bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2024–11–17
eighty-six papers selected by
Catalina Vasilescu, Helmholz Munich
  1. A PRKN-independent Mechanism Regulating Cardiac Mitochondrial Quality Control.
  2. Structural basis of 3'-tRNA maturation by the human mitochondrial RNase Z complex.
  3. CRISPR-Cas9 mediated knockout of NDUFS4 in human iPSCs: A model for mitochondrial complex I deficiency.
  4. POLG p.A962T Mutation Leads to Neuronal Mitochondrial Dysfunction That is Restored After Mitochondrial Transplantation.
  5. The mitochondrial mRNA-stabilizing protein SLIRP regulates skeletal muscle mitochondrial structure and respiration by exercise-recoverable mechanisms.
  6. Mitochondrial pyruvate transport regulates presynaptic metabolism and neurotransmission.
  7. eIF5A controls mitoprotein import by relieving ribosome stalling at TIM50 translocase mRNA.
  8. Mitochondrial complex I inhibition enhances astrocyte responsiveness to pro-inflammatory stimuli.
  9. Significantly reduced, but balanced, rates of mitochondrial fission and fusion are sufficient to maintain the integrity of yeast mitochondrial DNA.
  10. Variants in MICOS10 Identified by Whole Genome Sequencing and RNA Sequencing in a New Type of Hepatocerebral Mitochondrial DNA Depletion Syndrome.
  11. Expanding the genetic and clinical spectrum of SLC25A42-associated disorders and testing of pantothenic acid to improve CoA level in vitro.
  12. Mitochondria: great balls of fire.
  13. Mitochondrial E3 ligase TRIM71 affects mitochondrial complex assembly and sensitizes dopaminergic neuronal cells to apoptosis in Parkinson's Disease (PD).
  14. Metabolic Phenotyping of Synaptic Mitochondria Using MitoPlates™ and Synaptoneurosomes.
  15. Stem cell models of TAFAZZIN deficiency reveal novel tissue-specific pathologies in Barth syndrome.
  16. Genetic landscape of primary mitochondrial diseases in children and adults using molecular genetics and genomic investigations of mitochondrial and nuclear genome.
  17. Current global vitamin and cofactor prescribing practices for primary mitochondrial diseases: Results of a European reference network survey.
  18. Leber Hereditary Optic Neuropathy With Significant Visual Recovery: An MT-ND6 Mutation in a Malay Patient.
  19. Isolation and Analysis of Mitochondrial Small RNAs from Rat Liver Tissue and HepG2 Cells.
  20. A novel missense mutation in ISCA2 causes aberrant splicing and leads to multiple mitochondrial dysfunctions syndrome 4.
  21. Imaging Mitochondrial Axonal Transport in Human Induced Pluripotent Stem Cell-Derived Neurons.
  22. Methodologies for Mitochondrial Omic Profiling During Spaceflight.
  23. ATF5-mediated mitochondrial unfolded protein response protects against Pb-induced mitochondria damage in SH-SY5Y cell.
  24. Graph-Theoretical Prediction and Analysis of Biologically Relevant Substructures in an Open and Closed Conformation of Respiratory Complex I.
  25. Engineered bacterial lipoate protein ligase A (lplA) restores lipoylation in cell models of lipoylation deficiency.
  26. High-Resolution Respirometry Methodology for Bioenergetic and Metabolic Studies in Intact Brain Slices.
  27. Understanding Mitochondrial and Lysosomal Dynamics by Fluorescent Microscopy.
  28. Mitochondrial disorders are associated with morphological neuromuscular junction defects.
  29. Editorial: Mitochondrial dysfunction and genetic variations in neuro-ophthalmology diseases.
  30. Leigh Syndrome Caused by Compound Heterozygous Variants c.1162A_C and c.1138G_C in the NDUFV1 Gene: A Case Report.
  31. Mitochondrial calcium uptake orchestrates vertebrate pigmentation via transcriptional regulation of keratin filaments.
  32. HSF-1 promotes longevity through ubiquilin-1-dependent mitochondrial network remodelling.
  33. Nuclear localization of MTHFD2 is required for correct mitosis progression.
  34. Klf9 is essential for cardiac mitochondrial homeostasis.
  35. Absolute Quantification of Cellular and Cell-Free Mitochondrial DNA Copy Number from Human Blood and Urinary Samples Using Real Time Quantitative PCR.
  36. AI protein-prediction tool AlphaFold3 is now more open.
  37. FMRP gains mitochondrial fission control.
  38. Wars1 downregulation in hepatocytes induces mitochondrial stress and disrupts metabolic homeostasis.
  39. FMRP regulates MFF translation to locally direct mitochondrial fission in neurons.
  40. NAD+ enhancers as therapeutic agents in the cardiorenal axis.
  41. Efficient PHB2 (prohibitin 2) exposure during mitophagy depends on VDAC1 (voltage dependent anion channel 1).
  42. Mitochondrial Morphofunctional Profiling in Primary Human Skin Fibroblasts Using TMRM and Mitotracker Green Co-staining.
  43. The phenotypic spectrum of PTCD3 deficiency.
  44. Restoration of mitochondrial function alleviates trigeminal neuropathic pain in mice.
  45. Mitochondrial Dynamics Drive Muscle Stem Cell Progression from Quiescence to Myogenic Differentiation.
  46. Non-cell autonomous regulation of cell-cell signaling and differentiation by mitochondrial ROS.
  47. The Relation Between Mitochondrial Membrane Potential and Reactive Oxygen Species Formation.
  48. Plate-Based Measurement of Respiration by Isolated Mitochondria and by Intact Cells.
  49. Opposing roles for AMPK in regulating distinct mitophagy pathways.
  50. Pathogenic LRRK2 mutations cause loss of primary cilia and Neurturin in striatal parvalbumin interneurons.
  51. TAp73 regulates mitochondrial dynamics and multiciliated cell homeostasis through an OPA1 axis.
  52. Integrative Metabolome and Proteome Analysis of Cerebrospinal Fluid in Parkinson's Disease.
  53. Overcoming genetic neuromuscular diagnostic pitfalls in a middle-income country.
  54. NK2R control of energy expenditure and feeding to treat metabolic diseases.
  55. Hepatic SerpinA1 improves energy and glucose metabolism through regulation of preadipocyte proliferation and UCP1 expression.
  56. Peripheral immune cell abundance differences link blood mitochondrial DNA copy number and Parkinson's disease.
  57. Rescue of mitochondrial dysfunction through alteration of extracellular matrix composition in barth syndrome cardiac fibroblasts.
  58. Mitochondrial dysfunction in febrile illness and sepsis: no clear picture yet.
  59. HMGCS1 variants cause rigid spine syndrome amenable to mevalonic acid treatment in an animal model.
  60. Mitochondrial dysfunction as a therapeutic strategy for neurodegenerative diseases: Current insights and future directions.
  61. Enhancing mitochondrial pyruvate metabolism ameliorates ischemic reperfusion injury in the heart.
  62. N-terminal cleavage of cyclophilin D boosts its ability to bind F-ATP synthase.
  63. Mitochondrial Membrane Potential (ΔΨ) Fluctuations Associated with the Metabolic States of Mitochondria.
  64. Cell type-specific gene therapy confers protection against motor neuron disease caused by a TFG variant.
  65. PINK1-deficiency facilitates mitochondrial iron accumulation and colon tumorigenesis.
  66. Evaluation of Respiration with a Clark-Type Electrode in Isolated Mitochondria, Intact and Permeabilized Cells, and Explants from Animal Tissues.
  67. Improving reporting standards for genetic variants.
  68. Unveiling tryptophan dynamics and functions across model organisms via quantitative imaging.
  69. FDA approves L-amino acid decarboxylase deficiency gene therapy.
  70. Mitochondrial Bioenergetics Deficiency in cisd-1 Mutants is Linked to AMPK-Mediated Lipid Metabolism.
  71. Late-Onset Mitochondrial Neurogastrointestinal Encephalopathy Presenting With Isolated Ophthalmic Findings.
  72. Targeting NAMPT-OPA1 for treatment of senile osteoporosis.
  73. Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles.
  74. SSEmb: A joint embedding of protein sequence and structure enables robust variant effect predictions.
  75. Biallelic Variants in LIPT2 as a Cause of Infantile-Onset Dystonia: Expanding the Clinical and Molecular Spectrum.
  76. The function of nicotinamide phosphoribosyl transferase (NAMPT) and its role in diseases.
  77. A homozygous TARS2 variant is a novel cause of syndromic neonatal diabetes.
  78. Modulatory Effect of Nicotinamide Adenine Dinucleotide Phosphate (NADPH) on the 2-Oxoglutarate Mitochondrial Carrier.
  79. Molecular and cellular mechanisms of mitochondria transfer in models of central nervous system disease.
  80. Circular logic: understanding RNA's strangest form yet.
  81. A proteolytic AAA+ machine poised to unfold protein substrates.
  82. Targeted Next-Generation Sequencing in Rare Diseases.
  83. Transfer RNA supplementation rescues HARS deficiency in a humanized yeast model of Charcot-Marie-Tooth disease.
  84. The node of Ranvier influences the in vivo axonal transport of mitochondria and signaling endosomes.
  85. A review of multiple diagnostic approaches in the undiagnosed diseases network to identify inherited metabolic diseases.
  86. Barth syndrome: a rare cause of cardiomyopathy in neonates.
  1. Autophagy. 2024 Nov 09.
    A PRKN-independent Mechanism Regulating Cardiac Mitochondrial Quality Control.
    Wenjuan Wang, Jinbao Liu, Jie Li, Huabo Su.
      PRKN-dependent mitophagy plays a crucial role in maintaining mitochondrial health. Yet, PRKN-deficient mice do not exhibit mitochondrial and cardiac phenotypes at baseline, suggesting the existence of other mitochondrial ubiquitin (Ub) ligases. Here, we discuss our recent work identifying RNF7/RBX2 as a novel mitochondrial Ub ligase. Upon mitochondrial depolarization, RNF7 proteins are recruited to the mitochondria, where they directly ubiquitinate mitochondrial proteins and stabilize PINK1 expression, thereby promoting the clearance of damaged mitochondria and regulating mitochondrial turnover in the heart. The actions of RNF7 in mitochondria do not require PRKN. Ablation of Rnf7 in mouse hearts results in severe mitochondrial dysfunction and heart failure. Our findings demonstrate that RNF7 is indispensable for mitochondrial turnover and cardiac homeostasis. These results open new avenues for exploring new PRKN-independent pathways that regulate mitophagy, which could have significant implications for developing therapeutic interventions for cardiac diseases.
    Keywords:  Heart failure; RBX2/SAG; mitophagy; parkin; ubiquitination
    DOI:  https://doi.org/10.1080/15548627.2024.2423329
  2. EMBO J. 2024 Nov 08.
    Structural basis of 3'-tRNA maturation by the human mitochondrial RNase Z complex.
    Genís Valentín Gesé, B Martin Hällberg.
      Maturation of human mitochondrial tRNA is essential for cellular energy production, yet the underlying mechanisms remain only partially understood. Here, we present several cryo-EM structures of the mitochondrial RNase Z complex (ELAC2/SDR5C1/TRMT10C) bound to different maturation states of mitochondrial tRNAHis, showing the molecular basis for tRNA-substrate selection and catalysis. Our structural insights provide a molecular rationale for the 5'-to-3' tRNA processing order in mitochondria, the 3'-CCA antideterminant effect, and the basis for sequence-independent recognition of mitochondrial tRNA substrates. Furthermore, our study links mutations in ELAC2 to clinically relevant mitochondrial diseases, offering a deeper understanding of the molecular defects contributing to these conditions.
    Keywords:  Cryo-EM; ELAC2; Mitochondria; RNA Processing; RNase Z
    DOI:  https://doi.org/10.1038/s44318-024-00297-w
  3. Biochim Biophys Acta Mol Basis Dis. 2024 Nov 13. pii: S0925-4439(24)00563-5. [Epub ahead of print] 167569
    CRISPR-Cas9 mediated knockout of NDUFS4 in human iPSCs: A model for mitochondrial complex I deficiency.
    Shivani Goolab, Karin Terburgh, Charl du Plessis, Janine Scholefield, Roan Louw.
      Mitochondrial diseases, often caused by defects in complex I (CI) of the oxidative phosphorylation system, currently lack curative treatments. Human-relevant, high-throughput drug screening platforms are crucial for the discovery of effective therapeutics, with induced pluripotent stem cells (iPSCs) emerging as a valuable technology for this purpose. Here, we present a novel iPSC model of NDUFS4-related CI deficiency that displays a strong metabolic phenotype in the pluripotent state. Human iPSCs were edited using CRISPR-Cas9 to target the NDUFS4 gene, generating isogenic NDUFS4 knockout (KO) cell lines. Sanger sequencing detected heterozygous biallelic deletions, whereas no indel mutations were found in isogenic control cells. Western blotting confirmed the absence of NDUFS4 protein in KO iPSCs and CI enzyme kinetics showed a ~56 % reduction in activity compared to isogenic controls. Comprehensive metabolomic profiling revealed a distinct metabolic phenotype in NDUFS4 KO iPSCs, predominantly associated with an elevated NADH/NAD+ ratio, consistent with alterations observed in other models of mitochondrial dysfunction. Additionally, β-lapachone, a recognized NAD+ modulator, alleviated reductive stress in KO iPSCs by modifying the redox state in both the cytosol and mitochondria. Although undifferentiated iPSCs cannot fully replicate the complex cellular dynamics of the disease seen in vivo, these findings highlight the utility of iPSCs in providing a relevant metabolic milieu that can facilitate early-stage, high-throughput exploration of therapeutic strategies for mitochondrial dysfunction.
    Keywords:  CI deficiency; CRISPR-Cas9; Mitochondrial disease; iPSC
    DOI:  https://doi.org/10.1016/j.bbadis.2024.167569
  4. Physiol Res. 2024 Nov 15. 73(5): 801-808
    POLG p.A962T Mutation Leads to Neuronal Mitochondrial Dysfunction That is Restored After Mitochondrial Transplantation.
    W Hu, C Shi, H Guo, B Zhang.
      Mutations in DNA polymerase gamma (POLG) are known as the predominant cause of inherited mitochondrial disorders. But how these POLG mutations disturb mitochondrial function remains to be determined. Furthermore, no effective therapy, to date, has been reported for POLG diseases. Using differentiated SH-SY5Y cells, a human neuronal model cell line, the current study investigated whether the novel POLG variant p.A962T impairs mitochondrial function. This involved quantifying mitochondrial DNA (mtDNA) content using PCR and assessing the expression levels of the subunits of complex IV (COXI-IV), a complex I subunit NDUFV1 and Cytochrome C (Cyto C) release using Western blotting. Activities of mitochondrial complex I, II, and IV were measured using colorimetric assays. Mitochondrial membrane potential (delta Psim) and ATP were evaluated using fluorescence assays and luminescent assays, respectively. In addition, we investigated whether mitochondrial transplantation (MT) using Pep-1-conjugated mitochondria could compensate for mitochondrial defects caused by the variant in cells carrying mutant POLG. The results of this study showed that POLG p.A962T mutation resulted in mitochondrial defects, including mitochondrial DNA (mtDNA) depletion, membrane potential (delta Psim) depolarization and adenosine triphosphate (ATP) reduction. Mechanistically, POLG mutation-caused mtDNA depletion led to the loss of mtDNA-encoded subunits of complex I and IV and thus compromised their activities. POLG p.A962T mutation is a pathogenic mutation leading to mitochondrial malfunction and mtDNA depletion in neurons. Cell-penetrating peptide Pep-1-mediated MT treatment compensated for mitochondrial defects induced by these POLG variants, suggesting the therapeutic application of this method in POLG diseases.
  5. Nat Commun. 2024 Nov 13. 15(1): 9826
    The mitochondrial mRNA-stabilizing protein SLIRP regulates skeletal muscle mitochondrial structure and respiration by exercise-recoverable mechanisms.
    Tang Cam Phung Pham, Steffen Henning Raun, Essi Havula, Carlos Henriquez-Olguín, Diana Rubalcava-Gracia, Emma Frank, Andreas Mæchel Fritzen, Paulo R Jannig, Nicoline Resen Andersen, Rikke Kruse, Mona Sadek Ali, Andrea Irazoki, Jens Frey Halling, Stine Ringholm, Elise J Needham, Solvejg Hansen, Anders Krogh Lemminger, Peter Schjerling, Maria Houborg Petersen, Martin Eisemann de Almeida, Thomas Elbenhardt Jensen, Bente Kiens, Morten Hostrup, Steen Larsen, Niels Ørtenblad, Kurt Højlund, Michael Kjær, Jorge L Ruas, Aleksandra Trifunovic, Jørgen Frank Pind Wojtaszewski, Joachim Nielsen, Klaus Qvortrup, Henriette Pilegaard, Erik Arne Richter, Lykke Sylow.
      Decline in mitochondrial function is linked to decreased muscle mass and strength in conditions like sarcopenia and type 2 diabetes. Despite therapeutic opportunities, there is limited and equivocal data regarding molecular cues controlling muscle mitochondrial plasticity. Here we uncovered that the mitochondrial mRNA-stabilizing protein SLIRP, in complex with LRPPRC, is a PGC-1α target that regulates mitochondrial structure, respiration, and mtDNA-encoded-mRNA pools in skeletal muscle. Exercise training effectively counteracts mitochondrial defects caused by genetically-induced LRPPRC/SLIRP loss, despite sustained low mtDNA-encoded-mRNA pools, by increasing mitoribosome translation capacity and mitochondrial quality control. In humans, exercise training robustly increases muscle SLIRP and LRPPRC protein across exercise modalities and sexes, yet less prominently in individuals with type 2 diabetes. SLIRP muscle loss reduces Drosophila lifespan. Our data points to a mechanism of post-transcriptional mitochondrial regulation in muscle via mitochondrial mRNA stabilization, offering insights into how exercise enhances mitoribosome capacity and mitochondrial quality control to alleviate defects.
