bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2024–12–22
sixty-four papers selected by
Catalina Vasilescu, Helmholz Munich
  1. Mapping mitochondrial aging.
  2. SLMO transfers phosphatidylserine between the outer and inner mitochondrial membrane in Drosophila.
  3. Subcellular NAD+ pools are interconnected and buffered by mitochondrial NAD.
  4. Mechanism and Clinical Application Prospects of Mitochondrial DNA Single Nucleotide Polymorphism in Neurodegenerative Diseases.
  5. Crucial role and conservation of the three [2Fe-2S] clusters in the human mitochondrial ribosome.
  6. Biochemical and neurophysiological effects of deficiency of the mitochondrial import protein TIMM50.
  7. A molecular glue for Prkn/parkin.
  8. Metformin targets mitochondrial complex I to lower blood glucose levels.
  9. A Kinetic Model for Compound Heterozygous Pathogenic Variants in Tyrosyl-tRNA Synthetase Gene YARS2-Associated Neonatal Phenotype.
  10. Neuronal activity inhibits mitochondrial transport only in synaptically connected segments of the axon.
  11. Role of Fatty Acids β-Oxidation in the Metabolic Interactions Between Organs.
  12. Guardians of the cell: mitochondria as a rheostat for cellular NAD+ levels.
  13. Bi-allelic variants in DAP3 result in reduced assembly of the mitoribosomal small subunit with altered apoptosis and a Perrault-syndrome-spectrum phenotype.
  14. Proteolytic regulation of mitochondrial magnesium channel MRS2 by m-AAA protease and prohibitin complex.
  15. Updates on neurologic manifestations of mitochondrial disease.
  16. Exercise as Mitochondrial Medicine: How Does the Exercise Prescription Affect Mitochondrial Adaptations to Training?
  17. Peripheral Neuropathy in Mitochondrial Trifunctional Protein Deficiency due to a Variant in HADHA Gene.
  18. Mitochondria-targeted oligomeric α-synuclein induces TOM40 degradation and mitochondrial dysfunction in Parkinson's disease and parkinsonism-dementia of Guam.
  19. Mitochondrial respiration atlas reveals differential changes in mitochondrial function across sex and age.
  20. Increased mitochondrial mutation heteroplasmy induces aging phenotypes in pluripotent stem cells and their differentiated progeny.
  21. Regulation of SR and mitochondrial Ca2+ signaling by L-type Ca2+ channels and Na/Ca exchanger in hiPSC-CMs.
  22. Inter- and intracellular mitochondrial communication: signaling hubs in aging and age-related diseases.
  23. Rhabdomyolysis in a Patient With a Possible Mitochondrial Pathogenic Variant in the Peri-operative Period: A Case Report.
  24. Measurement of Lipid Transport in Mitochondria by the MTL Complex.
  25. Metaxin-2 tunes mitochondrial transportation and neuronal function in Drosophila.
  26. Label-Free Visualization and Segmentation of Endothelial Cell Mitochondria Using Holotomographic Microscopy and U-Net.
  27. The Utility of Long-Read Sequencing in Diagnosing Early Onset Parkinson's Disease.
  28. NDUFAF5 variants cause early onset Leigh syndrome.
  29. Aged neurons don't register energy need.
  30. Transfer RNA and small molecule therapeutics for aminoacyl-tRNA synthetase diseases.
  31. Mitochondrial Dynamics in Brain Cells During Normal and Pathological Aging.
  32. UniVar: A variant interpretation platform enhancing rare disease diagnosis through robust filtering and unified analysis of SNV, INDEL, CNV and SV.
  33. Mitochondrial metabolism and epigenetic crosstalk drive the SASP.
  34. Meeting metformin again for the first time.
  35. Aging promotes an increase in mitochondrial fragmentation in astrocytes.
  36. Ultrastructural Analysis Reveals Mitochondrial Placement Independent of Synapse Placement in Fine Caliber C. elegans Neurons.
  37. Human mitochondrial RNA polymerase structures reveal transcription start-site and slippage mechanism.
  38. NAD+ Boosting Strategies.
  39. Clinical trials in Leber hereditary optic neuropathy: outcomes and opportunities.
  40. Renal phenotyping in a hypomorphic murine model of propionic aciduria reveals common pathomechanisms in organic acidurias.
  41. In-Gel Activity Assay of Mammalian Mitochondrial and Cytosolic Aconitases, Surrogate Markers of Compartment-Specific Oxidative Stress and Iron Status.
  42. A Commentary on Mitochondrial Dysfunction and Compromised DNA Repair in Neurodegeneration: The Emerging Role of FUS in ALS.
  43. Phosphatase activity-based PPM1K: a key player in the regulation of mitochondrial function and its multifaceted impact in diseases.
  44. Endogenous interactomes of MFN1 and MFN2 provide novel insights into interorganelle communication and autophagy.
  45. Targeting mitochondrial fitness for cardioprotection.
  46. Boosting neuronal activity-driven mitochondrial DNA transcription improves cognition in aged mice.
  47. Dynamic mitophagy trajectories hallmark brain aging.
  48. Intramolecular feedback regulation of the LRRK2 Roc G domain by a LRRK2 kinase-dependent mechanism.
  49. Novel PNPLA8 variants associated with primary ovarian insufficiency, tremors, cerebellar ataxia and limb weakness: a case report and literature review.
  50. Epigenome-wide Association Analysis of Mitochondrial Heteroplasmy Provides Insight into Molecular Mechanisms of Disease.
  51. Exome and Genome Sequencing to Diagnose the Genetic Basis of Neonatal Hypotonia: An International Consortium Study.
  52. Optimization of ACE-tRNAs function in translation for suppression of nonsense mutations.
  53. Making sense of missense: challenges and opportunities in variant pathogenicity prediction.
  54. SGLT2 inhibition alters substrate utilization and mitochondrial redox in healthy and failing rat hearts.
  55. Predicting absolute protein folding stability using generative models.
  56. Single-Eye Gene Therapy for Leber Hereditary Optic Neuropathy.
  57. Conditional ablation of MCU exacerbated cardiac pathology in a genetic arrhythmic model of CPVT.
  58. Efficient reinterpretation of rare disease cases using Exomiser.
  59. Inter-organ communication is a critical machinery to regulate metabolism and aging.
  60. CoCrMo nanoparticle induces neurotoxicity mediated via mitochondrial dysfunction: a study model for implant derived nanoparticle effects.
  61. Development of a riboflavin-responsive model of riboflavin transporter deficiency in zebrafish.
  62. Maternal Low-Protein Diet Leads to Mitochondrial Dysfunction and Impaired Energy Metabolism in the Skeletal Muscle of Male Rats.
  63. Consultation informs strategies to improve functional evidence use in variant classification.
  64. Advancing rare disease measurement through the Rare Disease Clinical Outcome Assessment Consortium.
  1. Elife. 2024 Dec 20. pii: e105191. [Epub ahead of print]13
    Mapping mitochondrial aging.
    Alessandro Bitto.
      Measuring mitochondrial respiration in frozen tissue samples provides the first comprehensive atlas of how aging affects mitochondrial function in mice.
    Keywords:  aging; cellular respiration; computational biology; mitochondria; mouse; respiration atlas; sex; systems biology
    DOI:  https://doi.org/10.7554/eLife.105191
  2. PLoS Biol. 2024 Dec;22(12): e3002941
    SLMO transfers phosphatidylserine between the outer and inner mitochondrial membrane in Drosophila.
    Siwen Zhao, Xuguang Jiang, Ning Li, Tao Wang.
      Phospholipids are critical building blocks of mitochondria, and proper mitochondrial function and architecture rely on phospholipids that are primarily transported from the endoplasmic reticulum (ER). Here, we show that mitochondrial form and function rely on synthesis of phosphatidylserine (PS) in the ER through phosphatidylserine synthase (PSS), trafficking of PS from ER to mitochondria (and within mitochondria), and the conversion of PS to phosphatidylethanolamine (PE) by phosphatidylserine decarboxylase (PISD) in the inner mitochondrial membrane (IMM). Using a forward genetic screen in Drosophila, we found that Slowmo (SLMO) specifically transfers PS from the outer mitochondrial membrane (OMM) to the IMM within the inner boundary membrane (IBM) domain. Thus, SLMO is required for shaping mitochondrial morphology, but its putative conserved binding partner, dTRIAP, is not. Importantly, SLMO's role in maintaining mitochondrial morphology is conserved in humans via the SLMO2 protein and is independent of mitochondrial dynamics. Our results highlight the importance of a conserved PSS-SLMO-PISD pathway in maintaining the structure and function of mitochondria.
    DOI:  https://doi.org/10.1371/journal.pbio.3002941
  3. Nat Metab. 2024 Dec;6(12): 2319-2337
    Subcellular NAD+ pools are interconnected and buffered by mitochondrial NAD.
    Lena E Høyland, Magali R VanLinden, Marc Niere, Øyvind Strømland, Suraj Sharma, Jörn Dietze, Ingvill Tolås, Eva Lucena, Ersilia Bifulco, Lars J Sverkeli, Camila Cimadamore-Werthein, Hanan Ashrafi, Kjellfrid F Haukanes, Barbara van der Hoeven, Christian Dölle, Cédric Davidsen, Ina K N Pettersen, Karl J Tronstad, Svein A Mjøs, Faisal Hayat, Mikhail V Makarov, Marie E Migaud, Ines Heiland, Mathias Ziegler.
      The coenzyme NAD+ is consumed by signalling enzymes, including poly-ADP-ribosyltransferases (PARPs) and sirtuins. Ageing is associated with a decrease in cellular NAD+ levels, but how cells cope with persistently decreased NAD+ concentrations is unclear. Here, we show that subcellular NAD+ pools are interconnected, with mitochondria acting as a rheostat to maintain NAD+ levels upon excessive consumption. To evoke chronic, compartment-specific overconsumption of NAD+, we engineered cell lines stably expressing PARP activity in mitochondria, the cytosol, endoplasmic reticulum or peroxisomes, resulting in a decline of cellular NAD+ concentrations by up to 50%. Isotope-tracer flux measurements and mathematical modelling show that the lowered NAD+ concentration kinetically restricts NAD+ consumption to maintain a balance with the NAD+ biosynthesis rate, which remains unchanged. Chronic NAD+ deficiency is well tolerated unless mitochondria are directly targeted. Mitochondria maintain NAD+ by import through SLC25A51 and reversibly cleave NAD+ to nicotinamide mononucleotide and ATP when NMNAT3 is present. Thus, these organelles can maintain an additional, virtual NAD+ pool. Our results are consistent with a well-tolerated ageing-related NAD+ decline as long as the vulnerable mitochondrial pool is not directly affected.
    DOI:  https://doi.org/10.1038/s42255-024-01174-w
  4. Neurochem Res. 2024 Dec 14. 50(1): 61
    Mechanism and Clinical Application Prospects of Mitochondrial DNA Single Nucleotide Polymorphism in Neurodegenerative Diseases.
    Mengying Xu, Tianjiao Li, Xuan Liu, Binish Islam, Yuyue Xiang, Xiyan Zou, Jianwu Wang.
      Mitochondrial dysfunction is well recognized as a critical component of the complicated pathogenesis of neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and Huntington's disease. This review investigates the influence of mitochondrial DNA single nucleotide polymorphisms on mitochondrial function, as well as their role in the onset and progression of these neurodegenerative diseases. Furthermore, the contemporary approaches to mitochondrial regulation in these disorders are discussed. Our objective is to uncover early diagnostic targets and formulate precision medicine strategies for neurodegenerative diseases, thereby offering new paths for preventing and treating these conditions.
    Keywords:  Mitochondrial dysfunction; Mitochondrial regulation technologies; Neurodegenerative diseases; SNPs; mtDNA
    DOI:  https://doi.org/10.1007/s11064-024-04311-9
  5. J Biol Chem. 2024 Dec 13. pii: S0021-9258(24)02589-4. [Epub ahead of print] 108087
    Crucial role and conservation of the three [2Fe-2S] clusters in the human mitochondrial ribosome.
    Linda Boß, Oliver Stehling, Hans-Peter Elsässer, Roland Lill.
      Mitochondria synthesize only a small set of their proteins on endogenous mitoribosomes. These particles differ in structure and composition from both their bacterial 70S ancestors and cytosolic 80S ribosomes. Recently published high resolution structures of the human mitoribosome revealed the presence of three [2Fe-2S] clusters in the small and large subunits. Each of these clusters is coordinated in a bridging fashion by cysteine residues from two different mitoribosomal proteins. Here, we investigated the cell biological and biochemical roles of all three Fe/S clusters in mitochondrial function and assembly. First, we found a requirement of both early and late factors of the mitochondrial iron-sulfur cluster assembly machinery for protein translation indicating that not only the mitoribosome [2Fe-2S] clusters but also the [4Fe-4S] cluster of the mitoribosome assembly factor METTL17 are required for mitochondrial translation. Second, siRNA-mediated depletion of the cluster-coordinating ribosomal proteins bS18m, mS25 or mL66 and complementation with either the respective wild-type or cysteine-exchange proteins unveiled the importance of the clusters for assembly, stability, and function of the human mitoribosome. As a consequence, the lack of cluster binding to mitoribosomes impaired the activity of the mitochondrial respiratory chain complexes and led to altered mitochondrial morphology with a loss of cristae membranes. Finally, in silico investigation of the phylogenetic distribution of the cluster-coordinating cysteine motifs indicated their presence in most metazoan mitoribosomes, with exception of ray-finned fish. Collectively, our study highlights the functional need of mitochondrial Fe/S protein biogenesis for both protein translation and respiratory energy supply in most metazoan mitochondria.
