mitochondrial stress signatures, which may be applied to a range of systems.
    Keywords:  CP: Metabolism; CP: Systems biology; cancer metabolism; integrated multi-omics; integrated stress response; metabolomics; mitochondria; mitochondrial stress response; mitochondrial unfolded protein response; stress signatures
    DOI:  https://doi.org/10.1016/j.crmeth.2025.101027
  4. Nat Biotechnol. 2025 Apr;43(4): 501
    Engineering mitochondrial DNA deletions in human cells improves disease modeling.
    Iris Marchal.
      
    DOI:  https://doi.org/10.1038/s41587-025-02652-6
  5. Biol Chem. 2025 Apr 17.
    The mitochondrial unfolded protein response: acting near and far.
    Nikolaos Charmpilas, Qiaochu Li, Thorsten Hoppe.
      Mitochondria are central hubs of cellular metabolism and their dysfunction has been implicated in a variety of human pathologies and the onset of aging. To ensure proper mitochondrial function under misfolding stress, a retrograde mitochondrial signaling pathway known as UPRmt is activated. The UPRmt ensures that mitochondrial stress is communicated to the nucleus, where gene expression for several mitochondrial proteases and chaperones is induced, forming a protective mechanism to restore mitochondrial proteostasis and function. Importantly, the UPRmt not only acts within cells, but also exhibits a conserved cell-nonautonomous activation across species, where mitochondrial stress in a defined tissue triggers a systemic response that affects distant organs. Here, we summarize the molecular basis of the UPRmt in the invertebrate model organism Caenorhabditis elegans and in mammals. We also describe recent findings on cell-nonautonomous activation of the UPRmt in worms, flies and mice, and how UPRmt activation in specific tissues affects organismal metabolism and longevity.
    Keywords:  cell-nonautonomous regulation; integrated stress response; mitochondria; mitochondrial unfolded protein response; stress signaling
    DOI:  https://doi.org/10.1515/hsz-2025-0107
  6. Biochim Biophys Acta Mol Cell Res. 2025 Apr 15. pii: S0167-4889(25)00060-6. [Epub ahead of print] 119955
    In vivo composition of the mitochondrial nucleoid in mice.
    Rodolfo García-Villegas, Franka Odenthal, Yvonne Giannoula, Nina A Bonekamp, Inge Kühl, Chan Bae Park, Henrik Spåhr, Elisa Motori, Fredrik Levander, Nils-Göran Larsson.
      Mitochondrial DNA (mtDNA) is compacted into dynamic structures called mitochondrial nucleoids (mt-nucleoids), with the mitochondrial transcription factor A (TFAM) as the core packaging protein. We generated bacterial artificial chromosome (BAC) transgenic mice expressing FLAG-tagged TFAM protein (Tfam-FLAGBAC mice) to investigate the mt-nucleoid composition in vivo. Importantly, we show that the TFAM-FLAG protein is functional and complements the absence of the wild-type TFAM protein in homozygous Tfam knockout mice. We performed immunoprecipitation experiments from different mouse tissues and identified 12 proteins as core mt-nucleoid components by proteomics analysis. Among these, eight proteins correspond to mtDNA replication and transcription factors, while the other four are involved in the mitoribosome assembly. In addition, we used the Tfam-FLAGBAC mice to identify ten proteins that may stabilize TFAM-FLAG upon depletion of the mitochondrial RNA polymerase despite the absence of mtDNA and induction of the LONP1 protease. Finally, we evaluated the changes in mt-nucleoids caused by very high levels of TFAM unraveling nine interactors that could counteract the high TFAM levels to maintain active mtDNA transcription. Altogether, we demonstrate that the Tfam-FLAGBAC mice are a valuable tool for investigating the mt-nucleoid composition in vivo.
    Keywords:  Mitochondrial nucleoid; Mitochondrial translation; TFAM; Transgenic mice; mtDNA expression
    DOI:  https://doi.org/10.1016/j.bbamcr.2025.119955
  7. Am J Physiol Heart Circ Physiol. 2025 Apr 15.
    Mitochondrial Dynamics: Deciphering the Role of HDL-C in Regulating Mitochondrial Function and Fatty Acid Oxidation in Human Skeletal Muscle.
    Mauricio Castro-Sepulveda, Francesca Amati.
      XXXX.
    Keywords:  Mitochondria; cholesterol; metabolism; physiology; skeletal muscle
    DOI:  https://doi.org/10.1152/ajpheart.00219.2025
  8. J Cell Biol. 2025 May 05. pii: e202503010. [Epub ahead of print]224(5):
    Mitochondrial mayhem: Disrupting conserved N-terminal motifs in TANGO2 impacts its localization and function.
    Sarah E Sandkuhler, Samuel J Mackenzie.
      TANGO2 deficiency in humans leads to progressive neurological impairment, punctuated by life-threatening metabolic crises. In this issue, Lujan and colleagues demonstrate that TANGO2 localizes within the mitochondrial lumen and binds acyl-CoA species, potentially implicating it as a lipid trafficking protein.
    DOI:  https://doi.org/10.1083/jcb.202503010
  9. Nat Commun. 2025 Apr 17. 16(1): 3401
    Mitochondrial complexity is regulated at ER-mitochondria contact sites via PDZD8-FKBP8 tethering.
    Koki Nakamura, Saeko Aoyama-Ishiwatari, Takahiro Nagao, Mohammadreza Paaran, Christopher J Obara, Yui Sakurai-Saito, Jake Johnston, Yudan Du, Shogo Suga, Masafumi Tsuboi, Makoto Nakakido, Kouhei Tsumoto, Yusuke Kishi, Yukiko Gotoh, Chulhwan Kwak, Hyun-Woo Rhee, Jeong Kon Seo, Hidetaka Kosako, Clint Potter, Bridget Carragher, Jennifer Lippincott-Schwartz, Franck Polleux, Yusuke Hirabayashi.
      Mitochondria-ER membrane contact sites (MERCS) represent a fundamental ultrastructural feature underlying unique biochemistry and physiology in eukaryotic cells. The ER protein PDZD8 is required for the formation of MERCS in many cell types, however, its tethering partner on the outer mitochondrial membrane (OMM) is currently unknown. Here we identify the OMM protein FKBP8 as the tethering partner of PDZD8 using a combination of unbiased proximity proteomics, CRISPR-Cas9 endogenous protein tagging, Cryo-electron tomography, and correlative light-electron microscopy. Single molecule tracking reveals highly dynamic diffusion properties of PDZD8 along the ER membrane with significant pauses and captures at MERCS. Overexpression of FKBP8 is sufficient to narrow the ER-OMM distance, whereas independent versus combined deletions of these two proteins demonstrate their interdependence for MERCS formation. Furthermore, PDZD8 enhances mitochondrial complexity in a FKBP8-dependent manner. Our results identify a novel ER-mitochondria tethering complex that regulates mitochondrial morphology in mammalian cells.
    DOI:  https://doi.org/10.1038/s41467-025-58538-3
  10. Nat Commun. 2025 Apr 17. 16(1): 3641
    Coupling of ribosome biogenesis and translation initiation in human mitochondria.
    Marleen Heinrichs, Anna Franziska Finke, Shintaro Aibara, Angelique Krempler, Angela Boshnakovska, Peter Rehling, Hauke S Hillen, Ricarda Richter-Dennerlein.
      Biogenesis of mitoribosomes requires dedicated chaperones, RNA-modifying enzymes, and GTPases, and defects in mitoribosome assembly lead to severe mitochondriopathies in humans. Here, we characterize late-step assembly states of the small mitoribosomal subunit (mtSSU) by combining genetic perturbation and mutagenesis analysis with biochemical and structural approaches. Isolation of native mtSSU biogenesis intermediates via a FLAG-tagged variant of the GTPase MTG3 reveals three distinct assembly states, which show how factors cooperate to mature the 12S rRNA. In addition, we observe four distinct primed initiation mtSSU states with an incompletely matured rRNA, suggesting that biogenesis and translation initiation are not mutually exclusive processes but can occur simultaneously. Together, these results provide insights into mtSSU biogenesis and suggest a functional coupling between ribosome biogenesis and translation initiation in human mitochondria.
    DOI:  https://doi.org/10.1038/s41467-025-58827-x
  11. J Child Neurol. 2025 Apr 16. 8830738251328199
    NDUFS8-Related Leigh Syndrome Mimicking a Leukodystrophy.
    Bailyn Hogue, Mekka R Garcia, Connolly G Steigerwald, Maria J Borja, Nicolas J Abreu.
      Leigh syndrome is a progressive infantile neurodegenerative disorder of mitochondrial metabolism that often leads to decompensation in the setting of metabolic stress. It is genetically heterogenous with varied inheritance patterns. One subtype includes NDUFS8-related autosomal recessive Leigh syndrome. This nuclear gene encodes a complex I subunit of the mitochondrial complex chain. Although Leigh syndrome is typically associated with basal ganglia and brainstem involvement, cases of confluent white matter disease have been described with NDUFS8-related disorders. We present the case of a 6-month-old girl with initial imaging suggestive of a leukodystrophy, later found to have a novel homozygous variant in NDUFS8. In conjunction with the clinical course, a diagnosis of Leigh syndrome was made. This case highlights that mitochondrial disorders should be considered on the differential for confluent cerebral white matter disease in early childhood.
    Keywords:  Leigh syndrome; NDUFS8; leukodystrophy; leukoencephalopathy; white matter
    DOI:  https://doi.org/10.1177/08830738251328199
  12. Trends Biochem Sci. 2025 Apr 11. pii: S0968-0004(25)00056-8. [Epub ahead of print]
    Emerging mechanisms of human mitochondrial translation regulation.
    Michele Brischigliaro, Ahram Ahn, Seungwoo Hong, Flavia Fontanesi, Antoni Barrientos.
      Mitochondrial translation regulation enables precise control over the synthesis of hydrophobic proteins encoded by the organellar genome, orchestrating their membrane insertion, accumulation, and assembly into oxidative phosphorylation (OXPHOS) complexes. Recent research highlights regulation across all translation stages (initiation, elongation, termination, and recycling) through a complex interplay of mRNA structures, specialized translation factors, and unique regulatory mechanisms that adjust protein levels for stoichiometric assembly. Key discoveries include mRNA-programmed ribosomal pausing, frameshifting, and termination-dependent re-initiation, which fine-tune protein synthesis and promote translation of overlapping open reading frames (ORFs) in bicistronic transcripts. In this review, we examine these advances, which are significantly enhancing our understanding of mitochondrial gene expression.
    Keywords:  RNA folding; mitochondrial translation; programmed ribosomal frameshifting; ribosome stalling; termination-reinitiation
    DOI:  https://doi.org/10.1016/j.tibs.2025.03.007
  13. Proc Natl Acad Sci U S A. 2025 Apr 22. 122(16): e2503531122
    RRM2B deficiency causes dATP and dGTP depletion through enhanced degradation and slower synthesis.
    Ololade Folajimi Awoyomi, Choco Michael Gorospe, Biswajit Das, Pradeep Mishra, Sushma Sharma, Olena Diachenko, Anna Karin Nilsson, Phong Tran, Paulina H Wanrooij, Andrei Chabes.
      Mitochondrial DNA (mtDNA) replication requires a steady supply of deoxyribonucleotides (dNTPs), synthesized de novo by ribonucleotide reductase (RNR). In nondividing cells, RNR consists of RRM1 and RRM2B subunits. Mutations in RRM2B cause mtDNA depletion syndrome, linked to muscle weakness, neurological decline, and early mortality. The impact of RRM2B deficiency on dNTP pools in nondividing tissues remains unclear. Using a mouse knockout model, we demonstrate that RRM2B deficiency selectively depletes dATP and dGTP, while dCTP and dTTP levels remain stable or increase. This depletion pattern resembles the effects of hydroxyurea, an inhibitor that reduces overall RNR activity. Mechanistically, we propose that the depletion of dATP and dGTP arises from their preferred degradation by the dNTPase SAMHD1 and the lower production rate of dATP by RNR. Identifying dATP and dGTP depletion as a hallmark of RRM2B deficiency provides insights for developing nucleoside bypass therapies to alleviate the effects of RRM2B mutations.
    Keywords:  dNTP metabolism; genome stability; mtDNA stability; ribonucleotide reductase
    DOI:  https://doi.org/10.1073/pnas.2503531122
  14. Mol Ther Nucleic Acids. 2025 Jun 10. 36(2): 102521
    Optimization of mtDNA-targeted platinum TALENs for bi-directionally modifying heteroplasmy levels in patient-derived m.3243A>G-iPSCs.
    Naoki Yahata, Yu-Ichi Goto, Ryuji Hata.
      Patient-derived induced pluripotent stem cells (iPSCs) are a useful pathological model for debilitating diseases caused by mitochondrial DNA (mtDNA) mutations. We established iPSCs derived from mitochondrial disease patients, heteroplasmic for the m.3243A>G mutation. The proportion of a selected mtDNA can be reduced by delivering a programmable nuclease into the mitochondria, and we developed various mtDNA-targeted Platinum TALENs (mpTALENs) to modify m.3243A>G-iPSC heteroplasmy levels in either wild-type or mutant direction. For TALEN optimization, the use of non-conventional repeat-variable di-residues (ncRVD)-LK/WK or NM-enhanced cleavage activity and specificity, and the replacement of conventional with obligate heterodimeric FokI nuclease domains increased target specificity and protected mtDNA from copy number depletion. In vitro, depending on whether wild-type or mutant mtDNA was targeted, we could obtain m.3243A>G-iPSCs with a higher or lower mutation load, while the cells retained their ability to differentiate into three germ layers. These results demonstrate that our mpTALEN optimization created a useful tool for altering heteroplasmy levels in m.3243A>G-iPSCs, improving the potential for studying mutation pathology. The enhanced efficiency also holds promise for using m.3243G(MUT)-mpTALEN as a therapeutic strategy for treating patients suffering from m.3243A>G mitochondrial diseases.
    Keywords:  MELAS; MT: RNA/DNA Editing; diabetes mellitus; induced pluripotent stem cells, iPSCs; mitochondria; mitochondrial DNA, mtDNA; transcription activator-like effector nuclease, TALEN
    DOI:  https://doi.org/10.1016/j.omtn.2025.102521
  15. Sci Adv. 2025 Apr 18. 11(16): eads1842
    Metabolic rewiring caused by mitochondrial dysfunction promotes mTORC1-dependent skeletal aging.
    Kristina Bubb, Julia Etich, Kristina Probst, Tanvi Parashar, Maximilian Schuetter, Frederik Dethloff, Susanna Reincke, Janica L Nolte, Marcus Krüger, Ursula Schlötzer-Schrehard, Julian Nüchel, Constantinos Demetriades, Patrick Giavalisco, Jan Riemer, Bent Brachvogel.