    DOI:  https://doi.org/10.1038/s41467-024-54183-4
  6. Sci Adv. 2024 Nov 15. 10(46): eadp7423
    Mitochondrial pyruvate transport regulates presynaptic metabolism and neurotransmission.
    Anupama Tiwari, Jongyun Myeong, Arsalan Hashemiaghdam, Marion I Stunault, Hao Zhang, Xiangfeng Niu, Marissa A Laramie, Jasmin Sponagel, Leah P Shriver, Gary J Patti, Vitaly A Klyachko, Ghazaleh Ashrafi.
      Glucose has long been considered the primary fuel source for the brain. However, glucose levels fluctuate in the brain during sleep or circuit activity, posing major metabolic stress. Here, we demonstrate that the mammalian brain uses pyruvate as a fuel source, and pyruvate can support neuronal viability in the absence of glucose. Nerve terminals are sites of metabolic vulnerability, and we show that mitochondrial pyruvate uptake is a critical step in oxidative ATP production in hippocampal terminals. We find that the mitochondrial pyruvate carrier is post-translationally modified by lysine acetylation, which, in turn, modulates mitochondrial pyruvate uptake. Our data reveal that the mitochondrial pyruvate carrier regulates distinct steps in neurotransmission, namely, the spatiotemporal pattern of synaptic vesicle release and the efficiency of vesicle retrieval-functions that have profound implications for synaptic plasticity. In summary, we identify pyruvate as a potent neuronal fuel and mitochondrial pyruvate uptake as a critical node for the metabolic control of neurotransmission in hippocampal terminals.
    DOI:  https://doi.org/10.1126/sciadv.adp7423
  7. J Cell Biol. 2024 Dec 02. pii: e202404094. [Epub ahead of print]223(12):
    eIF5A controls mitoprotein import by relieving ribosome stalling at TIM50 translocase mRNA.
    Marina Barba-Aliaga, Vanessa Bernal, Cynthia Rong, Madeleine E Volfbeyn, Keguang Zhang, Brian M Zid, Paula Alepuz.
      Efficient import of nuclear-encoded proteins into mitochondria is crucial for proper mitochondrial function. The conserved translation factor eIF5A binds ribosomes, alleviating stalling at polyproline-encoding sequences. eIF5A impacts mitochondrial function across species, though the precise molecular mechanism is unclear. We found that eIF5A depletion in yeast reduces the translation and levels of the TCA cycle and oxidative phosphorylation proteins. Loss of eIF5A causes mitoprotein precursors to accumulate in the cytosol and triggers a mitochondrial import stress response. We identify an essential polyproline protein as a direct target of eIF5A: the mitochondrial inner membrane protein and translocase component Tim50. Thus, eIF5A controls mitochondrial protein import by alleviating ribosome stalling along Tim50 mRNA at the mitochondrial surface. Removal of polyprolines from Tim50 partially rescues the mitochondrial import stress response and translation of oxidative phosphorylation genes. Overall, our findings elucidate how eIF5A impacts the mitochondrial function by promoting efficient translation and reducing ribosome stalling of co-translationally imported proteins, thereby positively impacting the mitochondrial import process.
    DOI:  https://doi.org/10.1083/jcb.202404094
  8. Sci Rep. 2024 11 08. 14(1): 27182
    Mitochondrial complex I inhibition enhances astrocyte responsiveness to pro-inflammatory stimuli.
    Lena Wischhof, Amal John Mathew, Lorenzo Bonaguro, Marc Beyer, Dan Ehninger, Pierluigi Nicotera, Daniele Bano.
      Inhibition of the mitochondrial oxidative phosphorylation (OXPHOS) system can lead to metabolic disorders and neurodegenerative diseases. In primary mitochondrial disorders, reactive astrocytes often accompany neuronal degeneration and may contribute to neurotoxic inflammatory cascades that elicit brain lesions. The influence of mitochondria to astrocyte reactivity as well as the underlying molecular mechanisms remain elusive. Here we report that mitochondrial Complex I dysfunction promotes neural progenitor cell differentiation into astrocytes that are more responsive to neuroinflammatory stimuli. We show that the SWItch/Sucrose Non-Fermentable (SWI/SNF/BAF) chromatin remodeling complex takes part in the epigenetic regulation of astrocyte responsiveness, since its pharmacological inhibition abrogates the expression of inflammatory genes. Furthermore, we demonstrate that Complex I deficient human iPSC-derived astrocytes negatively influence neuronal physiology upon cytokine stimulation. Together, our data describe the SWI/SNF/BAF complex as a sensor of altered mitochondrial OXPHOS and a downstream epigenetic regulator of astrocyte-mediated neuroinflammation.
    Keywords:  ATP-dependent chromatin remodeling SWI/SNF/BAF complex; Mitochondria; Reactive astrocytes
    DOI:  https://doi.org/10.1038/s41598-024-78434-y
  9. Mol Biol Cell. 2024 Nov 13. mbcE24070306
    Significantly reduced, but balanced, rates of mitochondrial fission and fusion are sufficient to maintain the integrity of yeast mitochondrial DNA.
    Brett T Wisniewski, Jason C Casler, Laura L Lackner.
      Mitochondria exist as dynamic tubular networks and the morphology of these networks impacts organelle function and cell health. Mitochondrial morphology is maintained in part by the opposing activities of mitochondrial fission and fusion. Mitochondrial fission and fusion are also required to maintain mitochondrial DNA (mtDNA) integrity. In Saccharomyces cerevisiae, the simultaneous inhibition of mitochondrial fission and fusion results in increased mtDNA mutation and the consequent loss of respiratory competence. The mechanism by which fission and fusion maintain mtDNA integrity is not fully understood. Previous work demonstrates that mtDNA is spatially linked to mitochondrial fission sites. Here, we extend this finding using live-cell imaging to localize mtDNA to mitochondrial fusion sites. While mtDNA is present at sites of mitochondrial fission and fusion, mitochondrial fission and fusion rates are not altered in cells lacking mtDNA. Using alleles that alter mitochondrial fission and fusion rates, we find that mtDNA integrity can be maintained in cells with significantly reduced, but balanced, rates of fission and fusion. In addition, we find that increasing mtDNA copy number reduces the loss of respiratory competence in double mitochondrial fission-fusion mutants. Our findings add novel insights into the relationship between mitochondrial dynamics and mtDNA integrity.
    DOI:  https://doi.org/10.1091/mbc.E24-07-0306
  10. Liver Int. 2024 Nov 07.
    Variants in MICOS10 Identified by Whole Genome Sequencing and RNA Sequencing in a New Type of Hepatocerebral Mitochondrial DNA Depletion Syndrome.
    Yoshihito Kishita, Ayumu Sugiura, Nanako Omichi, Masaru Shimura, Yukiko Yatsuka, Kohta Nakamura, Toju Tanaka, Mitsuru Kubota, Kei Murayama, Akira Ohtake, Yasushi Okazaki.
       BACKGROUND: The mitochondrial contact site and cristae organising system (MICOS) complex is required for cristae formation and is composed of seven proteins. Among the genes of MICOS complex, variants of MICOS13, IMMT and APOO have been reported to cause diseases.
    METHODS AND RESULTS: We report a case in which whole genome sequencing identified a variant of the MICOS10 gene associated with mitochondrial hepatopathy along with mitochondrial DNA depletion. We identified the deletion g.19596826_19601303del and the single nucleotide variant c.173G>C (p.Cys58Ser). The deletion including exon 1 might have caused complete loss of gene expression, indicating monoallelic expression from RNA sequencing. MIC10 was lost at the protein level in the patient's fibroblasts, and mitochondrial oxygen consumption was impaired. These were restored by overexpression of MICOS10 in the patient's fibroblasts.
    CONCLUSION: Taken together, these findings indicate that MICOS10 is a causative gene for hepatopathy and neuropathy, a disease very similar to that associated with MICOS13.
    Keywords:  MICOS complex; RNA sequencing; hepatopathy; mitochondrial DNA; whole genome sequencing
    DOI:  https://doi.org/10.1111/liv.16148
  11. JIMD Rep. 2024 Nov;65(6): 417-425
    Expanding the genetic and clinical spectrum of SLC25A42-associated disorders and testing of pantothenic acid to improve CoA level in vitro.
    Katharina Heckmann, Arcangela Iuso, Janine Reunert, Marianne Grüneberg, Anja Seelhöfer, Stephan Rust, Giuseppe Fiermonte, Eleonora Paradies, Carmela Piazzolla, Manoj Mannil, Thorsten Marquardt.
      SLC25A42 encodes the mitochondrial coenzyme A (CoA) transporter localized at the inner mitochondrial membrane. SLC25A42 deficiency leads to a congenital disease with a heterogeneous clinical presentation, including myopathy, developmental delay, lactic acidosis, and encephalopathy. Twenty-one patients have been described so far. In the current study, we report on the identification of new biallelic variants in SLC25A42 in three siblings. Patients presented with symmetrical T2 hyperintensity of the putamen with minor volume depression at the brain MRI, elevated lactate, reduced oxygen consumption rates in muscle and fibroblasts, and reduced CoA levels in fibroblasts. Administration of pantothenic acid led to clinical stabilization and increased CoA levels in fibroblasts, thus confirming a role for SLC25A42 in energy metabolism and CoA homeostasis.
    Keywords:  SLC25A42; cellular CoA; mitochondrial coenzyme transporter; mitochondrial respiration; pantothenic acid
    DOI:  https://doi.org/10.1002/jmd2.12441
  12. FEBS J. 2024 Nov 14.
    Mitochondria: great balls of fire.
    Howard T Jacobs, Pierre Rustin, Paule Bénit, Dan Davidi, Mügen Terzioglu.
      Recent experimental studies indicate that mitochondria in mammalian cells are maintained at temperatures of at least 50 °C. While acknowledging the limitations of current experimental methods and their interpretation, we here consider the ramifications of this finding for cellular functions and for evolution. We consider whether mitochondria as heat-producing organelles had a role in the origin of eukaryotes and in the emergence of homeotherms. The homeostatic responses of mitochondrial temperature to externally applied heat imply the existence of a molecular heat-sensing system in mitochondria. While current findings indicate high temperatures for the innermost compartments of mitochondria, those of the mitochondrial surface and of the immediately surrounding cytosol remain to be determined. We ask whether some aspects of mitochondrial dynamics and motility could reflect changes in the supply and demand for mitochondrial heat, and whether mitochondrial heat production could be a factor in diseases and immunity.
    Keywords:  cold‐shock; eukaryote origins; heat‐shock; homeothermy; immunity; mitochondria; mitochondrial disease; mitochondrial dynamics; temperature gradients; thermogenesis
    DOI:  https://doi.org/10.1111/febs.17316
  13. Int J Biochem Cell Biol. 2024 Nov 08. pii: S1357-2725(24)00182-1. [Epub ahead of print] 106689
    Mitochondrial E3 ligase TRIM71 affects mitochondrial complex assembly and sensitizes dopaminergic neuronal cells to apoptosis in Parkinson's Disease (PD).
    Shanikumar Goyani, Shatakshi Shukla, Minal Mane, M V Saranga, Nisha Chandak, Anjali Shinde, Fatema Currim, Jyoti Singh, Rajesh Singh.
      Parkinson's Disease (PD) is a chronic neurodegenerative disorder that impacts the substantia niagra region of the midbrain leading to impaired motor as well as non-motor symptoms of the central nervous system (CNS). Mitochondrial dysfunction has been characterized as the primary cause of dopaminergic neuronal loss, however, the molecular mechanisms leading to mitochondrial dysfunction are not completely understood. PARKIN, E3 ubiquitin ligase, plays a crucial role in maintaining mitochondrial quality control, albeit the role of other E3 ligases in regulating mitochondrial functions is not understood. In the current study, we explored the implication of TRIM71, E3 ubiquitin ligase, in the modulation of mitochondrial functions and neuronal death in PD stress conditions induced by rotenone and 6-OHDA. Ectopic expression of TRIM71 in SH-SY5Y dopaminergic neuronal cells sensitizes to PD stress-induced cell death, while its knock-down rescues neuronal cell death. TRIM71 turnover is enhanced in neurons under PD stress conditions. TRIM71 predominantly localizes on the outer mitochondrial membrane and translocation increases during PD stress conditions. TRIM71 regulates mitochondrial complex I and IV assembly and activity. TRIM71 knock-down decreases mitochondrial ROS and enhances ATP level as well as mitochondrial membrane potential in PD stress conditions. TRIM71-mediated mitochondrial ROS and cell death were rescued by mitoTEMPO, a mitochondrial-targeted antioxidant. Altogether, the evidence strongly suggests TRIM71-mediated modulation of mitochondrial functions and neuronal apoptosis in PD stress conditions.
    Keywords:  Parkinson’s disease; ROS; TRIM71; cell death; mitochondria
    DOI:  https://doi.org/10.1016/j.biocel.2024.106689
  14. Methods Mol Biol. 2025 ;2878 67-74
    Metabolic Phenotyping of Synaptic Mitochondria Using MitoPlates™ and Synaptoneurosomes.
    Aleksandra Stawikowska, Magdalena Dziembowska, Bozena Kuzniewska.
      Mitochondrial functional assays using MitoPlates™ S-1 allow us to characterize mitochondria in terms of substrate metabolism. MitoPlates™ are 96-well microplates pre-coated with a diverse set of substrates. The electron flow from NADH and FADH2 producing mitochondrial substrates is measured based on the reduction of redox dye, that acts as a terminal electron acceptor. Here, we describe the application of MitoPlates™ to characterize the metabolism of synaptic mitochondria enclosed in isolated pre- and postsynaptic terminals (synaptoneurosomes).
    Keywords:  MitoPlates™; Mitochondrial substrate metabolism; Synaptic mitochondria; Synaptoneurosomes
    DOI:  https://doi.org/10.1007/978-1-0716-4264-1_4
  15. Hum Mol Genet. 2024 Nov 13. pii: ddae152. [Epub ahead of print]
    Stem cell models of TAFAZZIN deficiency reveal novel tissue-specific pathologies in Barth syndrome.
    Olivia Sniezek Carney, Kodi W Harris, Yvonne Wohlfarter, Kyuna Lee, Grant Butschek, Arianna F Anzmann, Anne Hamacher-Brady, Markus A Keller, Hilary J Vernon.
      Barth syndrome (BTHS) is a rare mitochondrial disease caused by pathogenic variants in the gene TAFAZZIN, which leads to abnormal cardiolipin (CL) metabolism on the inner mitochondrial membrane. Although TAFAZZIN is ubiquitously expressed, BTHS involves a complex combination of tissue specific phenotypes including cardiomyopathy, neutropenia, skeletal myopathy, and growth delays, with a relatively minimal neurological burden. To understand both the developmental and functional effects of TAZ-deficiency in different tissues, we generated isogenic TAZ knockout (TAZ-KO) and WT cardiomyocytes (CMs) and neural progenitor cells (NPCs) from CRISPR-edited induced pluripotent stem cells (iPSCs). In TAZ-KO CMs we discovered evidence of dysregulated mitophagy including dysmorphic mitochondria and mitochondrial cristae, differential expression of key autophagy-associated genes, and an inability of TAZ-deficient CMs to properly initiate stress-induced mitophagy. In TAZ-deficient NPCs we identified novel phenotypes including a reduction in CIV abundance and CIV activity in the CIII2&CIV2 intermediate complex. Interestingly, while CL acyl chain manipulation was unable to alter mitophagy defects in TAZ-KO CMs, we found that linoleic acid or oleic acid supplementation was able to partially restore CIV abundance in TAZ-deficient NPCs. Taken together, our results have implications for understanding the tissue-specific pathology of BTHS and potential for tissue-specific therapeutic targeting. Moreover, our results highlight an emerging role for mitophagy in the cardiac pathophysiology of BTHS and reveal a potential neuron-specific bioenergetic phenotype.
    Keywords:  Barth syndrome; TAFAZZIN; cardiomyopathy; mitophagy
    DOI:  https://doi.org/10.1093/hmg/ddae152
  16. Orphanet J Rare Dis. 2024 Nov 12. 19(1): 424
    Genetic landscape of primary mitochondrial diseases in children and adults using molecular genetics and genomic investigations of mitochondrial and nuclear genome.
    Anastasia Ambrose, Shalini Bahl, Saloni Sharma, Dan Zhang, Clara Hung, Shailly Jain-Ghai, Alicia Chan, Saadet Mercimek-Andrews.
       BACKGROUND: Primary mitochondrial diseases (PMD) are one of the most common metabolic genetic disorders. They are due to pathogenic variants in the mitochondrial genome (mtDNA) or nuclear genome (nDNA) that impair mitochondrial function and/or structure. We hypothesize that there is overlap between PMD and other genetic diseases that are mimicking PMD. For this reason, we performed a retrospective cohort study.
    METHODS: All individuals with suspected PMD that underwent molecular genetic and genomic investigations were included. Individuals were grouped for comparison: (1) individuals with mtDNA-PMD; (2) individuals with nDNA-PMD; (3) individuals with other genetic diseases mimicking PMD (non-PMD); (4) individuals without a confirmed genetic diagnosis.