    Keywords:  Protein synthesis; biogenesis; iron-sulfur protein assembly; mitochondria; mitochondrial respiratory chain; ribosome assembly
    DOI:  https://doi.org/10.1016/j.jbc.2024.108087
  6. Elife. 2024 Dec 16. pii: RP99914. [Epub ahead of print]13
    Biochemical and neurophysiological effects of deficiency of the mitochondrial import protein TIMM50.
    Eyal Paz, Sahil Jain, Irit Gottfried, Orna Staretz-Chacham, Muhammad Mahajnah, Pritha Bagchi, Nicholas T Seyfried, Uri Ashery, Abdussalam Azem.
      TIMM50, an essential TIM23 complex subunit, is suggested to facilitate the import of ~60% of the mitochondrial proteome. In this study, we characterized a TIMM50 disease-causing mutation in human fibroblasts and noted significant decreases in TIM23 core protein levels (TIMM50, TIMM17A/B, and TIMM23). Strikingly, TIMM50 deficiency had no impact on the steady-state levels of most of its putative substrates, suggesting that even low levels of a functional TIM23 complex are sufficient to maintain the majority of TIM23 complex-dependent mitochondrial proteome. As TIMM50 mutations have been linked to severe neurological phenotypes, we aimed to characterize TIMM50 defects in manipulated mammalian neurons. TIMM50 knockdown in mouse neurons had a minor effect on the steady state level of most of the mitochondrial proteome, supporting the results observed in patient fibroblasts. Amongst the few affected TIM23 substrates, a decrease in the steady state level of components of the intricate oxidative phosphorylation and mitochondrial ribosome complexes was evident. This led to declined respiration rates in fibroblasts and neurons, reduced cellular ATP levels, and defective mitochondrial trafficking in neuronal processes, possibly contributing to the developmental defects observed in patients with TIMM50 disease. Finally, increased electrical activity was observed in TIMM50 deficient mice neuronal cells, which correlated with reduced levels of KCNJ10 and KCNA2 plasma membrane potassium channels, likely underlying the patients' epileptic phenotype.
    Keywords:  Action potential; TIM23; TIMM50; TIMM50 disease; biochemistry; chemical biology; human; import disease; mitochondria; mitochondrial protein import; mouse; neuroscience
    DOI:  https://doi.org/10.7554/eLife.99914
  7. Autophagy. 2024 Dec 19.
    A molecular glue for Prkn/parkin.
    Véronique Sauvé, Kalle Gehring.
      Parkinson disease (PD) is a neurodegenerative disease characterized by the loss of dopaminergic neurons in the substantia nigra, primarily due to mitochondria dysfunction. PRKN (parkin RBR E3 ubiquitin protein ligase) and PINK1 (PTEN induced kinase 1) are linked to early-onset cases of PD and essential for the clearance of damaged mitochondria via selective mitochondrial autophagy (mitophagy). In a recent publication, we detail how a small molecule can activate PRKN mutants that are unable to be phosphorylated, restoring mitophagy in cellular assays. These findings offer hope for the design of therapeutic drugs for some forms of PD.
    Keywords:  Activator; PARK2; mitochondria; neurodegeneration; parkinson disease; ubiquitin
    DOI:  https://doi.org/10.1080/15548627.2024.2443232
  8. Sci Adv. 2024 Dec 20. 10(51): eads5466
    Metformin targets mitochondrial complex I to lower blood glucose levels.
    Colleen R Reczek, Ram P Chakrabarty, Karis B D'Alessandro, Zachary L Sebo, Rogan A Grant, Peng Gao, G R Budinger, Navdeep S Chandel.
      Metformin is among the most prescribed antidiabetic drugs, but the primary molecular mechanism by which metformin lowers blood glucose levels is unknown. Previous studies have proposed numerous mechanisms by which acute metformin lowers blood glucose, including the inhibition of mitochondrial complex I of the electron transport chain (ETC). Here, we used transgenic mice that globally express the Saccharomyces cerevisiae internal alternative NADH dehydrogenase (NDI1) protein to determine whether the glucose-lowering effect of acute oral administration of metformin requires inhibition of mitochondrial complex I of the ETC in vivo. NDI1 is a yeast NADH dehydrogenase enzyme that complements the loss of mammalian mitochondrial complex I electron transport function and is insensitive to pharmacologic mitochondrial complex I inhibitors including metformin. We demonstrate that NDI1 expression attenuates metformin's ability to lower blood glucose levels under standard chow and high-fat diet conditions. Our results indicate that acute oral administration of metformin targets mitochondrial complex I to lower blood glucose.
    DOI:  https://doi.org/10.1126/sciadv.ads5466
  9. J Biol Chem. 2024 Dec 13. pii: S0021-9258(24)02594-8. [Epub ahead of print] 108092
    A Kinetic Model for Compound Heterozygous Pathogenic Variants in Tyrosyl-tRNA Synthetase Gene YARS2-Associated Neonatal Phenotype.
    Thomas Christian, Sunita Maharjan, Sitao Yin, Yuka Yamaki, Isao Masuda, Fenglin Li, Colleen Muraresku, Sheila Clever, Rebecca D Ganetzky, Ya-Ming Hou.
      Human genetic disorders are often caused by mutations of compound heterozygosity, where each allele of the mutant gene harbors a different genetic lesion. However, studies of such mutations are hampered, due to the lack of an appropriate model. Here we describe a kinetic model of compound heterozygous variants in an obligate enzyme dimer that contains one mutation in one monomer and the other mutation in the second monomer. This enzyme is encoded by human YARS2 for mitochondrial tyrosyl-tRNA synthetase (mt-TyrRS), which aminoacylates tyrosine to mt-tRNATyr. YARS2 is a member of the genes for mt-aminoacyl-tRNA synthetases, where pathogenic mutations present limited correlation between disease severity and enzyme activity. We identify a pair of compound heterozygous variants in YARS2 that is associated with neonatal fatality. We show that, while each mutation causes a minor-to-modest defect in aminoacylation in the homodimer of mt-TyrRS, the two mutations in trans synergistically reduce the enzyme activity to a greater effect. This kinetic model thus accurately recapitulates the disease severity, emphasizing its utility to study YARS2 mutations and its potential for generalization to other diseases with compound heterozygous mutations.
    Keywords:  MLASA; heterodimer; homodimer; mt-TyrRS; mt-tRNA(Tyr)
    DOI:  https://doi.org/10.1016/j.jbc.2024.108092
  10. Front Cell Neurosci. 2024 ;18 1509283
    Neuronal activity inhibits mitochondrial transport only in synaptically connected segments of the axon.
    Tom Venneman, Pieter Vanden Berghe.
      Due to their large scale and uniquely branched architecture, neurons critically rely on active transport of mitochondria in order to match energy production and calcium buffering to local demand. Consequently, defective mitochondrial trafficking is implicated in various neurological and neurodegenerative diseases. A key signal regulating mitochondrial transport is intracellular calcium. Elevated Ca2+ levels have been demonstrated to inhibit mitochondrial transport in many cell types, including neurons. However, it is currently unclear to what extent calcium-signaling regulates axonal mitochondrial transport during realistic neuronal activity patterns. We created a robust pipeline to quantify with high spatial resolution, absolute Ca2+ concentrations. This allows us to monitor Ca2+ dynamics with pixel precision in the axon and other neuronal compartments. We found that axonal calcium levels scale with firing frequency in the range of 0.1-1 μM, whereas KCl-induced depolarization generated levels almost a magnitude higher. As expected, prolonged KCl-induced depolarization did inhibit axonal mitochondrial transport in primary hippocampal neurons. However, physiologically relevant neuronal activity patterns only inhibited mitochondrial transport in axonal segments which made connections to a target neuron. In "non-connecting" axonal segments, we were unable to trigger this inhibitory mechanism using realistic firing patterns. Thus, we confirm that neuronal activity can indeed regulate axonal mitochondrial transport, and reveal a spatial pattern to this regulation which went previously undetected. Together, these findings indicate a potent, but localized role for activity-related calcium fluctuations in the regulation of axonal mitochondrial transport.
    Keywords:  axonal mitochondrial transport; neuronal activity; ratiometric calcium imaging; synaptic connections; transport regulation
    DOI:  https://doi.org/10.3389/fncel.2024.1509283
  11. Int J Mol Sci. 2024 Nov 27. pii: 12740. [Epub ahead of print]25(23):
    Role of Fatty Acids β-Oxidation in the Metabolic Interactions Between Organs.
    Alexander V Panov, Vladimir I Mayorov, Sergey I Dikalov.
      In recent decades, several discoveries have been made that force us to reconsider old ideas about mitochondria and energy metabolism in the light of these discoveries. In this review, we discuss metabolic interaction between various organs, the metabolic significance of the primary substrates and their metabolic pathways, namely aerobic glycolysis, lactate shuttling, and fatty acids β-oxidation. We rely on the new ideas about the supramolecular structure of the mitochondrial respiratory chain (respirasome), the necessity of supporting substrates for fatty acids β-oxidation, and the reverse electron transfer via succinate dehydrogenase during β-oxidation. We conclude that ATP production during fatty acid β-oxidation has its upper limits and thus cannot support high energy demands alone. Meanwhile, β-oxidation creates conditions that significantly accelerate the cycle: glucose-aerobic glycolysis-lactate-gluconeogenesis-glucose. Therefore, glycolytic ATP production becomes an important energy source in high energy demand. In addition, lactate serves as a mitochondrial substrate after converting to pyruvate + H+ by the mitochondrial lactate dehydrogenase. All coupled metabolic pathways are irreversible, and the enzymes are organized into multienzyme structures.
    Keywords:  aerobic glycolysis; beta-oxidation; fatty acids; gluconeogenesis; lactate; metabolism; mitochondria; respirasome
    DOI:  https://doi.org/10.3390/ijms252312740
  12. Nat Metab. 2024 Dec;6(12): 2215-2217
    Guardians of the cell: mitochondria as a rheostat for cellular NAD+ levels.
    Fiona M Fitzpatrick, Nora Kory.
      
    DOI:  https://doi.org/10.1038/s42255-024-01160-2
  13. Am J Hum Genet. 2024 Dec 14. pii: S0002-9297(24)00416-6. [Epub ahead of print]
    Bi-allelic variants in DAP3 result in reduced assembly of the mitoribosomal small subunit with altered apoptosis and a Perrault-syndrome-spectrum phenotype.
    DDD Study
      The mitochondrial ribosome (mitoribosome) synthesizes 13 protein subunits of the oxidative phosphorylation system encoded by the mitochondrial genome. The mitoribosome is composed of 12S rRNA, 16S rRNA, and 82 mitoribosomal proteins encoded by nuclear genes. To date, variants in 12 genes encoding mitoribosomal proteins are associated with rare monogenic disorders and frequently show combined oxidative phosphorylation deficiency. Here, we describe five unrelated individuals with bi-allelic variants in death-associated protein 3 (DAP3), a nuclear gene encoding mitoribosomal small subunit 29 (MRPS29), with variable clinical presentations ranging from Perrault syndrome (sensorineural hearing loss and ovarian insufficiency) to an early childhood neurometabolic phenotype. Assessment of respiratory-chain function and proteomic profiling of fibroblasts from affected individuals demonstrated reduced MRPS29 protein amounts and, consequently, decreased levels of additional protein components of the mitoribosomal small subunit, as well as an associated combined deficiency of complexes I and IV. Lentiviral transduction of fibroblasts from affected individuals with wild-type DAP3 cDNA increased DAP3 mRNA expression and partially rescued protein levels of MRPS7, MRPS9, and complex I and IV subunits, demonstrating the pathogenicity of the DAP3 variants. Protein modeling suggested that DAP3 disease-associated missense variants can impact ADP binding, and in vitro assays demonstrated that DAP3 variants can consequently reduce both intrinsic and extrinsic apoptotic sensitivity, DAP3 thermal stability, and DAP3 GTPase activity. Our study presents genetic and functional evidence that bi-allelic variants in DAP3 result in a multisystem disorder of combined oxidative phosphorylation deficiency with pleiotropic presentations, consistent with mitochondrial dysfunction.
    Keywords:  DAP3; MRPS29; Perrault syndrome; leukodystrophy; mitochondria; mitoribosomal small subunit; mitoribosome; ovarian insufficiency; rare disease; sensorineural hearing loss
    DOI:  https://doi.org/10.1016/j.ajhg.2024.11.007
  14. Genetics. 2024 Dec 05. pii: iyae203. [Epub ahead of print]
    Proteolytic regulation of mitochondrial magnesium channel MRS2 by m-AAA protease and prohibitin complex.
    Alaumy Joshi, Rachel A Stanfield, Andrew T Spletter, Vishal M Gohil.
      Mitochondrial membrane phospholipid cardiolipin is essential for the stability of several inner mitochondrial membrane protein complexes. We recently showed that the abundance of mitochondrial magnesium channel MRS2 is reduced in models of Barth syndrome, an X-linked genetic disorder caused by a remodeling defect in cardiolipin. However, the mechanism underlying the reduced abundance of MRS2 in cardiolipin-depleted mitochondria remained unknown. In this study, we utilized yeast mutants of mitochondrial proteases to identify an evolutionarily conserved m-AAA protease, Yta10/Yta12, responsible for degrading Mrs2. The activity of m-AAA protease is regulated by the inner mitochondrial membrane scaffolding complex prohibitin, and consistent with this role, we find that Mrs2 turnover is increased in yeast prohibitin mutants. Importantly, we find that deleting Yta10 in cardiolipin-deficient yeast cells restores the steady-state levels of Mrs2 to the wild-type cells, and the knockdown of AFG3L2, a mammalian homolog of Yta12, increases the abundance of MRS2 in a murine muscle cell line. Thus, our work has identified the m-AAA protease/prohibitin complex as an evolutionarily conserved regulator of Mrs2 that can be targeted to restore Mrs2 abundance in cardiolipin-depleted cells.