      Decline of mitochondrial respiratory chain (mtRC) capacity is a hallmark of mitochondrial diseases. Patients with mtRC dysfunction often present reduced skeletal growth as a sign of premature cartilage degeneration and aging, but how metabolic adaptations contribute to this phenotype is poorly understood. Here we show that, in mice with impaired mtRC in cartilage, reductive/reverse TCA cycle segments are activated to produce metabolite-derived amino acids and stimulate biosynthesis processes by mechanistic target of rapamycin complex 1 (mTORC1) activation during a period of massive skeletal growth and biomass production. However, chronic hyperactivation of mTORC1 suppresses autophagy-mediated organelle recycling and disturbs extracellular matrix secretion to trigger chondrocytes death, which is ameliorated by targeting the reductive metabolism. These findings explain how a primarily beneficial metabolic adaptation response required to counterbalance the loss of mtRC function, eventually translates into profound cell death and cartilage tissue degeneration. The knowledge of these dysregulated key nutrient signaling pathways can be used to target skeletal aging in mitochondrial disease.
    DOI:  https://doi.org/10.1126/sciadv.ads1842
  16. Cell Chem Biol. 2025 Apr 17. pii: S2451-9456(25)00097-2. [Epub ahead of print]32(4): 620-630.e6
    Genetically encoded tool for manipulation of ΔΨm identifies its role as the driver of ISR induced by ATP synthase dysfunction.
    Mangyu Choe, Alex E Ekvik, Gretchen Stalnaker, Hijai R Shin, Denis V Titov.
      Mitochondrial membrane potential (ΔΨm) is one of the key parameters controlling cellular bioenergetics. Investigation of the role of ΔΨm in live cells is complicated by a lack of tools for its direct manipulation without off-target effects. Here, we adopted the uncoupling protein UCP1 from brown adipocytes as a genetically encoded tool for direct manipulation of ΔΨm. We validated the ability of exogenously expressed UCP1 to induce uncoupled respiration and lower ΔΨm in mammalian cells. UCP1 expression lowered ΔΨm to the same extent as chemical uncouplers but did not inhibit cell proliferation, suggesting that it manipulates ΔΨm without the off-target effects of chemical uncouplers. Using UCP1, we revealed that elevated ΔΨm is the driver of the integrated stress response induced by ATP synthase inhibition in mammalian cells.
    Keywords:  ATP synthase inhibition; GEMMs; ISR; UCP1; genetically encoded tools for manipulation of metabolism; integrated stress response,; mitochondrial membrane potential; ΔΨm
    DOI:  https://doi.org/10.1016/j.chembiol.2025.03.007
  17. Mol Cell. 2025 Apr 17. pii: S1097-2765(25)00196-0. [Epub ahead of print]85(8): 1487-1508
    Mitochondria-organelle crosstalk in establishing compartmentalized metabolic homeostasis.
    Brandon Chen, Costas A Lyssiotis, Yatrik M Shah.
      Mitochondria serve as central hubs in cellular metabolism by sensing, integrating, and responding to metabolic demands. This integrative function is achieved through inter-organellar communication, involving the exchange of metabolites, lipids, and signaling molecules. The functional diversity of metabolite exchange and pathway interactions is enabled by compartmentalization within organelle membranes. Membrane contact sites (MCSs) are critical for facilitating mitochondria-organelle communication, creating specialized microdomains that enhance the efficiency of metabolite and lipid exchange. MCS dynamics, regulated by tethering proteins, adapt to changing cellular conditions. Dysregulation of mitochondrial-organelle interactions at MCSs is increasingly recognized as a contributing factor in the pathogenesis of multiple diseases. Emerging technologies, such as advanced microscopy, biosensors, chemical-biology tools, and functional genomics, are revolutionizing our understanding of inter-organellar communication. These approaches provide novel insights into the role of these interactions in both normal cellular physiology and disease states. This review will highlight the roles of metabolite transporters, lipid-transfer proteins, and mitochondria-organelle interfaces in the coordination of metabolism and transport.
    Keywords:  endoplasmic reticulum; inter-organellar communication; mitochondria; organellar metabolism; organelle membrane contact sites
    DOI:  https://doi.org/10.1016/j.molcel.2025.03.003
  18. NPJ Syst Biol Appl. 2025 Apr 17. 11(1): 37
    MIRO1 mutation leads to metabolic maladaptation resulting in Parkinson's disease-associated dopaminergic neuron loss.
    Alise Zagare, Thomas Sauter, Kyriaki Barmpa, Maria Pacheco, Rejko Krüger, Jens Christian Schwamborn, Claudia Saraiva.
      MIRO1 is a mitochondrial outer membrane protein important for mitochondrial distribution, dynamics and bioenergetics. Over the last decade, evidence has pointed to a link between MIRO1 and Parkinson's disease (PD) pathogenesis. Moreover, a heterozygous MIRO1 mutation (p.R272Q) was identified in a PD patient, from which an iPSC-derived midbrain organoid model was derived, showing MIRO1 mutant-dependent selective loss of dopaminergic neurons. Herein, we use patient-specific iPSC-derived midbrain organoids carrying the MIRO1 p.R272Q mutation to further explore the cellular and molecular mechanisms involved in dopaminergic neuron degeneration. Using single-cell RNA sequencing (scRNAseq) analysis and metabolic modeling we show that the MIRO1 p.R272Q mutation affects the dopaminergic neuron developmental path leading to metabolic deficits and disrupted neuron-astrocyte metabolic crosstalk, which might represent an important pathogenic mechanism leading to their loss.
    DOI:  https://doi.org/10.1038/s41540-025-00509-x
  19. J Cell Physiol. 2025 Apr;240(4): e70033
    Mechanism of MCUB-Dependent Inhibition of Mitochondrial Calcium Uptake.
    Neeraj K Rai, David R Eberhardt, Anthony M Balynas, Melissa J S MacEwen, Ashley R Bratt, Yasemin Sancak, Dipayan Chaudhuri.
      Mitochondrial Ca2+ levels are regulated to balance stimulating respiration against the harm of Ca2+ overload. Contributing to this balance, the main channel transporting Ca2+ into the matrix, the mitochondrial Ca2+ uniporter, can incorporate a dominant-negative subunit (MCUB). MCUB is homologous to the pore-forming subunit MCU, but when present in the pore-lining tetramer, inhibits Ca2+ transport. Here, using cell lines deleted of both MCU and MCUB, we identify three factors that contribute to MCUB-dependent inhibition. First, MCUB protein requires MCU to express. The effect is mediated via the N-terminal domain (NTD) of MCUB. Replacement of the MCUB NTD with the MCU NTD recovers autonomous expression but fails to rescue Ca2+ uptake. Surprisingly, mutations to MCUB that affect interactions with accessory subunits or the conduction pore all failed to rescue Ca2+ uptake, suggesting the mechanism of inhibition may involve more global domain rearrangements. Second, using concatemeric tetramers with varying MCU:MCUB ratios, we find that MCUB incorporation does not abolish conduction, but rather inhibits Ca2+ influx proportional to the amount of MCUB present in the channel. Reducing rather than abolishing Ca2+ transport is consistent with MCUB retaining the highly-conserved selectivity filter DIME sequence. Finally, we apply live-cell Förster resonance energy transfer to establish that the endogenous stoichiometry is 2:2 MCU:MCUB. Taken together, our results suggest MCUB preferentially incorporates into nascent uniporters, and the amount of MCUB protein present linearly correlates with the degree of inhibition of Ca2+ transport, creating a precise, tunable mechanism for cells to regulate mitochondrial Ca2+ uptake.
    Keywords:  EMRE; Förster resonance energy transfer; MICU1; calcium channels; ischemia‐reperfusion injury; mitochondrial calcium uniporter
    DOI:  https://doi.org/10.1002/jcp.70033
  20. Sci Adv. 2025 Apr 18. 11(16): eads6830
    Spatial analysis of mitochondrial gene expression reveals dynamic translation hubs and remodeling in stress.
    Adam Begeman, John A Smolka, Ahmad Shami, Tejashree Pradip Waingankar, Samantha C Lewis.
      Protein- and RNA-rich bodies contribute to the spatial organization of gene expression in the cell and are also sites of quality control critical to cell fitness. In most eukaryotes, mitochondria harbor their own genome, and all steps of mitochondrial gene expression co-occur within a single compartment-the matrix. Here, we report that processed mitochondrial RNAs are consolidated into micrometer-scale translation hubs distal to mitochondrial DNA transcription and RNA processing sites in human cells. We find that, during stress, mitochondrial messenger and ribosomal RNA are sequestered in mesoscale bodies containing mitoribosome components, concurrent with suppression of active translation. Stress bodies are triggered by proteotoxic stress downstream of double-stranded RNA accumulation in cells lacking unwinding activity of the highly conserved helicase SUPV3L1/SUV3. We propose that the spatial organization of nascent polypeptide synthesis into discrete domains serves to throttle the flow of genetic information to support recovery of mitochondrial quality control.
    DOI:  https://doi.org/10.1126/sciadv.ads6830
  21. Trends Biochem Sci. 2025 Apr 15. pii: S0968-0004(25)00060-X. [Epub ahead of print]
    Lipids: emerging actors in mitochondrial protein import.
    Mayra A Borrero-Landazabal, Vanessa Linke, Agnieszka Chacinska.
      Lipids are emerging as functional players in mitochondrial protein import beyond constituting membranes. Cryo-electron microscopy structures of protein translocases such as translocase of the outer membrane (TOM) and insertases such as translocase of the inner membrane (TIM22) link lipids to protein import by suggesting structural and functional roles for lipids in protein translocation and insertion, and for protein insertases in lipid scrambling.
    Keywords:  membrane complexes; mitochondrial biology; mitochondrial protein import; protein–lipid interactions
    DOI:  https://doi.org/10.1016/j.tibs.2025.03.011
  22. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub. 2025 Apr 14.
    Mitochondria in focus: From structure and function to their role in human diseases. A review.
    Daniel Follprecht, Jakub Vavricka, Viktorie Johankova, Pavel Broz, Ales Krouzecky.
      Mitochondria, double-membraned organelles within all eukaryotic cells, are essential for the proper functioning of the human organism. The frequently used phrase "powerhouses of the cell" fails to adequately capture their multifaceted roles. In addition to producing energy in the form of adenosine triphosphate through oxidative phosphorylation, mitochondria are also involved in apoptosis (programmed cell death), calcium regulation, and signaling through reactive oxygen species. Recent research suggests that they can communicate with one another and influence cellular processes. Impaired mitochondrial function on the one hand, can have widespread and profound effects on cellular and organismal health, contributing to various diseases and age-related conditions. Regular exercise on the other hand, promotes mitochondrial health by enhancing their volume, density, and functionality. Although research has made significant progress in the last few decades, mainly through the use of modern technologies, there is still a need to intensify research efforts in this field. Exploring new approaches to enhance mitochondrial health could potentially impact longevity. In this review, we focus on mitochondrial research and discoveries, examine the structure and diverse roles of mitochondria in the human body, explore their influence on energy metabolism and cellular signaling and emphasize their importance in maintaining overall health.
    Keywords:  mitochondria; mitochondrial disease; mitochondrial function; oxidative phosphorylation; reactive oxygen species
    DOI:  https://doi.org/10.5507/bp.2025.009
  23. bioRxiv. 2025 Apr 10. pii: 2025.04.03.647084. [Epub ahead of print]
    STAR/STARD1: a mitochondrial intermembrane space cholesterol shuttle degraded through mitophagy.
    Prasanthi P Koganti, Amy H Zhao, Michael C Kern, Auriole C R Fassinou, Vimal Selvaraj.
      The import of cholesterol to the inner mitochondrial membrane by the steroidogenic acute regulatory protein (STAR/STARD1) is essential for de novo steroid hormone biosynthesis and the acidic pathway of bile acid synthesis. This robust system, evolved to start and stop colossal cholesterol movement, ensures pulsatile yet swift mitochondrial steroid metabolism in cells. Nonetheless, the proposed mechanism and components involved in this process has remained a topic of ongoing debate. In this study, we elucidate the mitochondrial import machinery and structural aspects of STAR, revealing its role as an intermembrane space cholesterol shuttle that subsequently undergoes rapid degradation by mitophagy. This newfound mechanism illuminates a fundamental process in cell biology and provides precise interpretations for the full range of human STAR mutation-driven lipoid congenital adrenal hyperplasia in patients.
    DOI:  https://doi.org/10.1101/2025.04.03.647084
  24. Sci Adv. 2025 Apr 18. 11(16): eadw1489
    Molecular basis of pyruvate transport and inhibition of the human mitochondrial pyruvate carrier.
    Maximilian Sichrovsky, Denis Lacabanne, Jonathan J Ruprecht, Jessica J Rana, Klaudia Stanik, Mariangela Dionysopoulou, Alice P Sowton, Martin S King, Scott A Jones, Lee Cooper, Steven W Hardwick, Giulia Paris, Dimitri Y Chirgadze, Shujing Ding, Ian M Fearnley, Shane M Palmer, Els Pardon, Jan Steyaert, Vanessa Leone, Lucy R Forrest, Sotiria Tavoulari, Edmund R S Kunji.
      The mitochondrial pyruvate carrier transports pyruvate, produced by glycolysis from sugar molecules, into the mitochondrial matrix, as a crucial transport step in eukaryotic energy metabolism. The carrier is a drug target for the treatment of cancers, diabetes mellitus, neurodegeneration, and metabolic dysfunction-associated steatotic liver disease. We have solved the structure of the human MPC1L/MPC2 heterodimer in the inward- and outward-open states by cryo-electron microscopy, revealing its alternating access rocker-switch mechanism. The carrier has a central binding site for pyruvate, which contains an essential lysine and histidine residue, important for its ΔpH-dependent transport mechanism. We have also determined the binding poses of three chemically distinct inhibitor classes, which exploit the same binding site in the outward-open state by mimicking pyruvate interactions and by using aromatic stacking interactions.
    DOI:  https://doi.org/10.1126/sciadv.adw1489
  25. J Cell Sci. 2025 Apr 16. pii: jcs.263925. [Epub ahead of print]
    Approaches to reduce succinate accumulation by restoration of succinate dehydrogenase activity in cultured adrenal cells.
    Fatimah Al Khazal, Leili Rahimi, Fan Feng, Nicole A Becker, Clifford D Folmes, Judith Favier, L James Maher.
      The rare human neuroendocrine tumors pheochromocytoma and paraganglioma (PPGL) can result from loss of mitochondrial succinate dehydrogenase. The resulting succinate accumulation is tumorigenic in certain neuroendocrine cells. Here we explore two theoretical approaches to mitigate tumorigenic succinate accumulation in a cell culture model of PPGL. We first study a gene replacement strategy using transposition technology and conclude that many aspects of mitochondrial morphology, oxidative cell metabolism and succinate accumulation are reversible by this process. We then investigate if riboflavin supplementation has the potential to rescue succinate dehydrogenase activity in the intact SDHA catalytic subunit to suppress succinate accumulation even in the absence of SDHB. We show that this latter strategy is not successful.
    Keywords:  Paraganglioma; Pheochromocytoma; Riboflavin; Succinate dehydrogenase
    DOI:  https://doi.org/10.1242/jcs.263925
  26. Genome Biol. 2025 Apr 15. 26(1): 97
    Guidelines for releasing a variant effect predictor.
    Benjamin J Livesey, Mihaly Badonyi, Mafalda Dias, Jonathan Frazer, Sushant Kumar, Kresten Lindorff-Larsen, David M McCandlish, Rose Orenbuch, Courtney A Shearer, Lara Muffley, Julia Foreman, Andrew M Glazer, Ben Lehner, Debora S Marks, Frederick P Roth, Alan F Rubin, Lea M Starita, Joseph A Marsh.