    RESULTS: 297 individuals fulfilled inclusion criteria. The diagnostic yield of molecular genetics and genomic investigations was 31.3%, including 37% for clinical exome sequencing and 15.8% for mitochondrial genome sequencing. We identified 71 individuals with PMD (mtDNA n = 41, nDNA n = 30) and 22 individuals with non-PMD. Adults had higher percentage of mtDNA-PMD compared to children (p-value = 0.00123). There is a statistically significant phenotypic difference between children and adults with PMD.
    CONCLUSION: We report a large cohort of individuals with PMD and the diagnostic yield of urine mitochondrial genome sequencing (16.1%). We think liver phenotype might be progressive and should be studied further in PMD. We showed a relationship between non-PMD genes and their indirect effects on mitochondrial machinery. Differentiation of PMD from non-PMD can be achieved using specific phenotypes as there was a statistically significant difference for muscular, cardiac, and ophthalmologic phenotypes, seizures, hearing loss, peripheral neuropathy in PMD group compared to non-PMD group.
    Keywords:  Exome sequencing; Mitochondrial genome sequencing; Primary mitochondrial diseases
    DOI:  https://doi.org/10.1186/s13023-024-03437-x
  17. J Inherit Metab Dis. 2024 Nov 11.
    Current global vitamin and cofactor prescribing practices for primary mitochondrial diseases: Results of a European reference network survey.
    MetabERN PM‐MD Consortium authors
      Primary mitochondrial diseases (PMD) account for a group of approximately 400 different genetic disorders with diverse clinical presentations and pathomechanisms. Although each individual disorder is rare, collectively they represent one of the largest groups in the field of inherited metabolic disorders. The complexity of PMD results in a continued lack of therapeutic options, necessitating a predominantly symptomatic treatment approach for affected patients. While a subset of diseases responds exceptionally well to treatment with specific vitamins or cofactors, for most PMD systematic reviews were not able to show significant benefit. This is in discrepancy to their continued frequent use among specialists. To gain further insight into the current clinical practice of vitamin and cofactor supplementation among clinicians treating children and adults affected by PMD, we conducted a worldwide cross-sectional questionnaire study exploring the choice of substances and the specific diseases where they are applied. To our knowledge, this is the first global study exploring this topic and featuring a high response rate from paediatricians. The vast majority (95%, 106/112) of responding specialists recommended the use of vitamins and cofactors, either in an agnostic approach irrespective of the specific PMD or directed to the treatment of specific diseases or phenotypes. Our study highlights significant regional and specialty-specific differences in supplementation practices. We provide some preliminary insights into specialist-based opinions regarding the use of vitamins and cofactors in PMD and highlight the need for more rigorous clinical and preclinical investigations and/or clear consensus statements.
    Keywords:  cofactors; cross sectional study; inherited metabolic disease; primary mitochondrial disease; survey; treatment; vitamins
    DOI:  https://doi.org/10.1002/jimd.12805
  18. Cureus. 2024 Oct;16(10): e71210
    Leber Hereditary Optic Neuropathy With Significant Visual Recovery: An MT-ND6 Mutation in a Malay Patient.
    Muhammad Arif Ozir, Mohammad Hudzaifah Nordin, Syaratul Emma Hashim, Sumaiyah Adzahar, Muhammad Aizuddin Ahmad, Kwang Sheng Ng, Wan-Hazabbah Wan Hitam.
      Leber hereditary optic neuropathy (LHON) is a rare maternally inherited mitochondrial disorder that predominantly affects young men, leading to optic nerve degeneration and subsequent vision loss. The rarity of LHON and its clinical similarity to optic neuritis complicates diagnosis, necessitating genetic testing to confirm specific point mutations and predict visual outcomes. We report a rare case of an 18-year-old Malay male with m.14484T>C/MT-ND6 mutation of LHON, who demonstrated remarkable spontaneous visual recovery over a three-year follow-up period. This report highlights the pivotal role of genetic testing in diagnosing LHON, explores the variability in visual outcomes associated with different mutations, and underscores the potential for spontaneous recovery in specific mutation variants. Early diagnosis, genetic counseling, and supportive management are critical for optimizing outcomes and improving quality of life.
    Keywords:  idebenone; leber hereditary optic neuropathy; mitochondrial disease; optic neuritis; optic neuropathy
    DOI:  https://doi.org/10.7759/cureus.71210
  19. Methods Mol Biol. 2025 ;2878 259-271
    Isolation and Analysis of Mitochondrial Small RNAs from Rat Liver Tissue and HepG2 Cells.
    Julian Geiger, Louise T Dalgaard.
      The presence of non-coding RNAs, such as microRNAs (miRNAs), in mitochondria has been reported by several studies. The biological roles and functions of these mitochondrial miRNAs ("mitomiRs") have not been sufficiently characterized, but the mitochondrial localization of miRNAs has recently gained significance due to modified mitomiR-populations in certain states of diseases. Here, we describe the isolation and analysis of mitochondrial RNAs from rat liver tissue and HepG2 cells. The principle of the analysis is to prepare mitochondria by differential centrifugation. Cytosolic RNA contamination is eliminated by RNase A treatment followed by percoll gradient-purification and RNA-extraction. Small RNA content is verified by capillary electrophoresis. Mitochondrial miRNAs are detected by Q-PCR following synthesis of cDNA. After Q-PCR based mitomiR-profiling, the Normfinder algorithm is applied to identify suitable reference miRNAs to use as normalizers for mitochondrial input and data analysis. The described procedure depicts a simple way of isolating and quantifying mitomiRs in tissue and cell culture samples.
    Keywords:  MicroRNA; Mito-miR; Mitochondria; Mitochondrial purification; Normfinder; Percoll gradient; Q-PCR; RNA
    DOI:  https://doi.org/10.1007/978-1-0716-4264-1_14
  20. Front Psychiatry. 2024 ;15 1428175
    A novel missense mutation in ISCA2 causes aberrant splicing and leads to multiple mitochondrial dysfunctions syndrome 4.
    Zuhair Al-Hassnan, Mazhor AlDosary, Aljouhra AlHargan, Hanan AlQudairy, Rawan Almass, Khaled Omar Alahmadi, Saif AlShahrani, Albandary AlBakheet, Mohammad A Almuhaizea, Robert W Taylor, Dilek Colak, Namik Kaya.
       Background: Iron-sulfur cluster assembly 2 (ISCA2) deficiency is linked to an autosomal recessive disorder known as multiple mitochondrial dysfunctions syndrome 4 (MMDS4). This disorder is characterized by leukodystrophy and neuroregression. Currently, most of the reported patients are from Saudi Arabia. All these patients carry a homozygous founder variant (NM_194279.2:c.229G>A:p.Gly77Ser) in ISCA2.
    Methods: We describe a patient who underwent full clinical evaluation, including metabolic, neurological, and radiological examinations. Standard genetic testing, including whole exome sequencing coupled with autozygome analysis, was undertaken, as were assessments of mitochondrial DNA (mtDNA) copy number and mtDNA sequencing on DNA extracted from blood and cultured fibroblasts. Functional workup consisted of splicing assessment of ISCA2 using RT-PCR, biochemical assessment of complex I status using dipstick assays, and mitochondrial respiration measurements using a Seahorse XFp analyzer.
    Results: We present the clinical and functional characterization of a novel homozygous ISCA2 missense variant (NM_194279.3:c.70A>G:p.Arg24Gly), leading to aberrant splicing in a patient presenting with neuroregression, generalized spasticity with exaggerated deep tendon reflexes and head lag, and progressive loss of acquired milestones. The novel variant was fully segregated in a wider family and was absent in a large control cohort, ethnically matching in-house exomes, local databases such as CGMdb and Saudi Human Genome Program, and ClinVar.
    Conclusions: Our analyses revealed that the variant is pathogenic, disrupting normal ISCA2 splicing and presumably leading to a truncated protein that disturbs metabolic pathways in patient-derived cells.
    Keywords:  ISCA2 founder variant; depletion; leukodystrophy; mtDNA; neuroregression; novel splicing variant
    DOI:  https://doi.org/10.3389/fpsyt.2024.1428175
  21. Methods Mol Biol. 2025 ;2878 201-209
    Imaging Mitochondrial Axonal Transport in Human Induced Pluripotent Stem Cell-Derived Neurons.
    Carla Lopes.
      Neuronal mitochondria are essential organelles to maintain synaptic activity due to the high calcium buffering capacity and ATP production. In neurons, mitochondria transport occurs along the microtubules mediated by motor proteins, kinesins and dynein, to drive mitochondria toward the synapses. Disruption of axonal transport is an early pathogenic event in neurodegenerative disorders and growing evidence supports that it may precede neurodegeneration. Here, we describe a method to label mitochondria with fluorescent proteins to monitor their movement along the axons in hiPSC-derived medium spiny neuron-like cells. We also included a detailed protocol for differentiation of hiPSC that produces electrophysiologically mature GABAergic striatal neurons with low amount of glial population.
    Keywords:  Kymographs; Medium spiny neurons; Mitochondria; Transport; iPSC
    DOI:  https://doi.org/10.1007/978-1-0716-4264-1_10
  22. Methods Mol Biol. 2025 ;2878 273-291
    Methodologies for Mitochondrial Omic Profiling During Spaceflight.
    Joseph W Guarnieri, JangKeun Kim, Douglas C Wallace, Christopher E Mason, Masafumi Muratani, Afshin Beheshti.
      To be able to understand how spaceflight can affect human biology, there is a need for maximizing the amount of information that can be obtained from experiments flown to space. Recently there has been an influx of data obtained from astronauts through multi-omics approaches based on both governmental and commercial spaceflight missions. In addition to data from humans, mitochondrial specific data is gathered for other experiments from rodents and other organisms that are flown in space. This data has started to universally demonstrate that mitochondrial dysfunction is the key regulator associated with increasing health risks associated with spaceflight. This mitochondrial dysfunction can have influence downstream on immune suppression, inflammation, circadian rhythm issues, and more. Due to the space environment, standard methodologies have to be altered for performing mitochondrial specific analysis and in general sample collection for omics. To perform mitochondrial specific analysis and data collection from samples flown to space we will outline the current sample collection methods, processing of the samples, and specific analysis. Specifically we will highlight the different mitochondrial methodologies and challenges involved with research associated with spaceflight.
    Keywords:  Astronauts; ImmunoblottingImmunoblotting; Mitochondria; Mitochondrial DNA; Multi-omics; Omics; PBMCs; RNA-sequence; Transcriptomics; mtDNA
    DOI:  https://doi.org/10.1007/978-1-0716-4264-1_15
  23. Neurotoxicology. 2024 Nov 13. pii: S0161-813X(24)00133-5. [Epub ahead of print]
    ATF5-mediated mitochondrial unfolded protein response protects against Pb-induced mitochondria damage in SH-SY5Y cell.
    Yihan Xu, Min Liu, Sikang Gao, Xiaoyi Li, Jun Chen, Fang Ye.
      Mitochondria is the primary target of lead (Pb) in neural cells, and Pb exposure can cause impairment to mitochondrial function and morphology. Recent studies have reported that a conserved cellular stress response, called mitochondrial unfolded protein response (mtUPR), is activated in response to mitochondrial dysfunction and protein misfolding and play protective roles in aging and neurodegeneration, but it's unknown whether mtUPR could protect against Pb-induced neurotoxicity. In this study, we found that sublethal level exposure of PbAc (2.5μM) could cause mitochondria damage and then activate mtUPR by promoting the expression of mitochondrial proteases (LonP1 and ClpP), molecular chaperone (HSPA1A). ATF5 mediated mtUPR activation as knocking out ATF5 significantly inhibited Pb-induced LonP1 and ClpP expression. Moreover, ATF5 deficiency exacerbated Pb-induced mitochondrial morphological and oxidative phosphorylation (OXPHOS) functional damage, resulting in oxidative stress and ultimately promoting cell death. Conversely, overexpression of ATF5 confers protection against Pb-induced oxidative stress and cell death. Collectively, thess results highlight that mtUPR mediated by ATF5 safeguards against mitochondria damage caused by Pb exposure, providing insights into the development of new strategies for mitigating the Pb neurotoxicity.
    Keywords:  ATF5; Lead; Mitochondrial unfolded protein response; Neurotoxicity
    DOI:  https://doi.org/10.1016/j.neuro.2024.11.001
  24. Methods Mol Biol. 2025 ;2870 289-314
    Graph-Theoretical Prediction and Analysis of Biologically Relevant Substructures in an Open and Closed Conformation of Respiratory Complex I.
    Florian J Gisdon, Jörg Ackermann, Christoph Welsch, Ina Koch.
      Protein complexes are functional modules within the hierarchy of the cellular organization. Large protein complexes often consist of smaller functional modules, which are biologically relevant substructures with specific functions. The first protein complex of the respiratory chain, complex I, consists of functional modules for the electron transfer from NADH to quinone and the translocation of protons across the inner mitochondrial membrane. Complex I is well-characterized and biological modules have been experimentally assigned. Nevertheless, there is an ongoing discussion about the coupling of the electron transfer and the proton translocation, and about the proton translocation pathways.We modelled a mammalian complex I in open and closed conformations as complex graphs, with vertices representing protein chains and edges representing chain-chain contacts. Using a graph-theoretical method, we computed the structural modules of complex I, which indicated functional, biological substructures. We described characteristic structural features of complex I and observed a rearrangement of the structural modules. The changes in the structural modules indicated the formation of a functional module in the membrane arm of complex I during the conformational change.
    Keywords:  Clustering; Community detection; Complex graph; Graph partitioning; Respiratory complex I
    DOI:  https://doi.org/10.1007/978-1-0716-4213-9_15
  25. J Biol Chem. 2024 Nov 13. pii: S0021-9258(24)02497-9. [Epub ahead of print] 107995
    Engineered bacterial lipoate protein ligase A (lplA) restores lipoylation in cell models of lipoylation deficiency.
    Nolan Bick, Margaret Dreishpoon, Ava Perry, Anna Rogachevskaya, Sylvia S Bottomley, Mark D Fleming, Sarah Ducamp, Peter Tsvetkov.
      Protein lipoylation, a vital lysine posttranslational modification (PTM), plays a crucial role in the function of key mitochondrial TCA cycle enzymatic complexes. In eukaryotes, lipoyl PTM synthesis occurs exclusively through de novo pathways, relying on lipoyl synthesis/transfer enzymes, dependent upon mitochondrial fatty acid and Fe-S cluster biosynthesis. Dysregulation in any of these pathways leads to diminished cellular lipoylation. Efficient restoration of lipoylation in lipoylation deficiency cell states using either chemical or genetic approaches has been challenging due to pathway complexity and multiple upstream regulators. To address this challenge, we explored the possibility that a bacterial lipoate protein ligase (lplA) enzyme, that can salvage free lipoic acid bypassing the dependency on de novo synthesis, could be engineered to be functional in human cells. Overexpression of the engineered lplA in lipoylation null cells restored lipoylation levels, cellular respiration, and growth in low glucose conditions. Engineered lplA restored lipoylation in all tested lipoylation null cell models, mimicking defects in mitochondrial fatty acid synthesis (MECR KO), Fe-S cluster biosynthesis (BOLA3 KO), and specific lipoylation regulating enzymes (FDX1, LIAS and LIPT1 KOs). Furthermore, we describe a patient with a homozygous c.212C>T variant LIPT1 with a previously uncharacterized syndromic congenital sideroblastic anemia. K562 erythroleukemia cells engineered to harbor this missense LIPT1 allele recapitulate the lipoylation deficient phenotype and exhibit impaired proliferation in low glucose that is completely restored by engineered lplA. This synthetic approach offers a potential therapeutic strategy for treating lipoylation disorders.
    DOI:  https://doi.org/10.1016/j.jbc.2024.107995
  26. Methods Mol Biol. 2025 ;2878 35-48
    High-Resolution Respirometry Methodology for Bioenergetic and Metabolic Studies in Intact Brain Slices.
    Cândida Dias, Cátia F Lourenço, João Laranjinha, Ana Ledo.
      The brain is critically dependent on energetic substrates as it consumes circa 20% of glucose and oxygen under normal physiological conditions. Although different cell types and at different locations might experience particular specificities in the utilization of these substrates, overall, mitochondrial oxidative phosphorylation supports the most efficient energy transduction process, enabling the complete oxidation of glucose to CO2 coupled to ATP synthesis in the presence of O2. Impairment of mitochondrial bioenergetics has been identified as an early event in many brain diseases and aging. Thus, novel methodologies to readily assess mitochondrial respiration in brain tissue, while preserving cellular and mitochondrial architecture and overcoming the serious drawbacks of studies using isolated mitochondrial preparations, are needed. Here we describe a methodology for studying functional parameters defining tissue metabolic respiration in brain hippocampal slices. The methodology can be used for physiological, pharmacological, and toxicological studies.
    Keywords:  Brain tissue bioenergetics; High-resolution respirometry; Oxidative phosphorylation; Oxygen consumption rate; Whole brain slices
    DOI:  https://doi.org/10.1007/978-1-0716-4264-1_2
  27. Methods Mol Biol. 2025 ;2878 211-221
    Understanding Mitochondrial and Lysosomal Dynamics by Fluorescent Microscopy.
    Pedro A Dionísio, Vilma A Sardão, Nuno Raimundo.
      Live cell imaging is a robust method to visualize dynamic cellular structures, especially organelles with network-like structures such as mitochondria. In this regard, mitochondrial dynamics, namely mitochondrial fission and fusion, are highly dynamic processes that regulate mitochondrial size and morphology depending on a plethora of cellular cues. Likewise, lysosome size and distribution may hint at their function and state.Here, we describe how to perform live cell confocal imaging using commercially available organelle dyes (MitoTracker, LysoTracker), followed by either 2D or 3D analyses of mitochondrial morphology/network connectivity and lysosomal morphology using the freely available Mitochondria Analyzer plugin for ImageJ/Fiji.