    Keywords:   m-AAA protease; MRS2; Mitochondria; cardiolipin; prohibitin
    DOI:  https://doi.org/10.1093/genetics/iyae203
  15. Curr Opin Pediatr. 2025 Feb 01. 37(1): 107-111
    Updates on neurologic manifestations of mitochondrial disease.
    Britta Kuusik, Divakar S Mithal.
       PURPOSE OF REVIEW: Primary mitochondrial disease (PMD) is diverse both genetically and phenotypically. Neurologic manifestations are present at a high rate and often pose complications for providers. The review will discuss common manifestations and how advances in genetic testing have broadened understanding of PMDs.
    RECENT FINDINGS: Across all areas of PMD research, genetic advancements are notable both for mitochondrial and nuclear DNA.
    SUMMARY: Global understanding of PMDs is driving deeper and broader research. Neurologic manifestations primarily include neuromuscular disease, epilepsy, stroke-like episodes and neurodegeneration, and advances in all areas have benefitted from global reporting of genetic studies.
    DOI:  https://doi.org/10.1097/MOP.0000000000001418
  16. Annu Rev Physiol. 2024 Dec 10.
    Exercise as Mitochondrial Medicine: How Does the Exercise Prescription Affect Mitochondrial Adaptations to Training?
    David J Bishop, Matthew J-C Lee, Martin Picard.
      Mitochondria are multifaceted organelles with several life-sustaining functions beyond energy transformation, including cell signaling, calcium homeostasis, hormone synthesis, programmed cell death (apoptosis), and others. A defining aspect of these dynamic organelles is their remarkable plasticity, which allows them to sense, respond, and adapt to various stressors. In particular, it is well-established that the stress of exercise provides a powerful stimulus that can trigger transient or enduring changes to mitochondrial molecular features, activities, integrated functions, behaviors, and cell-dependent mitochondrial phenotypes. Evidence documenting the many beneficial mitochondrial adaptations to exercise has led to the notion of exercise as a mitochondrial medicine. However, as with other medicines, it is important to understand the optimal prescription (i.e., type, dose, frequency, duration). In this review, we build on a systematic biological framework that distinguishes between domains of mitochondrial biology to critically evaluate how different exercise prescription variables influence mitochondrial adaptations to training.
    DOI:  https://doi.org/10.1146/annurev-physiol-022724-104836
  17. Iran J Pathol. 2024 ;19(3): 355-358
    Peripheral Neuropathy in Mitochondrial Trifunctional Protein Deficiency due to a Variant in HADHA Gene.
    Samaneh Abedidoust, Reza-Shervin Badv, Amitis Saliani, Aileen Azari-Yam.
      We report a 4.5-year-old girl with recurrent episodes of bilateral lower limb weakness following periods of upper respiratory tract infection since the age of 1.5 years. Nerve conduction velocity and electromyography studies suggested distal motor neuropathy. The whole exome sequencing analysis revealed a homozygous variant, c.955G>A (p.Gly319Ser), of the mitochondrial trifunctional protein α-subunit (HADHA) gene. This variant has already been reported as pathogenic in an Iranian consanguineous family with a probable diagnosis of Charcot-Marie-Tooth disease. In addition, this variant, in compound heterozygosity with another likely pathogenic variant, has been known to be linked with mitochondrial trifunctional protein deficiency.
    Keywords:  Fatty acid ß-oxidation; HADHA gene; Mitochondrial trifunctional protein; Neuropathy; Whole exome sequencing
    DOI:  https://doi.org/10.30699/IJP.2024.2010490.3163
  18. Cell Death Dis. 2024 Dec 18. 15(12): 914
    Mitochondria-targeted oligomeric α-synuclein induces TOM40 degradation and mitochondrial dysfunction in Parkinson's disease and parkinsonism-dementia of Guam.
    Velmarini Vasquez, Manohar Kodavati, Joy Mitra, Indira Vedula, Dale J Hamilton, Ralph M Garruto, K S Rao, Muralidhar L Hegde.
      Mitochondrial dysfunction is a central aspect of Parkinson's disease (PD) pathology, yet the underlying mechanisms are not fully understood. This study investigates the link between α-Synuclein (α-Syn) pathology and the loss of translocase of the outer mitochondrial membrane 40 (TOM40), unraveling its implications for mitochondrial dysfunctions in neurons. We discovered that TOM40 protein depletion occurs in the brains of patients with Guam Parkinsonism-Dementia (Guam PD) and cultured neurons expressing α-Syn proteinopathy, notably, without corresponding changes in TOM40 mRNA levels. Cultured neurons expressing α-Syn mutants, with or without a mitochondria-targeting signal (MTS) underscores the role of α-Syn's mitochondrial localization in inducing TOM40 degradation. PDe-related etiological factors, such as 6-hydroxydopamine or ROS/metal ions stress, which promotes α-Syn oligomerization, exacerbate TOM40 depletion in PD patient-derived cells with SNCA gene triplication. Although α-Syn interacts with both TOM40 and TOM20 in the outer mitochondrial membrane, degradation is selective for TOM40, which occurs via the ubiquitin-proteasome system (UPS) pathway. Our comprehensive analyses using Seahorse technology, mitochondrial DNA sequencing, and damage assessments, demonstrate that mutant α-Syn-induced TOM40 loss results in mitochondrial dysfunction, characterized by reduced membrane potential, accumulation of mtDNA damage, deletion/insertion mutations, and altered oxygen consumption rates. Notably, ectopic supplementation of TOM40 or reducing pathological forms of α-Syn using ADP-ribosylation inhibitors ameliorate these mitochondrial defects, suggesting potential therapeutic avenues. In conclusion, our findings provide crucial mechanistic insights into how α-Syn accumulation leads to TOM40 degradation and mitochondrial dysfunction, offering insights for targeted interventions to alleviate mitochondrial defects in PD.
    DOI:  https://doi.org/10.1038/s41419-024-07258-5
  19. Elife. 2024 Dec 20. pii: RP96926. [Epub ahead of print]13
    Mitochondrial respiration atlas reveals differential changes in mitochondrial function across sex and age.
    Dylan C Sarver, Muzna Saqib, Fangluo Chen, G William Wong.
      Organ function declines with age, and large-scale transcriptomic analyses have highlighted differential aging trajectories across tissues. The mechanism underlying shared and organ-selective functional changes across the lifespan, however, still remains poorly understood. Given the central role of mitochondria in powering cellular processes needed to maintain tissue health, we therefore undertook a systematic assessment of respiratory activity across 33 different tissues in young (2.5 months) and old (20 months) mice of both sexes. Our high-resolution mitochondrial respiration atlas reveals: (1) within any group of mice, mitochondrial activity varies widely across tissues, with the highest values consistently seen in heart, brown fat, and kidney; (2) biological sex is a significant but minor contributor to mitochondrial respiration, and its contributions are tissue-specific, with major differences seen in the pancreas, stomach, and white adipose tissue; (3) age is a dominant factor affecting mitochondrial activity, especially across most brain regions, different fat depots, skeletal muscle groups, eyes, and different regions of the gastrointestinal tract; (4) age effects can be sex- and tissue-specific, with some of the largest effects seen in pancreas, heart, adipose tissue, and skeletal muscle; and (5) while aging alters the functional trajectories of mitochondria in a majority of tissues, some are remarkably resilient to age-induced changes. Altogether, our data provide the most comprehensive compendium of mitochondrial respiration and illuminate functional signatures of aging across diverse tissues and organ systems.
    Keywords:  aging; computational biology; mitochondria; mouse; respiration atlas; sex; systems biology
    DOI:  https://doi.org/10.7554/eLife.96926
  20. Aging Cell. 2024 Dec 16. e14402
    Increased mitochondrial mutation heteroplasmy induces aging phenotypes in pluripotent stem cells and their differentiated progeny.
    Amy R Vandiver, Alejandro Torres, Amberly Sanden, Thang L Nguyen, Jasmine Gasilla, Mary T Doan, Vahan Martirosian, Austin Hoang, Jonathan Wanagat, Michael A Teitell.
      The mitochondrial genome (mtDNA) is an important source of inherited extranuclear variation. Clonal increases in mtDNA mutation heteroplasmy have been implicated in aging and disease, although the impact of this shift on cell function is challenging to assess. Reprogramming to pluripotency affects mtDNA mutation heteroplasmy. We reprogrammed three human fibroblast lines with known heteroplasmy for deleterious mtDNA point or deletion mutations. Quantification of mutation heteroplasmy in the resulting 76 induced pluripotent stem cell (iPSC) clones yielded a bimodal distribution, creating three sets of clones with high levels or absent mutation heteroplasmy with matched nuclear genomes. iPSC clones with elevated deletion mutation heteroplasmy show altered growth dynamics, which persist in iPSC-derived progenitor cells. We identify transcriptomic and metabolic shifts consistent with increased investment in neutral lipid synthesis as well as increased epigenetic age in high mtDNA deletion mutation iPSC, consistent with changes occurring in cellular aging. Together, these data demonstrate that high mtDNA mutation heteroplasmy induces changes occurring in cellular aging.
    Keywords:  aging; iPSC; mitochondria; mtDNA mutation
    DOI:  https://doi.org/10.1111/acel.14402
  21. Cell Calcium. 2024 Dec 12. pii: S0143-4160(24)00143-X. [Epub ahead of print]125 102985
    Regulation of SR and mitochondrial Ca2+ signaling by L-type Ca2+ channels and Na/Ca exchanger in hiPSC-CMs.
    Xiao-Hua Zhang, Martin Morad.
       RATIONALE & METHODS: While signaling of cardiac SR by surface membrane proteins (ICa & INCX) is well studied, the regulation of mitochondrial Ca2+ by plasmalemmal proteins remains less explored. Here we have examined the signaling of mitochondria and SR by surface-membrane calcium-transporting proteins, using genetically engineered targeted fluorescent probes, mito-GCamP6 and R-CEPIA1er.
    RESULTS: In voltage-clamped and TIRF-imaged cardiomyocytes, low Na+ induced SR Ca2+ release was suppressed by short pre-exposures to ∼100 nM FCCP, suggesting mitochondrial Ca2+ contribution to low Na+ triggered SR Ca2+release. Even though low Na+- or caffeine-triggered SR Ca2+ release activated global mitochondrial Ca2+ uptake, focal mitochondrial Ca2+ signals varied in kinetics and magnitude, showing uptake or release of calcium, depending on cellular location of mitochondria. In spontaneously pacing cells, sustained caffeine exposures depleted the SR Ca2+ content activating mitochondrial Ca2+ uptake followed by sustained mitochondrial pacing. Spontaneous hiPSCCMs pacing was strongly suppressed by L-type calcium channels blockers, but not by inhibiting SERCA2a by CPA.
    CONCLUSION: Spontaneous hiPSCCMs pacing is triggered by influx of calcium through L-type Ca2+ channel that gates the release of SR pools supplemented by NCX-mediated mitochondrial calcium contribution.
    Keywords:  Genetically targeted fluorescence probes; I(NCX) and I(Ca); Mitochondria Ca(2+) signaling; Sarcoplasmic reticulum; hiPSC—CMs
    DOI:  https://doi.org/10.1016/j.ceca.2024.102985
  22. Cell Mol Biol Lett. 2024 Dec 18. 29(1): 153
    Inter- and intracellular mitochondrial communication: signaling hubs in aging and age-related diseases.
    Meng Zhang, Jin Wei, Chang He, Liutao Sui, Chucheng Jiao, Xiaoyan Zhu, Xudong Pan.
      Mitochondria are versatile and complex organelles that can continuously communicate and interact with the cellular milieu. Deregulated communication between mitochondria and host cells/organelles has significant consequences and is an underlying factor of many pathophysiological conditions, including the process of aging. During aging, mitochondria lose function, and mitocellular communication pathways break down; mitochondrial dysfunction interacts with mitochondrial dyscommunication, forming a vicious circle. Therefore, strategies to protect mitochondrial function and promote effective communication of mitochondria can increase healthy lifespan and longevity, which might be a new treatment paradigm for age-related disorders. In this review, we comprehensively discuss the signal transduction mechanisms of inter- and intracellular mitochondrial communication, as well as the interactions between mitochondrial communication and the hallmarks of aging. This review emphasizes the indispensable position of inter- and intracellular mitochondrial communication in the aging process of organisms, which is crucial as the cellular signaling hubs. In addition, we also specifically focus on the status of mitochondria-targeted interventions to provide potential therapeutic targets for age-related diseases.
    Keywords:  Age-related diseases; Aging; Mitochondrial communication; Mitochondrial dysfunction; Signaling hubs
    DOI:  https://doi.org/10.1186/s11658-024-00669-4
  23. Cureus. 2024 Nov;16(11): e73577
    Rhabdomyolysis in a Patient With a Possible Mitochondrial Pathogenic Variant in the Peri-operative Period: A Case Report.
    Joyce Kam, Rabiu Momoh.