      Computational methods for assessing the likely impacts of mutations, known as variant effect predictors (VEPs), are widely used in the assessment and interpretation of human genetic variation, as well as in other applications like protein engineering. Many different VEPs have been released, and there is tremendous variability in their underlying algorithms, outputs, and the ways in which the methodologies and predictions are shared. This leads to considerable difficulties for users trying to navigate the selection and application of VEPs. Here, to address these issues, we provide guidelines and recommendations for the release of novel VEPs.
    DOI:  https://doi.org/10.1186/s13059-025-03572-z
  27. Proc Natl Acad Sci U S A. 2025 Apr 22. 122(16): e2421953122
    Active control of mitochondrial network morphology by metabolism-driven redox state.
    Gaurav Singh, Vineeth Vengayil, Aayushee Khanna, Swagata Adhikary, Sunil Laxman.
      Mitochondria are dynamic organelles that constantly change morphology. What controls mitochondrial morphology however remains unresolved. Using actively respiring yeast cells growing in distinct carbon sources, we find that mitochondrial morphology and activity are unrelated. Cells can exhibit fragmented or networked mitochondrial morphology in different nutrient environments independent of mitochondrial activity. Instead, mitochondrial morphology is controlled by the intracellular redox state, which itself depends on the nature of electron entry into the electron transport chain (ETC)-through complex I/II or directly to coenzyme Q/cytochrome c. In metabolic conditions where direct electron entry is high, reactive oxygen species (ROS) increase, resulting in an oxidized cytosolic environment and rapid mitochondrial fragmentation. Decreasing direct electron entry into the ETC by genetic or chemical means, or reducing the cytosolic environment rapidly restores networked morphologies. Using controlled disruptions of electron flow to alter ROS and redox state, we demonstrate minute-scale, reversible control between networked and fragmented forms in an activity-independent manner. Mechanistically, the fission machinery through Dnm1 responds in minute-scale to redox state changes, preceding the change in mitochondrial form. Thus, the metabolic state of the cell and its consequent cellular redox state actively control mitochondrial form.
    Keywords:  electron transport chain; mitochondrial network; reactive oxygen species; redox state
    DOI:  https://doi.org/10.1073/pnas.2421953122
  28. Mol Genet Metab Rep. 2025 Jun;43 101214
    The recurrent p.Glu3Lys variant in EHHADH is responsible for Fanconi syndrome with early liver dysfunction and mitochondrial abnormalities.
    P Rollier, A Cospain, M Barth, V Milon, N Gueguen, C Homedan, V Desquiret, C Bris, E Colin, L Damaj, A Ryckewaert, P Reynier, S Odent, P Amati-Bonneau, V Procaccio, D Bonneau, A Ziegler.
       Background: The recurrent pathogenic variant c.7G>A p.Glu3Lys in the EHHADH gene is responsible for an autosomal dominant form of Fanconi renotubular syndrome. This variant leads to mislocalization of peroxisomal EHHADH protein to the mitochondria, thereby impairing mitochondrial function. To date, this variant has been reported in only two unrelated families, with affected individuals presenting with isolated renotubular Fanconi syndrome. No other pathogenic variant has been documented in this gene.
    Methods: A boy followed from four months-old to twelve years-old underwent clinical evaluation, mitochondrial analyses and exome sequencing.
    Results: The four-month-old infant boy presented with hypoglycemia, ketonuria, lactic acidosis and hepatic cytolysis. Three months later, a Fanconi tubulopathy with nephrocalcinosis appeared. Mitochondrial respiratory chain analyses performed on hepatocytes showed a decreased activity of complex I and IV of the mitochondrial respiratory chain and a quantitative decrease of these complexes. Exome sequencing revealed the missense variant c.7G>A p.Glu3Lys, inherited from his father who was asymptomatic at 54 years old. A diet supplemented in medium-chain fatty acids was experimented.
    Conclusion: This case widens the phenotypic spectrum of the recurrent p.Glu3Lys variant in EHHADH, which may be responsible for Fanconi syndrome and early onset hepatic dysfunction with cytolysis and hypoglycemia. Medium-chain fatty acids supplemented diet did not improve the disease.
    Keywords:  EHHADH; Fanconi renotubular syndrome; Hepatic dysfunction; Hypoglycemia; Medium-chain fatty acids
    DOI:  https://doi.org/10.1016/j.ymgmr.2025.101214
  29. bioRxiv. 2025 Apr 01. pii: 2025.03.31.646474. [Epub ahead of print]
    Mitochondrial function regulates cell growth kinetics to actively maintain mitochondrial homeostasis.
    Leeba Ann Chacko, Hidenori Nakaoka, Richard Morris, Wallace Marshall, Vaishnavi Ananthanarayanan.
      Mitochondria are not produced de novo in newly divided daughter cells, but are inherited from the mother cell during mitosis. While mitochondrial homeostasis is crucial for living cells, the feedback responses that maintain mitochondrial volume across generations of dividing cells remain elusive. Here, using a microfluidic yeast 'mother machine', we tracked several generations of fission yeast cells and observed that cell size and mitochondrial volume grew exponentially during the cell cycle. We discovered that while mitochondrial homeostasis relied on the 'sizer' mechanism of cell size maintenance, mitochondrial function was a critical determinant of the timing of cell division: cells born with lower than average amounts of mitochondria grew slower and thus added more mitochondria before they divided. Thus, mitochondrial addition during the cell cycle was tailored to the volume of mitochondria at birth, such that all cells ultimately contained the same mitochondrial volume at cell division. Quantitative modelling and experiments with mitochondrial DNA-deficient rho0 cells additionally revealed that mitochondrial function was essential for driving the exponential growth of cells. Taken together, we demonstrate a central role for mitochondrial activity in dictating cellular growth rates and ensuring mitochondrial volume homeostasis.
    DOI:  https://doi.org/10.1101/2025.03.31.646474
  30. Cureus. 2025 Mar;17(3): e80439
    Leber Hereditary Optic Neuropathy With Magnetic Resonance Imaging Findings Suggestive of Optic Perineuritis and Optic Neuritis: A Diagnostic Challenge.
    Kazuhiro Horiuchi, Shuntaro Nakamura, Kazuki Yamada.
      Leber hereditary optic neuropathy (LHON) is a rare mitochondrial disorder characterized by subacute, painless, and bilateral vision loss, typically affecting young men. LHON is caused by mitochondrial DNA mutations, most commonly m.11778G>A, m.14484T>C, and m.3460G>A. LHON has incomplete penetrance, with a higher prevalence in men, and its diagnosis is often delayed because of clinical overlap with other optic nerve disorders, such as optic neuritis. Herein, we report the case of a 37-year-old man presenting with progressive vision loss in both eyes over two months. Early magnetic resonance imaging (MRI) findings were suggestive of optic neuritis or peripapillary optic neuritis. Based on the MRI findings, the differential diagnoses for the patient's condition included multiple sclerosis, neuromyelitis optica spectrum disorders, anti-myelin oligodendrocyte glycoprotein (MOG) antibody-related diseases, sarcoidosis, Behçet's disease, systemic lupus erythematosus, Sjögren's syndrome, and idiopathic optic neuritis and peripapillary optic neuritis. The patient was treated with intravenous methylprednisolone and plasmapheresis. Despite immunotherapy, the patient's symptoms worsened. Comprehensive evaluation revealed normal cerebrospinal fluid and negative autoimmune markers. Mitochondrial DNA testing confirmed the m.11778G>A mutation, which led to the diagnosis of LHON. The patient was treated with ubidecarenone because of the unavailability of idebenone; however, no significant visual improvement occurred. His vision stabilized at 0.3 in the right eye, whereas the left eye became completely blind. This case highlights the diagnostic challenges of LHON, particularly when MRI findings mimic optic neuritis. The preservation of the pupillary light reflex and nonresponse to immunotherapy are key diagnostic clues. Early genetic testing is crucial in cases with atypical progression to confirm LHON and guide management. This case underscores the need for heightened awareness of the incidence of LHON in patients with subacute vision loss unresponsive to conventional treatments.
    Keywords:  genetic testing; leber hereditary optic neuropathy; mitochondrial disease; optic neuritis; optic perineuritis
    DOI:  https://doi.org/10.7759/cureus.80439
  31. Cell Calcium. 2025 Apr 08. pii: S0143-4160(25)00026-0. [Epub ahead of print]127 103017
    Calcium acts as a critical determinant of mitochondria-nuclear networking driven retrograde signaling.
    Kriti Ahuja, Rajender K Motiani.
      Mitochondria are robust signaling organelle that regulate a variety of cellular functions. One of the key mechanisms that drive mitochondrial signaling is inter-organelle crosstalk. Mitochondria communicates with other organelles primarily via exchange of calcium (Ca2+), reactive oxygen species (ROS) and lipids across organelle membranes. Mitochondria has its own genome but a majority of mitochondrial proteins are encoded by nuclear genome. Therefore, several mitochondrial functions are controlled by nucleus via anterograde signaling. However, the role of mitochondria in driving expression of genes encoded by nuclear genome has recently gained attention. Recent studies from independent groups have demonstrated a critical role for mitochondrial Ca2+signaling in stimulating nuclear gene expression. These studies report that inhibition of mitochondrial Ca2+uptake through silencing of Mitochondrial Ca2+Uniporter (MCU) leads to Ca2+oscillations in the cytosol. The rise in cytosolic Ca2+ results in activation of Ca2+ sensitive transcription factors such as NFATs and NF-κB. These transcription factors consequently induce expression of their target genes in the nuclear genome. It is important to highlight that these groups used different cell types and elegantly presented a phenomenon that is conserved across various systems. Notably, mitochondrial Ca2+ signaling mediated transcriptional regulation controls diverse cellular functions ranging from B-cell activation, melanogenesis and aging associated inflammation. Future studies on this signaling module would result in better understanding of this axis in human pathophysiology and could lead to development of novel therapeutic strategies.
    Keywords:  Calcium sensitive transcription factors; Mitochondrial calcium signaling; Nuclear transcription; Retrograde signaling
    DOI:  https://doi.org/10.1016/j.ceca.2025.103017
  32. Orphanet J Rare Dis. 2025 Apr 15. 20(1): 181
    Transcriptome analysis of atad3-null zebrafish embryos elucidates possible disease mechanisms.
    Shlomit Ezer, Nathan Ronin, Shira Yanovsky-Dagan, Shahar Rotem-Bamberger, Orli Halstuk, Yair Wexler, Zohar Ben-Moshe, Inbar Plaschkes, Hadar Benyamini, Ann Saada, Adi Inbal, Tamar Harel.
       BACKGROUND: ATAD3A, a nuclear gene encoding the ATAD3A protein, has diverse roles in mitochondrial processes, encompassing mitochondrial dynamics, mitochondrial DNA maintenance, metabolic pathways and inter-organellar interactions. Pathogenic variants in this gene cause neurological diseases in humans with recognizable genotype-phenotype correlations. Yet, gaps in knowledge remain regarding the underlying pathogenesis.
    METHODS: To further investigate the gene function and its implication in health and disease, we utilized CRISPR/Cas9 genome editing to generate a knockout model of the zebrafish ortholog gene, atad3. We characterized the phenotype of the null model, performed mitochondrial and functional tests, and compared the transcriptome of null embryos to their healthy siblings.
    RESULTS: Analysis of atad3-null zebrafish embryos revealed microcephaly, small eyes, pericardial edema and musculature thinning, closely mirroring the human rare disease phenotype. Larvae exhibited delayed hatching and embryonic lethality by 13 days post-fertilization (dpf). Locomotor activity, ATP content, mitochondrial content, and mitochondrial activity were all reduced in the mutant embryos. Transcriptome analysis at 3 dpf via RNA-sequencing indicated decline in most mitochondrial pathways, accompanied by a global upregulation of cytosolic tRNA synthetases, presumably secondary to mitochondrial stress and possibly endoplasmic reticulum (ER)-stress. Differential expression of select genes was corroborated in fibroblasts from an affected individual.
    CONCLUSIONS: The atad3-null zebrafish model emerges as a reliable representation of human ATAD3A-associated disorders, with similarities in differentially expressed pathways and processes. Furthermore, our study underscores mitochondrial dysfunction as the primary underlying pathogenic mechanism in ATAD3A-associated disorders and identifies potential readouts for therapeutic studies.
    Keywords:   ATAD3A ; CRISPR/Cas9; Mitochondria; RNA-seq; Transcriptome; Zebrafish knockout model
    DOI:  https://doi.org/10.1186/s13023-025-03709-0
  33. Mol Biol Rep. 2025 Apr 18. 52(1): 401
    The mitochondrial LONP1 protease: molecular targets and role in pathophysiology.
    Pei Tang, Qun Zeng, Yihao Li, Jing Wang, Meihua She.
      Lon peptidase 1 (LONP1), a member of the AAA + family, is essential for maintaining mitochondrial function. Recent studies have revealed that LONP1 serves as a multifunctional enzyme, acting not only as a protease but also as a molecular chaperone, interacting with mitochondrial DNA (mtDNA), and playing roles in mitochondrial dynamics, oxidative stress, cellular respiration, and energy metabolism. LONP1 is evolutionarily highly conserved, and mutations or dysfunctions in LONP1 can lead to diseases. There is growing evidence linking LONP1 to various human diseases, such as tumors, neurodegenerative diseases, and heart diseases. This review discusses the discovery, molecular structure, subcellular localization, tissue distribution, and mitochondrial function of LONP1. Furthermore, it summarizes the associations between LONP1 and tumors, neurodegenerative diseases, and heart diseases, exploring its role in different diseases and potential molecular mechanisms. It also analyzes the regulatory effects of related inhibitors and agonists on LONP1. Considering the pleiotropic effects of LONP1, the study of LONP1 is crucial to understanding the relevant pathophysiological processes and developing strategies to modulate and control these related diseases.
    Keywords:  Heart disease; LONP1; Mitochondria; Neurodegenerative disease; Tumor
    DOI:  https://doi.org/10.1007/s11033-025-10500-8
  34. Sci Rep. 2025 Apr 14. 15(1): 12839
    Mipep deficiency in adipocytes impairs mitochondrial protein maturation and leads to systemic inflammation and metabolic dysfunctions.
    Yuka Nozaki, Masaki Kobayashi, Tomoyoshi Fukuoh, Mamiko Ishimatsu, Takumi Narita, Kanari Taki, Yuto Hirao, Shota Ayabe, Miku Yokoyama, Yuina Otani, Yuhei Mizunoe, Mami Matsumoto, Nobuhiko Ohno, Tomonori Kaifu, Shogo Okazaki, Ryo Goitsuka, Yoshimi Nakagawa, Hitoshi Shimano, Yoichiro Iwakura, Yoshikazu Higami.