    Keywords:  Cell imaging; Fluorescent probes; LysoTracker; Lysosomes; Microscopy; MitoTracker; Mitochondria; Mitochondrial dynamics
    DOI:  https://doi.org/10.1007/978-1-0716-4264-1_11
  28. Neuromuscul Disord. 2024 Oct 25. pii: S0960-8966(24)01731-0. [Epub ahead of print]45 105235
    Mitochondrial disorders are associated with morphological neuromuscular junction defects.
    Lola E R Lessard, Emmanuelle Girard, Nathalie Streichenberger, Philippe Petiot, Cécile Acquaviva, Cécile Pagan, Peter Mulligan, Françoise Bouhour, Laurent Schaeffer, Arnaud Jacquier.
      We aimed to evaluate whether inherited mitochondrial dysfunction is associated with neuromuscular junction remodeling in patients with mitochondrial disorders. Muscle biopsies from 15 patients with mitochondrial disorders and 10 control patients were analyzed through immunostaining for various neuromuscular junction components. The patient group, with a mean age of 49.9 years, exhibited various mitochondrial disorders including chronic progressive external ophthalmoplegia, Kearns-Sayre syndrome, and mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes. Patients with mitochondrial disorders had a high percentage of remodeled (p= 0.0001), neoformed (p= 0.0049) and dilated (p= 0.016) endplates. There was a trend toward an increased proportion of neuromuscular junctions with terminal Schwann cell extension in these patients (p= 0.052). No significant difference was found in myofiber diameter between the groups. The observed neuromuscular junction defects varied widely across different mitochondrial disorder phenotypes and were present even without accompanying muscle weakness or neuropathy. This suggest that mitochondrial disorders are associated with a primary NMJ remodeling independent of muscle structural damage. Pathomechanisms underpinning this remodeling of the neuromuscular junction, as well as clinical factors predictive of this remodeling, remain to be fully characterized.
    Keywords:  Confocal microscopy; Denervation; Fatigability; Ptosis; Reinnervation; Remodeling
    DOI:  https://doi.org/10.1016/j.nmd.2024.105235
  29. Front Ophthalmol (Lausanne). 2024 ;4 1483607
    Editorial: Mitochondrial dysfunction and genetic variations in neuro-ophthalmology diseases.
    Neeru A Vallabh, Ian Trounce.
      
    Keywords:  OXPHOS; glaucoma; mitochondria; mtDNA; ophthalmic disease; retina
    DOI:  https://doi.org/10.3389/fopht.2024.1483607
  30. Cureus. 2024 Oct;16(10): e71127
    Leigh Syndrome Caused by Compound Heterozygous Variants c.1162A_C and c.1138G_C in the NDUFV1 Gene: A Case Report.
    Josef Finsterer.
      Early-onset Leigh syndrome is usually a genetically and phenotypically heterogeneous, severe, rapidly progressive mitochondrial disorder with a fatal outcome. Leigh syndrome is genetically heterogeneous as it is based on mutations in mtDNA or nDNA genes, which mostly encode subunits of respiratory chain complexes or assembly factors. It is phenotypically heterogeneous because it is genetically heterogeneous and due to the peculiarities of mitochondrial genetics. One of the more than 100 mutated genes responsible for Leigh syndrome is NDUFV1. Here we present the case of an infant with Leigh syndrome who suffered from a novel heterozygous variant of the NDUFV1 gene, which is phenotypically characterized by a number of previously unknown features. The patient was a four-month-old girl with Leigh syndrome due to the compound heterozygous variants c.1162+4A>C (previously described, inherited from the mother) and c.1138G>C (novel, inherited from the father) in NDUFV1. The mutation c.1162+4A>C is a non-canonical splice site variant that has been demonstrated to result in loss of function. The bioinformatic analysis supports that the missense variant c. 1138G>C has a deleterious effect on protein structure or function. The mutations manifested phenotypically with typical cerebral lesions on imaging, developmental delay, cognitive decline, epileptiform discharges in the electroencephalography without seizures, atrioventricular (AV) block II, agenesis of a subclavian vein, right heart failure, patent foramen ovale, pulmonary hypertension, hypoaldosteronism, and abdominal hernias. Within five weeks of hospitalization, the disease took a progressive course, and the patient died of infectious complications despite maximum treatment. This case shows that the described new heterozygous variant in NDUFV1 can occur with previously undescribed phenotypic features. It is important to diagnose mitochondrial disorders due to NDUFV1 mutations early in order not to miss the time for appropriate symptomatic treatment.
    Keywords:  complex-i deficiency; leigh-like syndrome; mitochondrial dna; ndufv1; respiratory chain
    DOI:  https://doi.org/10.7759/cureus.71127
  31. PLoS Biol. 2024 Nov 11. 22(11): e3002895
    Mitochondrial calcium uptake orchestrates vertebrate pigmentation via transcriptional regulation of keratin filaments.
    Jyoti Tanwar, Kriti Ahuja, Akshay Sharma, Paras Sehgal, Gyan Ranjan, Farina Sultan, Anushka Agrawal, Donato D'Angelo, Anshu Priya, Vamsi K Yenamandra, Archana Singh, Anna Raffaello, Muniswamy Madesh, Rosario Rizzuto, Sridhar Sivasubbu, Rajender K Motiani.
      Mitochondria regulate several physiological functions through mitochondrial Ca2+ dynamics. However, role of mitochondrial Ca2+ signaling in melanosome biology remains unknown. Here, we show that pigmentation requires mitochondrial Ca2+ uptake. In vitro gain and loss of function studies demonstrate that mitochondrial Ca2+ uniporter (MCU) is crucial for melanogenesis while MCU rheostat, MCUb negatively control melanogenesis. Zebrafish, MCU+/- and MCUb-/- mice models show that MCU complex drives pigmentation in vivo. Mechanistically, MCU silencing activates transcription factor NFAT2 to induce expression of keratin (5, 7, and 8) filaments. Interestingly, keratin5 in turn augments mitochondrial Ca2+ uptake and potentiates melanogenesis by regulating melanosome biogenesis and maturation. Hence this signaling module acts as a negative feedback loop that fine-tunes both mitochondrial Ca2+ signaling and pigmentation. Notably, mitoxantrone, an FDA approved drug that inhibits MCU, reduces pigmentation thereby highlighting therapeutic potential of targeting mitochondrial Ca2+ uptake for clinical management of pigmentary disorders. Taken together, we reveal an MCU-NFAT2-Keratin5 driven signaling axis that acts as a critical determinant of mitochondrial Ca2+ uptake and pigmentation. Given the vital role of mitochondrial Ca2+ signaling and keratin filaments in cellular physiology, this feedback loop could be operational in a variety of other patho-physiological processes.
    DOI:  https://doi.org/10.1371/journal.pbio.3002895
  32. Nat Commun. 2024 Nov 12. 15(1): 9797
    HSF-1 promotes longevity through ubiquilin-1-dependent mitochondrial network remodelling.
    Annmary Paul Erinjeri, Xunyan Wang, Rhianna Williams, Riccardo Zenezini Chiozzi, Konstantinos Thalassinos, Johnathan Labbadia.
      Increased activity of the heat shock factor, HSF-1, suppresses proteotoxicity and enhances longevity. However, the precise mechanisms by which HSF-1 promotes lifespan are unclear. Using an RNAi screen, we identify ubiquilin-1 (ubql-1) as an essential mediator of lifespan extension in worms overexpressing hsf-1. We find that hsf-1 overexpression leads to transcriptional downregulation of all components of the CDC-48-UFD-1-NPL-4 complex, which is central to both endoplasmic reticulum and mitochondria associated protein degradation, and that this is complemented by UBQL-1-dependent turnover of NPL-4.1. As a consequence, mitochondrial network dynamics are altered, leading to increased lifespan. Together, our data establish that HSF-1 mediates lifespan extension through mitochondrial network adaptations that occur in response to down-tuning of components associated with organellar protein degradation pathways.
    DOI:  https://doi.org/10.1038/s41467-024-54136-x
  33. Nat Commun. 2024 Nov 12. 15(1): 9529
    Nuclear localization of MTHFD2 is required for correct mitosis progression.
    Natalia Pardo-Lorente, Anestis Gkanogiannis, Luca Cozzuto, Antoni Gañez Zapater, Lorena Espinar, Ritobrata Ghose, Jacqueline Severino, Laura García-López, Rabia Gül Aydin, Laura Martin, Maria Victoria Neguembor, Evangelia Darai, Maria Pia Cosma, Laura Batlle-Morera, Julia Ponomarenko, Sara Sdelci.
      Subcellular compartmentalization of metabolic enzymes establishes a unique metabolic environment that elicits specific cellular functions. Indeed, the nuclear translocation of certain metabolic enzymes is required for epigenetic regulation and gene expression control. Here, we show that the nuclear localization of the mitochondrial enzyme methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) ensures mitosis progression. Nuclear MTHFD2 interacts with proteins involved in mitosis regulation and centromere stability, including the methyltransferases KMT5A and DNMT3B. Loss of MTHFD2 induces severe methylation defects and impedes correct mitosis completion. MTHFD2 deficient cells display chromosome congression and segregation defects and accumulate chromosomal aberrations. Blocking the catalytic nuclear function of MTHFD2 recapitulates the phenotype observed in MTHFD2 deficient cells, whereas restricting MTHFD2 to the nucleus is sufficient to ensure correct mitotic progression. Our discovery uncovers a nuclear role for MTHFD2, supporting the notion that translocation of metabolic enzymes to the nucleus is required to meet precise chromatin needs.
    DOI:  https://doi.org/10.1038/s41467-024-51847-z
  34. Nat Cardiovasc Res. 2024 Nov;3(11): 1318-1336
    Klf9 is essential for cardiac mitochondrial homeostasis.
    Lei Zhang, Menglin Zhang, Jinlong Huang, Jincan Huang, Yujie Zhang, Yinliang Zhang, Houzao Chen, Cuizhe Wang, Xiangwen Xi, Heng Fan, Jikui Wang, Dingsheng Jiang, Jinwei Tian, Jun Zhang, Yongsheng Chang.
      Mitochondrial dynamics and mitophagy are intimately linked physiological processes that are essential for cardiac homeostasis. Here we show that cardiac Krüppel-like factor 9 (Klf9) is dysregulated in human and rodent cardiomyopathy. Both global and cardiac-specific Klf9-deficient mice displayed hypertrophic cardiomyopathy. Klf9 knockout led to mitochondrial disarray and fragmentation, impairing mitochondrial respiratory function in cardiomyocytes. Furthermore, cardiac Klf9 deficiency inhibited mitophagy, thereby causing accumulation of dysfunctional mitochondria and acceleration of heart failure in response to angiotensin II treatment. In contrast, cardiac-specific Klf9 transgene improved cardiac systolic function. Mechanistically, Klf9 knockout decreased the expression of PGC-1α and its target genes involved in mitochondrial energy metabolism. Moreover, Klf9 controlled the expression of Mfn2, thereby regulating mitochondrial dynamics and mitophagy. Finally, adeno-associated virus-mediated Mfn2 rescue in Klf9-CKO hearts improved cardiac mitochondrial and systolic function. Thus, Klf9 integrates cardiac energy metabolism, mitochondrial dynamics and mitophagy. Modulating Klf9 activity may have therapeutic potential in the treatment of heart failure.
    DOI:  https://doi.org/10.1038/s44161-024-00561-6
  35. Methods Mol Biol. 2025 ;2878 233-257
    Absolute Quantification of Cellular and Cell-Free Mitochondrial DNA Copy Number from Human Blood and Urinary Samples Using Real Time Quantitative PCR.
    Eliane Caseiro Soares de Menezes, Afshan Navid Malik.
      Mitochondrial DNA copy number (mtDNA-CN) in human body fluids is widely used as a biomarker of mitochondrial dysfunction in common metabolic diseases. Here we describe protocols to measure cellular and/or cell free (cf)-mtDNA-CN in human peripheral blood and urine. Cellular mtDNA is located inside the mitochondria where it encodes key subunits of the respiratory complexes in mitochondria and is usually normalized with reference to the nuclear genome as the mitochondrial genome to nuclear genome ratio (Mt/N) in either whole blood, peripheral blood mononuclear cells (PBMCs), or whole urine. Cf -mtDNA is usually found outside of the mitochondria, often released following mitochondrial damage, can trigger inflammatory pathways, and is usually measured as mtDNA-CN per volume of the starting material. Here we describe how to (1) separate whole blood into PBMCs, plasma, and serum fractions and whole urine into urinary supernatant and pellet, (2) prepare DNA from each of these fractions, (3) prepare reference standards for absolute quantification, (4) carry out qPCR for either relative or absolute quantification from test samples, (5) analyze qPCR data, and (6) calculate the sample size to adequately power studies. The protocol presented here is suitable for high throughput use and can be modified to quantify mtDNA from other body fluids, human cells, and tissues.
    Keywords:  Absolute quantification; Circulating mtDNA; Mitochondrial DNA; Mt/N ratio; PBMCs; Plasma; Serum; Urinary pellet; Urinary supernatant; Urine; mtDNA; mtDNA content; mtDNA copy number; qPCR
    DOI:  https://doi.org/10.1007/978-1-0716-4264-1_13
  36. Nature. 2024 Nov 11.
    AI protein-prediction tool AlphaFold3 is now more open.
    Ewen Callaway.
      
    Keywords:  Drug discovery; Machine learning; Structural biology
    DOI:  https://doi.org/10.1038/d41586-024-03708-4
  37. Nat Cell Biol. 2024 Nov 15.
    FMRP gains mitochondrial fission control.
    Carissa L Sirois, Soraya O Sandoval, Xinyu Zhao.
      
    DOI:  https://doi.org/10.1038/s41556-024-01567-9
  38. Metabolism. 2024 Nov 06. pii: S0026-0495(24)00289-0. [Epub ahead of print] 156061
    Wars1 downregulation in hepatocytes induces mitochondrial stress and disrupts metabolic homeostasis.
    Francesca Pontanari, Hadrien Demagny, Adrien Faure, Xiaoxu Li, Giorgia Benegiamo, Antoine Jalil, Alessia Perino, Johan Auwerx, Kristina Schoonjans.
      Several laboratories, including ours, have employed the Slc25a47tm1c(EUCOMM)Hmgu mouse model to investigate the role of SLC25A47, a hepatocyte-specific mitochondrial carrier, in regulating hepatic metabolism and systemic physiology. In this study, we reveal that the hepatic and systemic phenotypes observed following recombination of the Slc25a47-Wars1 locus in hepatocytes are primarily driven by the unexpected downregulation of Wars1, a cytosolic tryptophan aminoacyl-tRNA synthetase located adjacent to Slc25a47. While the downregulation of Wars1 predictably affects cytosolic translation, we also observed a significant impairment in mitochondrial protein synthesis within hepatocytes. This disturbance in mitochondrial function leads to an activation of the mitochondrial unfolded protein response (UPRmt), a critical component of the mitochondrial stress response (MSR). Our findings clarify the distinct roles of Slc25a47 and Wars1 in maintaining both systemic and hepatic metabolic homeostasis. This study sheds new light on the broader implications of aminoacyl-tRNA synthetases in mitochondrial physiology and stress responses.
    Keywords:  Hepatocytes; ISR; MSR; SLC25A47; Translation; UPR(mt); WARS1
    DOI:  https://doi.org/10.1016/j.metabol.2024.156061
  39. Nat Cell Biol. 2024 Nov 15.
    FMRP regulates MFF translation to locally direct mitochondrial fission in neurons.
    Adam R Fenton, Ruchao Peng, Charles Bond, Siewert Hugelier, Melike Lakadamyali, Yi-Wei Chang, Erika L F Holzbaur, Thomas A Jongens.
      Fragile X messenger ribonucleoprotein (FMRP) is a critical regulator of translation, whose dysfunction causes fragile X syndrome. FMRP dysfunction disrupts mitochondrial health in neurons, but it is unclear how FMRP supports mitochondrial homoeostasis. Here we demonstrate that FMRP granules are recruited to the mitochondrial midzone, where they mark mitochondrial fission sites in axons and dendrites. Endolysosomal vesicles contribute to FMRP granule positioning around mitochondria and facilitate FMRP-associated fission via Rab7 GTP hydrolysis. Cryo-electron tomography and real-time translation imaging reveal that mitochondria-associated FMRP granules are ribosome-rich structures that serve as sites of local protein synthesis. Specifically, FMRP promotes local translation of mitochondrial fission factor (MFF), selectively enabling replicative fission at the mitochondrial midzone. Disrupting FMRP function dysregulates mitochondria-associated MFF translation and perturbs fission dynamics, resulting in increased peripheral fission and an irregular distribution of mitochondrial nucleoids. Thus, FMRP regulates local translation of MFF in neurons, enabling precise control of mitochondrial fission.
    DOI:  https://doi.org/10.1038/s41556-024-01544-2
  40. Cell Commun Signal. 2024 Nov 08. 22(1): 537
    NAD+ enhancers as therapeutic agents in the cardiorenal axis.
    Mariano Marín-Blázquez, Jordi Rovira, María José Ramírez-Bajo, Rubén Zapata-Pérez, Rubén Rabadán-Ros.