      Mitochondrial disorders are often underrecognized as potential causes of rhabdomyolysis, a condition characterized by acute muscle breakdown that can lead to local and potentially systemic complications, with the possibility of being life-threatening. Accounts of rhabdomyolysis as a peri-operative complication associated with mitochondrial disorders are rare; therefore, this study is noteworthy. We describe a case of rhabdomyolysis that occurred during the peri-operative period in a middle-aged male with Charcot-Marie-Tooth (CMT) disease-like peripheral neuropathy. Importantly, genetic studies confirmed that the patient's mother, sister, and maternal uncle carried the m.9176T>C (ATP6) mitochondrial pathogenic variant, which follows a maternal inheritance pattern. This suggests that the patient may have inherited the disorder as well.
    Keywords:  compartment syndrome; creatine kinase; dialysis; genetic disorders; hyperkalemia; m.9176t>c (atp6) mitochondrial pathogenic variant; maternal inheritance; mitochondrial disorder; renal failure; rhabdomyolysis
    DOI:  https://doi.org/10.7759/cureus.73577
  24. Methods Mol Biol. 2025 ;2888 167-191
    Measurement of Lipid Transport in Mitochondria by the MTL Complex.
    Juliette Jouhet, Valérie Gros, Morgane Michaud.
      Membrane biogenesis requires an extensive traffic of lipids between different cell compartments. Two main pathways, the vesicular and non-vesicular pathways, are involved in such a process. Whereas the mechanisms involved in vesicular trafficking are well understood, less is known about non-vesicular lipid trafficking, particularly in plants. This pathway involves the direct exchange of lipids at membrane contact sites (MCSs) between organelles. In plants, extensive traffic of the chloroplast-synthesized digalactosyldiacylglycerol (DGDG) to mitochondria is specifically promoted during phosphate starvation. This lipid exchange likely occurs by non-vesicular trafficking pathways at MCSs between mitochondria and plastids. By a biochemical approach, a mitochondrial lipoproteic super-complex called MTL (mitochondrial transmembrane lipoprotein complex) involved in mitochondrial lipid trafficking has been identified in Arabidopsis thaliana. This protocol describes the method used to separate the MTL complex and to study the implication of a component of this complex (AtMic60) in mitochondrial lipid transport.
    Keywords:  CN-PAGE; Lipid transfer; MTL complex; Mass spectrometry; Mitochondria
    DOI:  https://doi.org/10.1007/978-1-0716-4318-1_12
  25. Genetics. 2024 Dec 05. pii: iyae204. [Epub ahead of print]
    Metaxin-2 tunes mitochondrial transportation and neuronal function in Drosophila.
    Ting Zhang, Ling Li, Xiaoyu Fan, Xinyi Shou, Yina Ruan, Xiaojun Xie.
      Metaxins are a family of evolutionarily conserved proteins that reside on the mitochondria outer membrane (MOM) and participate in the protein import into the mitochondria. Metaxin-2 (Mtx2), a member of this family, has been identified as a key component in the machinery for mitochondrial transport in both C. elegans and human neurons. To deepen our understanding of Mtx2's role in neurons, we examined the homologous genes CG5662 and CG8004 in Drosophila. The CG5662 is a non-essential gene while CG8004 null mutants die at late pupal stages. The CG8004 protein is widely expressed throughout the Drosophila nervous system and is targeted to mitochondria. However, neuronal CG8004 is dispensable for animal survival and is partially required for mitochondrial distribution in certain neuropil regions. Conditional knockout of CG8004 in adult gustatory receptor neurons (GRNs) impairs mitochondrial trafficking along GRN axons and diminishes the mitochondrial quantities in axon terminals. The absence of CG8004 also leads to mitochondrial fragmentation within GRN axons, a phenomenon that may be linked to mitochondrial transport through its genetic interaction with the fusion proteins Marf and Opa1. While the removal of neuronal CG8004 is not lethal during the developmental stage, it does have consequences for the lifespan and healthspan of adult Drosophila. At last, double knockout (KO) of CG5662 and CG8004 shows similar phenotypes as the CG8004 single KO, suggesting that CG5662 does not compensate for the loss of CG8004. In summary, our findings suggest that CG8004 plays a conserved and context-dependent role in axonal mitochondrial transport, as well it is important for sustaining neuronal function. Therefore, we refer to CG8004 as the Drosophila Metaxin-2 (dMtx2).
    Keywords:   Drosophila ; Mandibuloacral dysplasia; Metaxin; Mitochondria dynamics; Mitochondria transport
    DOI:  https://doi.org/10.1093/genetics/iyae204
  26. bioRxiv. 2024 Dec 02. pii: 2024.11.26.625487. [Epub ahead of print]
    Label-Free Visualization and Segmentation of Endothelial Cell Mitochondria Using Holotomographic Microscopy and U-Net.
    Raul Michael, Tallah Modirzadeh, Tahir Bachar Issa, Patrick Jurney.
      Understanding the physiological processes underlying age-related cardiovascular disease (CVD) requires examination of endothelial cell (EC) mitochondrial networks, because mitochondrial function and adenosine triphosphate production are crucial in EC metabolism, and consequently influence CVD progression. Although current biochemical assays and immunofluorescence microscopy can reveal how mitochondrial function influences cellular metabolism, they cannot achieve live observation and tracking changes in mitochondrial networks through fusion and fission events. Holotomographic microscopy (HTM) has emerged as a promising technique for real-time, label-free visualization of ECs and their organelles, such as mitochondria. This non-destructive, non-interfering live cell imaging method offers unprecedented opportunities to observe mitochondrial network dynamics. However, because existing image processing tools based on immunofluorescence microscopy techniques are incompatible with HTM images, a machine-learning model is required. Here, we developed a model using a U-net learner with a Resnet18 encoder to identify four classes within HTM images: mitochondrial networks, cell borders, ECs, and background. This method accurately identifies mitochondrial structures and positions. With high accuracy and similarity metrics, the output image successfully provides visualization of mitochondrial networks within HTM images of ECs. This approach enables the study of mitochondrial networks and their effects, and holds promise in advancing understanding of CVD mechanisms.
    DOI:  https://doi.org/10.1101/2024.11.26.625487
  27. Ann Neurol. 2024 Dec 19.
    The Utility of Long-Read Sequencing in Diagnosing Early Onset Parkinson's Disease.
    Kensuke Daida, Hiroyo Yoshino, Laksh Malik, Breeana Baker, Mayu Ishiguro, Rylee Genner, Kimberly Paquette, Yuanzhe Li, Kenya Nishioka, Satoshi Masuzugawa, Makito Hirano, Kenta Takahashi, Mikhail Kolmogorov, Kimberley J Billingsley, Manabu Funayama, Cornelis Blauwendraat, Nobutaka Hattori.
       OBJECTIVE: Variants in PRKN and PINK1 are the leading cause of early-onset autosomal recessive Parkinson's disease, yet many cases remain genetically unresolved. We previously identified a 7 megabases complex structural variant in a pair of monozygotic twins using Oxford Nanopore Technologies (ONT) long-read sequencing. This study aims to determine if ONT long-read sequencing can detect a second variant in other unresolved early-onset Parkinson's disease (EOPD) cases with 1 heterozygous PRKN or PINK1 variant.
    METHODS: ONT long-read sequencing was performed on EOPD patients with 1 reported PRKN/PINK1 pathogenic variant, with onset age under 50. Positive controls included EOPD patients with 2 known PRKN pathogenic variants. Initial testing involved short-read targeted panel sequencing for single nucleotide variants and multiplex ligation-dependent probe amplification for copy number variants.
    RESULTS: A total of 47 patients were studied (PRKN "one-variant," n = 23; PINK1 "one-variant," n = 12; PRKN "two-variants," n = 12). ONT long-read sequencing identified a second pathogenic variant in 26% of PRKN "one-variant" patients (6/23), but none in PINK1 "one-variant" patients (0/12). Detected variants included 1 complex inversion, 2 structural variant overlaps, and 3 duplications. In the PRKN "two-variants" group, both variants were identified in all patients (100%, 12/12).
    INTERPRETATION: ONT long-read sequencing effectively identifies pathogenic structural variants in the PRKN locus missed by conventional methods. It should be considered for unresolved EOPD cases when a second variant is not detected through conventional approaches. ANN NEUROL 2024.
    DOI:  https://doi.org/10.1002/ana.27155
  28. Parkinsonism Relat Disord. 2024 Dec 09. pii: S1353-8020(24)01239-2. [Epub ahead of print]131 107227
    NDUFAF5 variants cause early onset Leigh syndrome.
    Breno Kazuo Massuyama, Amanda Monteiro Viagi, Rafael Chaves Claudino de Queiroga, Raphael Pinheiro Camurugy da Hora, Victor Rebelo Procaci, Augusto Bragança Reis Rosa, Thiago Yoshinaga Tonholo Silva, Orlando Graziani Povoas Barsottini, José Luiz Pedroso.
      
    Keywords:  Leigh disease; Mitochondrial diseases; NDUFAF5
    DOI:  https://doi.org/10.1016/j.parkreldis.2024.107227
  29. Science. 2024 Dec 20. 386(6728): 1349-1350
    Aged neurons don't register energy need.
    Deniz Bingul, Scott F Owen.
      Neuronal activity and mitochondrial gene expression become decoupled in aged mice.
    DOI:  https://doi.org/10.1126/science.adu4935
  30. FEBS J. 2024 Dec 19.
    Transfer RNA and small molecule therapeutics for aminoacyl-tRNA synthetase diseases.
    Tristan N Samuels, Fanqi Wu, Maria Mahmood, Wajd A Abuzaid, Nancy Sun, Angelica Moresco, Victoria M Siu, Patrick O'Donoghue, Ilka U Heinemann.
      Aminoacyl-tRNA synthetases catalyze the ligation of a specific amino acid to its cognate tRNA. The resulting aminoacyl-tRNAs are indispensable intermediates in protein biosynthesis, facilitating the precise decoding of the genetic code. Pathogenic alleles in the aminoacyl-tRNA synthetases can lead to several dominant and recessive disorders. To date, disease-specific treatments for these conditions are largely unavailable. We review pathogenic human synthetase alleles, the molecular and cellular mechanisms of tRNA synthetase diseases, and emerging approaches to allele-specific treatments, including small molecules and nucleic acid-based therapeutics. Current treatment approaches to rescue defective or dysfunctional tRNA synthetase mutants include supplementation with cognate amino acids and delivery of cognate tRNAs to alleviate bottlenecks in translation. Complementary approaches use inhibitors to target the integrated stress response, which can be dysregulated in tRNA synthetase diseases.
    Keywords:  GCN2; aminoacyl‐tRNA synthetase; genetic disorders; tRNA therapeutics
    DOI:  https://doi.org/10.1111/febs.17361
  31. Int J Mol Sci. 2024 Nov 29. pii: 12855. [Epub ahead of print]25(23):
    Mitochondrial Dynamics in Brain Cells During Normal and Pathological Aging.
    Vladimir S Sukhorukov, Tatiana I Baranich, Anna V Egorova, Anastasia V Akateva, Kseniia M Okulova, Maria S Ryabova, Krisitina A Skvortsova, Oscar V Dmitriev, Natalia M Mudzhiri, Dmitry N Voronkov, Sergey N Illarioshkin.
      Mitochondrial dynamics significantly play a major role in the pathogenesis of neurodegenerative diseases, such as Parkinson's disease and Alzheimer's disease. The dysregulation of mitochondrial biogenesis and function, characterized by impaired fission and fusion processes mediated by a number of proteins, in particular, Drp1, Mfn1, Mfn2, Opa1, and PGC-1α, contributes to neuronal vulnerability and degeneration. Insufficient mitophagy and disrupted mitochondrial transport exacerbate oxidative stress and neurotoxicity. Emerging therapeutic strategies that target mitochondrial dynamics, including various pharmacological agents, demonstrate potential for restoring mitochondrial balance and enhancing neuroprotection. This growing body of research underscores the importance of mitochondrial health in developing effective interventions for neurodegenerative conditions. This review highlights well-established links between the disruption of mitochondrial dynamics and the development of neurodegenerative processes. We also discuss different therapeutic strategies that target mitochondrial function in neurons that have been proposed as perspective neuroprotective treatments.
    Keywords:  mitochondrial dynamics; mitophagy; neurodegeneration; neuroprotection
    DOI:  https://doi.org/10.3390/ijms252312855
  32. Comput Biol Med. 2024 Dec 17. pii: S0010-4825(24)01645-7. [Epub ahead of print]185 109560
    UniVar: A variant interpretation platform enhancing rare disease diagnosis through robust filtering and unified analysis of SNV, INDEL, CNV and SV.
    Cherie C Y Au-Yeung, Yuen-Ting Cheung, Joshua Y T Cheng, Ken W H Ip, Sau-Dan Lee, Victor Y T Yang, Amy Y T Lau, Chit K C Lee, Peter K H Chong, King Wai Lau, Jurgen T J van Lunenburg, Damon F D Zheng, Brian H M Ho, Crystal Tik, Kingsley K K Ho, Ramesh Rajaby, Chun-Hang Au, Mullin H C Yu, Wing-Kin Sung.
       BACKGROUND: Interpreting the pathogenicity of genetic variants associated with rare diseases is a laborious and time-consuming endeavour. To streamline the diagnostic process and lighten the burden of variant interpretation, it is crucial to automate variant annotation and prioritization. Unfortunately, currently available variant interpretation tools lack a unified and comprehensive workflow that can collectively assess the clinical significance of these types of variants together: small nucleotide variants (SNVs), small insertions/deletions (INDELs), copy number variants (CNVs) and structural variants (SVs).