      Most mitochondrial proteins encoded in the nuclear genome are synthesized in the cytoplasm. These proteins subsequently undergo maturation through the cleavage of a signal sequence at the N-terminus by one or two mitochondrial signal peptidases, which is essential for their function within mitochondria. The present study demonstrates that adipocyte-specific knockout of one mitochondrial signal peptidase, mitochondrial intermediate peptidase (MIPEP), resulted in disordered mitochondrial proteostasis of MIPEP substrate proteins and their defective maturation. MIPEP deficiency in white and brown adipocytes suppressed the expression of adipocyte differentiation, lipid metabolism, and mitochondrial biogenesis genes. These alterations led to lipoatrophy in white adipose tissue and the whitening of brown adipose tissue. Additionally, it induced an atypical mitochondrial unfolded protein response and local inflammation in white and brown adipose tissue. Furthermore, it induced fatty liver and splenomegaly and caused systemic impairments in glucose metabolism and inflammation. These findings indicate that maturation defects of certain mitochondrial proteins and subsequent proteostasis disorders in white and brown adipocytes cause chronic and systemic inflammatory and metabolic dysfunctions.
    DOI:  https://doi.org/10.1038/s41598-025-97307-6
  35. Stem Cell Res Ther. 2025 Apr 15. 16(1): 180
    Mitochondrial quality control in hematopoietic stem cells: mechanisms, implications, and therapeutic opportunities.
    Yun Liao, Stacia Octaviani, Zhen Tian, Samuel R Wang, Chunlan Huang, Jian Huang.
      Mitochondrial quality control (MQC) is a critical mechanism for maintaining mitochondrial function and cellular metabolic homeostasis, playing an essential role in the self-renewal, differentiation, and long-term stability of hematopoietic stem cells (HSCs). Recent research highlights the central importance of MQC in HSC biology, particularly the roles of mitophagy, mitochondrial biogenesis, fission, fusion and mitochondrial transfer in regulating HSC function. Mitophagy ensures the removal of damaged mitochondria, maintaining low levels of reactive oxygen species (ROS) in HSCs, thereby preventing premature aging and functional decline. Concurrently, mitochondrial biogenesis adjusts key metabolic regulators such as mitochondrial transcription factor A (TFAM) and peroxisome proliferator-activated receptor-γ coactivator 1α (PGC-1α) to meet environmental demands, ensuring the metabolic needs of HSCs are met. Additionally, mitochondrial transfer, as an essential form of intercellular material exchange, facilitates the transfer of functional mitochondria from bone marrow stromal cells to HSCs, contributing to damage repair and metabolic support. Although existing studies have revealed the significance of MQC in maintaining HSC function, the precise molecular mechanisms and interactions among different regulatory pathways remain to be fully elucidated. Furthermore, the potential role of MQC dysfunction in hematopoietic disorders, including its involvement in disease progression and therapeutic resistance, is not yet fully understood. This review discusses the molecular mechanisms of MQC in HSCs, its functions under physiological and pathological conditions, and its potential therapeutic applications. By summarizing the current progress in this field, we aim to provide insights for further research and the development of innovative treatment strategies.
    Keywords:  Hematopoietic stem cell; Mitochondrial biogenesis; Mitochondrial dynamics; Mitochondrial metabolism; Mitochondrial quality control; Mitochondrial transfer; Mitophagy
    DOI:  https://doi.org/10.1186/s13287-025-04304-7
  36. Hum Mutat. 2025 ;2025 6096758
    Genome Sequencing of Rare Disease Patients Through the Korean Regional Rare Disease Diagnostic Support Program.
    Rin Khang, Hane Lee, Jihye Kim, Dongseok Moon, Seokhui Jang, Eugene Lee, Yongjun Song, Seung Woo Ryu, Sohyun Lee, Heonjong Han, Sukwon Kim, Sohyun Jang, Young Bae Sohn, Won Seop Kim, Ji-Eun Lee, Juwon Kim, Yonggon Cho, Bo Lyun Lee, Han Hyuk Lim, Hoon Kook, Ki-Soo Kang, Soonhak Kwon, Jiwon Lee, Go Hun Seo, Seung Hwan Oh, Chong Kun Cheon.
      Affecting fewer than 20,000 people as defined in South Korea, rare diseases pose significant diagnostic challenges due to their diverse manifestations and genetic heterogeneity. Genome sequencing (GS) offers a promising solution by enabling simultaneous screening for thousands of rare genetic disorders. This study explores the diagnostic utility and necessity of GS within the government-funded Korean Regional Rare Disease Diagnostic Support Program (KR-RDSP), a collaborative initiative involving 11 regional rare disease centers across Korea. The program was launched as a proof-of-concept study in 2023 to equip the genetic clinics with a diagnostic tool to expedite the diagnoses for rare disease patients who reside outside the urban Seoul region where diagnostic resources are limited. The study leveraged GS to diagnose a cohort of 400 patients exhibiting a wide spectrum of symptoms. The overall diagnostic yield was 36.3% (145/400), with 4.8% (7/145) of the diagnosed patients being reported with variants that could not have been identified by chromosomal microarray or exome sequencing (ES), highlighting the added value of comprehensive genomic analysis. The implementation of a centralized GS analysis system streamlined the diagnostic process, enabling timely reporting within a reasonable turnaround time of ≤ 35 days. Segregation analysis by Sanger sequencing played a crucial role in confirming or reclassifying variant pathogenicity by elucidating inheritance patterns. Here, we summarize diagnostic statistics from the 400 GS dataset gathered from June 2023 to December 2023 and show interesting and informative case examples that illustrate the diagnostic efficacy of GS, highlighting its ability to uncover elusive genetic etiologies and provide personalized treatment insights. The study also highlights the successful implementation of the program for the 11 regional rare disease centers across Korea with a practical workflow, comprehensive testing, comparable diagnostic yield to previous reports, and, most importantly, reasonable turnaround time.
    DOI:  https://doi.org/10.1155/humu/6096758
  37. Front Cell Neurosci. 2025 ;19 1591313
    Editorial: Metabolic dysregulation in neurodegenerative diseases.
    Maria Jimenez-Gonzalez.
      
    Keywords:  brain; glucose; metabolism; mitochondria; neurodegeneration
    DOI:  https://doi.org/10.3389/fncel.2025.1591313
  38. Nature. 2025 Apr 17.
    Whole-genome sequencing susses out rare diseases.
    Amanda B Keener.
      
    Keywords:  DNA sequencing; Diseases; Non-coding RNAs
    DOI:  https://doi.org/10.1038/d41586-025-01014-1
  39. Biochim Biophys Acta Mol Basis Dis. 2025 Apr 10. pii: S0925-4439(25)00184-X. [Epub ahead of print] 167839
    Mitochondrial classic metabolism and its often-underappreciated facets.
    João P Moura, Paulo J Oliveira, Ana M Urbano.
      For many decades, mitochondria were essentially regarded as the main providers of the adenosine triphosphate (ATP) required to maintain the viability and function of eukaryotic cells, thus the widely popular metaphor "powerhouses of the cell". Besides ATP generation - via intermediary metabolism - these organelles have also traditionally been known, albeit to a lesser degree, for their notable role in biosynthesis, both as generators of biosynthetic intermediates and/or as the sites of biosynthesis. From the 1990s onwards, the concept of mitochondria as passive organelles providing the rest of the cell, from which they were otherwise isolated, with ATP and biomolecules on an on-demand basis has been challenged by a series of paradigm-shifting discoveries. Namely, it was shown that mitochondria act as signaling effectors to upregulate ATP generation in response to growth-promoting stimuli and that they are actively engaged, through signaling and epigenetics, in the regulation of a plethora of cellular processes, ultimately deciding cell function and fate. With the focus of mitochondrial research increasingly placed in these "non-classical" functions, the centrality of mitochondrial intermediary metabolism to biosynthesis and other mitochondrial functions tends to be overlooked. In this article, we revisit mitochondrial intermediary metabolism and illustrate how its intermediates, by-products and molecular machinery underpin other mitochondrial functions. A certain emphasis is given to frequently overlooked functions, namely the biosynthesis of iron‑sulfur (FeS) clusters, the only known function shared by all mitochondria and mitochondrion-related organelles. The generation of reactive oxygen species (ROS) and their putative role in signaling is also discussed in detail.
    Keywords:  Educational article; Intermediary metabolism; Iron‑sulfur clusters; Metabolic energy; Mitochondrion-related organelles; ROS signaling
    DOI:  https://doi.org/10.1016/j.bbadis.2025.167839
  40. Stem Cell Reports. 2025 Apr 12. pii: S2213-6711(25)00078-5. [Epub ahead of print] 102474
    Perinuclear mitochondrial clustering for mesenchymal-to-epithelial transition in pluripotency induction.
    Ge Xiang, Zihuang Liu, Zebin Yuan, Zhongfu Ying, Yingzhe Ding, Dongtong Lin, Haihao Qin, Shanshan Dong, Shihe Zhou, Hao Yuan, Wei Xie, Zhihong Zheng, Yongqiang Chen, Linpeng Li, Qi Long, Liang Yang, Yi Wu, Keshi Chen, Feixiang Bao, Yile Huang, Wei Li, Junwei Wang, Yang Liu, Dajiang Qin, Xingguo Liu.
      Remodeled mitochondria are characteristic of pluripotent stem cells. However, a role for mitochondrial movement and distribution in pluripotency remains unknown. Here, we show that mitochondrial retrograde transport-mediated perinuclear clustering via dynein complex occurs at the early phase of pluripotency induction. Interestingly, this mitochondrial redistribution is regulated by Yamanaka factor OCT4 but not SOX2 or KLF4. This mitochondrial redistribution, which has effect on the efficiency of somatic cell reprogramming, also depends on DRP1-mediated mitochondrial fission. Importantly, perinuclear mitochondrial clustering is required for mesenchymal-to-epithelial transition (MET), an early step in reprogramming, during which β-catenin regulates the MET process. Furthermore, sufficient amount of β-catenin plays a key role in maintaining stabilization of E-CADHERIN. Taken together, these studies show that perinuclear mitochondrial clustering is an essential organellar step for MET process of pluripotency induction, which may shed light on the subcellular relationship between mitochondrial dynamics, pluripotency, and cellular morphology.
    Keywords:  Drp1; Dynein; Oct4; Wnt signaling; mesenchymal-to-epithelial transition
    DOI:  https://doi.org/10.1016/j.stemcr.2025.102474
  41. Clin Case Rep. 2025 Apr;13(4): e70421
    Role of Comprehensive Renal Genetic Testing in Diagnosing a RMND-1 Mitochondrial Disease in Two Adult Cases Exhibiting Variable Disease Phenotypes.
    Quinn Stein, Ryan Mascarenhas, Sumit Punj, Maggie Westemeyer, Emily Hendricks, Tessa Pitman, Meg Hager, Nour Al Haj Baddar, Kristen Connors, Alexa Bacher, Robin Larson, Lauren Zec, Jennifer Stoddard.
      RMND1-related mitochondrial disease is a rare genetic condition that affects multiple organs, including the kidneys. We describe two adult patients whose diagnosis, initiated in childhood, was established through renal gene panel testing, emphasizing the value of genetic testing in uncovering kidney-related conditions that have a high degree of clinical heterogeneity.
    Keywords:  RMND1; RMND1‐related mitochondrial disease; genetic testing; kidney gene panel
    DOI:  https://doi.org/10.1002/ccr3.70421
  42. bioRxiv. 2025 Apr 01. pii: 2025.03.31.646376. [Epub ahead of print]
    An Msp1-Protease Chimera Captures Transient AAA+ Interactions and Unveils Ost4 Mislocalization Errors.
    Deepika Gaur, Brian Acquaviva, Matthew L Wohlever.
      Membrane protein homeostasis (proteostasis) is essential for maintaining the integrity of eukaryotic organelles. Msp1 is a membrane anchored AAA+ (ATPase Associated with cellular Activities) protein that maintains mitochondrial proteostasis by extracting aberrant proteins from the outer mitochondrial membrane. A comprehensive understanding of the physiological roles of Msp1 has been hindered because AAA+ proteins interact with substrates transiently and common strategies to stabilize this interaction lead to undesirable mitochondrial phenotypes. To circumvent these drawbacks, we fused catalytically active Msp1 to the inactivated protease domain of the AAA+ protease Yme1. The resulting chimera sequesters substrates in the catalytically inactive degradation chamber formed by the protease domain. We performed mass spectrometry analysis with the Msp1-protease chimera and identified the signal anchored protein Ost4 as a novel Msp1 substrate. Topology experiments show that Ost4 adopts mixed orientations when mislocalized to mitochondria and that Msp1 extracts mislocalized Ost4 regardless of orientation. Together, this work develops new tools for capturing transient interactions with AAA+ proteins, identifies new Msp1 substrates, and shows a surprising error in targeting of Ost4.
    DOI:  https://doi.org/10.1101/2025.03.31.646376
  43. Hum Mutat. 2023 ;2023 5493978
    A Comprehensive LOVD Database for Fatty Acid Oxidation Disorders in Chinese Populations.
    Ting Zhang, Zinan Yu, Lingwei Hu, Chao Zhang, Haixia Miao, Rulai Yang, Ming Qi, Benqing Wu, Xinwen Huang.
      Fatty acid oxidation disorders (FAODs) are a group of rare, autosomal recessive, metabolic disorders with clinical symptoms from mild types of fatigue, muscle weakness to severe types of hypoketotic hypoglycemia, (cardio)myopathy, arrhythmia, and rhabdomyolysis, especially during prolonged fasting, exercise, and illness. There are eleven diseases caused by thirteen FAOD genes (SLC22A5, ETFDH, ETFA, ETFB, SLC25A20, ACADS, ACADM, ACADVL, ACAT1, CPT1A, CPT2, HADHA, and HADHB) which are specific enzymes or transport proteins involved in the mitochondrial catabolism of fatty acids. We built the LOVD database for FAODs focused on the Chinese population, in which we recorded all the reported variants by literature peer review. In addition, the unpublished variant data of patients from Zhejiang province were also incorporated into the database. Currently, a total of 538 unique variants have been recorded. We also compared the incidence of high-frequency variants of certain FAOD genes among different populations. The database would provide the guidance for genetic screening of Chinese patients.
    DOI:  https://doi.org/10.1155/2023/5493978
  44. Cell Metab. 2025 Apr 08. pii: S1550-4131(25)00149-4. [Epub ahead of print]
    Cytosolic cytochrome c represses ferroptosis.
    Xinxin Song, Zhuan Zhou, Jiao Liu, Jingbo Li, Chunhua Yu, Herbert J Zeh, Daniel J Klionsky, Brent R Stockwell, Jiayi Wang, Rui Kang, Guido Kroemer, Daolin Tang.
      The release of cytochrome c, somatic (CYCS) from mitochondria to the cytosol is an established trigger of caspase-dependent apoptosis. Here, we unveil an unexpected role for cytosolic CYCS in inhibiting ferroptosis-a form of oxidative cell death driven by uncontrolled lipid peroxidation. Mass spectrometry and site-directed mutagenesis revealed the existence of a cytosolic complex composed of inositol polyphosphate-4-phosphatase type I A (INPP4A) and CYCS. This CYCS-INPP4A complex is distinct from the CYCS-apoptotic peptidase activating factor 1 (APAF1)-caspase-9 apoptosome formed during mitochondrial apoptosis. CYCS boosts INPP4A activity, leading to increased formation of phosphatidylinositol-3-phosphate, which prevents phospholipid peroxidation and plasma membrane rupture, thus averting ferroptotic cell death. Unbiased screening led to the identification of the small-molecule compound 10A3, which disrupts the CYCS-INPP4A interaction. 10A3 sensitized cultured cells and tumors implanted in immunocompetent mice to ferroptosis. Collectively, these findings redefine our understanding of cytosolic CYCS complexes that govern diverse cell death pathways.