      Cardiorenal diseases represent a complex interplay between heart failure and renal dysfunction, being clinically classified as cardiorenal syndromes (CRS). Recently, the contributions of altered nicotinamide adenine dinucleotide (NAD+) metabolism, through deficient NAD+ synthesis and/or elevated consumption, have proved to be decisive in the onset and progress of cardiorenal disease. NAD+ is a pivotal coenzyme in cellular metabolism, being significant in various signaling pathways, such as energy metabolism, DNA damage repair, gene expression, and stress response. Convincing evidence suggests that strategies designed to boost cellular NAD+ levels are a promising therapeutic option to address cardiovascular and renal disorders. Here, we review and discuss the implications of NAD+ metabolism in cardiorenal diseases, focusing on the propitious NAD+ boosting therapeutic strategies, based on the use of NAD+ precursors, poly(ADP-ribose) polymerase inhibitors, sirtuin activators, and other alternative approaches, such as CD38 blockade, nicotinamide phosphoribosyltransferase activation and combined interventions.
    Keywords:  AKI; Animal models; CD38; Cardiorenal syndrome; Clinical trial; Ischemia/reperfusion; NAD+ metabolism; NMNH; NRH; Niacin; Niacinamide; Nicotinamide; Nicotinamide mononucleotide; Nicotinamide riboside; Poly(ADP-ribose) polymerases; Sirtuins; Trigonelline
    DOI:  https://doi.org/10.1186/s12964-024-01903-4
  41. Autophagy. 2024 Nov 08.
    Efficient PHB2 (prohibitin 2) exposure during mitophagy depends on VDAC1 (voltage dependent anion channel 1).
    Moumita Roy, Sumangal Nandy, Elena Marchesan, Chayan Banerjee, Rupsha Mondal, Federico Caicci, Elena Ziviani, Joy Chakraborty.
      Exposure of inner mitochondrial membrane resident protein PHB2 (prohibitin 2) during autophagic removal of depolarized mitochondria (mitophagy) depends on the ubiquitin-proteasome system. This uncovering facilitates the PHB2 interaction with phagophore membrane-associated protein MAP1LC3/LC3. It is unclear whether PHB2 is exposed randomly at mitochondrial rupture sites. Prior knowledge and initial screening indicated that VDAC1 (voltage dependent anion channel 1) might play a role in this phenomenon. Through in vitro biochemical assays and imaging, we have found that VDAC1-PHB2 interaction increases during mitochondrial depolarization. Subsequently, this interaction enhances the efficiency of PHB2 exposure and mitophagy. To investigate the relevance in vivo, we utilized porin (equivalent to VDAC1) knockout Drosophila line. Our findings demonstrate that during mitochondrial stress, porin is essential for Phb2 exposure, Phb2-Atg8 interaction and mitophagy. This study highlights that VDAC1 predominantly synchronizes efficient PHB2 exposure through mitochondrial rupture sites during mitophagy. These findings may provide insights to understand progressive neurodegeneration.
    Keywords:  Neurodegeneration; PHB2-LC3 interaction; PINK1-PRKN; parkinson disease; porin; ubiquitin-proteasome system
    DOI:  https://doi.org/10.1080/15548627.2024.2426116
  42. Methods Mol Biol. 2025 ;2878 223-232
    Mitochondrial Morphofunctional Profiling in Primary Human Skin Fibroblasts Using TMRM and Mitotracker Green Co-staining.
    Jesper M M Bergmans, Els M A van de Westerlo, Sander Grefte, Merel J W Adjobo-Hermans, Werner J H Koopman.
      Mitochondrial morphology and membrane potential (Δψ) are important readouts of mitochondrial function. Integrated analysis of these parameters in living cells can be performed using fluorescent lipophilic cations, which enter cells and accumulate in the mitochondrial matrix in a Δψ-dependent manner. Here, we describe the use of tetramethylrhodamine methyl ester (TMRM) and Mitotracker Green FM (MG) for mitochondrial morphology and semiquantitative Δψ analysis in living primary human skin fibroblasts (PHSFs). Practically, we present an integrated protocol to quantify mitochondrial morphology parameters and signal intensity using epifluorescence microscopy of PHSFs co-stained with TMRM and MG. This approach performs best using large flat cells like PHSFs, which display a high mitochondria-specific fluorescence signal and are imaged at a relatively high (x40) magnification.
    Keywords:  FCCP; Mitochondrial morphology; Mitotracker Green; TMRM
    DOI:  https://doi.org/10.1007/978-1-0716-4264-1_12
  43. JIMD Rep. 2024 Sep;65(5): 297-304
    The phenotypic spectrum of PTCD3 deficiency.
    Baiba Lace, Eissa Faqeih, Namik Kaya, Zita Krumina, Johannes A Mayr, Ieva Micule, Nathan Thompson Wright, Melanie T Achleitner, Hanan AlQudairy, Sander Pajusalu, Janis Stavusis, Pawel Zayakin, Inna Inashkina.
      The PTCD3 gene product (protein PTCD3 or MRPS39) forms the entry channel of the mitochondrial small ribosomal subunit and binds to single-stranded mRNA. Here, we expand on the clinical manifestations of PTCD3 pathogenic variants by describing an early-onset patient with Leigh-like syndrome and two patients with milder form of disease, with combined oxidative phosphorylation deficiency. A 34-year-old male and his 33-year-old sister both have horizontal nystagmus, pronounced rough tremor, truncal ataxia, dysmetria, spasticity and hyperreflexia. The basal respiration rate decreased significantly for the male patient and his mother (p < 0.0001) compared to the controls. The whole genome sequencing analysis revealed two heterozygous variants in the PTCD3: c.1182T>A, p.(Tyr394Ter) and c.805C>T, p.(His269Tyr). Tyr394Ter variant ablates the C-terminal half of the protein, including a significant portion of the central fold. In silico modelling for the variant His269Tyr shows that the inclusion of the slightly larger tyrosine sidechain is well tolerated, with no significant change in either the position or the movement of the surrounding area. The third case is a 9-year-old boy, who has a global developmental delay, central hypotonia, hyperreflexia and abnormal MRI. PTCD3 pathogenic variant c.538+4A>G was identified by whole exome sequencing. To test the variant's effect on splicing, an RT-PCR experiment was performed, which revealed skipping of an out-of-frame exon 7.
    Keywords:  Leigh‐like syndrome; PTCD3; pentatricopeptide repeat
    DOI:  https://doi.org/10.1002/jmd2.12424
  44. Free Radic Biol Med. 2024 Nov 09. pii: S0891-5849(24)01040-2. [Epub ahead of print]
    Restoration of mitochondrial function alleviates trigeminal neuropathic pain in mice.
    Jiajun Yang, Song Xie, Jiahao Guo, Yujuan Zhou, Yaning Yang, Zhaoxia Sun, Peng Cai, Chenchen Zhang, Shangying Jiang, Xuxia Cao, Yuanlan Fan, Xing Chen, Xiaokun Li, Yi Zhang.
      Craniofacial pain is prevalent and a debilitating condition. Managing craniofacial pain is particularly challenging due to its multifaceted nature. Among the most severe forms of craniofacial pain is trigeminal neuralgia, often described as one of the most excruciating pain syndromes encountered in clinical practice. Utilizing a mouse model of trigeminal neuropathic pain, we found severe mitochondrial impairment in the injured trigeminal ganglion (TG), spanning transcription and translation to functionality. Our findings demonstrated that rejuvenating mitochondria by boosting NAD+ levels enhanced mitochondrial fitness and significantly ameliorated trigeminal neuropathic pain. Additionally, we showed that the analgesic effects of nicotinamide riboside (NR) supplementation mainly depend on Sirt1. Importantly, our multi-omics studies revealed that activated Sirt1 by NR suppresses a broad range of key pain genes and exerts anti-inflammatory effects in the TG. Together, we present a comprehensive view of how mitochondrial dysfunction is involved in trigeminal neuropathic pain. Therefore, targeting mitochondrial dysfunction offers a novel and promising approach to craniofacial pain management.
    Keywords:  NAD(+); Sirt1; craniofacial pain; mitochondria; pain genes
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2024.11.011
  45. Cells. 2024 Oct 26. pii: 1773. [Epub ahead of print]13(21):
    Mitochondrial Dynamics Drive Muscle Stem Cell Progression from Quiescence to Myogenic Differentiation.
    Olivia Sommers, Rholls A Tomsine, Mireille Khacho.
      From quiescence to activation and myogenic differentiation, muscle stem cells (MuSCs) experience drastic alterations in their signaling activity and metabolism. Through balanced cycles of fission and fusion, mitochondria alter their morphology and metabolism, allowing them to affect their decisive role in modulating MuSC activity and fate decisions. This tightly regulated process contributes to MuSC regulation by mediating changes in redox signaling pathways, cell cycle progression, and cell fate decisions. In this review, we discuss the role of mitochondrial dynamics as an integral modulator of MuSC activity, fate, and maintenance. Understanding the influence of mitochondrial dynamics in MuSCs in health and disease will further the development of therapeutics that support MuSC integrity and thus may aid in restoring the regenerative capacity of skeletal muscle.
    Keywords:  DRP1; OPA1; differentiation; glutathione; metabolism; mitochondria; mitochondrial dynamics; muscle stem cells; myogenesis; reactive oxygen species (ROS)
    DOI:  https://doi.org/10.3390/cells13211773
  46. J Cell Biol. 2024 Dec 02. pii: e202401084. [Epub ahead of print]223(12):
    Non-cell autonomous regulation of cell-cell signaling and differentiation by mitochondrial ROS.
    Yipeng Du, Lei Wang, Lizbeth Perez-Castro, Maralice Conacci-Sorrell, Matthew Sieber.
      Mitochondrial reactive oxygen species (ROS) function intrinsically within cells to induce cell damage, regulate transcription, and cause genome instability. However, we know little about how mitochondrial ROS production non-cell autonomously impacts cell-cell signaling. Here, we show that mitochondrial dysfunction inhibits the plasma membrane localization of cell surface receptors that drive cell-cell communication during oogenesis. Within minutes, we found that mitochondrial ROS impairs exocyst membrane binding and leads to defective endosomal recycling. This endosomal defect impairs the trafficking of receptors, such as the Notch ligand Delta, during oogenesis. Remarkably, we found that overexpressing RAB11 restores ligand trafficking and rescues the developmental defects caused by ROS production. ROS production from adjacent cells acutely initiates a transcriptional response associated with growth and migration by suppressing Notch signaling and inducing extra cellualr matrix (ECM) remodeling. Our work reveals a conserved rapid response to ROS production that links mitochondrial dysfunction to the non-cell autonomous regulation of cell-cell signaling.
    DOI:  https://doi.org/10.1083/jcb.202401084
  47. Methods Mol Biol. 2025 ;2878 133-162
    The Relation Between Mitochondrial Membrane Potential and Reactive Oxygen Species Formation.
    Magdalena Lebiedzinska-Arciszewska, Jan Suski, Massimo Bonora, Barbara Pakula, Paolo Pinton, Jerzy Duszynski, Patrycja Jakubek-Olszewska, Mariusz R Wieckowski.
      Mitochondria are considered one of the main sites of reactive oxygen species (ROS) production in the eukaryotic cells. For this reason, mitochondrial dysfunction associated with increased ROS production underlies various pathological conditions as well as promotes aging. Chronically increased rates of ROS production contribute to oxidative damage to macromolecules, i.e., DNA, proteins, and lipids. Accumulation of unrepaired oxidative damage may result in progressive cell dysfunction, which can finally trigger cell death. The main by-product of mitochondrial oxidative phosphorylation is superoxide, which is generated by the leak of electrons from the mitochondrial respiratory chain complexes leading to one-electron reduction of oxygen. Mitochondrial superoxide dismutase (MnSOD, SOD2) as well as cytosolic superoxide dismutase (Cu/ZnSOD, SOD1), whose smaller pool is localized in the mitochondrial intermembrane space, converts superoxide to H2O2, which can be then degraded by the catalase to harmless H2O.In this chapter, we focus on the relationship between one of the bioenergetic parameters, which is mitochondrial membrane potential, and the rate of ROS formation. We present a set of various methods enabling the characterization of these parameters applicable to isolated mitochondria or intact cells. We also present examples of experimental data demonstrating that the magnitude and direction (increase or decrease) of a change in mitochondrial ROS production depend on the mitochondrial metabolic state.
    Keywords:  Confocal microscopy; Hydrogen peroxide; Mitochondria; Oxygen consumption; Resazurin; Superoxide
    DOI:  https://doi.org/10.1007/978-1-0716-4264-1_8
  48. Methods Mol Biol. 2025 ;2878 49-66
    Plate-Based Measurement of Respiration by Isolated Mitochondria and by Intact Cells.
    Shona A Mookerjee.
      Measuring respiration rate can be a powerful way to assess energetic function in isolated mitochondria and intact cells. Current plate-based methods have several advantages over older suspension-based systems, including greater throughput and the requirement of only microgram quantities of material. In this chapter, we provide an update to our previously published methods for plate-based measurement of oxygen consumption in isolated adherent mitochondria in a 96-well format plate. We also describe methods for performing the same measurements on intact cells in a 96-well format.
    Keywords:  ATP production; Electron flow; Mitochondrial respiration; Oxygen consumption; Respiratory control ratio
    DOI:  https://doi.org/10.1007/978-1-0716-4264-1_3
  49. Mol Cell. 2024 Nov 05. pii: S1097-2765(24)00865-7. [Epub ahead of print]
    Opposing roles for AMPK in regulating distinct mitophagy pathways.
    Marianna Longo, Aniketh Bishnu, Pierpaolo Risiglione, Lambert Montava-Garriga, Joyceline Cuenco, Kei Sakamoto, Carol MacKintosh, Ian G Ganley.
      Mitophagy degrades damaged mitochondria, but we show here that it can also target functional mitochondria. This latter scenario occurs during programmed mitophagy and involves the mitophagy receptors NIX and BNIP3. Although AMP-activated protein kinase (AMPK), the energy-sensing protein kinase, can influence damaged-induced mitophagy, its role in programmed mitophagy is unclear. We found that AMPK directly inhibits NIX-dependent mitophagy by triggering 14-3-3-mediated sequestration of ULK1, via ULK1 phosphorylation at two sites: Ser556 and an additional identified site, Ser694. By contrast, AMPK activation increases Parkin phosphorylation and enhances the rate of depolarization-induced mitophagy, independently of ULK1. We show that this happens both in cultured cells and tissues in vivo, using the mito-QC mouse model. Our work unveils a mechanism whereby AMPK activation downregulates mitophagy of functional mitochondria but enhances that of dysfunctional/damaged ones.
    Keywords:  14-3-3; AMPK; NIX; Parkin; ULK1; autophagy; liver; mito-QC; mitophagy; skeletal muscle
    DOI:  https://doi.org/10.1016/j.molcel.2024.10.025
  50. Life Sci Alliance. 2025 Jan;pii: e202402922. [Epub ahead of print]8(1):
    Pathogenic LRRK2 mutations cause loss of primary cilia and Neurturin in striatal parvalbumin interneurons.
    Yu-En Lin, Ebsy Jaimon, Francesca Tonelli, Suzanne R Pfeffer.
      Parkinson's disease-associated, activating mutations in the LRRK2 kinase block primary cilium formation in cell culture and in specific cell types in the brain. In the striatum that is important for movement control, about half of astrocytes and cholinergic interneurons, but not the predominant medium spiny neurons, lose their primary cilia. Here, we show that mouse and human striatal parvalbumin interneurons that are inhibitory regulators of movement also lose primary cilia. Without cilia, these neurons are not able to respond to Sonic hedgehog signals that normally induce the expression of Patched RNA, and their numbers decrease. In addition, in mouse, glial cell line-derived neurotrophic factor-related Neurturin RNA is significantly decreased. These experiments highlight the importance of parvalbumin neurons in cilium-dependent, neuroprotective signaling pathways and show that LRRK2 activation correlates with decreased Neurturin production, resulting in less neuroprotection for dopamine neurons.
    DOI:  https://doi.org/10.26508/lsa.202402922
  51. Cell Death Dis. 2024 Nov 08. 15(11): 807
    TAp73 regulates mitochondrial dynamics and multiciliated cell homeostasis through an OPA1 axis.
    Niall A Buckley, Andrew Craxton, Xiao-Ming Sun, Emanuele Panatta, Lucia Giraldez Pinon, Sina Beier, Lajos Kalmar, Jaime Llodrá, Nobuhiro Morone, Ivano Amelio, Gerry Melino, L Miguel Martins, Marion MacFarlane.
      Dysregulated mitochondrial fusion and fission has been implicated in the pathogenesis of numerous diseases. We have identified a novel function of the p53 family protein TAp73 in regulating mitochondrial dynamics. TAp73 regulates the expression of Optic Atrophy 1 (OPA1), a protein responsible for controlling mitochondrial fusion, cristae biogenesis and electron transport chain function. Disruption of this axis results in a fragmented mitochondrial network and an impaired capacity for energy production via oxidative phosphorylation. Owing to the role of OPA1 in modulating cytochrome c release, TAp73-/- cells display an increased sensitivity to apoptotic cell death, e.g., via BH3-mimetics. We additionally show that the TAp73/OPA1 axis has functional relevance in the upper airway, where TAp73 expression is essential for multiciliated cell differentiation and function. Consistently, ciliated epithelial cells of Trp73-/- (global p73 knock-out) mice display decreased expression of OPA1 and perturbations of the mitochondrial network, which may drive multiciliated cell loss. In support of this, Trp73 and OPA1 gene expression is decreased in chronic obstructive pulmonary disease (COPD) patients, a disease characterised by alterations in mitochondrial dynamics. We therefore highlight a potential mechanism involving the loss of p73 in COPD pathogenesis. Our findings also add to the growing body of evidence for growth-promoting roles of TAp73 isoforms.