    RESULTS: The Unified Variant Interpretation Platform (UniVar) is a free web server tool that offers an automated and comprehensive workflow on annotation, filtering and prioritization for SNV, INDEL, CNV and SV collectively to identify disease-causing variants for rare diseases in one interface, ensuring accessibility for users even without programming expertise. To filter common CNVs/SVs, a diverse SV catalogue has been generated, that enables robust filtering of common SVs based on population allele frequency. Through benchmarking our SV catalogue, we showed that it is more complete and accurate than the state-of-the-art SV catalogues. Furthermore, to cope with those patients without detailed clinical information, we have developed a novel computational method that enables variant prioritization from gene panels. Our analysis shows that our approach could prioritize pathogenic variants as effective as using HPO terms assigned by clinicians, which adds value for cases without specific clinically assigned HPO terms. Lastly, through a practical case study of disease-causing compound heterozygous variants across SNV and SV, we demonstrated the uniqueness and effectiveness in variant interpretation of UniVar, edging over any existing interpretation tools.
    CONCLUSIONS: UniVar is a unified and versatile platform that empowers researchers and clinicians to identify and interpret disease-causing variants in rare diseases efficiently through a single holistic interface and without a prerequisite for HPO terms. It is freely available without login and installation at https://univar.live/.
    Keywords:  Copy number variants; Genetic diagnosis; Rare diseases; SNV and INDEL; Structural variants; Variant interpretation; Variant prioritization
    DOI:  https://doi.org/10.1016/j.compbiomed.2024.109560
  33. Res Sq. 2024 Dec 05. pii: rs.3.rs-5278203. [Epub ahead of print]
    Mitochondrial metabolism and epigenetic crosstalk drive the SASP.
    Joao Passos, Helene Martini, Jodie Birch, Francisco Marques, Stella Victorelli, Anthony Lagnado, Nicholas Pirius, Ana Franco, Gung Lee, Yeaeun Han, Jennifer Rowsey, Alexandre Gaspar-Maia, Aaron Havas, Rabi Murad, Xue Lei, Rebecca Porritt, Oliver Maddocks, Diana Jurk, Sundeep Khosla, Peter Adams.
      Senescent cells drive tissue dysfunction through the senescence-associated secretory phenotype (SASP). We uncovered a central role for mitochondria in the epigenetic regulation of the SASP, where mitochondrial-derived metabolites, specifically citrate and acetyl-CoA, fuel histone acetylation at SASP gene loci, promoting their expression. We identified the mitochondrial citrate carrier (SLC25A1) and ATP-citrate lyase (ACLY) as critical for this process. Inhibiting these pathways selectively suppresses SASP without affecting cell cycle arrest, highlighting their potential as therapeutic targets for age-related inflammation. Notably, SLC25A1 inhibition reduces systemic inflammation and extends healthspan in aged mice, establishing mitochondrial metabolism as pivotal to the epigenetic control of aging.
    DOI:  https://doi.org/10.21203/rs.3.rs-5278203/v1
  34. Sci Adv. 2024 Dec 20. 10(51): eadu7436
    Meeting metformin again for the first time.
    Douglas R Green.
      New evidence convincingly shows that metformin, a drug that reduces circulating glucose, acts by inhibiting mitochondrial complex I.
    DOI:  https://doi.org/10.1126/sciadv.adu7436
  35. Front Cell Neurosci. 2024 ;18 1496163
    Aging promotes an increase in mitochondrial fragmentation in astrocytes.
    Ana Paula Bergamo Araujo, Gabriele Vargas, Lívia de Sá Hayashide, Isadora Matias, Cherley Borba Vieira Andrade, Jorge José de Carvalho, Flávia Carvalho Alcantara Gomes, Luan Pereira Diniz.
       Introduction: Brain aging involves a complex interplay of cellular and molecular changes, including metabolic alterations and the accumulation of senescent cells. These changes frequently manifest as dysregulation in glucose metabolism and mitochondrial function, leading to reduced energy production, increased oxidative stress, and mitochondrial dysfunction-key contributors to age-related neurodegenerative diseases.
    Methods: We conducted experiments on two models: young (3-4 months) and aged (over 18 months) mice, as well as cultures of senescent and control mouse astrocytes. Mitochondrial content and biogenesis were analyzed in astrocytes and neurons from aged and young animals. Cultured senescent astrocytes were examined for mitochondrial membrane potential and fragmentation. Quantitative PCR (qPCR) and immunocytochemistry were used to measure fusion- and fission-related protein levels. Additionally, transmission electron microscopy provided morphological data on mitochondria.
    Results: Astrocytes and neurons from aged animals showed a significant reduction in mitochondrial content and a decrease in mitochondrial biogenesis. Senescent astrocytes in culture exhibited lower mitochondrial membrane potential and increased mitochondrial fragmentation. qPCR and immunocytochemistry analyses revealed a 68% increase in fusion-related proteins (mitofusin 1 and 2) and a 10-fold rise in DRP1, a key regulator of mitochondrial fission. Transmission electron microscopy showed reduced perimeter, area, and length-to-diameter ratio of mitochondria in astrocytes from aged mice, supported by elevated DRP1 phosphorylation in astrocytes of the cerebral cortex.
    Discussion: Our findings provide novel evidence of increased mitochondrial fragmentation in astrocytes from aged animals. This study sheds light on mechanisms of astrocytic metabolic dysfunction and mitochondrial dysregulation in brain aging, highlighting mitochondrial fragmentation as a potential target for therapeutic interventions in age-related neurodegenerative diseases.
    Keywords:  astrocytes; brain aging; mitochondrial biogenesis and neurodegeneration; mitochondrial dysfunction; mitochondrial fragmentation
    DOI:  https://doi.org/10.3389/fncel.2024.1496163
  36. J Comp Neurol. 2024 Dec;532(12): e70002
    Ultrastructural Analysis Reveals Mitochondrial Placement Independent of Synapse Placement in Fine Caliber C. elegans Neurons.
    Danielle V Riboul, Sarah Crill, Carlos D Oliva, Maria Gabriela Restifo, Reggie Joseph, Kerdes Joseph, Ken C Q Nguyen, David H Hall, Yaouen Fily, Gregory T Macleod.
      Neurons rely on mitochondria for an efficient supply of ATP and other metabolites. However, while neurons are highly elongated, mitochondria are discrete and limited in number. Due to the slow rates of metabolite diffusion over long distances, it follows that neurons would benefit from an ability to control the distribution of mitochondria to sites of high metabolic activity such as synapses. Ultrastructural data over substantial portions of a neuron's extent that would allow for tests of such hypotheses are scarce. Here, we mined the Caenorhabditis elegans' electron micrographs of John White and Sydney Brenner and found systematic differences in average mitochondrial length (ranging from 1.3 to 2.4 µm), diameter (0.18-0.24 µm) and volume density (3.7%-6.5%) between neurons of different function and neurotransmitter type, but found limited differences in mitochondrial length, diameter, and density between axons and dendrites of the same neurons. In analyses of mitochondrial distribution, mitochondria were found to be distributed randomly with respect to presynaptic sites. Presynaptic sites were primarily localized to varicosities, but mitochondria were no more likely to be found in synaptic varicosities than non-synaptic varicosities. Consistently, mitochondrial volume density was no greater in synaptic varicosities than non-synaptic varicosities. Therefore, beyond the capacity to disperse mitochondria throughout their length, at least in C. elegans, fine caliber neurons manifest limited subcellular control of mitochondrial size and distribution.
    Keywords:  electron microscopy; mitochondria; synapses
    DOI:  https://doi.org/10.1002/cne.70002
  37. bioRxiv. 2024 Dec 02. pii: 2024.12.02.626445. [Epub ahead of print]
    Human mitochondrial RNA polymerase structures reveal transcription start-site and slippage mechanism.
    Jiayu Shen, Quinten Goovaerts, Yogeeshwar Ajjugal, Brent De Wijngaert, Kalyan Das, Smita S Patel.
      Human mitochondrial RNA polymerase (POLRMT) and protein factors TFAM and TFB2M assemble on mitochondrial DNA promoters to initiate promoter-specific transcription. We present cryo-EM structures of two initiation complexes, IC3 and slipped-IC3, with fully resolved transcription bubbles containing RNA transcripts starting from +1 and -1 positions, respectively. These structures reveal the mechanisms of promoter melting, start site selection, and slippage synthesis. Promoter melting begins at -4 with base-specific interactions of -4 and -3 template guanines with POLRMT and -1 non-template adenine with TFB2M, stabilizing the bubble and facilitating initiation from +1. Slippage occurs when a synthesized 2-mer RNA shifts to -1; the -1 position is not an alternative start-site. The conserved non-template sequence (-1)AAA(+2) is recognized by a non-template stabilizing loop (K153LDPRSGGVIKPP165) and Y209 from TFB2M and W1026 of POLRMT. The initiation complex on cryo-EM grids exist in equilibrium with apo and dimeric POLRMTs, whose relative concentrations may regulate transcription initiation.
    Keywords:  POLRMT; TFAM; TFB2M; abortive synthesis; promoter melting; transcription initiation
    DOI:  https://doi.org/10.1101/2024.12.02.626445
  38. Subcell Biochem. 2024 ;107 63-90
    NAD+ Boosting Strategies.
    Jared Rice, Sofie Lautrup, Evandro F Fang.
      Nicotinamide adenine dinucleotide (oxidized form, NAD+) serves as a co-substrate and co-enzyme in cells to execute its key roles in cell signalling pathways and energetic metabolism, arbitrating cell survival and death. It was discovered in 1906 by Arthur Harden and William John Young in yeast extract which could accelerate alcohol fermentation. NAD acts as an electron acceptor and cofactor throughout the processes of glycolysis, Tricarboxylic Acid Cycle (TCA), β oxidation, and oxidative phosphorylation (OXPHOS). NAD has two forms: NAD+ and NADH. NAD+ is the oxidising coenzyme that is reduced when it picks up electrons. NAD+ levels steadily decline with age, resulting in an increase in vulnerability to chronic illness and perturbed cellular metabolism. Boosting NAD+ levels in various model organisms have resulted in improvements in healthspan and lifespan extension. These results have prompted a search for means by which NAD+ levels in the body can be augmented by both internal and external means. The aim of this chapter is to provide an overview of NAD+, appraise clinical evidence of its importance and success in potentially extending health- and lifespan, as well as to explore NAD+ boosting strategies.
    Keywords:  Ageing; Caloric restriction; NAD+; Neurodegeneration; Nicotinamide mononucleotide; Nicotinamide riboside; Oxidative stress; Supplementation
    DOI:  https://doi.org/10.1007/978-3-031-66768-8_4
  39. Curr Opin Neurol. 2024 Dec 23.
    Clinical trials in Leber hereditary optic neuropathy: outcomes and opportunities.
    Benson S Chen, Nancy J Newman.
       PURPOSE OF REVIEW: Leber hereditary optic neuropathy (LHON) is a mitochondrial DNA disease characterised by sequential bilateral vision loss due to loss of retinal ganglion cells. The purpose of this review is to provide an update on the results of recent clinical trials for LHON, focusing on studies of idebenone and lenadogene nolparvovec gene therapy.
    RECENT FINDINGS: Evidence from three clinical studies (RHODOS, RHODOS-OFU, and LEROS) suggest that idebenone should be started early and continued for at least 24 months. Treatment effect varies according to the stage of LHON and the underlying mutation. Favourable outcomes are associated with the m.11778G>A mutation and chronic eyes with the m.14484T>C mutation. Caution should be taken in subacute/dynamic eyes with the m.3460G>A mutation, due to possible clinical worsening with idebenone. Compared to eyes from an external natural history cohort, pooled data from four clinical studies (RESCUE, REVERSE, RESTORE and REFLECT) show that a single intravitreal injection of lenadogene nolparvovec can result in sustained bilateral visual improvement in m.11778G>A LHON patients aged ≥15 years when treated within 1 year of onset. Although the treatment effect is modest, the final visual acuity of treated patients (∼1.2 logMAR) significantly differs from the published natural history of LHON and the treatment benefit is more pronounced than the effect of idebenone alone in patients with the m.11778G>A mutation.
    SUMMARY: There is increasing evidence for the potential therapeutic benefit of idebenone and lenadogene nolparvovec gene therapy.
    DOI:  https://doi.org/10.1097/WCO.0000000000001343
  40. Sci Rep. 2024 12 16. 14(1): 30478
    Renal phenotyping in a hypomorphic murine model of propionic aciduria reveals common pathomechanisms in organic acidurias.
    Anke Schumann, Ainhoa Martinez-Pizarro, Eva Richard, Christoph Schell, Anna Laura Kössinger, Karina A Zeyer, Stefan Tholen, Oliver Schilling, Michael Barry, Björn Neubauer, Michael Köttgen, Luciana Hannibal, Lourdes R Desviat, Ute Spiekerkötter.
      Mutations in the mitochondrial enzyme propionyl-CoA carboxylase (PCC) cause propionic aciduria (PA). Chronic kidney disease (CKD) is a known long-term complication. However, good metabolic control and standard therapy fail to prevent CKD. The pathophysiological mechanisms of CKD are unclear. We investigated the renal phenotype of a hypomorphic murine PA model (Pcca-/-(A138T)) to identify CKD-driving mechanisms. Pcca-/-(A138T) mice show elevated retention parameters and express markers of kidney damage progressing with time. Morphological assessment of the Pcca-/-(A138T) mouse kidneys indicated partial flattening of tubular epithelial cells and focal tubular-cystic dilation. We observed altered renal mitochondrial ultrastructure and mechanisms acting against oxidative stress were active. LC-MS/MS analysis confirmed disease-specific metabolic signatures and revealed disturbances in mitochondrial energy generation via the TCA cycle. Our investigations revealed altered mitochondrial networks shifted towards fission and a marked reduction of mitophagy. We observed a steep reduction of PGC-1-α, the key mediator modulating mitochondrial functions and a counter actor of mitochondrial fission. Our results suggest that impairment of mitochondrial homeostasis and quality control are involved in CKD development in PA. Therapeutic targeting of the identified pathways might help to ameliorate CKD in addition to the current treatment strategies.