    Keywords:  apoptosis; cytochrome c; ferroptosis; protein complex
    DOI:  https://doi.org/10.1016/j.cmet.2025.03.014
  45. Orphanet J Rare Dis. 2025 Apr 14. 20(1): 177
    A population-based cohort study of mitochondrial disease and mental health conditions in Ontario, Canada.
    Laura C Rosella, Mackenzie Hurst, Emmalin Buajitti, Thomas Samson, L Trevor Young, Ana C Andreazza.
       BACKGROUND: Mitochondrial disease has been linked to mental health disorder in clinical cohorts and post-mortem studies. However, a lack of population-level studies examining the relationship between mitochondrial disease and mental health has resulted in an evidence gap and creates a challenge for identifying and addressing care needs for the mitochondrial disease population. Using multiple linked population health databases in a single-payer health system that covers the full population, this study aimed to investigate the prevalence of mood disorders and other mental health conditions in patients with mitochondrial disease and to examine the joint impact of mitochondrial disease and mental health conditions on healthcare use and health system costs. To contextualize these findings, a clinical comparator cohort of multiple sclerosis (MS) patients was analyzed.
    RESULTS: Overall, co-prevalent mental health conditions are common in the mitochondrial population. Double the proportion of patients in the mitochondrial disease cohort had a co-prevalent mental health illness as compared to the MS population (18% vs 9%). Healthcare utilization was highest among patients with co-prevalent mitochondrial disease and mental illness, with 49% hospitalized within 1 year prior to cohort entry (compared to 12% of MS patients with no mental health condition). Costs were likewise highest among mitochondrial disease patients with mental health conditions.
    CONCLUSIONS: This study presents the first comprehensive, population-wide cohort study of mitochondrial disease and co-prevalent mental health conditions. Our findings demonstrate a high burden of mental health conditions among mitochondrial disease patients, with high associated health care needs. We also find that patients with concurrent mental illness and mitochondrial disease represent a high-burden, high-cost population in a single-payer health insurance setting.
    Keywords:  Epidemiology; Health care costs; Health care utilization; Mental health; Mitochondrial disease
    DOI:  https://doi.org/10.1186/s13023-025-03688-2
  46. Hum Mutat. 2024 ;2024 6411444
    CAVaLRi: An Algorithm for Rapid Identification of Diagnostic Germline Variation.
    Robert J Schuetz, Austin A Antoniou, Grant E Lammi, David M Gordon, Harkness C Kuck, Bimal P Chaudhari, Peter White.
      Clinical exome and genome sequencing (ES/GS) have become indispensable diagnostic tools for rare genetic diseases (RGD). However, the interpretation of ES/GS presents a substantial operational challenge in clinical settings. Test interpretation requires the review of hundreds of genetic variants, a task that has become increasingly challenging given the rising use of ES/GS. In response, we present Clinical Assessment of Variants by Likelihood Ratios (CAVaLRi), which employ a modified likelihood ratio (LR) framework to assign diagnostic probabilities to candidate germline disease genes. CAVaLRi models aspects of the clinical variant assessment process, taking into consideration the predicted impact of the variant, the proband and parental genotypes, and the proband's clinical characteristics. It also factors in computational phenotype noise and weighs the relative significance of genotype, phenotype, and variant segregation information. We trained and tested CAVaLRi on variant and phenotype data from an internal cohort of 655 clinical ES cases. For validation, CAVaLRi's performance was benchmarked against four leading gene prioritization algorithms (Exomiser's hiPHIVE and PhenIX prioritizers, LIRICAL, and XRare) using a distinct cohort of 12,832 ES cases. Our findings reveal that CAVaLRi significantly outperforms its counterparts when clinician-curated phenotype sets are used, as evidenced by its superior precision-recall curve (PR AUC: 0.701) and average diagnostic gene rank (1.59). Notably, even when substituting highly focused clinician-curated phenotype sets with large and potentially nonspecific computationally derived phenotypes, CAVaLRi retains its precision (PR AUC: 0.658; diagnostic gene average rank: 1.68) and markedly outperforms other tools. In a large, heterogeneous validation cohort, CAVaLRi stood out as the most precise prioritization algorithm (PR AUC: 0.335; average diagnostic rank: 1.91). In conclusion, CAVaLRi presents a robust solution for prioritizing diagnostic genes, surpassing current methods. It demonstrates resilience to noisy, computationally-derived phenotypes, providing a scalable strategy to help labs focus on the most diagnostically relevant variants, thus addressing the growing demand for ES/GS interpretation.
    DOI:  https://doi.org/10.1155/2024/6411444
  47. Genome Med. 2025 Apr 14. 17(1): 40
    Systematic identification of disease-causing promoter and untranslated region variants in 8040 undiagnosed individuals with rare disease.
    Alexandra C Martin-Geary, Alexander J M Blakes, Ruebena Dawes, Scott D Findlay, Jenny Lord, Shan Dong, Susan Walker, Jonathan Talbot-Martin, Nechama Wieder, Elston N D'Souza, Maria Fernandes, Sarah Hilton, Nayana Lahiri, Christopher Campbell, Sarah Jenkinson, Christian G E L DeGoede, Emily R Anderson, Toby Candler, Helen Firth, Christopher B Burge, Stephan J Sanders, Jamie Ellingford, Diana Baralle, Siddharth Banka, Nicola Whiffin.
       BACKGROUND: Both promoters and untranslated regions (UTRs) have critical regulatory roles, yet variants in these regions are largely excluded from clinical genetic testing due to difficulty in interpreting pathogenicity. The extent to which these regions may harbour diagnoses for individuals with rare disease is currently unknown.
    METHODS: We present a framework for the identification and annotation of potentially deleterious proximal promoter and UTR variants in known dominant disease genes. We use this framework to annotate de novo variants (DNVs) in 8040 undiagnosed individuals in the Genomics England 100,000 genomes project, which were subject to strict region-based filtering, clinical review, and validation studies where possible. In addition, we performed region and variant annotation-based burden testing in 7862 unrelated probands against matched unaffected controls.
    RESULTS: We prioritised eleven DNVs and identified an additional variant overlapping one of the eleven. Ten of these twelve variants (82%) are in genes that are a strong match to the individual's phenotype and six had not previously been identified. Through burden testing, we did not observe a significant enrichment of potentially deleterious promoter and/or UTR variants in individuals with rare disease collectively across any of our region or variant annotations.
    CONCLUSIONS: Whilst screening promoters and UTRs can uncover additional diagnoses for individuals with rare disease, including these regions in diagnostic pipelines is not likely to dramatically increase diagnostic yield. Nevertheless, we provide a framework to aid identification of these variants.
    Keywords:  Non-coding; Promoters; Rare disease; Regulatory regions; Splicing; Untranslated regions
    DOI:  https://doi.org/10.1186/s13073-025-01464-2
  48. Brain Res. 2025 Apr 16. pii: S0006-8993(25)00206-9. [Epub ahead of print] 149647
    Effects of mitochondrial O-GlcNAcylation in pericytes after mechanical injury.
    Ji Hyun Park, Dong Bin Back, Shuzhen Guo, Masayoshi Tanaka, Hajime Takase, Michael J Whalen, Ken Arai, Kazuhide Hayakawa, Eng H Lo.
      Damage to vascular cells comprise an important part of traumatic brain injury (TBI) but the underlying pathophysiology remains to be fully elucidated. Here, we investigate the loss of O-Linked β-N-acetylglucosamine(O-GlcNAc) modification (O-GlcNAcylation) and mitochondrial disruption in vascular pericytes as a candidate mechanism. In mouse models in vivo, TBI rapidly induces vascular oxidative stress and down-regulates mitochondrial O-GlcNAcylation. In pericytes but not brain endothelial cultures in vitro, mechanical stretch injury down-regulates mitochondrial O-GlcNAcylation. This is accompanied by disruptions in mitochondrial dynamics, comprising a decrease in mitochondrial fusion and an increase in mitochondrial fission proteins. Pharmacologic rescue of endogenous mitochondrial O-GlcNAcylation with an O-GlcNAcase inhibitor Thiamet-G or addition of exogenous O-GlcNAc-enhanced extracellular mitochondria ameliorates the mitochondrial disruption in pericytes damaged by mechanical injury. Finally, in a pericyte-endothelial co-culture model, mechanical injury increased trans-cellular permeability; adding Thiamet-G or O-GlcNAc-enhanced extracellular mitochondria rescued trans-cellular permeability following mechanical injury. These proof-of-concept findings suggest that mitochondrial O-GlcNAcylation in pericytes may represent a novel therapeutic target for ameliorating oxidative stress and vascular damage after mechanical injury following TBI.
    Keywords:  Mitochondrial dynamics; O-GlcNAcylation; Oxidative stress; Traumatic brain injury; Vascular pericyte
    DOI:  https://doi.org/10.1016/j.brainres.2025.149647
  49. Am J Physiol Endocrinol Metab. 2025 Apr 17.
    Ketone body supported respiration in murine isolated brain mitochondria is augmented by alpha-ketoglutarate and is optimized by neuronal SCOT expression.
    Xin C Davis, Colin S McCoin, E Matthew Morris, Julie Allen, Harrison D Stierwalt, Edziu Franczak, Eric D Queathem, Kyle L Fulghum, Patrycja Puchalska, Peter A Crawford, John P Thyfault.
      Ketone bodies are increasingly examined as an alternative fuel source for the known decreases in glucose utilization that occur with neurodegeneration. Here, we established a protocol to maximize ketone body respiration in isolated brain mitochondria, while quantifying acetyl-CoA and energy charge via liquid chromatography-tandem mass spectrometry in control mice compared to mice with neuron-specific deletion of succinyl- CoA-3-oxoacid-CoA transferase (SCOT), required for CoA transfer from succinyl-CoA to AcAc to support its oxidation. Maximal ADP-dependent AcAc respiration occurred at 1 mM; however, the percent increase above basal was minimal (~15%). Alpha- ketoglutarate (αKG) substantially increased AcAc-dependent respiration in isolated brain mitochondria, putatively through the generation of succinyl-CoA. Using mice with neuron- specific deletion of SCOT, we also examined brain mitochondrial respiration of AcAc and resulting acetyl CoA and energy charge (cellular energy availability via adenosine nucleotide ratios of ATP, ADP, and AMP). As expected, isolated brain mitochondria from SCOT-KO mice had lower AcAc State 3 respiration than control mice. Surprisingly, we did not find differences in mitochondrial energy charge between SCOT control and neuron SCOT-KO mice despite decreased acetyl-CoA level in SCOT-KO mice when AcAc was used as the substrate. In conclusion, we show that KG enhances ketone-supported respiration rate in isolated brain mitochondria, and ketone metabolism in neurons affects acetyl-CoA level in brain mitochondria but not energy charge. Future work will determine if diet, exercise, sex, or age impacts ketone-supported respiration rates in conjunction with differences in markers of brain health.
    Keywords:  Brain; Ketone; Mitochondria respiration; SCOT
    DOI:  https://doi.org/10.1152/ajpendo.00058.2025
  50. Adv Mater. 2025 Apr 14. e2500495
    Artificial Mitochondrial Nanorobots Deliver Energy In Vivo by Oral Administration.
    Nan Li, Min Zhou, Ziyu Wu, Yu Chen, Yu Duan, Ziqiang Zhang, Zhuolin Wu, Xue Xia, Jian Shen, Chun Mao, Mimi Wan.
      Delivering energy in vivo is essential for treating mitochondrial damage-related diseases. Current methods, including natural mitochondrial transplantation and artificial energy delivery systems, lack non-destructive, external energy-free, and clinically viable potential solutions. Here, artificial mitochondrial nanorobots (AMNs) carrying high-energy phosphate bonds rebuild the in vivo energy supply system to provide energy. Using ischemic heart disease (IHD) as an energy-deficient disease model and the oral route, which has high patient compliance and facilitates long-term administration, to investigate the therapeutic efficacy of AMNs. AMNs remain stable in the gastrointestinal tract, cross the intestinal barrier via a barrier-crossing unit, and target damaged heart tissue and cardiomyocytes using a motion unit chemotactically. Intracellularly, their energy-generating unit provides high-energy phosphate bonds for ATP synthesis (duration 12 h), while synergistically reducing inflammation and restoring cell viability. At the same frequency of administration, oral AMNs (50 mg kg-1) match intravenous AMNs (10 mg kg-1) in therapeutic efficacy, offering a convenient approach to improving cardiac function. Transcriptomics confirm that 200 µg AMNs emulate 5 × 10⁶ natural mitochondria, restoring energy metabolism and structural function in damaged hearts at the genetic level. This innovative design opens a new pathway for the construction of artificial energy delivery systems in vivo.
    Keywords:  artificial mitochondria; energy delivery; ischemic heart disease; nanorobots; oral administration
    DOI:  https://doi.org/10.1002/adma.202500495
  51. Antioxidants (Basel). 2025 Feb 24. pii: 259. [Epub ahead of print]14(3):
    Sauchinone Ameliorates Senescence Through Reducing Mitochondrial ROS Production.
    Myeong Uk Kuk, Yun Haeng Lee, Duyeol Kim, Kyeong Seon Lee, Ji Ho Park, Jee Hee Yoon, Yoo Jin Lee, Byeonghyeon So, Minseon Kim, Hyung Wook Kwon, Youngjoo Byun, Ki Yong Lee, Joon Tae Park.
      One of the major causes of senescence is oxidative stress caused by ROS, which is mainly generated from dysfunctional mitochondria. Strategies to limit mitochondrial ROS production are considered important for reversing senescence, but effective approaches to reduce them have not yet been developed. In this study, we screened the secondary metabolites that plants produce under oxidative stress and discovered sauchinone as a potential candidate. Sauchinone induced mitochondrial function recovery, enabling efficient electron transport within the electron transport chain (ETC). This led to a decrease in ROS production, a byproduct of inefficient electron transport. The reduction in ROS by sauchinone rejuvenated senescence-associated phenotypes. To understand the underlying mechanism by which sauchinone rejuvenates senescence, we carried out RNA sequencing and found VAMP8 as a key gene. VAMP8 was downregulated by sauchinone. Knockdown of VAMP8 decreased mitochondrial ROS levels and subsequently rejuvenated mitochondrial function, which was similar to the effect of sauchinone. Taken together, these studies revealed a novel mechanism by which sauchinone reduces mitochondrial ROS production by regulating mitochondrial function and VAMP8 expression. Our results open a new avenue for aging research to control senescence by regulating mitochondrial ROS production.
    Keywords:  ROS; mitochondria; mitochondrial oxidative stress; senescence amelioration
    DOI:  https://doi.org/10.3390/antiox14030259
  52. Geroscience. 2025 Apr 12.
    HDAC11 deficiency regulates age-related muscle decline and sarcopenia.