    DOI:  https://doi.org/10.1038/s41419-024-07130-6
  52. Int J Mol Sci. 2024 Oct 23. pii: 11406. [Epub ahead of print]25(21):
    Integrative Metabolome and Proteome Analysis of Cerebrospinal Fluid in Parkinson's Disease.
    Seok Gi Kim, Ji Su Hwang, Nimisha Pradeep George, Yong Eun Jang, Minjun Kwon, Sang Seop Lee, Gwang Lee.
      Parkinson's disease (PD) is a common neurodegenerative disorder characterized by the loss of dopaminergic neurons in the substantia nigra. Recent studies have highlighted the significant role of cerebrospinal fluid (CSF) in reflecting pathophysiological PD brain conditions by analyzing the components of CSF. Based on the published literature, we created a single network with altered metabolites in the CSF of patients with PD. We analyzed biological functions related to the transmembrane of mitochondria, respiration of mitochondria, neurodegeneration, and PD using a bioinformatics tool. As the proteome reflects phenotypes, we collected proteome data based on published papers, and the biological function of the single network showed similarities with that of the metabolomic network. Then, we analyzed the single network of integrated metabolome and proteome. In silico predictions based on the single network with integrated metabolomics and proteomics showed that neurodegeneration and PD were predicted to be activated. In contrast, mitochondrial transmembrane activity and respiration were predicted to be suppressed in the CSF of patients with PD. This review underscores the importance of integrated omics analyses in deciphering PD's complex biochemical networks underlying neurodegeneration.
    Keywords:  Parkinson’s disease; cerebrospinal fluid; integrated omics; metabolomics; proteomics
    DOI:  https://doi.org/10.3390/ijms252111406
  53. Brain Commun. 2024 ;6(6): fcae342
    Overcoming genetic neuromuscular diagnostic pitfalls in a middle-income country.
    Rodrigo Siqueira Soares Frezatti, Pedro José Tomaselli, Christopher J Record, Lindsay A Wilson, Gustavo Maximiano Alves, Natalia Dominik, Stephanie Efthymiou, Krutik Patel, Jana Vandrovcova, Roope Männikkö, Robert D S Pitceathly, Claudia Ferreira da Rosa Sobreira, Robert McFarland, Robert W Taylor, Henry Houlden, Michael G Hanna, Mary M Reilly, Wilson Marques.
      Neuromuscular disorders affect almost 20 million people worldwide. Advances in molecular diagnosis have provided valuable insights into neuromuscular disorders, allowing for improved standards of care and targeted therapeutic approaches. Despite this progress, access to genomic diagnosis remains scarce and inconsistent in middle-income countries such as Brazil. The lack of public health policies to enable feasible genetic diagnosis and the shortage of neuromuscular disorders specialists are the main reasons in this process. We report our experience in a transcontinental genomic consortium for neuromuscular disorders highlighting how collaborative efforts have helped overcome various obstacles in diagnosing our patients. We describe several challenging cases categorized into three major themes, underlining significant gaps in genetic diagnosis: (i) reverse phenotyping and variant validation, (ii) deep phenotyping and identifying a bespoke molecular approach, and (iii) exploring the use of genomic tests beyond whole exome sequencing. We applied a qualitative case-based approach to exemplify common pitfalls in genomic diagnosis in a middle-income country. Our experience has shown that establishing a virtual transcontinental partnership is viable, offering effective exchange of scientific experiences, providing both guidance for rational decision-making and specialized training on a local level and access to diverse molecular diagnosis strategies and functional analyses. Collaborative efforts such as these have the potential to overcome local obstacles, strengthen scientific capabilities, foster diverse multi-ethnic cohorts, and ultimately provide improved care for patients.
    Keywords:  capacity building; diagnostic pitfalls; genomic medicine; middle income country; transcontinental consortium
    DOI:  https://doi.org/10.1093/braincomms/fcae342
  54. Nature. 2024 Nov 13.
    NK2R control of energy expenditure and feeding to treat metabolic diseases.
    Frederike Sass, Tao Ma, Jeppe H Ekberg, Melissa Kirigiti, Mario G Ureña, Lucile Dollet, Jenny M Brown, Astrid L Basse, Warren T Yacawych, Hayley B Burm, Mette K Andersen, Thomas S Nielsen, Abigail J Tomlinson, Oksana Dmytiyeva, Dan P Christensen, Lindsay Bader, Camilla T Vo, Yaxu Wang, Dylan M Rausch, Cecilie K Kristensen, María Gestal-Mato, Wietse In Het Panhuis, Kim A Sjøberg, Stace Kernodle, Jacob E Petersen, Artem Pavlovskyi, Manbir Sandhu, Ida Moltke, Marit E Jørgensen, Anders Albrechtsen, Niels Grarup, M Madan Babu, Patrick C N Rensen, Sander Kooijman, Randy J Seeley, Anna Worthmann, Joerg Heeren, Tune H Pers, Torben Hansen, Magnus B F Gustafsson, Mads Tang-Christensen, Tuomas O Kilpeläinen, Martin G Myers, Paul Kievit, Thue W Schwartz, Jakob B Hansen, Zachary Gerhart-Hines.
      The combination of decreasing food intake and increasing energy expenditure represents a powerful strategy for counteracting cardiometabolic diseases such as obesity and type 2 diabetes1. Yet current pharmacological approaches require conjugation of multiple receptor agonists to achieve both effects2-4, and so far, no safe energy-expending option has reached the clinic. Here we show that activation of neurokinin 2 receptor (NK2R) is sufficient to suppress appetite centrally and increase energy expenditure peripherally. We focused on NK2R after revealing its genetic links to obesity and glucose control. However, therapeutically exploiting NK2R signalling has previously been unattainable because its endogenous ligand, neurokinin A, is short-lived and lacks receptor specificity5,6. Therefore, we developed selective, long-acting NK2R agonists with potential for once-weekly administration in humans. In mice, these agonists elicit weight loss by inducing energy expenditure and non-aversive appetite suppression that circumvents canonical leptin signalling. Additionally, a hyperinsulinaemic-euglycaemic clamp reveals that NK2R agonism acutely enhances insulin sensitization. In diabetic, obese macaques, NK2R activation significantly decreases body weight, blood glucose, triglycerides and cholesterol, and ameliorates insulin resistance. These findings identify a single receptor target that leverages both energy-expending and appetite-suppressing programmes to improve energy homeostasis and reverse cardiometabolic dysfunction across species.
    DOI:  https://doi.org/10.1038/s41586-024-08207-0
  55. Nat Commun. 2024 Nov 12. 15(1): 9585
    Hepatic SerpinA1 improves energy and glucose metabolism through regulation of preadipocyte proliferation and UCP1 expression.
    Shota Okagawa, Masaji Sakaguchi, Yuma Okubo, Yuri Takekuma, Motoyuki Igata, Tatsuya Kondo, Naoki Takeda, Kimi Araki, Bruna Brasil Brandao, Wei-Jun Qian, Yu-Hua Tseng, Rohit N Kulkarni, Naoto Kubota, C Ronald Kahn, Eiichi Araki.
      Lipodystrophy and obesity are associated with insulin resistance and metabolic syndrome accompanied by fat tissue dysregulation. Here, we show that serine protease inhibitor A1 (SerpinA1) expression in the liver is increased during recovery from lipodystrophy caused by the adipocyte-specific loss of insulin signaling in mice. SerpinA1 induces the proliferation of white and brown preadipocytes and increases the expression of uncoupling protein 1 (UCP1) to promote mitochondrial activation in mature white and brown adipocytes. Liver-specific SerpinA1 transgenic mice exhibit increased browning of adipose tissues, leading to increased energy expenditure, reduced adiposity and improved glucose tolerance. Conversely, SerpinA1 knockout mice exhibit decreased adipocyte mitochondrial function, impaired thermogenesis, obesity, and systemic insulin resistance. SerpinA1 forms a complex with the Eph receptor B2 and regulates its downstream signaling in adipocytes. These results demonstrate that SerpinA1 is an important hepatokine that improves obesity, energy expenditure and glucose metabolism by promoting preadipocyte proliferation and activating mitochondrial UCP1 expression in adipocytes.
    DOI:  https://doi.org/10.1038/s41467-024-53835-9
  56. NPJ Parkinsons Dis. 2024 Nov 14. 10(1): 219
    Peripheral immune cell abundance differences link blood mitochondrial DNA copy number and Parkinson's disease.
    Longfei Wang, Jiru Han, Liam G Fearnley, Michael Milton, Haloom Rafehi, Joshua Reid, Zachary F Gerring, Shashank Masaldan, Tali Lang, Terence P Speed, Melanie Bahlo.
      Mitochondrial dysfunction plays an important role in Parkinson's disease (PD), with mitochondrial DNA copy number (mtDNA-CN) emerging as a potential marker for mitochondrial health. We investigated the links between blood mtDNA-CN and PD severity and risk using the Accelerating Medicines Partnership program for Parkinson's Disease dataset, replicating our results in the UK Biobank. Our findings reveal that reduced blood mtDNA-CN levels are associated with heightened PD risk and increased severity of motor symptoms and olfactory dysfunction. We estimated blood cell composition using complete blood cell profile when available or RNA-sequencing data as a surrogate. After adjusting for blood cell composition, the associations between mtDNA-CN and PD risk and clinical symptoms became non-significant. Bidirectional Mendelian randomization analysis also found no evidence of a direct causal relationship between blood mtDNA-CN and PD susceptibility. Hence peripheral inflammatory immune responses rather than mitochondrial dysfunction underpin these previously identified associations in PD.
    DOI:  https://doi.org/10.1038/s41531-024-00831-x
  57. Biomaterials. 2024 Oct 26. pii: S0142-9612(24)00456-3. [Epub ahead of print]315 122922
    Rescue of mitochondrial dysfunction through alteration of extracellular matrix composition in barth syndrome cardiac fibroblasts.
    Janny Piñeiro-Llanes, Silveli Suzuki-Hatano, Ananya Jain, Sree Venigalla, Manasi Kamat, Kari B Basso, William T Cade, Chelsey S Simmons, Christina A Pacak.
      Fibroblast-ECM (dys)regulation is associated with a plethora of diseases. The ECM acts as a reservoir of inflammatory factors and cytokines that mediate molecular mechanisms within cardiac cell populations. The role of ECM-mitochondria crosstalk in the development and progression of cardiac disorders remains uncertain. We evaluated the influence of ECM produced by stromal cells from patients with the mitochondrial cardiomyopathy (Barth syndrome, BTHS) and unaffected healthy controls on cardiac fibroblast (CF) metabolic function. To do this, cell-derived matrices CDMs were generated from BTHS and healthy human pluripotent stem cell-derived CFs (hPSC-CF) and used as cell culture substrates. BTHS CDMs negatively impacted the mitochondrial function of healthy hPSC-CFs while healthy CDMs improved mitochondrial function in BTHS hPSC-CFs. Mass spectrometry comparisons identified 5 matrisome proteins differentially expressed in BTHS compared to healthy CDM. Our results highlight a key role for the ECM in disease through its impact on mitochondrial function.
    Keywords:  Barth syndrome; Cardiac fibroblasts; Cell derived matrices; Extracellular matrix; Mitochondria
    DOI:  https://doi.org/10.1016/j.biomaterials.2024.122922
  58. Pediatr Res. 2024 Nov 07.
    Mitochondrial dysfunction in febrile illness and sepsis: no clear picture yet.
    Tara Sudhadevi, Anantha Harijith.
      
    DOI:  https://doi.org/10.1038/s41390-024-03696-1
  59. Brain. 2024 Nov 12. pii: awae371. [Epub ahead of print]
    HMGCS1 variants cause rigid spine syndrome amenable to mevalonic acid treatment in an animal model.
    Lein N H Dofash, Lee B Miles, Yoshihiko Saito, Eloy Rivas, Vanessa Calcinotto, Sara Oveissi, Rita J Serrano, Rachel Templin, Georg Ramm, Alison Rodger, Joel Haywood, Evan Ingley, Joshua S Clayton, Rhonda L Taylor, Chiara L Folland, David Groth, Daniella H Hock, David A Stroud, Svetlana Gorokhova, Sandra Donkervoort, Carsten G Bönnemann, Malika Sud, Grace E VanNoy, Brian E Mangilog, Lynn Pais, Anne O'Donnell-Luria, Marcos Madruga-Garrido, Marcello Scala, Chiara Fiorillo, Serena Baratto, Monica Traverso, Edoardo Malfatti, Claudio Bruno, Federico Zara, Carmen Paradas, Katsuhisa Ogata, Ichizo Nishino, Nigel G Laing, Robert J Bryson-Richardson, Macarena Cabrera-Serrano, Gianina Ravenscroft.
      Rigid spine syndrome is a rare childhood-onset myopathy characterised by slowly progressive or non-progressive scoliosis, neck and spine contractures, hypotonia, and respiratory insufficiency. Biallelic variants in SELENON account for most cases of rigid spine syndrome, however, the underlying genetic cause in some patients remains unexplained. We used exome and genome sequencing to investigate the genetic basis of rigid spine syndrome in patients without a genetic diagnosis. In five patients from four unrelated families, we identified biallelic variants in HMGCS1 (3-hydroxy-3-methylglutaryl-coenzyme A synthase). These included six missense variants and one frameshift variant distributed throughout HMGCS1. All patients presented with spinal rigidity primarily affecting the cervical and dorsolumbar regions, scoliosis, and respiratory insufficiency. Creatine kinase levels were variably elevated. The clinical course worsened with intercurrent disease or certain drugs in some patients; one patient died from respiratory failure following infection. Muscle biopsies revealed irregularities in oxidative enzyme staining with occasional internal nuclei and rimmed vacuoles. HMGCS1 encodes a critical enzyme of the mevalonate pathway and has not yet been associated with disease. Notably, biallelic hypomorphic variants in downstream enzymes including HMGCR and GGPS1 are associated with muscular dystrophy resembling our cohort's presentation. Analyses of recombinant human HMGCS1 protein and four variants (p.S447P, p.Q29L, p.M70T, p.C268S) showed that all mutants maintained their dimerization state. Three of the four mutants exhibited reduced thermal stability, and two mutants showed subtle changes in enzymatic activity compared to the wildtype. Hmgcs1 mutant zebrafish displayed severe early defects, including immobility at 2 days and death by day 3 post-fertilisation and were rescued by HMGCS1 mRNA. We demonstrate that the four variants tested (S447P, Q29L M70T, and C268S) have reduced function compared to wildtype HMGCS1 in zebrafish rescue assays. Additionally, we demonstrate the potential for mevalonic acid supplementation to reduce phenotypic severity in mutant zebrafish. Overall, our analyses suggest that these missense variants in HMGCS1 act through a hypomorphic mechanism. Here, we report an additional component of the mevalonate pathway associated with disease and suggest biallelic variants in HMGCS1 should be considered in patients presenting with an unresolved rigid spine myopathy phenotype. Additionally, we highlight mevalonoic acid supplementation as a potential treatment for patients with HMGCS1-related disease.
    Keywords:  HMGCS1; enzymopathy; mevalonate pathway; neuromuscular disease; rigid spine myopathy
    DOI:  https://doi.org/10.1093/brain/awae371
  60. Ageing Res Rev. 2024 Nov 10. pii: S1568-1637(24)00395-7. [Epub ahead of print]102 102577
    Mitochondrial dysfunction as a therapeutic strategy for neurodegenerative diseases: Current insights and future directions.
    Ying-Ying Gu, Xin-Ru Zhao, Nan Zhang, Yuan Yang, Ying Yi, Qian-Hang Shao, Ming-Xuan Liu, Xiao-Ling Zhang.
      Neurodegenerative diseases, as common diseases in the elderly, tend to become younger due to environmental changes, social development and other factors. They are mainly characterized by progressive loss or dysfunction of neurons in the central or peripheral nervous system, and common diseases include Parkinson's disease, Alzheimer's disease, Huntington's disease and so on. Mitochondria are important organelles for adenosine triphosphate (ATP) production in the brain. In recent years, a large amount of evidence has shown that mitochondrial dysfunction plays a direct role in neurodegenerative diseases, which is expected to provide new ideas for the treatment of related diseases. This review will summarize the main mechanisms of mitochondrial dysfunction in neurodegenerative diseases, as well as collating recent advances in the study of mitochondrial disorders and new therapies.
    Keywords:  Mitochondrial dynamics; Mitochondrial dysfunction; Mitophagy; Neurodegenerative diseases; Oxidative stress
    DOI:  https://doi.org/10.1016/j.arr.2024.102577
  61. JCI Insight. 2024 Nov 08. pii: e187849. [Epub ahead of print]9(21):
    Enhancing mitochondrial pyruvate metabolism ameliorates ischemic reperfusion injury in the heart.
    Joseph R Visker, Ahmad A Cluntun, Jesse N Velasco-Silva, David R Eberhardt, Luis Cedeño-Rosario, Thirupura S Shankar, Rana Hamouche, Jing Ling, Hyoin Kwak, J Yanni Hillas, Ian Aist, Eleni Tseliou, Sutip Navankasattusas, Dipayan Chaudhuri, Gregory S Ducker, Stavros G Drakos, Jared Rutter.
      
    DOI:  https://doi.org/10.1172/jci.insight.187849
  62. Commun Biol. 2024 Nov 11. 7(1): 1486
    N-terminal cleavage of cyclophilin D boosts its ability to bind F-ATP synthase.