    Keywords:  Chronic kidney disease; Mitochondrial dysfunction; Mitochondrial energy metabolism; Mitochondrial fission; Mitochondrial homeostasis; Mitochondrial quality control; Propionic aciduria
    DOI:  https://doi.org/10.1038/s41598-024-79572-z
  41. Bio Protoc. 2024 Dec 05. 14(23): e5126
    In-Gel Activity Assay of Mammalian Mitochondrial and Cytosolic Aconitases, Surrogate Markers of Compartment-Specific Oxidative Stress and Iron Status.
    Wing-Hang Tong, Tracey A Rouault.
      Two aconitase isoforms are present in mammalian cells: the mitochondrial aconitase (ACO2) that catalyzes the reversible isomerization of citrate to isocitrate in the citric acid cycle, and the bifunctional cytosolic enzyme (ACO1), which also plays a role as an RNA-binding protein in the regulation of intracellular iron metabolism. Aconitase activities in the different subcellular compartments can be selectively inactivated by different genetic defects, iron depletion, and oxidative or nitrative stress. Aconitase contains a [4Fe-4S]2+ cluster that is essential for substrate coordination and catalysis. Many Fe-S clusters are sensitive to oxidative stress, nitrative stress, and reduced iron availability, which forms the basis of redox- and iron-mediated regulation of intermediary metabolism via aconitase and other Fe-S cluster-containing metabolic enzymes, such as succinate dehydrogenase. As such, ACO1 and ACO2 activities can serve as compartment-specific surrogate markers of oxygen levels, reactive oxygen species (ROS), reactive nitrogen species (RNS), iron bioavailability, and the status of intermediary and iron metabolism. Here, we provide a protocol describing a non-denaturing polyacrylamide gel electrophoresis (PAGE)-based procedure that has been successfully used to monitor ACO1 and ACO2 aconitase activities simultaneously in human and mouse cells and tissues. Key features • Monitoring aconitase activity changes in the mitochondria and cytosol simultaneously in response to oxidative or nitrative stress, iron depletion, and various pathophysiological conditions. • Optimized for human and mouse cell lines and tissue samples. • Semi-quantitative detection of aconitase isoforms with different states of phosphorylation and/or post-translational modification.
    Keywords:  ACO1; ACO2; Aconitase; IRE-BP1; IRP1; Iron metabolism; Iron regulatory protein 1; Iron response element binding protein 1; Nitrative stress; Oxidative stress
    DOI:  https://doi.org/10.21769/BioProtoc.5126
  42. Neurosci Insights. 2024 ;19 26331055241305151
    A Commentary on Mitochondrial Dysfunction and Compromised DNA Repair in Neurodegeneration: The Emerging Role of FUS in ALS.
    Manohar Kodavati, Muralidhar L Hegde.
      Mitochondrial dysfunction plays a pivotal role in the progression of neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), Alzheimer's, and Parkinson's disease. Recent discoveries have highlighted the involvement of DNA damage and repair processes, particularly mitochondrial DNA (mtDNA) damage, in these conditions. This commentary reflects on our recent findings, demonstrating the RNA/DNA binding protein fused in sarcoma (FUS)'s crucial role in maintaining mtDNA integrity through interactions with mitochondrial DNA ligase IIIα (mtLig3). Our studies provide direct evidence of increased mtDNA damage in ALS-linked FUS mutant cells, emphasizing the potential of targeting DNA repair pathways to mitigate neurodegeneration. Furthermore, the restoration of mitochondrial function through targeted expression of human DNA ligase 1 (Lig1) in FUS mutant models showcases the therapeutic promise of DNA repair mechanisms in neurodegenerative diseases. These insights offer new molecular understanding and open up future avenues for therapeutic interventions, particularly in FUS-associated ALS and related disorders.
    Keywords:  ALS; DNA damage; DNA ligase; mitochondria; neurodegeneration
    DOI:  https://doi.org/10.1177/26331055241305151
  43. Mol Cell Biochem. 2024 Dec 18.
    Phosphatase activity-based PPM1K: a key player in the regulation of mitochondrial function and its multifaceted impact in diseases.
    Yuanling Mao, Jing Feng.
      PPM1K is a significant metal-dependent phosphatase predominantly located in the mitochondrial matrix, where it plays a crucial role in the metabolism of branched-chain amino acids (BCAAs). It is implicated in cellular function and development across various tissues and is associated with diseases like Alzheimer's, cardiomyopathy, and maple syrup urine disease (MSUD). This article reviews PPM1K's impact on mitochondrial function and cellular metabolism, as well as its role in disease progression. The regulation of PPM1K expression and activity by various factors is complex and highlights its therapeutic potential. PPM1K's dysfunction can lead to the accumulation of BCAAs and the excessive opening of the mitochondrial permeability transition pore (MPTP), disrupting physiological metabolism and function. It also regulates the degradation of BCAAs by acting as a specific phosphatase for the E1α subunit of the BCKD complex. Outside the mitochondria, PPM1K suppresses de novo fatty acid synthesis and promotes fatty acid oxidation by dephosphorylating ACL. Furthermore, PPM1K has anti-inflammatory effects and modulates immune cell infiltration in tumor tissues. The expression and activity of PPM1K are influenced by factors such as BCAA concentration, fructose intake, and drug treatments, making it a promising target for therapeutic applications and further basic research.
    Keywords:  BCAAs; Cellular metabolism; Disease regulation; Mitochondrial function; PPM1K; Therapeutic potential
    DOI:  https://doi.org/10.1007/s11010-024-05188-6
  44. Autophagy. 2024 Dec 15.
    Endogenous interactomes of MFN1 and MFN2 provide novel insights into interorganelle communication and autophagy.
    Isabel Gordaliza-Alaguero, Paula Sànchez-Fernàndez-de-Landa, Dragana Radivojevikj, Laura Villarreal, Gianluca Arauz-Garofalo, Marina Gay, Marta Martinez-Vicente, Jorge Seco, Pau Martin-Malpartida, Marta Vilaseca, María J Macías, Manuel Palacin, Saška Ivanova, Antonio Zorzano.
      MFN1 (mitofusin 1) and MFN2 are key players in mitochondrial fusion, endoplasmic reticulum (ER)-mitochondria juxtaposition, and macroautophagy/autophagy. However, the mechanisms by which these proteins participate in these processes are poorly understood. Here, we studied the interactomes of these two proteins by using CRISPR-Cas9 technology to insert an HA-tag at the C terminus of MFN1 and MFN2, and thus generating HeLa cell lines that endogenously expressed MFN1-HA or MFN2-HA. HA-affinity isolation followed by mass spectrometry identified potential interactors of MFN1 and MFN2. A substantial proportion of interactors were common for MFN1 and MFN2 and were regulated by nutrient deprivation. We validated novel ER and endosomal partners of MFN1 and/or MFN2 with a potential role in interorganelle communication. We characterized RAB5C (RAB5C, member RAS oncogene family) as an endosomal modulator of mitochondrial homeostasis, and SLC27A2 (solute carrier family 27 (fatty acid transporter), member 2) as a novel partner of MFN2 relevant in autophagy. We conclude that MFN proteins participate in nutrient-modulated pathways involved in organelle communication and autophagy.
    Keywords:  Autophagosomes; endosomes; mitochondria; mitochondria-endoplasmic reticulum contact sites; mitochondrial dynamics; nutrient deprivation
    DOI:  https://doi.org/10.1080/15548627.2024.2440843
  45. Eur Heart J. 2024 Dec 06. pii: ehae821. [Epub ahead of print]
    Targeting mitochondrial fitness for cardioprotection.
    Sauri Hernandez-Resendiz, Derek J Hausenloy.
      
    DOI:  https://doi.org/10.1093/eurheartj/ehae821
  46. Science. 2024 Dec 20. 386(6728): eadp6547
    Boosting neuronal activity-driven mitochondrial DNA transcription improves cognition in aged mice.
    Wenwen Li, Jiarui Li, Jing Li, Chen Wei, Tal Laviv, Meiyi Dong, Jingran Lin, Mariah Calubag, Lesley A Colgan, Kai Jin, Bing Zhou, Ying Shen, Haohong Li, Yihui Cui, Zhihua Gao, Tao Li, Hailan Hu, Ryohei Yasuda, Huan Ma.
      Deciphering the complex interplay between neuronal activity and mitochondrial function is pivotal in understanding brain aging, a multifaceted process marked by declines in synaptic function and mitochondrial performance. Here, we identified an age-dependent coupling between neuronal and synaptic excitation and mitochondrial DNA transcription (E-TCmito), which operates differently compared to classic excitation-transcription coupling in the nucleus (E-TCnuc). We demonstrated that E-TCmito repurposes molecules traditionally associated with E-TCnuc to regulate mitochondrial DNA expression in areas closely linked to synaptic activation. The effectiveness of E-TCmito weakens with age, contributing to age-related neurological deficits in mice. Boosting brain E-TCmito in aged animals ameliorated these impairments, offering a potential target to counteract age-related cognitive decline.
    DOI:  https://doi.org/10.1126/science.adp6547
  47. Autophagy. 2024 Dec 19. 1-3
    Dynamic mitophagy trajectories hallmark brain aging.
    Anna Rappe, Thomas G McWilliams.
      Studies using mitophagy reporter mice have established steady-state landscapes of mitochondrial destruction in mammalian tissues, sparking intense interest in basal mitophagy. Yet how basal mitophagy is modified by healthy aging in diverse brain cell types has remained a mystery. We present a comprehensive spatiotemporal analysis of mitophagy and macroautophagy dynamics in the aging mammalian brain, reporting critical region- and cell-specific turnover trajectories in a longitudinal study. We demonstrate that the physiological regulation of mitophagy in the mammalian brain is cell-specific, dynamic and complex. Mitophagy increases significantly in the cerebellum and hippocampus during midlife, while remaining unchanged in the prefrontal cortex (PFC). Conversely, macroautophagy decreases in the hippocampus and PFC, but remains stable in the cerebellum. We also describe emergent lysosomal heterogeneity, with subsets of differential acidified lysosomes accumulating in the aging brain. We further establish midlife as a critical inflection point for autophagy regulation, which may be important for region-specific vulnerability and resilience to aging. By mapping in vivo autophagy dynamics at the single cell level within projection neurons, interneurons and microglia, to astrocytes and secretory cells, we provide a new framework for understanding brain aging and offer potential targets and timepoints for further study and intervention in neurodegenerative diseases.
    Keywords:  Aging; autophagy; brain; mitochondria; mitophagy
    DOI:  https://doi.org/10.1080/15548627.2024.2426115
  48. Elife. 2024 Dec 19. pii: RP91083. [Epub ahead of print]12
    Intramolecular feedback regulation of the LRRK2 Roc G domain by a LRRK2 kinase-dependent mechanism.
    Bernd K Gilsbach, Franz Y Ho, Benjamin Riebenbauer, Xiaojuan Zhang, Giambattista Guaitoli, Arjan Kortholt, Christian Johannes Gloeckner.
      The Parkinson's disease (PD)-linked protein Leucine-Rich Repeat Kinase 2 (LRRK2) consists of seven domains, including a kinase and a Roc G domain. Despite the availability of several high-resolution structures, the dynamic regulation of its unique intramolecular domain stack is nevertheless still not well understood. By in-depth biochemical analysis, assessing the Michaelis-Menten kinetics of the Roc G domain, we have confirmed that LRRK2 has, similar to other Roco protein family members, a KM value of LRRK2 that lies within the range of the physiological GTP concentrations within the cell. Furthermore, the R1441G PD variant located within a mutational hotspot in the Roc domain showed an increased catalytic efficiency. In contrast, the most common PD variant G2019S, located in the kinase domain, showed an increased KM and reduced catalytic efficiency, suggesting a negative feedback mechanism from the kinase domain to the G domain. Autophosphorylation of the G1+2 residue (T1343) in the Roc P-loop motif is critical for this phosphoregulation of both the KM and the kcat values of the Roc-catalyzed GTP hydrolysis, most likely by changing the monomer-dimer equilibrium. The LRRK2 T1343A variant has a similar increased kinase activity in cells compared to G2019S and the double mutant T1343A/G2019S has no further increased activity, suggesting that T1343 is crucial for the negative feedback in the LRRK2 signaling cascade. Together, our data reveal a novel intramolecular feedback regulation of the LRRK2 Roc G domain by a LRRK2 kinase-dependent mechanism. Interestingly, PD mutants differently change the kinetics of the GTPase cycle, which might in part explain the difference in penetrance of these mutations in PD patients.
    Keywords:  GTPase; LRRK2; Michaelis–Menten kinetics; PD; biochemistry; chemical biology; negative feedback loop; none; parkinson's disease
    DOI:  https://doi.org/10.7554/eLife.91083
  49. J Neurol. 2024 Dec 16. 272(1): 78
    Novel PNPLA8 variants associated with primary ovarian insufficiency, tremors, cerebellar ataxia and limb weakness: a case report and literature review.
    Bin Chen, Cuiping Zhang, Yun Yuan, Zhan Wang, Tao Cui, Gehong Dong, Hua Pan, Zaiqiang Zhang, Wei Li.