    Renato Odria, Aina Cardús, Clara Gomis-Coloma, Marta Balanyà-Segura, Alexandra Mercado-Amarilla, Pau Maestre-Mora, Andrea Poveda-Sabuco, Joan Carles Domingo, Gisela Nogales-Gadea, Jose A Gomez-Sanchez, Erica Hurtado, Mònica Suelves.
      Sarcopenia, defined as the progressive loss of skeletal muscle mass and function associated with ageing, has devastating effects in terms of reducing the quality of life of older people. Muscle ageing is characterised by muscle atrophy and decreased capacity for muscle repair, including a reduction in the muscle stem cell pool that impedes recovery after injury. Histone deacetylase 11 (HDAC11) is the newest member of the HDAC family and it is highly expressed in skeletal muscle. Our group recently showed that genetic deficiency in HDAC11 increases skeletal muscle regeneration, mitochondrial function and globally improves muscle performance in young mice. Here, we explore for the first time the functional consequences of HDAC11 deficiency in old mice, in homeostasis and during muscle regeneration. Aged mice lacking HDAC11 show attenuated muscle atrophy and postsynaptic fragmentation of the neuromuscular junction, but no significant differences in the number or diameter of myelinated axons of peripheral nerves. Maintenance of the muscle stem cell reservoir and advanced skeletal muscle regeneration after injury are also observed. HDAC11 depletion enhances mitochondrial fatty acid oxidation and attenuates age-associated alterations in skeletal muscle fatty acid composition, reducing drastically the omega-6/omega-3 fatty acid ratio and improving significantly the omega-3 index, providing an explanation for improved muscle strength and fatigue resistance and decreased mortality. Taken together, our results point to HDAC11 as a new target for the treatment of sarcopenia. Importantly, selective HDAC11 inhibitors have recently been developed that could offer a new therapeutic approach to slow the ageing process.
    Keywords:  Fatty acid oxidation; HDAC11; Muscle atrophy; Omega-6/omega-3 fatty acid ratio; Sarcopenia; Skeletal muscle regeneration
    DOI:  https://doi.org/10.1007/s11357-025-01611-y
  53. Neurol India. 2025 Apr 16.
    Broadening the Horizons of Mitochondrial Parkinsonism.
    Mridula Singh, Deepti Grover, Suman Kushwaha.
      
    DOI:  https://doi.org/10.4103/neurol-india.Neurol-India-D-24-00768
  54. CEN Case Rep. 2025 Apr 16.
    Taurine supplementation improves physical activity level in a hemodialysis patient with mitochondrial disease: a case report.
    Ryuto Yoshida, Ryunosuke Mitsuno, Takashin Nakayama, Tatsuhiko Azegami, Akinori Hashiguchi, Takuto Torimitsu, Norifumi Yoshimoto, Akihito Hisikawa, Aika Hagiwara, Toshifumi Nakamura, Shu Meguro, Masahiro Katsumata, Jin Endo, Tatsuo Matsunaga, Jun Yoshino, Takeshi Kanda, Kohkichi Morimoto, Toshiaki Monkawa, Tadashi Yoshida, Jin Nakahara, Shintaro Yamaguchi, Kaori Hayashi.
      Mitochondrial diseases (MDs) are inherited metabolic disorders that affect multiple organ systems, including the kidneys. Variability in disease onset and phenotypic expression, combined with the absence of specific kidney pathological findings, pose significant challenges in diagnosing MD. Consequently, many undiagnosed cases of MD may exist among patients undergoing dialysis. No effective treatment for mitochondrial nephropathy has been established. We report the case of a 27-year-old female patient who presented with leg edema, nephrotic range proteinuria attributed to focal segmental glomerulosclerosis, and bilateral sensorineural hearing loss. Immunosuppressive therapy failed to achieve remission, resulting in progressive kidney function decline and eventual end-stage kidney disease. At hemodialysis initiation, worsening atypical cardiac function and hypertrophy prompted genetic testing, which identified an MT-TL1 m.3243 A > G mutation and confirmed the diagnosis of MD. After hemodialysis initiation, the patient experienced persistent fatigue and decreased physical activity levels despite dry weight management. Suspected stroke-like symptoms prompted the initiation of taurine supplementation, which significantly improved headache severity, cardiac function, and physical activity levels. This case highlights the therapeutic potential of taurine supplementation in patients with MD undergoing dialysis and the importance of maintaining clinical vigilance for MD across all stages of chronic kidney disease, even without characteristic renal pathological findings of mitochondrial nephropathy.
    Keywords:  Focal segmental glomerulosclerosis; Mitochondrial disease; Taurine
    DOI:  https://doi.org/10.1007/s13730-025-00992-5
  55. J Mater Chem B. 2025 Apr 17.
    A red-shifted donor-acceptor hemicyanine-based probe for mitochondrial pH in live cells.
    Fouzia Kalim, Gandhi Sivaraman, Himanshu Vankhede, Arati Ramesh, Sufi O Raja, Akash Gulyani.
      pH dynamically regulates diverse cellular functions and processes. At the inner mitochondrial membrane (IMM), nanoscale pH gradients generated by the electron transport chain (ETC) play a critical role in contributing to mitochondrial membrane potential that drives ATP synthesis and thermogenesis. However, tools to decouple pH gradients from the overall IMM potential in living cells are limited. This study integrates a fluorescent "benzo-indole" chromophore with a pH-sensitive "phenol" moiety into a single covalent skeleton to build a sensitive, red-shifted, cell-permeable pH probe (Mito-pH2). Mito-pH2 localizes inside mitochondria with high specificity presumably to the mitochondrial inner membrane by virtue of being an amphiphilic cation and can report dynamic changes in mitochondrial pH in living cells. Our design ensures that Mito-pH2 exhibits pH-sensitive dual-excitation and dual-emission peaks enabling ratiometric pH-sensing. Furthermore, Mito-pH2 reports an increase in pH in the pH range of 3-9 through a striking colour change from yellow to purple making it a sensitive all-purpose colorimetric pH probe. A combination of DFT calculations and spectroscopy shed light on likely sensing mechanisms including photophysics. Quantitative live-cell fluorescence imaging reveals that Mito-pH2 can detect dynamic changes in mitochondrial pH upon extracellular pH modulation with little or no measurable cytotoxicity during live imaging. Red-emitting Mito-pH2 opens new avenues of quantitative mapping of physiological mitochondrial membrane pH and significantly enhances the repertoire of environment-sensitive and low-toxicity mitochondrial probes that link mitochondrial state and micro-environment.
    DOI:  https://doi.org/10.1039/d4tb01839g
  56. Nat Commun. 2025 Apr 16. 16(1): 3306
    Elevated mitochondrial membrane potential is a therapeutic vulnerability in Dnmt3a-mutant clonal hematopoiesis.
    Kira A Young, Mohsen Hosseini, Jayna J Mistry, Claudia Morganti, Taylor S Mills, Xiurong Cai, Brandon T James, Griffin J Nye, Natalie R Fournier, Veronique Voisin, Ali Chegini, Aaron D Schimmer, Gary D Bader, Grace Egan, Marc R Mansour, Grant A Challen, Eric M Pietras, Kelsey H Fisher-Wellman, Keisuke Ito, Steven M Chan, Jennifer J Trowbridge.
      The competitive advantage of mutant hematopoietic stem and progenitor cells (HSPCs) underlies clonal hematopoiesis (CH). Drivers of CH include aging and inflammation; however, how CH-mutant cells gain a selective advantage in these contexts is an unresolved question. Using a murine model of CH (Dnmt3aR878H/+), we discover that mutant HSPCs sustain elevated mitochondrial respiration which is associated with their resistance to aging-related changes in the bone marrow microenvironment. Mutant HSPCs have DNA hypomethylation and increased expression of oxidative phosphorylation gene signatures, increased functional oxidative phosphorylation capacity, high mitochondrial membrane potential (Δψm), and greater dependence on mitochondrial respiration compared to wild-type HSPCs. Exploiting the elevated Δψm of mutant HSPCs, long-chain alkyl-TPP molecules (MitoQ, d-TPP) selectively accumulate in the mitochondria and cause reduced mitochondrial respiration, mitochondrial-driven apoptosis and ablate the competitive advantage of HSPCs ex vivo and in vivo in aged recipient mice. Further, MitoQ targets elevated mitochondrial respiration and the selective advantage of human DNMT3A-knockdown HSPCs, supporting species conservation. These data suggest that mitochondrial activity is a targetable mechanism by which CH-mutant HSPCs gain a selective advantage over wild-type HSPCs.
    DOI:  https://doi.org/10.1038/s41467-025-57238-2
  57. Nature. 2025 Apr 16.
    Clinical trials test the safety of stem-cell therapy for Parkinson's disease.
    Hideyuki Okano.
      
    Keywords:  Medical research; Parkinson's disease; Regeneration; Stem cells
    DOI:  https://doi.org/10.1038/d41586-025-00688-x
  58. Genome Res. 2025 Apr 14. 35(4): 572-582
    Evolution of genome-wide methylation profiling technologies.
    Carolina Montano, Winston Timp.
      In this mini-review, we explore the advancements in genome-wide DNA methylation profiling, tracing the evolution from traditional methods such as methylation arrays and whole-genome bisulfite sequencing to the cutting-edge single-molecule profiling enabled by long-read sequencing (LRS) technologies. We highlight how LRS is transforming clinical and translational research, particularly by its ability to simultaneously measure genetic and epigenetic information, providing a more comprehensive understanding of complex disease mechanisms. We discuss current challenges and future directions in the field, emphasizing the need for innovative computational tools and robust, reproducible approaches to fully harness the capabilities of LRS in molecular diagnostics.
    DOI:  https://doi.org/10.1101/gr.278407.123
  59. BMC Neurol. 2025 Apr 16. 25(1): 160
    Investigating the genetic association of mitochondrial DNA copy number with neurodegenerative diseases.
    Huan Xia, Zi-Hao Wang, Xiao-Bei Wang, Mei-Rong Gao, Sen Jiang, Xin-Yu Du, Xin-Ling Yang.
       OBJECTIVE: This study aims to investigate the causal relationship between Mitochondrial DNA (mtDNA) copy number and several common neurodegenerative diseases (NDs).
    METHODS: We conducted a bidirectional two-sample Mendelian randomization (MR) analysis using data from genome-wide association studies (GWAS) as instrumental variables (IVs). After screening for relevance and potential confounders, we estimated the association between mtDNA copy number and NDs, including Alzheimer's disease (AD), Parkinson's disease (PD), Amyotrophic lateral sclerosis (ALS), and Multiple sclerosis (MS). Additionally, we validated our findings using GWAS data on mtDNA copy number from Longchamps et al., sourced from the Genetics Epidemiology Consortium and the UK Biobank (UKB) aging study cohort.
    RESULTS: A GWAS analysis of 395,718 UKB participants found no significant association between mtDNA copy number and the risk of NDs, including AD (OR = 0.956, P = 0.708), PD (OR = 1.223, P = 0.179), ALS (OR = 0.972, P = 0.374), and MS (OR = 0.932, P = 0.789). Similarly, reverse MR analysis revealed no significant relationship between genetic predictions of NDs and mtDNA copy number: AD (OR = 0.987, P = 0.062), PD (OR = 0.997, P = 0.514), ALS (OR = 0.974, P = 0.706), and MS (OR = 1.003, P = 0.181).
    CONCLUSION: Although mitochondrial dysfunction is implicated in the pathogenesis of NDs, no clear evidence supports a causal role for mtDNA copy number. The relationship between mtDNA copy number and NDs is likely mediated by more complex molecular regulatory mechanisms. Further research is required to elucidate these intricate interactions.
    Keywords:  Genome-wide association studies; Mendelian randomization analysis; Mitochondrial DNA copy number; Neurodegenerative diseases
    DOI:  https://doi.org/10.1186/s12883-025-04176-7
  60. Cell. 2025 Apr 10. pii: S0092-8674(25)00343-5. [Epub ahead of print]
    Integrator loss leads to dsRNA formation that triggers the integrated stress response.
    Apoorva Baluapuri, Nicole ChenCheng Zhao, Ryan J Marina, Kai-Lieh Huang, Anastasia Kuzkina, Maria E Amodeo, Chad B Stein, Lucie Y Ahn, Jordan S Farr, Ashleigh E Schaffer, Vikram Khurana, Eric J Wagner, Karen Adelman.
      Integrator (INT) is a metazoan-specific complex that targets promoter-proximally paused RNA polymerase II (RNAPII) for termination, preventing immature RNAPII from entering gene bodies and functionally attenuating transcription of stress-responsive genes. Mutations in INT subunits are associated with many human diseases, including cancer, ciliopathies, and neurodevelopmental disorders, but how reduced INT activity contributes to disease is unknown. Here, we demonstrate that the loss of INT-mediated termination in human cells triggers the integrated stress response (ISR). INT depletion causes upregulation of short genes such as the ISR transcription factor activating transcription factor 3 (ATF3). Further, immature RNAPII that escapes into genes upon INT depletion is prone to premature termination, generating incomplete pre-mRNAs with retained introns. Retroelements within retained introns form double-stranded RNA (dsRNA) that is recognized by protein kinase R (PKR), which drives ATF4 activation and prolonged ISR. Critically, patient cells with INT mutations exhibit dsRNA accumulation and ISR activation, thereby implicating chronic ISR in diseases caused by INT deficiency.
    Keywords:  IR-Alu; Integrator; RNA polymerase II pausing; double-stranded RNA; gene regulation; integrated stress response; premature cleavage and polyadenylation; premature termination; protein kinase R
    DOI:  https://doi.org/10.1016/j.cell.2025.03.025
  61. bioRxiv. 2025 Apr 04. pii: 2025.04.03.647028. [Epub ahead of print]
    Structural Basis for Promoter Recognition and Transcription Factor Binding and Release in Human Mitochondria.
    Karl Herbine, Ashok R Nayak, Angelica Zamudio-Ochoa, Dmitry Temiakov.
      Transcription in human mitochondria is driven by a core apparatus consisting of a Pol A family RNA polymerase (mtRNAP), the initiation factors TFAM and TFB2M, and the elongation factor TEFM. While earlier structures of initiation and elongation complexes provided valuable snapshots, they represent isolated stages of a highly dynamic and multistep process. Critical aspects of mitochondrial transcription-such as DNA recognition and melting, promoter escape, and the release of initiation factors-remain poorly understood. Here, we present a series of cryo-EM structures that capture the transcription complex as it transitions from the initial open promoter complex to the processive elongation complex through intermediate stages. Our data reveal new determinants of promoter specificity, the sequential disengagement of mtRNAP from TFAM and the promoter, the release of TFB2M, and the recruitment of TEFM. Together, these findings provide a detailed molecular mechanism underlying transcription in human mitochondria.
    DOI:  https://doi.org/10.1101/2025.04.03.647028
  62. BMC Pregnancy Childbirth. 2025 Apr 14. 25(1): 444
    Mitochondrial proteins and congenital birth defect risk: a mendelian randomization study.
    Xin-Yu Li, Da-Tao Li, Yi-Yuan Li, Zhi-Cheng Xu, Qun Zhang, Xia Chen, Feng Xu, Ru-Hong Zhang.