    Gabriele Coluccino, Alessandro Negro, Antonio Filippi, Camilla Bean, Valentina Pia Muraca, Clarissa Gissi, Diana Canetti, Maria Chiara Mimmi, Elisa Zamprogno, Francesco Ciscato, Laura Acquasaliente, Vincenzo De Filippis, Marina Comelli, Michela Carraro, Andrea Rasola, Christoph Gerle, Paolo Bernardi, Alessandra Corazza, Giovanna Lippe.
      Cyclophilin (CyP) D is a regulator of the mitochondrial F-ATP synthase. Here we report the discovery of a form of CyPD lacking the first 10 (mouse) or 13 (human) N-terminal residues (ΔN-CyPD), a protein region with species-specific features. NMR studies on recombinant human full-length CyPD (FL-CyPD) and ΔN-CyPD form revealed that the N-terminus is highly flexible, in contrast with the rigid globular part. We have studied the interactions of FL and ΔN-CyPD with F-ATP synthase at the OSCP subunit, a site where CyPD binding inhibits catalysis and favors the transition of the enzyme complex to the permeability transition pore. At variance from FL-CyPD, ΔN-CyPD binds OSCP in saline media, indicating that the N-terminus substantially decreases the binding affinity for OSCP. We also provide evidence that calpain 1 is responsible for generation of ΔN-CyPD in cells. Altogether, our work suggests the existence of a novel mechanism of modulation of CyPD through cleavage of its N-terminus that may have significant pathophysiological implications.
    DOI:  https://doi.org/10.1038/s42003-024-07172-8
  63. Methods Mol Biol. 2025 ;2878 117-131
    Mitochondrial Membrane Potential (ΔΨ) Fluctuations Associated with the Metabolic States of Mitochondria.
    Ivo F Machado, Raul G Miranda, João S Teodoro, Daniel J Dorta, Anabela P Rolo, Carlos M Palmeira.
      The proton electrochemical gradient generated by the respiratory chain activity accounts for over 90% of the available respiratory energy and, as such, its evaluation and accurate measurement regarding total values and fluctuations are an invaluable component of the understanding of mitochondrial function. Consequently, alterations in electric potential across the inner mitochondrial membrane generated by differential protonic accumulation and transport are known as the mitochondrial membrane potential, or Δψ, and are reflective of the functional metabolic status of mitochondria. There are several experimental approaches to measure Δψ, ranging from fluorometric evaluations to electrochemical probes. In this chapter, we describe how Δψ may be evaluated in isolated mitochondria and live cells using electrochemical and fluorescent methods, such as tetraphenylphosphonium (TPP+) and tetramethylrhodamine methyl ester (TMRM), respectively. These methods are dependent on the accumulation of cationic probes within mitochondria, which are assessed by using a TPP+-selective electrode or instruments that measure fluorescence (microplate reader and flow cytometer).
    Keywords:  Flow cytometry; Membrane potential; Metabolic states; Mitochondria; TMRM; TPP+-selective electrode
    DOI:  https://doi.org/10.1007/978-1-0716-4264-1_7
  64. Proc Natl Acad Sci U S A. 2024 Nov 19. 121(47): e2410996121
    Cell type-specific gene therapy confers protection against motor neuron disease caused by a TFG variant.
    Molly M Lettman, Caitlin A Mendina, Emma Burkard, James R Alvin, Yunyun Zhu, Joshua J Coon, Anjon Audhya.
      Inherited forms of motor neuron disease (MND), including hereditary spastic paraplegias (HSP), are associated with the death or dysfunction of nerve cells that control skeletal muscle activity. However, in some cases, the impacts of genetic variants underlying MND act in a non-cell autonomous manner, instead affecting the function of other cell types necessary for neuronal maintenance. Pathological mutations in TFG, which have been implicated in HSP, lead to axonopathy within the corticospinal tract, but it remains unclear whether this problem arises due to perturbations within neurons or supporting neuroglia. To address this question, we leveraged a rat model harboring the recessive TFG p.R106C mutation (mRATBN7.2, g.11:43897639C>T, c.316C>T), which recapitulates multiple phenotypes associated with HSP in humans, including progressive motor deficits, leg spasticity, and indications of an inflammatory response within the motor cortex. In particular, we took advantage of cell type-specific gene therapies to demonstrate that the reintroduction of wild-type TFG into synapsin 1-positive neurons provides robust protection against MND, whereas its expression in GFAP-positive glial cells provides no significant improvement in quantitative measures of gait, despite a dramatic reduction in the presence of reactive astrocytes throughout the brain. These data strongly suggest that therapeutic approaches targeting neurons should be pursued in cases of TFG-HSP, with our animal model offering a unique platform for preclinical assessment.
    Keywords:  SYN1; neurodegeneration; neuroinflammation; spastic paraparesis
    DOI:  https://doi.org/10.1073/pnas.2410996121
  65. Autophagy. 2024 Nov 08.
    PINK1-deficiency facilitates mitochondrial iron accumulation and colon tumorigenesis.
    Mariella Arcos, Lavanya Goodla, Hyeoncheol Kim, Sharina P Desai, Rui Liu, Kunlun Yin, Zhaoli Liu, David R Martin, Xiang Xue.
      Mitophagy, the process by which cells eliminate damaged mitochondria, is mediated by PINK1 (PTEN induced kinase 1). Our recent research indicates that PINK1 functions as a tumor suppressor in colorectal cancer by regulating cellular metabolism. Interestingly, PINK1 ablation activated the NLRP3 (NLR family pyrin domain containing 3) inflammasome, releasing IL1B (interleukin 1 beta). However, inhibiting the NLRP3-IL1B signaling pathway with an IL1R (interleukin 1 receptor) antagonist or NLRP3 inhibitor did not hinder colon tumor growth after PINK1 loss. To identify druggable targets in PINK1-deficient tumors, ribonucleic acid sequencing analysis was performed on colon tumors from pink1 knockout and wild-type mice. Gene Set Enrichment Analysis highlighted the enrichment of iron ion transmembrane transporter activity. Subsequent qualitative polymerase chain reaction and western blot analysis revealed an increase in mitochondrial iron transporters, including mitochondrial calcium uniporter, in PINK1-deficient colon tumor cells and tissues. Live-cell iron staining demonstrated elevated cellular and mitochondrial iron levels in PINK1-deficient cells. Clinically used drugs deferiprone and minocycline reduced mitochondrial iron and superoxide levels, resulting in decreased colon tumor cell growth in vitro and in vivo. Manipulating the mitochondrial iron uptake protein MCU (mitochondrial calcium uniporter) also affected cell and xenograft tumor growth. This study suggests that therapies aimed at reducing mitochondrial iron levels may effectively inhibit colon tumor growth, particularly in patients with low PINK1 expression.
    Keywords:  Colorectal cancer; deferiprone; iron chelation; minocycline; mitochondrial iron; mitophagy
    DOI:  https://doi.org/10.1080/15548627.2024.2425594
  66. Methods Mol Biol. 2025 ;2878 1-34
    Evaluation of Respiration with a Clark-Type Electrode in Isolated Mitochondria, Intact and Permeabilized Cells, and Explants from Animal Tissues.
    Ana M Silva, Paulo J Oliveira.
      Evaluation of mitochondrial function in aerobic cells is crucial for understanding the conditions that can potentially compromise their physiology. From the fields of Toxicology to Oncology, various approaches involving freshly isolated fractions of mitochondria, permeabilized cells, intact cells, or animal tissues have been employed to investigate metabolism through oxygen consumption.Several techniques are available for measuring oxygen consumption in liquids. These include polarography with oxygen electrodes, which can employ chemical, electrochemical, or optical detection methods, as well as the use of fluorescent or luminescent probes. In this chapter, we will review the concepts previously discussed in earlier editions, focusing on Clark-type electrodes for electrochemical detection. Additionally, we will explore other approaches that involve intact cells and tissue explants with minimal plasmatic membrane alterations. These techniques provide an integrated view of Glycolysis, Krebs Cycle and Oxidative Phosphorylation. Despite being a classical and cost-effective system, this elegant technique continues to amaze us with its versatility and generation of reliable data.
    Keywords:  Basal respiration; Clark-type electrode; Intact cells; Mitochondria; Mitochondrial respiratory chain; Oxygen consumption rate; Permeabilized cells; Respirometry; Tissue explants
    DOI:  https://doi.org/10.1007/978-1-0716-4264-1_1
  67. Nat Genet. 2024 Nov;56(11): 2283
    Improving reporting standards for genetic variants.
      
    DOI:  https://doi.org/10.1038/s41588-024-02002-3
  68. BMC Biol. 2024 Nov 14. 22(1): 258
    Unveiling tryptophan dynamics and functions across model organisms via quantitative imaging.
    Kui Wang, Tian-Lun Chen, Xin-Xin Zhang, Jian-Bin Cao, Pengcheng Wang, Mingcang Wang, Jiu-Lin Du, Yu Mu, Rongkun Tao.
       BACKGROUND: Tryptophan is an essential amino acid involved in critical cellular processes in vertebrates, serving as a precursor for serotonin and kynurenine, which are key neuromodulators to influence neural and immune functions. Systematic and quantitative measurement of tryptophan is vital to understanding these processes.
    RESULTS: Here, we utilized a robust and highly responsive green ratiometric indicator for tryptophan (GRIT) to quantitatively measure tryptophan dynamics in bacteria, mitochondria of mammalian cell cultures, human serum, and intact zebrafish. At the cellular scale, these quantitative analyses uncovered differences in tryptophan dynamics across cell types and organelles. At the whole-organism scale, we revealed that inflammation-induced tryptophan concentration increases in zebrafish brain led to elevated serotonin and kynurenine levels, prolonged sleep duration, suggesting a novel metabolic connection between immune response and behavior. Moreover, GRIT's application in detecting reduced serum tryptophan levels in patients with inflammation symptoms suggests its potential as a high-throughput diagnostic tool.
    CONCLUSIONS: In summary, this study introduces GRIT as a powerful method for studying tryptophan metabolism and its broader physiological implications, paving the way for new insights into the metabolic regulation of health and disease across multiple biological scales.
    Keywords:  Bacteria; Human serum; Mitochondria; Tryptophan quantitative imaging; Zebrafish
    DOI:  https://doi.org/10.1186/s12915-024-02058-x
  69. Nat Rev Drug Discov. 2024 Nov 15.
    FDA approves L-amino acid decarboxylase deficiency gene therapy.
    Asher Mullard.
      
    DOI:  https://doi.org/10.1038/d41573-024-00184-3
  70. Biomed J. 2024 Nov 07. pii: S2319-4170(24)00109-4. [Epub ahead of print] 100806
    Mitochondrial Bioenergetics Deficiency in cisd-1 Mutants is Linked to AMPK-Mediated Lipid Metabolism.
    Kuei-Ching Hsiung, Hsiang-Yu Tang, Mei-Ling Cheng, Li-Man Hung, Bertrand Chin-Ming Tan, Szecheng J Lo.
       BACKGROUND: CISD-1 is a mitochondrial iron-sulfate [2Fe-2S] protein known to be associated with various human diseases, including cancer and diabetes. Previously, we demonstrated that CISD-1 deficiency in worms lowers glucose and ATP levels. In this study, we further explored how worms compensate for lower ATP levels by analyzing changes in cytoplasmic and mitochondrial iron content, AMPK activities, and total lipid profiles.
    MATERIALS AND METHODS: Expression levels of CISD-1 and CISD-1::GFP fusion proteins in wild-type worms (N2), cisd-1-deletion mutants (tm4993 and syb923) and GFP insertion transgenic worms (PHX953 and SJL40) were examined by western blot. Fluorescence microscopy analyzed CISD-1::GFP pattern in PHX953 embryos and adults, and lipid droplet sizes in N2, cisd-1, aak-2 and aak-2;cisd-1 worms. Total and mitochondrial iron content, electron transport complex profiles, and AMPK activity were investigated in tm4993 and syb923 mutants. mRNA levels of mitochondrial β-oxidation genes, acs-2, cpt-5, and ech-1, were quantified by RT-qPCR in various genetic worm strains. Lipidomic analyses were performed in N2 and cisd-1(tm4993) worms.
    RESULTS: Defects in cisd-1 lead to an imbalance in iron transport and cause proton leak, resulting in lower ATP production by interrupting the mitochondrial electron transport chain. We identified a signaling pathway that links ATP deficiency-induced AMPK (AMP activated protein kinase) activation to the expression of genes that facilitate lipolysis via β-oxidation.
    CONCLUSION: Our data provide a functional coordination between CISD-1 and AMPK constitutes a mitochondrial bioenergetics quality control mechanism that provides compensatory energy resources.
    Keywords:  AMPK; C. elegans; iron-sulfate containing protein; lipid droplet size; lipidomic; mitochondria outer membrane protein
    DOI:  https://doi.org/10.1016/j.bj.2024.100806
  71. J Neuroophthalmol. 2024 Nov 11.
    Late-Onset Mitochondrial Neurogastrointestinal Encephalopathy Presenting With Isolated Ophthalmic Findings.
    Angelica Hanna, Edsel B Ing, Arun N Sundaram, Vera Bril, Rahul A Sharma.
      
    DOI:  https://doi.org/10.1097/WNO.0000000000002287
  72. Aging Cell. 2024 Nov 14. e14400
    Targeting NAMPT-OPA1 for treatment of senile osteoporosis.
    Chao-Wen Bai, Bo Tian, Ming-Chao Zhang, Qin Qin, Xin Shi, Xi Yang, Xiang Gao, Xiao-Zhong Zhou, Hua-Jian Shan, Jin-Yu Bai.
      Senescence of bone marrow mesenchymal stem cells (BMSCs) impairs their stemness and osteogenic differentiation, which is the principal cause of senile osteoporosis (SOP). Imbalances in nicotinamide phosphoribosyltransferase (NAMPT) homeostasis have been linked to aging and various diseases. Herein, reduction of NAMPT and impaired osteogenesis were observed in BMSCs from aged human and mouse. Knockdown of Nampt in BMSCs promotes lipogenic differentiation and increases age-related bone loss. Overexpression of Nampt ameliorates the senescence-associated (SA) phenotypes in BMSCs derived from aged mice, as well as promoting osteogenic potential. Mechanistically, NAMPT inhibits BMSCs senescence by facilitating OPA1 expression, which is essential for mitochondrial dynamics. The defect of NAMPT reduced mitochondrial membrane potential, interfered with mitochondrial fusion，and increased SA protein and phenotypes. More importantly, we have confirmed that P7C3, the NAMPT activator, is a novel strategy for reducing SOP bone loss. P7C3 treatment significantly prevents BMSCs senescence by improving mitochondrial function through the NAMPT-OPA1 signaling axis. Taken together, these results reveal that NAMPT is a regulator of BMSCs senescence and osteogenic differentiation. P7C3 is a novel molecule drug to prevent the pathological progression of SOP.
    Keywords:  NAMPT; Optic atrophy protein 1; cellular senescence; mesenchymal stem cell; mitochondrial function
    DOI:  https://doi.org/10.1111/acel.14400
  73. Nat Commun. 2024 Nov 07. 15(1): 9173
    Engineered PsCas9 enables therapeutic genome editing in mouse liver with lipid nanoparticles.
    Dmitrii Degtev, Jack Bravo, Aikaterini Emmanouilidi, Aleksandar Zdravković, Oi Kuan Choong, Julia Liz Touza, Niklas Selfjord, Isabel Weisheit, Margherita Francescatto, Pinar Akcakaya, Michelle Porritt, Marcello Maresca, David Taylor, Grzegorz Sienski.
      Clinical implementation of therapeutic genome editing relies on efficient in vivo delivery and the safety of CRISPR-Cas tools. Previously, we identified PsCas9 as a Type II-B family enzyme capable of editing mouse liver genome upon adenoviral delivery without detectable off-targets and reduced chromosomal translocations. Yet, its efficacy remains insufficient with non-viral delivery, a common challenge for many Cas9 orthologues. Here, we sought to redesign PsCas9 for in vivo editing using lipid nanoparticles. We solve the PsCas9 ribonucleoprotein structure with cryo-EM and characterize it biochemically, providing a basis for its rational engineering. Screening over numerous guide RNA and protein variants lead us to develop engineered PsCas9 (ePsCas9) with up to 20-fold increased activity across various targets and preserved safety advantages. We apply the same design principles to boost the activity of FnCas9, an enzyme phylogenetically relevant to PsCas9. Remarkably, a single administration of mRNA encoding ePsCas9 and its guide formulated with lipid nanoparticles results in high levels of editing in the Pcsk9 gene in mouse liver, a clinically relevant target for hypercholesterolemia treatment. Collectively, our findings introduce ePsCas9 as a highly efficient, and precise tool for therapeutic genome editing, in addition to the engineering strategy applicable to other Cas9 orthologues.
    DOI:  https://doi.org/10.1038/s41467-024-53418-8
  74. Nat Commun. 2024 Nov 07. 15(1): 9646
    SSEmb: A joint embedding of protein sequence and structure enables robust variant effect predictions.
    Lasse M Blaabjerg, Nicolas Jonsson, Wouter Boomsma, Amelie Stein, Kresten Lindorff-Larsen.
      The ability to predict how amino acid changes affect proteins has a wide range of applications including in disease variant classification and protein engineering. Many existing methods focus on learning from patterns found in either protein sequences or protein structures. Here, we present a method for integrating information from sequence and structure in a single model that we term SSEmb (Sequence Structure Embedding). SSEmb combines a graph representation for the protein structure with a transformer model for processing multiple sequence alignments. We show that by integrating both types of information we obtain a variant effect prediction model that is robust when sequence information is scarce. We also show that SSEmb learns embeddings of the sequence and structure that are useful for other downstream tasks such as to predict protein-protein binding sites. We envisage that SSEmb may be useful both for variant effect predictions and as a representation for learning to predict protein properties that depend on sequence and structure.