       BACKGROUND: PNPLA8 is a gene that causes an autosomal recessive mitochondrial disease characterised by microcephaly and intractable epilepsy in infants and cerebellar ataxia and limb weakness in adults. Herein, we report the clinical, muscle pathology, and brain imaging features of an adult patient with new variants of PNPLA8.
    METHODS: A 27-year-old Chinese woman presented with abnormal gait at age 11, remained amenorrhoeic with an infantile uterus at age 17, and presented with head and limb tremors at age 21. The results of brain magnetic resonance imaging suggested mild cerebellar atrophy. Whole-exome sequencing was performed, and mitochondrial and spinal cerebellar ataxia genes were screened. In addition, a biceps muscle biopsy was performed. Furthermore, a comprehensive literature search was conducted, and all patients with detailed clinical and genetic data up to October 2024 were included in the analysis.
    RESULTS: The patient's genetic screening revealed compound heterozygous variants c.1777T > G (p.Tyr593Asp) and c.1515-1516delTT (p.Tyr506Serfs*27) of PNPLA8 inherited from her parents. Her muscle biopsy showed mild myopathic changes on light microscopy and mitochondrial inclusions on electron microscopy. A total of 25 patients from 21 families were reviewed.
    CONCLUSION: Age of onset is a very important factor in terms of patient clinical phenotype and prognosis of PNPLA8-related disorders. It has been observed that adult females with PNPLA8 variants may present with primary ovarian dysfunction. The presence of mitochondrial inclusion bodies may serve as a pathological hallmark, extending the existing spectrum of the clinical phenotypes and pathogenic variants of PNPLA8.
    Keywords:   PNPLA8 ; Ataxia; Microcephaly; Mitochondrial inclusions; Primary ovarian insufficiency
    DOI:  https://doi.org/10.1007/s00415-024-12838-8
  50. medRxiv. 2024 Dec 08. pii: 2024.12.05.24318557. [Epub ahead of print]
    Epigenome-wide Association Analysis of Mitochondrial Heteroplasmy Provides Insight into Molecular Mechanisms of Disease.
    NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium
      The relationship between mitochondrial DNA (mtDNA) heteroplasmy and nuclear DNA (nDNA) methylation (CpGs) remains to be studied. We conducted an epigenome-wide association analysis of heteroplasmy burden scores across 10,986 participants (mean age 77, 63% women, and 54% non-White races/ethnicities) from seven population-based observational cohorts. We identified 412 CpGs (FDR p < 0.05) associated with mtDNA heteroplasmy. Higher levels of heteroplasmy burden were associated with lower nDNA methylation levels at most significant CpGs. Functional inference analyses of genes annotated to heteroplasmy-associated CpGs emphasized mitochondrial functions and showed enrichment in cardiometabolic conditions and traits. We developed CpG-scores based on heteroplasmy-count associated CpGs (MHC-CpG scores) using elastic net Cox regression in a training cohort. A one-unit higher level of the standardized MHC-CpG scores were associated with 1.26-fold higher hazard of all-cause mortality (95% CI: 1.14, 1.39) and 1.09-fold higher hazard of CVD (95% CI: 1.01-1.17) in the meta-analysis of testing cohorts, adjusting for age, sex, and smoking. These findings shed light on the relationship between mtDNA heteroplasmy and DNA methylation, and the role of heteroplasmy-associated CpGs as biomarkers in predicting all-cause mortality and cardiovascular disease.
    DOI:  https://doi.org/10.1101/2024.12.05.24318557
  51. Neurology. 2025 Jan 14. 104(1): e210106
    Exome and Genome Sequencing to Diagnose the Genetic Basis of Neonatal Hypotonia: An International Consortium Study.
    Sarah U Morton, Gregory Costain, Courtney E French, Emma Wakeling, Anna Szuto, John Christodoulou, Ronald Cohn, Basil T Darras, Monica H Wojcik, Alissa M D'Gama, James J Dowling, Sebastian Lunke, Francesco Muntoni, Lucy Raymond, David Rowitch, Alan H Beggs, Zornitza Stark, Pankaj B Agrawal.
       BACKGROUND AND OBJECTIVES: Hypotonia is a relatively common finding among infants in the neonatal intensive care unit (NICU). Consideration of genetic testing is recommended early in the care of infants with unexplained hypotonia. We aimed to assess the diagnostic yield and overall impact of exome and genome sequencing (ES and GS).
    METHODS: Consecutive infants with hypotonia were identified from research and clinical databases across 5 teaching hospitals in United States, Canada, United Kingdom, and Australia. Inclusion criteria included NICU admission and genetic evaluation. Infants with a known explanation for hypotonia were excluded. Data regarding infant characteristics, genetic testing, and diagnoses were collected. The primary outcome was identification of a molecular diagnosis. Impact on care was a secondary outcome. The Fisher exact and Wilcoxon rank-sum tests were used for statistical analysis.
    RESULTS: We identified 147 infants with unexplained hypotonia. The median gestational age was 39 weeks (interquartile range [IQR] 36-42 weeks), 77 (52%) were female, and the median age was 8 days at the time of evaluation (IQR 2-19 days). Eighty (54%) had hypotonia as the main clinical feature while 67 (46%) had additional multisystem involvement. Seventy-five (51%) underwent rapid ES, 44 (30%) rapid GS, 2 (1%) both ES and GS, and 26 (18%) were admitted before ES or GS became available. Of the 121 infants who underwent ES and/or GS, 72 (60%) had the primary outcome of a molecular diagnosis. In addition, 2 infants with mitochondrial genome variants were diagnosed by mitochondrial GS after negative ES, and one infant needed targeted testing to identify a short tandem repeat expansion missed by GS. The proportion diagnosed by ES and GS was not different between infants with hypotonia as the primary finding (37/56, 66%) and infants with multisystemic symptoms (35/65, 54%, odds ratio [OR] 1.7, CI 0.8-3.7, p value = 0.20). Testing was more likely to have an impact on care for infants receiving a genetic diagnosis (57/66 vs 14/33, OR 8.4, CI 2.9-26.1, p = 1.0E-05).
    DISCUSSION: Rapid ES and GS provided a molecular diagnosis for most of the infants with unexplained hypotonia who underwent testing. Further studies are needed to assess the generalizability of these findings as increased access to genetic testing becomes available.
    CLASSIFICATION OF EVIDENCE: This study provides Class IV evidence that in unexplained neonatal hypotonia, rapid ES or GS adds diagnostic specificity.
    DOI:  https://doi.org/10.1212/WNL.0000000000210106
  52. Nucleic Acids Res. 2024 Nov 30. pii: gkae1112. [Epub ahead of print]
    Optimization of ACE-tRNAs function in translation for suppression of nonsense mutations.
    Joseph J Porter, Wooree Ko, Emily G Sorensen, John D Lueck.
      Nonsense suppressor transfer RNAs (tRNAs) or AntiCodon-Edited tRNAs (ACE-tRNAs) have long been envisioned as a therapeutic approach to overcome genetic diseases resulting from the introduction of premature termination codons (PTCs). The ACE-tRNA approach for the rescue of PTCs has been hampered by ineffective delivery through available modalities for gene therapy. Here we have screened a series of ACE-tRNA expression cassette sequence libraries containing >1800 members in an effort to optimize ACE-tRNA function and provide a roadmap for optimization in the future. By optimizing PTC suppression efficiency of ACE-tRNAs, we have decreased the amount of ACE-tRNA required by ∼16-fold for the most common cystic fibrosis-causing PTCs.
    DOI:  https://doi.org/10.1093/nar/gkae1112
  53. Dis Model Mech. 2024 Dec 01. pii: dmm052218. [Epub ahead of print]17(12):
    Making sense of missense: challenges and opportunities in variant pathogenicity prediction.
    Ivan Molotkov, Elaine R Mardis, Mykyta Artomov.
      Computational tools for predicting variant pathogenicity are widely used to support clinical variant interpretation. Recently, several models, which do not rely on known variant classifications during training, have been developed. These approaches can potentially overcome biases of current clinical databases, such as misclassifications, and can potentially better generalize to novel, unclassified variants. AlphaMissense is one such model, built on the highly successful protein structure prediction model, AlphaFold. AlphaMissense has shown great performance in benchmarks of functional and clinical data, outperforming many supervised models that were trained on similar data. However, like other in silico predictors, AlphaMissense has notable limitations. As a large deep learning model, it lacks interpretability, does not assess the functional impact of variants, and provides pathogenicity scores that are not disease specific. Improving interpretability and precision in computational tools for variant interpretation remains a promising area for advancing clinical genetics.
    DOI:  https://doi.org/10.1242/dmm.052218
  54. J Clin Invest. 2024 Dec 16. pii: e176708. [Epub ahead of print]134(24):
    SGLT2 inhibition alters substrate utilization and mitochondrial redox in healthy and failing rat hearts.
    Leigh Goedeke, Yina Ma, Rafael C Gaspar, Ali Nasiri, Jieun Lee, Dongyan Zhang, Katrine Douglas Galsgaard, Xiaoyue Hu, Jiasheng Zhang, Nicole Guerrera, Xiruo Li, Traci LaMoia, Brandon T Hubbard, Sofie Haedersdal, Xiaohong Wu, John Stack, Sylvie Dufour, Gina Marie Butrico, Mario Kahn, Rachel J Perry, Gary W Cline, Lawrence H Young, Gerald I Shulman.
      Previous studies highlight the potential for sodium-glucose cotransporter type 2 (SGLT2) inhibitors (SGLT2i) to exert cardioprotective effects in heart failure by increasing plasma ketones and shifting myocardial fuel utilization toward ketone oxidation. However, SGLT2i have multiple in vivo effects and the differential impact of SGLT2i treatment and ketone supplementation on cardiac metabolism remains unclear. Here, using gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) methodology combined with infusions of [13C6]glucose or [13C4]βOHB, we demonstrate that acute SGLT2 inhibition with dapagliflozin shifts relative rates of myocardial mitochondrial metabolism toward ketone oxidation, decreasing pyruvate oxidation with little effect on fatty acid oxidation in awake rats. Shifts in myocardial ketone oxidation persisted when plasma glucose levels were maintained. In contrast, acute βOHB infusion similarly augmented ketone oxidation, but markedly reduced fatty acid oxidation and did not alter glucose uptake or pyruvate oxidation. After inducing heart failure, dapagliflozin increased relative rates of ketone and fatty acid oxidation, but decreased pyruvate oxidation. Dapagliflozin increased mitochondrial redox and reduced myocardial oxidative stress in heart failure, which was associated with improvements in left ventricular ejection fraction after 3 weeks of treatment. Thus, SGLT2i have pleiotropic effects on systemic and heart metabolism, which are distinct from ketone supplementation and may contribute to the long-term cardioprotective benefits of SGLT2i.
    Keywords:  Cardiology; Glucose metabolism; Intermediary metabolism; Metabolism; Mitochondria
    DOI:  https://doi.org/10.1172/JCI176708
  55. Protein Sci. 2025 Jan;34(1): e5233
    Predicting absolute protein folding stability using generative models.
    Matteo Cagiada, Sergey Ovchinnikov, Kresten Lindorff-Larsen.
      While there has been substantial progress in our ability to predict changes in protein stability due to amino acid substitutions, progress has been slower in methods to predict the absolute stability of a protein. Here, we show how a generative model for protein sequence can be leveraged to predict absolute protein stability. We benchmark our predictions across a broad set of proteins and find a mean error of 1.5 kcal/mol and a correlation coefficient of 0.7 for the absolute stability across a range of natural, small- to medium-sized proteins up to ca. 150 amino acid residues. We analyze current limitations and future directions including how such a model may be useful for predicting conformational free energies. Our approach is simple to use and freely available at an online implementation available via https://github.com/KULL-Centre/_2024_cagiada_stability.
    Keywords:  machine learning; protein folding; protein stability; thermodynamics
    DOI:  https://doi.org/10.1002/pro.5233
  56. JAMA Ophthalmol. 2024 Dec 19.
    Single-Eye Gene Therapy for Leber Hereditary Optic Neuropathy.
    Hendrik P N Scholl, Bence György.
      
    DOI:  https://doi.org/10.1001/jamaophthalmol.2024.5618
  57. J Mol Cell Cardiol Plus. 2024 Dec;pii: 100093. [Epub ahead of print]10
    Conditional ablation of MCU exacerbated cardiac pathology in a genetic arrhythmic model of CPVT.
    Arpita Deb, Brian D Tow, Jie Hao, Branden L Nguyen, Valeria Gomez, James A Stewart, Ashley J Smuder, Bjorn C Knollmann, Ying Wang, Bin Liu.
       Background: Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a genetic arrhythmic syndrome caused by mutations in the calcium (Ca2+) release channel ryanodine receptor (RyR2) and its accessory proteins. These mutations make the channel leaky, resulting in Ca2+-dependent arrhythmias. Besides arrhythmias, CPVT hearts typically lack structural cardiac remodeling, a characteristic often observed in other cardiac conditions (heart failure, prediabetes) also marked by RyR2 leak. Recent studies suggest that mitochondria are able to accommodate more Ca2+ influx to inhibit arrhythmias in CPVT. Thus, we hypothesize that CPVT mitochondria can absorb diastolic Ca2+ to protect the heart from cardiac remodeling.