       BACKGROUND: Mitochondrial dysfunction has been hypothesized to play a role in the etiology of congenital birth defects. However, evidence from observational studies is susceptible to bias and confounding. Mendelian randomization uses genetic variants as instrumental variables to investigate causal relationships. This study aimed to investigate the causal effect of mitochondrial proteins on risk of common congenital defects including orofacial clefts, congenital heart defects, external ear malformations, urinary system malformations, nervous system malformations, and limb malformations.
    METHODS: Summary statistics data on congenital birth defects were obtained from the FinnGen consortium. This included 1,994 cases of congenital heart malformations, 258 cases of nervous system malformations, 185 cases of ear malformations, 813 cases of urinary system malformations, 92 cases of limb malformations, and 181 cases of cleft lip and cleft palate, alongside 216,798 to 218,611 controls, depending on the defect type. Data on genetic variants associated with 66 mitochondrial proteins were extracted from the Human Plasma Proteome Atlas (n = 3,301 healthy individuals). The inverse-variance weighted method was applied as the primary analysis, with sensitivity analyses using MR-Egger regression, weighted median estimation, and MR-PRESSO to assess pleiotropy and outliers.
    RESULTS: Among the 66 mitochondrial protein traits examined, several displayed significant associations with congenital birth defects. Negative associations were found between pyruvate dehydrogenase kinase isozyme 1 and ATP synthase subunit beta mitochondrial levels and congenital heart malformation risk. GrpE protein homolog 1 mitochondrial was negatively associated with cleft lip/palate risk. 39S ribosomal protein L14 and GrpE protein homolog 1 mitochondrial showed positive and negative links with urinary malformations, respectively. Positive associations were noted between cytochrome c oxidase subunit 4 isoform 2, protein SCO1 homolog, and tRNA pseudouridine synthase A mitochondrial and nervous system malformations, while peptide chain release factor 1-like mitochondrial was negatively related. Cytochrome c oxidase subunit 7 A1 mitochondrial associated positively with ear malformations. Positive relationships were identified between cytochrome c oxidase subunit 7 A1, ADP-ribose pyrophosphatase, coiled-coil-helix-coiled-coil-helix domain-containing protein 10, NFU1 iron-sulfur cluster scaffold homolog mitochondrial, and limb malformation risk. Meanwhile, NADH dehydrogenase [ubiquinone] iron-sulfur protein 4 mitochondrial displayed a negative association.
    CONCLUSIONS: This Mendelian randomization study provides evidence that mitochondrial protein levels may be causally implicated in congenital heart, urinary, nervous system, ear, and limb malformations. The findings highlight potential etiological roles for mitochondrial dysfunction in the pathogenesis of structural birth defects. Further large-scale and functional investigations are warranted to corroborate these genetic inference results and elucidate underlying mechanisms that may inform translational applications.
    Keywords:  Congenital birth defect; Mendelian randomization; Mitochondria
    DOI:  https://doi.org/10.1186/s12884-025-07562-8
  63. Cell. 2025 Apr 08. pii: S0092-8674(25)00292-2. [Epub ahead of print]
    ALDH7A1 protects against ferroptosis by generating membrane NADH and regulating FSP1.
    Jia-Shu Yang, Andrew J Morris, Koki Kamizaki, Jianzhong Chen, Jillian Stark, William M Oldham, Toshitaka Nakamura, Eikan Mishima, Joseph Loscalzo, Yasuhiro Minami, Marcus Conrad, Whitney S Henry, Victor W Hsu.
      Ferroptosis is a form of cell death due to iron-induced lipid peroxidation. Ferroptosis suppressor protein 1 (FSP1) protects against this death by generating antioxidants, which requires nicotinamide adenine dinucleotide, reduced form (NADH) as a cofactor. We initially uncover that NADH exists at significant levels on cellular membranes and then find that this form of NADH is generated by aldehyde dehydrogenase 7A1 (ALDH7A1) to support FSP1 activity. ALDH7A1 activity also acts directly to decrease lipid peroxidation by consuming reactive aldehydes. Furthermore, ALDH7A1 promotes the membrane recruitment of FSP1, which is instigated by ferroptotic stress activating AMP-activated protein kinase (AMPK) to promote the membrane localization of ALDH7A1 that stabilizes FSP1 on membranes. These findings advance a fundamental understanding of NADH by revealing a previously unappreciated pool on cellular membranes, with the elucidation of its function providing a major understanding of how FSP1 acts and how an aldehyde dehydrogenase protects against ferroptosis.
    Keywords:  aldehyde dehydrogenase 7A1; ferroptosis; ferroptosis suppressor protein 1; nicotinamide adenine dinucleotide reduced form
    DOI:  https://doi.org/10.1016/j.cell.2025.03.019
  64. J Biol Chem. 2025 Apr 16. pii: S0021-9258(25)00359-X. [Epub ahead of print] 108510
    MitoSNO inhibits mitochondrial hydrogen peroxide (mtH2O2) generation by α-ketoglutarate dehydrogenase (KGDH).
    Olivia Chalifoux, Samantha Sterman, Ben Faerman, Meijing Li, Stephanie Trezza, Marek Michalak, Luis B Agellon, Ryan J Mailloux.
      Here, we demonstrate mitochondrial hydrogen peroxide (mtH2O2) production by α-ketoglutarate dehydrogenase (KGDH) can be inhibited by MitoSNO, alleviating lipotoxicity. MitoSNO in the nanomolar range inhibits mtH2O2 by ∼50% in isolated liver mitochondria without disrupting respiration, whereas the mitochondria-selective derivative used to synthesize MitoSNO, mitochondria-selective N-acetyl-penicillamine (MitoNAP), had no effect on either mtH2O2 generation or oxidative phosphorylation (OxPhos). Additionally, mtH2O2 generation in isolated liver mitochondria was almost abolished when MitoSNO was administered in the low micromolar range. The potent inhibitory effect of MitoSNO was comparable to 2-keto-3-methyl-valeric acid (KMV) and valproic acid (VA), selective inhibitors for KGDH-mediate mH2O2 production. S1QEL 1.1 (S1) and S3QEL (S3), which are known to selectively suppress mtH2O2 genesis through inhibition of complex I and complex III respectively, without disrupting respiration, had little to no effect on mtH2O2 production by liver mitochondria. We also identified it was a major mtH2O2 source as well but MitoSNO and MitoNAP did not affect mtH2O2 production by this ETC-linked enzyme. The MitoSNO also suppressed mtH2O2 production and partially rescued mitochondrial respiration in Huh-7 cells subjected to palmitate (PA) and fructose (Fruc) induced lipotoxicity. MitoSNO also prevented cell death and abrogated intrahepatic lipid accumulation in these Huh-7 cells. MitoSNO nullified mtH2O2 overgeneration and partially rescued OxPhos in liver mitochondria from mice fed a high fat diet (HFD). Our findings demonstrate that MitoSNO interferes with mtH2O2 production through KGDH S-nitrosation and may be useful in alleviating non-alcoholic fatty liver disease (NAFLD).
    DOI:  https://doi.org/10.1016/j.jbc.2025.108510
  65. Comput Struct Biotechnol J. 2025 ;27 1265-1277
    Modeling the different conformations of the human mitochondrial ADP/ATP carrier using AlphaFold and molecular dynamics simulations of the protein-ligand complexes.
    Virginia Quadrotta, Fabio Polticelli.
      The ADP/ATP Carrier (AAC), a member of the mitochondrial Solute Carrier Family 25 (SLC25), facilitates the exchange of cytosolic ADP for mitochondrial ATP across the inner mitochondrial membrane (IMM). It serves as a master regulator of the cellular ADP/ATP ratio and is involved in various pathologies, including cancer. Its transport mechanism involves a conformational transition that alternates the accessibility of the binding site between the cytoplasmic (c-state) and mitochondrial (m-state) sides of the IMM. In this study, the human AAC was used as a case study to evaluate the performance of AlphaFold2 (AF2) and AlphaFold3 (AF3) for structural modeling of members of the SLC25 family. The study also compared the AF3 approach for predicting protein-ligand complexes with the standard methodology of modeling followed by molecular docking. Both AF2 and AF3 display a bias toward the c-state conformation. On the other hand, ColabFold implementation of AF2 successfully generated the first ab initio structural model of the human AAC in the m-state conformation. Modeling of the complexes coupled to molecular dynamics (MD) simulations allowed to obtain structural insight into AAC's substrate binding and stabilization mechanisms, and the possible effects of pathogenic mutations on its conformational dynamics and functionality. These analyses provided a deeper understanding of AAC's alternating access mechanism and highlighted the potential of AF3 in modeling protein-ligand interactions, though only in the c-state. This work demonstrates the reliability of AlphaFold models when aligned with experimental data and provides further confirmation of their utility for investigating solute carriers and membrane proteins.
    Keywords:  ADP/ATP Carrier; AlphaFold; mitochondrial carrier; modeling; molecular dynamics; structural dynamics
    DOI:  https://doi.org/10.1016/j.csbj.2025.03.036
  66. Front Cell Dev Biol. 2025 ;13 1498902
    Rab11b is necessary for mitochondrial integrity and function in gut epithelial cells.
    Ivor Joseph, Jiangmeng Han, Jared Bianchi-Smak, Jiaxing Yang, Jagannatham Naidu Bhupana, Juan Flores, Jack Delucia, Tracy S Tran, James R Goldenring, Edward M Bonder, Nan Gao.
       Introduction: The RAB11 family of small GTPases are intracellular regulators of membrane and vesicular trafficking. We recently reported that RAB11A and RAB11B redundantly regulate spindle dynamics in dividing gut epithelial cells. However, in contrast to the well-studied RAB11A functions in transporting proteins and lipids through recycling endosomes, the distinct function of RAB11B is less clear.
    Methods and Results: Our proteomic analysis of RAB11A or RAB11B interactome suggested a potential RAB11B specific involvement in regulating mitochondrial functions. Transcriptomic analysis of Rab11b knockout mouse intestines revealed an enhanced mitochondrial protein targeting program with an altered mitochondrial functional integrity. Flow cytometry assessment of mitochondrial membrane potential and reactive oxygen species production revealed an impaired mitochondrial function in vivo. Electron microscopic analysis demonstrated a particularly severe mitochondrial membrane defect in Paneth cells.
    Conclusion: These genetic and functional data link RAB11B to mitochondrial structural and functional maintenance for the first time.
    Keywords:  Paneth cell; Rab11; intestine; mitochondria; proteomics
    DOI:  https://doi.org/10.3389/fcell.2025.1498902
  67. Nutrients. 2025 Mar 30. pii: 1214. [Epub ahead of print]17(7):
    Mitochondria at the Crossroads: Linking the Mediterranean Diet to Metabolic Health and Non-Pharmacological Approaches to NAFLD.
    Giovanna Mercurio, Antonia Giacco, Nicla Scopigno, Michela Vigliotti, Fernando Goglia, Federica Cioffi, Elena Silvestri.
      Nonalcoholic fatty liver disease (NAFLD) is a growing global health concern that is closely linked to metabolic syndrome, yet no approved pharmacological treatment exists. The Mediterranean diet (MD) emerged as a first-line dietary intervention for NAFLD, offering metabolic and hepatoprotective benefits. Now conceptualized as a complex chemical matrix rich in bioactive compounds, the MD exerts antioxidant and anti-inflammatory effects, improving insulin sensitivity and lipid metabolism. Mitochondria play a central role in NAFLD pathophysiology, influencing energy metabolism, oxidative stress, and lipid homeostasis. Emerging evidence suggests that the MD's bioactive compounds enhance mitochondrial function by modulating oxidative phosphorylation, biogenesis, and mitophagy. However, most research has focused on individual compounds rather than the MD as a whole, leaving gaps in understanding its collective impact as a complex dietary pattern. This narrative review explores how the MD and its bioactive compounds influence mitochondrial health in NAFLD, highlighting key pathways such as mitochondrial substrate control, dynamics, and energy efficiency. A literature search was conducted to identify relevant studies on the MD, mitochondria, and NAFLD. While the search was promising, our understanding remains incomplete, particularly when current knowledge is limited by the lack of mechanistic and comprehensive studies on the MD's holistic impact. Future research integrating cutting-edge experimental approaches is needed to elucidate the intricate diet-mitochondria interactions. A deeper understanding of how the MD influences mitochondrial health in NAFLD is essential for developing precision-targeted nutritional strategies that can effectively prevent and manage the disease.
    Keywords:  MASLD; MUFA; PUFA; fatty liver; fructose; lifestyle; metabolic syndrome; mitochondrial bioenergetics; mitochondrial quality control; polyphenols
    DOI:  https://doi.org/10.3390/nu17071214
  68. Exp Neurol. 2025 Apr 10. pii: S0014-4886(25)00117-7. [Epub ahead of print]389 115253
    Nicotinamide N-methyltransferase as a potential therapeutic target for neurodegenerative disorders: Mechanisms, challenges, and future directions.
    An Liu, Xiao-Juan Zhu, Wei-Dong Sun, Shuang-Zhou Bi, Chen-Ying Zhang, Shi-Yan Lai, Jiang-Hua Li.
      Neurodegenerative diseases (NDs), including Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD), are characterized by progressive neuronal loss and functional decline, posing significant global health challenges. Emerging evidence highlights nicotinamide N-methyltransferase (NNMT), a cytosolic enzyme regulating nicotinamide (NAM) methylation, as a pivotal player in NDs through its dual impact on epigenetic regulation and metabolic homeostasis. This review synthesizes current knowledge on NNMT's role in disease pathogenesis, focusing on its epigenetic modulation via DNA hypomethylation and histone modifications, alongside its disruption of NAD+ synthesis and homocysteine (Hcy) metabolism. Elevated NNMT activity depletes NAD+, exacerbating mitochondrial dysfunction and impairing energy metabolism, while increased Hcy levels drive oxidative stress, neuroinflammation, and aberrant protein aggregation (e.g., Aβ, tau, α-synuclein). Notably, NNMT overexpression in AD and PD correlates with neuronal hypomethylation and neurotoxicity, as observed in postmortem brain studies and transgenic models. Mechanistically, NNMT consumes S-adenosylmethionine (SAM), limiting methyl donor availability for DNA methyltransferases (DNMTs) and histone methyltransferases (HMTs), thereby altering gene expression patterns critical for neuronal survival. Concurrently, NNMT-mediated NAD+ depletion disrupts sirtuin activity (e.g., SIRT1) and mitochondrial biogenesis, accelerating axonal degeneration. Therapeutic strategies targeting NNMT, such as RNA interference (RNAi), small-molecule inhibitors and exercise therapy, show promise in preclinical models by restoring NAD+ levels and reducing Hcy toxicity. However, challenges persist in achieving cellular specificity, optimizing blood-brain barrier penetration, and mitigating off-target effects. This review underscores NNMT's potential as a multifactorial therapeutic target, bridging metabolic and epigenetic dysregulation in NDs. Future research should prioritize elucidating tissue-specific NNMT interactions, refining inhibitor pharmacokinetics, and validating translational efficacy in clinical trials. Addressing these gaps could pave the way for novel disease-modifying therapies to combat the rising burden of neurodegeneration.