    DOI:  https://doi.org/10.1038/s41467-024-53982-z
  75. Pediatr Neurol. 2024 Sep 18. pii: S0887-8994(24)00338-2. [Epub ahead of print]162 32-39
    Biallelic Variants in LIPT2 as a Cause of Infantile-Onset Dystonia: Expanding the Clinical and Molecular Spectrum.
    Kuntal Sen, Alonso Zea Vera, Anna Puronurmi, Andrea Gropman, Parith Wongkittichote, Rebecca Ganetzky, Kaija Autio, Alexander Kastaniotis.
       BACKGROUND: Lipoyl transferase 2 is involved in the biosynthesis of lipoate. Lipoate is the cofactor for the glycine cleavage system and four dehydrogenase enzymes. Biallelic variants in LIPT2 causing severe neonatal encephalopathy was first described in 2017.
    METHODS: Clinical data were collected by retrospective chart review after obtaining consent from parents. The pathogenicity of these variants was further delineated using a yeast model. The YEp352-LIPT2 plasmid was used as a template to generate the two patient variants using QuickChange Lightning Site-Directed Mutagenesis Kit.
    RESULTS: The patient was a 15-month-old female who presented at one month with dystonia, developmental delay, and feeding difficulties. Brain magnetic resonance imaging showed cortical malformations including colpocephaly, polymicrogyria, and heterotopia. Patient had elevations in lactate (6.1 mmol/L) and glycine. Exome sequencing showed two variants of uncertain significance in trans in the LIPT2 gene: c.346 G>T and c.418C>T. Patient was started on lipoic acid, thiamine, and COQ10. Yeast complementation experiments indicate that both patient mutant variants result in diminished function versions of the LIPT2 protein.
    CONCLUSION: We report the fourth case of LIPT2-related disorder. Proband shared significant overlap with previous patients; however, there was a distinct movement disorder and brain malformations, which have not been previously described. Unlike most neurometabolic disorders where dystonia develops later after metabolic stroke in basal ganglia, LIPT2-related disorder seems unique due to early onset of dystonia due to energy deficit in the developing brain. Lipoic acid supplementation has not led to significant clinical improvement. Analyses in yeast indicate that novel variants are deleterious but have retained some functionality.
    Keywords:  Dystonia; LIPT2; Lipoic acid biosynthesis disorder; Mitochondrial disorder
    DOI:  https://doi.org/10.1016/j.pediatrneurol.2024.09.013
  76. Front Mol Biosci. 2024 ;11 1480617
    The function of nicotinamide phosphoribosyl transferase (NAMPT) and its role in diseases.
    Aihong Peng, Junqin Li, Jianxiao Xing, Yuanjun Yao, Xuping Niu, Kaiming Zhang.
      Nicotinamide phosphoribosyl transferase (NAMPT) is a rate-limiting enzyme in the mammalian nicotinamide adenine dinucleotide (NAD) salvage pathway, and plays a vital role in the regulation of cell metabolic activity, reprogramming, aging and apoptosis. NAMPT synthesizes nicotinamide mononucleotide (NMN) through enzymatic action, which is a key protein involved in host defense mechanism and plays an important role in metabolic homeostasis and cell survival. NAMPT is involved in NAD metabolism and maintains intracellular NAD levels. Sirtuins (SIRTs) are a family of nicotinamide adenine dinucleotide (NAD)-dependent histone deacetylases (HDACs), the members are capable of sensing cellular NAD+ levels. NAMPT-NAD and SIRT constitute a powerful anti-stress defense system. In this paper, the structure, biological function and correlation with diseases of NAMPT are introduced, aiming to provide new ideas for the targeted therapy of related diseases.
    Keywords:  NAD metabolism; NAMPT; SIRTs; biological function; diseases
    DOI:  https://doi.org/10.3389/fmolb.2024.1480617
  77. Diabet Med. 2024 Nov 07. e15471
    A homozygous TARS2 variant is a novel cause of syndromic neonatal diabetes.
    Russell Donis, Kashyap A Patel, Matthew N Wakeling, Matthew B Johnson, Masha M Amoli, Melek Yildiz, Teoman Akçay, Irani Aspi, James Yong, Hanieh Yaghootkar, Michael N Weedon, Andrew T Hattersley, Sarah E Flanagan, Elisa De Franco.
       AIMS: Neonatal diabetes is a monogenic condition which can be the presenting feature of complex syndromes. The aim of this study was to identify novel genetic causes of neonatal diabetes with neurological features including developmental delay and epilepsy.
    METHODS: We performed genome sequencing in 27 individuals with neonatal diabetes plus epilepsy and/or developmental delay of unknown genetic cause. Replication studies were performed in 123 individuals with diabetes diagnosed aged ≤1 year without a known genetic cause using targeted next-generation sequencing.
    RESULTS: Three individuals, all diagnosed with diabetes in the first week of life, shared a rare homozygous missense variant, p.(Arg327Gln), in TARS2. Replication studies identified the same homozygous variant in a fourth individual diagnosed with diabetes at 1 year. One proband had epilepsy, one had development delay and two had both. Biallelic TARS2 variants cause a mitochondrial encephalopathy (COXPD-21) characterised by severe hypotonia, epilepsy and developmental delay. Diabetes is not a known feature of COXPD-21. Current evidence suggests that the p.(Arg327Gln) variant disrupts TARS2's regulation of the mTORC1 pathway which is essential for β-cells.
    CONCLUSIONS: Our findings establish the homozygous p.(Arg327Gln) TARS2 variant as a novel cause of syndromic neonatal diabetes and uncover a role for TARS2 in pancreatic β-cells.
    Keywords:  diabetes; genetic discovery; mitochondrial disease; mitochondrial dysfunction; monogenic diabetes; neonatal diabetes; β‐cells
    DOI:  https://doi.org/10.1111/dme.15471
  78. Molecules. 2024 Oct 31. pii: 5154. [Epub ahead of print]29(21):
    Modulatory Effect of Nicotinamide Adenine Dinucleotide Phosphate (NADPH) on the 2-Oxoglutarate Mitochondrial Carrier.
    Anna Spagnoletta, Daniela Valeria Miniero, Nicola Gambacorta, Francesca Oppedisano, Anna De Grassi, Orazio Nicolotti, Ciro Leonardo Pierri, Annalisa De Palma.
      The 2-oxoglutarate carrier (OGC), pivotal in cellular metabolism, facilitates the exchange of key metabolites between mitochondria and cytosol. This study explores the influence of NADPH on OGC transport activity using proteoliposomes. Experimental data revealed the ability of NADPH to modulate the OGC activity, with a significant increase of 60% at 0.010 mM. Kinetic analysis showed increased Vmax and a reduction in Km for 2-oxoglutarate, suggesting a direct regulatory role. Molecular docking pointed to a specific interaction between NADPH and cytosolic loops of OGC, involving key residues such as K206 and K122. This modulation was unique in mammalian OGC, as no similar effect was observed in a plant OGC structurally/functionally related mitochondrial carrier. These findings propose OGC as a responsive sensor for the mitochondrial redox state, coordinating with the malate/aspartate and isocitrate/oxoglutarate shuttles to maintain redox balance. The results underscore the potential role of OGC in redox homeostasis and its broader implications in cellular metabolism and oxidative stress responses.
    Keywords:  NADPH regulation; isocitrate/oxoglutarate shuttle; kinetic analysis; malate/aspartate shuttle; mitochondrial function; mitochondrial transport; molecular docking; oxoglutarate carrier
    DOI:  https://doi.org/10.3390/molecules29215154
  79. J Cereb Blood Flow Metab. 2024 Nov 14. 271678X241300223
    Molecular and cellular mechanisms of mitochondria transfer in models of central nervous system disease.
    Takafumi Nakano, Keiichi Irie, Koichi Matsuo, Kenichi Mishima, Yoshihiko Nakamura.
      In the central nervous system (CNS), neuronal function and dysfunction are critically dependent on mitochondrial integrity and activity. In damaged or diseased brains, mitochondrial dysfunction reduces adenosine triphosphate (ATP) levels and impairs ATP-dependent neural firing and neurotransmitter dynamics. Restoring mitochondrial capacity to generate ATP may be fundamental in restoring neuronal function. Recent studies in animals and humans have demonstrated that endogenous mitochondria may be released into the extracellular environment and transported or exchanged between cells in the CNS. Under pathological conditions in the CNS, intercellular mitochondria transfer contributes to new classes of signaling and multifunctional cellular activities, thereby triggering deleterious effects or promoting beneficial responses. Therefore, to take full advantage of the beneficial effects of mitochondria, it may be useful to transplant healthy and viable mitochondria into damaged tissues. In this review, we describe recent findings on the mechanisms of mitochondria transfer and provide an overview of experimental methodologies, including tissue sourcing, mitochondrial isolation, storage, and modification, aimed at optimizing mitochondria transplantation therapy for CNS disorders. Additionally, we examine the clinical relevance and potential strategies for the therapeutic application of mitochondria transplantation.
    Keywords:  Central nervous system; experimental disease models; mitochondria transplantation; therapeutic strategies; transfer mechanism
    DOI:  https://doi.org/10.1177/0271678X241300223
  80. Nature. 2024 Nov;635(8038): 511-513
    Circular logic: understanding RNA's strangest form yet.
    Amber Dance.
      
    Keywords:  Genetics; Molecular biology; Technology; Transcriptomics
    DOI:  https://doi.org/10.1038/d41586-024-03683-w
  81. Nat Commun. 2024 Nov 08. 15(1): 9681
    A proteolytic AAA+ machine poised to unfold protein substrates.
    Alireza Ghanbarpour, Robert T Sauer, Joseph H Davis.
      AAA+ proteolytic machines unfold proteins before degrading them. Here, we present cryoEM structures of ClpXP-substrate complexes that reveal a postulated but heretofore unseen intermediate in substrate unfolding/degradation. A ClpX hexamer draws natively folded substrates tightly against its axial channel via interactions with a fused C-terminal degron tail and ClpX-RKH loops that flexibly conform to the globular substrate. The specific ClpX-substrate contacts observed vary depending on the substrate degron and affinity tags, helping to explain ClpXP's ability to unfold/degrade a wide array of different cellular substrates. Some ClpX contacts with native substrates are enabled by upward movement of the seam subunit in the AAA+ spiral, a motion coupled to a rearrangement of contacts between the ClpX unfoldase and ClpP peptidase. Our structures additionally highlight ClpX's ability to translocate a diverse array of substrate topologies, including the co-translocation of two polypeptide chains.
    DOI:  https://doi.org/10.1038/s41467-024-53681-9
  82. Methods Mol Biol. 2025 ;2866 45-57
    Targeted Next-Generation Sequencing in Rare Diseases.
    Aleša Kristan, Nataša Debeljak.
      Targeted next-generation sequencing (NGS) in rare disease focuses on genetic analysis of specific regions in genome that are linked to a rare disease. In addition to library preparation, sequencing, and data analysis, targeted NGS includes an additional step of target enrichment of selected genes and regions. It allows for more sensitive and profound sequencing, as it is a fast and cost-effective approach with less data burden and is therefore often a method of choice for identifying rare variants in known genes, especially in diagnostics of rare diseases. Several in silico tools address the pathogenicity predictions of rare variants of unknown significance (VUS) and can therefore facilitate clinical interpretation.
    Keywords:  Data analysis; Disease-specific DNA probes; Hybridization capture; Library preparation; Pathogenicity prediction; Sequencing; Targeted enrichment
    DOI:  https://doi.org/10.1007/978-1-0716-4192-7_3
  83. Nucleic Acids Res. 2024 Nov 12. pii: gkae996. [Epub ahead of print]
    Transfer RNA supplementation rescues HARS deficiency in a humanized yeast model of Charcot-Marie-Tooth disease.
    Sarah D P Wilhelm, Jenica H Kakadia, Aruun Beharry, Rosan Kenana, Kyle S Hoffman, Patrick O'Donoghue, Ilka U Heinemann.
      Aminoacyl-tRNA synthetases are indispensable enzymes in all cells, ensuring the correct pairing of amino acids to their cognate tRNAs to maintain translation fidelity. Autosomal dominant mutations V133F and Y330C in histidyl-tRNA synthetase (HARS) cause the genetic disorder Charcot-Marie-Tooth type 2W (CMT2W). Treatments are currently restricted to symptom relief, with no therapeutic available that targets the cause of disease. We previously found that histidine supplementation alleviated phenotypic defects in a humanized yeast model of CMT2W caused by HARS V155G and S356N that also unexpectedly exacerbated the phenotype of the two HARS mutants V133F and Y330C. Here, we show that V133F destabilizes recombinant HARS protein, which is rescued in the presence of tRNAHis. HARS V133F and Y330C cause mistranslation and cause changes to the proteome without activating the integrated stress response as validated by mass spectrometry and growth defects that persist with histidine supplementation. The growth defects and reduced translation fidelity caused by V133F and Y330C mutants were rescued by supplementation with human tRNAHis in a humanized yeast model. Our results demonstrate the feasibility of cognate tRNA as a therapeutic that rescues HARS deficiency and ameliorates toxic mistranslation generated by causative alleles for CMT.
    DOI:  https://doi.org/10.1093/nar/gkae996
  84. iScience. 2024 Nov 15. 27(11): 111158
    The node of Ranvier influences the in vivo axonal transport of mitochondria and signaling endosomes.
    Andrew P Tosolini, Federico Abatecola, Samuele Negro, James N Sleigh, Giampietro Schiavo.
      Efficient long-range axonal transport is essential for maintaining neuronal function, and perturbations in this process underlie severe neurological diseases. Nodes of Ranvier (NoR) are short, specialized unmyelinated axonal domains with a unique molecular and structural composition. Currently, it remains unresolved how the distinct molecular structures of the NoR impact axonal transport dynamics. Using intravital time-lapse microscopy of sciatic nerves in live, anesthetized mice, we reveal (1) similar morphologies of the NoR in fast and slow motor axons, (2) signaling endosomes and mitochondria accumulate specifically at the distal node, and (3) unique axonal transport profiles of signaling endosomes and mitochondria transiting through the NoR. Collectively, these findings provide important insights into the fundamental physiology of peripheral nerve axons, motor neuron subtypes, and diverse organelle dynamics at the NoR. Furthermore, this work has relevance for several pathologies affecting peripheral nerves and the NoR.
    Keywords:  Cellular neuroscience; Molecular neuroscience
    DOI:  https://doi.org/10.1016/j.isci.2024.111158
  85. Orphanet J Rare Dis. 2024 Nov 14. 19(1): 427
    A review of multiple diagnostic approaches in the undiagnosed diseases network to identify inherited metabolic diseases.
    Undiagnosed Diseases Network
       BACKGROUND: The number of known inherited metabolic diseases (IMDs) has been expanding, and the rate of diagnosis is improving with the development of innovative approaches including next generation sequencing (NGS). However, a substantial proportion of IMDs remain undetected by traditional diagnostic approaches. We aim to highlight the spectrum of IMDs diagnosed by the Undiagnosed Diseases Network (UDN) and to learn from the UDN diagnostic processes that were able to detect IMDs.
    METHODS: We conducted a retrospective analysis of 757 UDN participants diagnosed from 2015 until 2023 using the cohort database, which were divided into a cohort with IMDs (n = 194; 27%) and a cohort whose phenotypes were not explained by an IMD (n = 563; 73%), based on the International Classification of Inherited Metabolic Disorders (ICIMD). Then, we divided the causes of the metabolic 194 diagnoses into seven groups that included all the ICIMD categories. We inspected which clinical and laboratory approaches contributed to a final UDN diagnosis. We also present a UDN case example from each group to highlight the diagnostic yields that resulted from combining newer diagnostic approaches in the UDN and illustrate potential pitfalls of current NGS methods.
    RESULTS: These 194 cases of IMDs included examples from 21/25 (84%) of the ICIMD categories. Of the UDN subjects 164/194 (85%) were diagnosed with IMDs through NGS.
    CONCLUSION: The spectrum of IMDs detected in the UDN cohort is large and growing and appropriate use of newer multiple diagnostic approaches should further increase diagnosis of IMDs that are presently missed by the traditional laboratory screening methods.
    Keywords:  Inherited metabolic diseases (IMDs); Next generation sequencing (NGS); Undiagnosed Diseases Network (UDN)
    DOI:  https://doi.org/10.1186/s13023-024-03423-3
  86. BMJ Case Rep. 2024 Nov 11. pii: e260799. [Epub ahead of print]17(11):
    Barth syndrome: a rare cause of cardiomyopathy in neonates.
    Neha Dalal, Kirti Naranje, Amita Moriangthem, Anita Singh.
      Barth syndrome (BTHS) is one of the rare X linked recessive diseases that appear in infancy with a triad of myocardial and skeletal muscle diseases, neutropenia and growth retardation. The pathogenic variant of TAFAZZIN gene leads to BTHS, which encodes the TAFAZZIN protein of the inner membrane of the mitochondria, a phosphatidyltransferase involved in cardiolipin remodelling and functional maturation. We present a case of a neonate presenting with early-onset cardiomyopathy, neutropenia and failure to thrive with no family history of cardiac diseases. Echocardiography suggested a dilated left ventricle with non-compaction and a low ejection fraction. The baby was managed with diuretics and decongestive measures. Clinical exome sequencing detected a hemizygous novel splice site variant c.541+2 T>C in TAFAZZIN, confirming the diagnosis of BTHS.
    Keywords:  Congenital disorders; Genetics; Mechanical ventilation; Neonatal intensive care
    DOI:  https://doi.org/10.1136/bcr-2024-260799
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