    Methods and results: The Mitochondrial Ca2+ uniporter (MCU), the main mitochondrial Ca2+ uptake protein, was conditionally knocked out in a CPVT model of calsequestrin 2 (CASQ2) KO. In vivo cardiac function was impaired in the CASQ2-/--MCUCKO model as assessed by echocardiography. Cardiac dilation and cellular hypertrophy were also observed in the CASQ2-/--MCUCKO hearts. Live-cell imaging identified altered Ca2+ handling and increased oxidative stress in CASQ2-/--MCUCKO myocytes. The activation status of Ca2+-dependent remodeling pathways (CaMKII, Calcineurin) was not altered in the CASQ2-/--MCUCKO model. RNAseq identified changes in the transcriptome of the CASQ2-/--MCUCKO hearts, distinct from the classic cardiac remodeling program of fetal gene re-expression.
    Conclusions: We present genetic evidence that mitochondria play a protective role in CPVT. MCU-dependent Ca2+ uptake is crucial for preventing pathological cardiac remodeling in CPVT.
    Keywords:  Ca2+-dependent cardiomyopathy; RyR2 leak
    DOI:  https://doi.org/10.1016/j.jmccpl.2024.100093
  58. NPJ Genom Med. 2024 Dec 18. 9(1): 65
    Efficient reinterpretation of rare disease cases using Exomiser.
    Letizia Vestito, Julius O B Jacobsen, Susan Walker, Valentina Cipriani, Nomi L Harris, Melissa A Haendel, Christopher J Mungall, Peter Robinson, Damian Smedley.
      Whole genome sequencing has transformed rare disease research; however, 50-80% of rare disease patients remain undiagnosed after such testing. Regular reanalysis can identify new diagnoses, especially in newly discovered disease-gene associations, but efficient tools are required to support clinical interpretation. Exomiser, a phenotype-driven variant prioritisation tool, fulfils this role; within the 100,000 Genomes Project (100kGP), diagnoses were identified after reanalysis in 463 (2%) of 24,015 unsolved patients after previous analysis for variants in known disease genes. However, extensive manual interpretation was required. This led us to develop a reanalysis strategy to efficiently reveal candidates from recent disease gene discoveries or newly designated pathogenic/likely pathogenic variants. Optimal settings to highlight new candidates from Exomiser reanalysis were identified with high recall (82%) and precision (88%) when including Exomiser's automated ACMG/AMP classifier, which correctly converted 92% of variants from unknown significance to pathogenic/likely pathogenic. In conclusion, Exomiser efficiently reinterprets previously unsolved cases.
    DOI:  https://doi.org/10.1038/s41525-024-00456-2
  59. Trends Endocrinol Metab. 2024 Dec 17. pii: S1043-2760(24)00320-5. [Epub ahead of print]
    Inter-organ communication is a critical machinery to regulate metabolism and aging.
    Kyohei Tokizane, Shin-Ichiro Imai.
      Inter-organ communication (IOC) is a complex mechanism involved in maintaining metabolic homeostasis and healthy aging. Dysregulation of distinct forms of IOC is linked to metabolic derangements and age-related pathologies, implicating these processes as a potential target for therapeutic intervention to promote healthy aging. In this review, we delve into IOC mediated by hormonal signaling, circulating factors, organelle signaling, and neuronal networks and examine their roles in regulating metabolism and aging. Given the role of the hypothalamus as a high-order control center for aging and longevity, we particularly emphasize the importance of its communication with peripheral organs and pave the way for a better understanding of this critical machinery in metabolism and aging.
    Keywords:  aging; hypothalamus; inter-organ communication; metabolism
    DOI:  https://doi.org/10.1016/j.tem.2024.11.013
  60. Nanotoxicology. 2024 Dec;18(8): 707-723
    CoCrMo nanoparticle induces neurotoxicity mediated via mitochondrial dysfunction: a study model for implant derived nanoparticle effects.
    Priyadarshini Vijayakumar, Yongchao Mou, Xuejun Li, Jahnavi Anil, Neeraja Revi, Kai-Yuan Cheng, Mathew T Mathew, Divya Bijukumar.
      Toxicity associated with elevated levels of cobalt-chromium-molybdenum (CoCrMo) nanoparticles in total hip replacement (THR) patients has been a rising concern. Recent investigations demonstrated that these particles can induce polyneuropathy in THR patients. The current study aims to address a detailed molecular investigation of CoCrMo nanoparticle-mediated mitochondrial dynamics using induced pluripotent stem cell-derived neurons (iPSC neurons). Telencephalic neurons from iPSCs were used in this study. A statistically significant dose-dependent reduction in membrane potential and mitochondrial superoxide generation was observed after CoCrMo nanoparticle treatment. The gene expression analysis confirmed that the oxidative-specific genes were significantly upregulated in particle-treated cells compared to untreated cells. When iPSCs were exposed to CoCrMo nanoparticles, there was a significant reduction in the area, perimeter, and length of mitochondria. Live cell imaging (mitochondrial tracking) revealed a significant reduction in mitochondrial movements in the presence of CoCrMo nanoparticles. Further protein expression confirmed increased mitochondrial fission in CoCrMo particle-treated cells by significantly upregulating Drp-1 protein and downregulating Mfn-2. In conclusion, the results show that CoCrMo nanoparticles can significantly alter neuronal mitochondrial dynamics. The disturbance in balance restricts mitochondrial movement, reduces energy production, increases oxidative stress, and can cause subsequent neurodegeneration.
    Keywords:  CoCrMo; THR; iPSC neurons; mitochondrial dynamics; nanoparticles
    DOI:  https://doi.org/10.1080/17435390.2024.2438118
  61. Hum Mol Genet. 2024 Dec 04. pii: ddae171. [Epub ahead of print]
    Development of a riboflavin-responsive model of riboflavin transporter deficiency in zebrafish.
    Catherine M Choueiri, Jarred Lau, Emily O'Connor, Alicia DiBattista, Brittany Y Wong, Sally Spendiff, Rita Horvath, Izabella Pena, Alexander MacKenzie, Hanns Lochmüller.
      Riboflavin transporter deficiency (RTD) is a rare and progressive neurodegenerative disease resulting from the disruption of RFVT2- and RFVT3- mediated riboflavin transport caused by biallelic mutations in SLC52A2 and SLC52A3, respectively. The resulting impaired mitochondrial metabolism leads to sensorimotor neurodegeneration and symptoms including muscle weakness, respiratory difficulty, and sensorineural deafness. Although over 70% of patients with RTD improve following high-dose riboflavin supplementation, remaining patients either stabilise or continue to deteriorate. This may be due to the rapid excretion of central nervous system (CNS) riboflavin by organic anion transporter 3 (OAT-3), highlighting the need for alternative or supplemental RTD treatments. Probenecid is a promising therapeutic candidate for RTD due to its known inhibitory effect on OAT-3. Therefore, this study aimed to generate morpholino-mediated knockdowns of human SLC52A3 ortholog slc52a3 in zebrafish larvae for use in therapeutic screening of riboflavin and probenecid. Knockdown of slc52a3 resulted in an RTD-like phenotype indicative of altered neurodevelopment, hearing loss, and reduced mobility. This RTD-like phenotype overlaps with the phenotype of CRISPR/Cas9-mediated knockout of slc52a3 in zebrafish, is maintained following slc52a3 morpholino + p53 morpholino co-injection, and is rescued following slc52a3 morpholino + human SLC52A3 mRNA co-injection, indicating specificity of the knockdown. Riboflavin treatment alone ameliorates locomotor activity and hearing ability in slc52a3 morphants. Riboflavin and probenecid co-treatment provides an additional small benefit to hearing but not to locomotion. Our findings demonstrate that this model recapitulates both the RTD phenotype and the riboflavin-responsiveness of RTD patients, and possible therapeutic benefit conferred by probenecid warrants further investigation.
    Keywords:  CRISPR/Cas9; neurogenetics; riboflavin transporter deficiency; zebrafish
    DOI:  https://doi.org/10.1093/hmg/ddae171
  62. Int J Mol Sci. 2024 Nov 29. pii: 12860. [Epub ahead of print]25(23):
    Maternal Low-Protein Diet Leads to Mitochondrial Dysfunction and Impaired Energy Metabolism in the Skeletal Muscle of Male Rats.
    Vipin A Vidyadharan, Ancizar Betancourt, Craig Smith, Chellakkan S Blesson, Chandra Yallampalli.
      A prenatal low-protein (LP) diet disrupts glucose homeostasis in adult offspring. Skeletal muscles are one of the main sites of glucose clearance, and mitochondria residing in the muscle fibers are central to glucose homeostasis. Our previous studies indicated that impaired mitochondrial health is central to dysregulated glucose metabolism in the gastrocnemius muscle of the LP-programmed female rats. In addition, dysfunctional mitochondria are often an indicator of underlying irregularities in energy metabolism and metabolic inflexibility. Therefore, this study examined the mitochondrial function and metabolic flexibility in the skeletal muscles of prenatal LP-programmed adult male rats. Pregnant Wistar rats were randomly allotted to a control diet (20% protein) or an isocaloric LP diet (6% protein). Standard laboratory rat chow was given to the dams and the pups after delivery and weaning. Gene and protein expressions, mtDNA copy number, and electron microscopy were assessed in gastrocnemius (GS) muscle, and the mitochondrial oxygen consumption rate was determined using isolated flexor digitorum brevis muscle fibers. The genes associated with mitochondrial outer membrane fusion, mitofusin1 and 2 (Mfn1 and Mfn2), fission (Fis1), and biogenesis (Pgc1B, Nrf1, and Esrra) were lower in the LP group. Further, our functional studies showed that the ATP-linked oxygen consumption rate (OCR), maximal, spare respiratory, and non-mitochondrial respiration-associated OCRs were lower in the LP rats. Further, the mRNA and protein expressions of Ndufb8, a key factor involved in the complex-I catalytic activity, were downregulated in the LP group. In addition, the expression of genes linked to mitochondrial pyruvate transport (Mpc1) and metabolism (Pdha1) was lower in the LP group. In contrast, the expression of mitochondrial fatty acid transporters (Cpt1a and Cpt2) was higher in the LP when compared to the control group. However, electron microscopic analysis exhibited no difference in the mitochondrial ultrastructure in the LP muscle compared to the control. Altogether, our results indicate that the LP diet affects the mitochondrial complex-I integrity and dynamics and leads to altered expression of genes associated with substrate oxidation and mitochondrial dysfunction in the skeletal muscle of the male LP offspring.
    Keywords:  energy metabolism; fetal programming; low-protein diet; mitochondria; mitochondrial dynamics; mitochondrial dysfunction; skeletal muscle
    DOI:  https://doi.org/10.3390/ijms252312860
  63. medRxiv. 2024 Dec 06. pii: 2024.12.04.24318523. [Epub ahead of print]
    Consultation informs strategies to improve functional evidence use in variant classification.
    Rehan M Villani, Bronwyn Terrill, Emma Tudini, Maddison E McKenzie, Corrina C Cliffe, Christopher N Hahn, Ben Lundie, Tessa Mattiske, Ebony Matotek, Abbye E McEwen, Sarah L Nickerson, James Breen, Douglas M Fowler, John Christodoulou, Lea Starita, Alan F Rubin, Amanda B Spurdle.
      To determine if a variant identified by diagnostic genetic testing is causal for disease, applied genetics professionals evaluate all available evidence to assign a clinical classification. Experimental assay data can provide strong functional evidence for or against pathogenicity in variant classification, but appears to be underutilised. We surveyed genetic diagnostic professionals in Australasia to assess their application of functional evidence in clinical practice. Results indicated that survey respondents are not confident to apply functional evidence, mainly due to uncertainty around practice recommendations. Respondents also identified need for support resources, educational opportunities, and in particular requested expert recommendations and updated practice guidelines to improve translation of experimental data to curation evidence. As an initial step, we have collated a list of functional assays recommended by 19 ClinGen Variant Curation Expert Panels as a source of international expert opinion on functional evidence evaluation. Additional support resources for diagnostic practice are in development.
    DOI:  https://doi.org/10.1101/2024.12.04.24318523
  64. Ther Adv Rare Dis. 2024 Jan-Dec;5:5 26330040241307962
    Advancing rare disease measurement through the Rare Disease Clinical Outcome Assessment Consortium.
    Naomi Knoble, Lindsey T Murray.
      There is a significant unmet need to develop and evaluate new treatments for people living with one of approximately 8000 rare diseases. Well-known difficulties in conducting clinical trials (e.g., small samples, wide geographic distribution, heterogeneous symptoms) and developing products for these rare indications persist. Identifying outcomes in rare disease clinical trials remains a hurdle that contributes to the challenges for drug and gene therapy development due to uncertainty about what aspects of a condition to measure for safety and efficacy and often with no regulatory approval precedent. To accelerate rare disease treatments by advancing outcomes measurement, the US Food and Drug Administration (FDA) funded a cooperative agreement to establish the Rare Disease COA Consortium (RD-COAC) in 2019. The RD-COAC officially launched on January 1, 2022, with the mission to enable pre-competitive, multi-stakeholder collaboration aimed at identifying scientifically sound tools and methodologies for collecting clinically meaningful and patient-centric outcomes data in treatment trials for rare diseases. The RD-COAC has four complementary workstreams to advance COA measurement for rare disease clinical trials: (1) Rare Disease COA Resource; (2) Advancing COA Measurement Topic-Focused Working Groups; (3) Rare Disease Discussion Sessions for pre-competitive collaboration and shared learnings among RD-COAC members; and (4) Dissemination. This review provides an overview of the RD-COAC's activities to date, as well as future directions and opportunities to collaborate.
    Keywords:  COAs; Rare Disease COA Resource; clinical outcome assessments; pre-competitive multi-stakeholder consortium; rare disease
    DOI:  https://doi.org/10.1177/26330040241307962
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