    Keywords:  Epigenetics; Homocysteine; NAD(+) metabolism; Neurodegenerative diseases; Nicotinamide N-methyltransferase (NNMT); Therapeutic targeting
    DOI:  https://doi.org/10.1016/j.expneurol.2025.115253
  69. Hum Cell. 2025 Apr 17. 38(3): 90
    Clinical characteristics and induced pluripotent stem cells (iPSCs) disease model of Harel-Yoon syndrome caused by compound heterozygous ATAD3A variants.
    Ziyi Jiang, Hongyu Chen, Xianghong Zhang, Xiaoling Jiang, Zhengqing Tong, Jingjing Ye, Shanshan Shi, Xucong Shi, Fengxia Li, Weiqin Shao, Qiang Shu, Lan Yu.
      ATPase family AAA-domain-containing protein 3 A (ATAD3A) is enriched on the mitochondrial membrane and is essential to the maintenance of mitochondrial structure and function. Variants of the ATAD3A gene can lead to Harel-Yoon syndrome (HAYOS), a developmental defect in neurological, cardiovascular, and other systems. This study aims to develop induced pluripotent stem cells (iPSCs) from the somatic cells of a patient (ZJUCHYLi001-A) and a negative control (ZJUCHYLi002-A) as effective tools for further investigations into the etiology of ATAD3A variant-related disease. We described and analyzed the clinical manifestations of the proband and her family members. Somatic cells from the proband and a negative control were collected and reprogrammed into iPSCs. Furthermore, we measured the ATAD3A expression levels in the iPSCs to confirm the validity of these cell lines. The proband and her elder sister were both critically ill and harbored compound heterozygous ATAD3A variants (F459S/T498 Nfs* 13). Their parents were carriers of these variants without any clinical manifestations. Both variants are located on the ATPase domain of the ATAD3A protein. Cell lines ZJUCHYLi001-A and ZJUCHYLi002-A presented typical features of pluripotent stem cells. The ATAD3A expression levels of ZJUCHYLi001-A were significantly reduced compared with ZJUCHYLi002-A. This study generated iPSCs from a patient with compound heterozygous variants of ATAD3A and a negative control as valuable tools for clarifying the molecular mechanisms underlying ATAD3A variant-related diseases.
    Keywords:  ATAD3A; Harel–Yoon Sysdrome; Induced pluripotent stem cells
    DOI:  https://doi.org/10.1007/s13577-025-01214-x
  70. Genome Res. 2025 Apr 14. 35(4): 593-598
    The impact of long-read sequencing on human population-scale genomics.
    Tobias Rausch, Tobias Marschall, Jan O Korbel.
      Long-read sequencing technologies, particularly those from Pacific Biosciences and Oxford Nanopore Technologies, are revolutionizing genome research by providing high-resolution insights into complex and repetitive regions of the human genome that were previously inaccessible. These advances have been particularly enabling for the comprehensive detection of genomic structural variants (SVs), which is critical for linking genotype to phenotype in population-scale and rare disease studies, as well as in cancer. Recent developments in sequencing throughput and computational methods, such as pangenome graphs and haplotype-resolved assemblies, are paving the way for the future inclusion of long-read sequencing in clinical cohort studies and disease diagnostics. DNA methylation signals directly obtained from long reads enhance the utility of single-molecule long-read sequencing technologies by enabling molecular phenotypes to be interpreted, and by allowing the identification of the parent of origin of de novo mutations. Despite this recent progress, challenges remain in scaling long-read technologies to large populations due to cost, computational complexity, and the lack of tools to facilitate the efficient interpretation of SVs in graphs. This perspective provides a succinct review on the current state of long-read sequencing in genomics by highlighting its transformative potential and key hurdles, and emphasizing future opportunities for advancing the understanding of human genetic diversity and diseases through population-scale long-read analysis.
    DOI:  https://doi.org/10.1101/gr.280120.124
  71. Nature. 2025 Apr 16.
    Deep Visual Proteomics maps proteotoxicity in a genetic liver disease.
    Florian A Rosenberger, Sophia C Mädler, Katrine Holtz Thorhauge, Sophia Steigerwald, Malin Fromme, Mikhail Lebedev, Caroline A M Weiss, Marc Oeller, Maria Wahle, Andreas Metousis, Maximilian Zwiebel, Niklas A Schmacke, Sönke Detlefsen, Peter Boor, Ondřej Fabián, Soňa Fraňková, Aleksander Krag, Pavel Strnad, Matthias Mann.
      Protein misfolding diseases, including α1-antitrypsin deficiency (AATD), pose substantial health challenges, with their cellular progression still poorly understood1-3. We use spatial proteomics by mass spectrometry and machine learning to map AATD in human liver tissue. Combining Deep Visual Proteomics (DVP) with single-cell analysis4,5, we probe intact patient biopsies to resolve molecular events during hepatocyte stress in pseudotime across fibrosis stages. We achieve proteome depth of up to 4,300 proteins from one-third of a single cell in formalin-fixed, paraffin-embedded tissue. This dataset reveals a potentially clinically actionable peroxisomal upregulation that precedes the canonical unfolded protein response. Our single-cell proteomics data show α1-antitrypsin accumulation is largely cell-intrinsic, with minimal stress propagation between hepatocytes. We integrated proteomic data with artificial intelligence-guided image-based phenotyping across several disease stages, revealing a late-stage hepatocyte phenotype characterized by globular protein aggregates and distinct proteomic signatures, notably including elevated TNFSF10 (also known as TRAIL) amounts. This phenotype may represent a critical disease progression stage. Our study offers new insights into AATD pathogenesis and introduces a powerful methodology for high-resolution, in situ proteomic analysis of complex tissues. This approach holds potential to unravel molecular mechanisms in various protein misfolding disorders, setting a new standard for understanding disease progression at the single-cell level in human tissue.
    DOI:  https://doi.org/10.1038/s41586-025-08885-4
  72. J Chem Theory Comput. 2025 Apr 16.
    Collective Variables and Facilitated Conformational Opening during Translocation of Human Mitochondrial RNA Polymerase (POLRMT) from Atomic Simulations.
    Shannon J McElhenney, Jin Yu.
      Collective variable (CV) identification is challenging in complex dynamical systems. To study the translocation of a single-subunit RNA polymerase (RNAP) during human mitochondrial transcription, we employed all-atom molecular dynamics (MD) as a vehicle to illustrate CV refinement in conformational samplings and dimension reduction analyses. RNAP translocation is an essential mechanical step of transcription elongation that dictates gene expression. The translocation generally follows from polymerization product release and proceeds to initial binding or preinsertion of incoming nucleotides. The human mitochondrial DNA-dependent RNAP (or POLRMT) plays a critical role in cellular metabolism and can be a key molecular off-target in the design of nucleotide analogue antiviral and antitumor drugs due to its structural similarities with many viral RNAPs or RNA-dependent RNA polymerases (RdRps). While POLRMT shares particularly high structural similarity with bacteriophage T7 RNAP, previous experimental studies and our current simulations suggest that POLRMT's mechanochemical coupling mechanisms may be distinct. In the current work, we modeled POLRMT elongation complexes and performed equilibrium MD simulations on the pre- and post-translocation models, with extensive samplings around two potential translocation paths (with or without coupling to the fingers subdomain conformational change). We then compared time-lagged independent component analysis (tICA) and the neural network implementation of the variational approach for Markov processes (VAMPnets) as dimensional reduction methods on selected atomic coordinate sets to best represent the sampled features from the MD simulations. Our results indicate that POLRMT translocation is likely coupled with NTP binding to enable fingers subdomain opening at post-translocation which would otherwise be nonstabilized, or the translocations may proceed futilely without the fingers opening for incoming NTP initial binding or incorporation. The time scale of the coupled translocation reaches over hundreds of microseconds, as predicted by the VAMPnets analyses. Such a time scale seems to match a last postcatalytic kinetic step suggested for the POLRMT elongation cycle by previous experimental measurements. Our MD simulation studies combining atomic coordinate refinements and dimension reduction analyses on top of extensive conformational samplings thus suggest a variation of Brownian ratcheting in POLRMT translocation, as if the Brownian motions of translocation are coupled with NTP binding, which captures transient fingers subdomain opening to couple the translocation with a sustained fingers opening.
    DOI:  https://doi.org/10.1021/acs.jctc.4c01568
  73. Commun Biol. 2025 Apr 16. 8(1): 619
    Structural and biochemical mechanism of short-chain enoyl-CoA hydratase (ECHS1) substrate recognition.
    Gengchen Su, Youwei Xu, Binxian Chen, Kaide Ju, Ye Jin, Houzao Chen, Shuyang Zhang, Xiaodong Luan.
      Deficiency of short-chain enoyl-CoA hydratase (ECHS1), a crucial enzyme in fatty acid metabolism through the mitochondrial β-oxidation pathway, has been strongly linked to various diseases, especially cardiomyopathy. However, the structural and biochemical mechanisms through which ECHS1 recognizes acyl-CoAs remain poorly understood. Herein, cryo-EM analysis reveals the apo structure of ECHS1 and structures of the ECHS1-crotonyl-CoA, ECHS1-acetoacetyl-CoA, ECHS1-hexanoyl-CoA, and ECHS1-octanoyl-CoA complexes at high resolutions. The mechanism through which ECHS1 recognizes its substrates varies with the fatty acid chain lengths of acyl-CoAs. Furthermore, crucial point mutations in ECHS1 have a great impact on substrate recognition, resulting in significant changes in binding affinity and enzyme activity, as do disease-related point mutations in ECHS1. The functional mechanism of ECHS1 is systematically elucidated from structural and biochemical perspectives. These findings provide a theoretical basis for subsequent work focused on determining the role of ECHS1 deficiency (ECHS1D) in the occurrence of diseases such as cardiomyopathy.
    DOI:  https://doi.org/10.1038/s42003-025-07924-0
  74. Proc Natl Acad Sci U S A. 2025 Apr 22. 122(16): e2419881122
    Mechanism of allosteric activation in human mitochondrial ClpP protease.
    Monica M Goncalves, Adwaith B Uday, Taylor J B Forrester, S Quinn W Currie, Angelina S Kim, Yue Feng, Yulia Jitkova, Algirdas Velyvis, Robert W Harkness, Matthew S Kimber, Aaron D Schimmer, Natalie Zeytuni, Siavash Vahidi.
      Human ClpP protease contributes to mitochondrial protein quality control by degrading misfolded proteins. ClpP is overexpressed in cancers such as acute myeloid leukemia (AML), where its inhibition leads to the accumulation of damaged respiratory chain subunits and cell death. Conversely, hyperactivating ClpP with small-molecule activators, such as the recently discovered ONC201, disrupts mitochondrial protein degradation and impairs respiration in cancer cells. Despite its critical role in human health, the mechanism underlying the structural and functional properties of human ClpP remains elusive. Notably, human ClpP is paradoxically activated by active-site inhibitors. All available structures of human ClpP published to date are in the inactive compact or compressed states, surprisingly even when ClpP is bound to an activator molecule such as ONC201. Here, we present structures of human mitochondrial ClpP in the active extended state, including a pair of structures where ClpP is bound to an active-site inhibitor. We demonstrate that amino acid substitutions in the handle region (A192E and E196R) recreate a conserved salt bridge found in bacterial ClpP, stabilizing the extended active state and significantly enhancing ClpP activity. We elucidate the ClpP activation mechanism, highlighting a hormetic effect where substoichiometric inhibitor binding triggers an allosteric transition that drives ClpP into its active extended state. Our findings link the conformational dynamics of ClpP to its catalytic function and provide high-resolution structures for the rational design of potent and specific ClpP inhibitors, with implications for targeting AML and other disorders with ClpP involvement.
    Keywords:  ClpP protease; HDX–MS; allostery; cryo-EM; intracellular protein degradation
    DOI:  https://doi.org/10.1073/pnas.2419881122
  75. Nature. 2025 Apr;640(8059): 623-633
    Towards multimodal foundation models in molecular cell biology.
    Haotian Cui, Alejandro Tejada-Lapuerta, Maria Brbić, Julio Saez-Rodriguez, Simona Cristea, Hani Goodarzi, Mohammad Lotfollahi, Fabian J Theis, Bo Wang.
      The rapid advent of high-throughput omics technologies has created an exponential growth in biological data, often outpacing our ability to derive molecular insights. Large-language models have shown a way out of this data deluge in natural language processing by integrating massive datasets into a joint model with manifold downstream use cases. Here we envision developing multimodal foundation models, pretrained on diverse omics datasets, including genomics, transcriptomics, epigenomics, proteomics, metabolomics and spatial profiling. These models are expected to exhibit unprecedented potential for characterizing the molecular states of cells across a broad continuum, thereby facilitating the creation of holistic maps of cells, genes and tissues. Context-specific transfer learning of the foundation models can empower diverse applications from novel cell-type recognition, biomarker discovery and gene regulation inference, to in silico perturbations. This new paradigm could launch an era of artificial intelligence-empowered analyses, one that promises to unravel the intricate complexities of molecular cell biology, to support experimental design and, more broadly, to profoundly extend our understanding of life sciences.
    DOI:  https://doi.org/10.1038/s41586-025-08710-y
  76. Nature. 2025 Apr 15.
    Twenty years of genome-wide association studies.
    Lorraine Southam, Eleftheria Zeggini.
      
    Keywords:  Diseases; Genetics; Genomics; Technology
    DOI:  https://doi.org/10.1038/d41586-025-01128-6
  77. Ageing Res Rev. 2025 Apr 11. pii: S1568-1637(25)00099-6. [Epub ahead of print]108 102753
    Transformative advances in modeling brain aging and longevity: Success, challenges and future directions.
    Varsha Pai, Bhisham Narayan Singh, Abhishek Kumar Singh.
      Research on brain aging is crucial for understanding age-related neurodegenerative disorders and developing several therapeutic interventions. Numerous models ranging from two-dimensional (2D) cell-based, invertebrate, vertebrate, and sophisticated three-dimensional (3D) models have been used to understand the process of brain aging. Invertebrate models are ideal for researching conserved aging processes because of their simplicity, short lifespans, and genetic tractability. Moreover, vertebrate models, including zebrafish and rodents, exhibit more complex nervous systems and behaviors, enabling the exploration of age-related neurodegeneration and cognitive decline. 2D cell culture models derived from primary cells or immortalized cell lines are widely used for mechanistic studies at the cellular level but lack the physiological complexity of brain tissue. Recent advancements have shifted focus to 3D models, which better recapitulate the brain's microenvironment. Organoids derived from induced pluripotent stem cells mimic human brain architecture and enable the study of cell-cell interactions and aging in a human-specific context. Brain-on-a-chip systems integrate microfluidics and 3D cultures to model blood-brain barrier dynamics and neuronal networks. Additionally, scaffold-based 3D cultures and spheroids provide intermediate complexity, allowing researchers to study extracellular matrix interactions and age-related changes in neuronal function. These 3D models bridge the gap between traditional 2D cultures and animal-based in vivo studies, offering unprecedented insights into brain aging mechanisms. By combining these diverse models, researchers can unravel the multifaceted processes of brain aging and accelerate the development of targeted therapies for age-related neurodegenerative disorders.
    Keywords:  3D brain aging models; Alzheimer’s disease; Antiaging; Brain aging; Neurodegenerative disorders; Parkinson’s disease
    DOI:  https://doi.org/10.1016/j.arr.2025.102753
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