bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2024–01–21
73 papers selected by
Catalina Vasilescu, Helmholz Munich
  1. A Homozygous NDUFS6 Variant Associated with Neuropathy and Optic Atrophy.
  2. A clinical approach to diagnosis and management of mitochondrial myopathies.
  3. The mitochondrial ATP-dependent potassium channel (mitoKATP) controls skeletal muscle structure and function.
  4. Partial loss of MCU mitigates pathology in vivo across a diverse range of neurodegenerative disease models.
  5. Activation of Ca2+ phosphatase Calcineurin regulates Parkin translocation to mitochondria and mitophagy in flies.
  6. Animal Models of Mitochondrial Diseases Associated with Nuclear Gene Mutations.
  7. Significance of quantitative analyses of the impact of heterogeneity in mitochondrial content and shape on cell differentiation.
  8. Identification of SLC25A46 interaction interfaces with mitochondrial membrane fusogens Mfn2 and Opa1.
  9. Multifaceted roles of t6A biogenesis in efficiency and fidelity of mitochondrial gene expression.
  10. Residual Complex I activity and amphidirectional Complex II operation support glutamate catabolism through mtSLP in anoxia.
  11. Mitochondrial Complex I Deficiency Masquerading as Stroke-Like Episode Clinically and as Alexander Disease Radiologically Following Chicken Pox.
  12. NAD+ dependent UPRmt activation underlies intestinal aging caused by mitochondrial DNA mutations.
  13. Mitochondrial permeability transition pore: a snapshot of a therapeutic target.
  14. Mitochondrial Dynamics, Diabetes, and Cardiovascular Disease.
  15. The expanding diagnostic toolbox for rare genetic diseases.
  16. Multi-level profiling unravels mitochondrial dysfunction in myotonic dystrophy type 2.
  17. In situ architecture of Opa1-dependent mitochondrial cristae remodeling.
  18. [Rare pathogenic nucleotide variants of mitochondrial DNA associated with Leber's hereditary optic neuropathy].
  19. Nuclear NAD+ deficiency by NMNAT1 deletion impaired hepatic insulin signaling, mitochondrial function and hepatokine expression in mice fed a high-fat diet.
  20. Angiogenic activity of mitochondria; beyond the sole bioenergetic organelle.
  21. Optimizing metabolism is a complex issue.
  22. Intracellular delivery of Parkin-RING0-based fragments corrects Parkin-induced mitochondrial dysfunction through interaction with SLP-2.
  23. Parkinson's Disease Is Predominantly an Environmental Disease.
  24. Cellular and Molecular Responses to Mitochondrial DNA Deletions in Kearns-Sayre Syndrome: Some Underlying Mechanisms.
  25. USP30 inhibition induces mitophagy and reduces oxidative stress in parkin-deficient human neurons.
  26. Mitochondrial stress activates YAP/TAZ through RhoA oxidation to promote liver injury.
  27. A Pair of Compound Heterozygous IARS2 Variants Manifesting West Syndrome and Electrolyte Disorders in a Chinese Patient.
  28. PMPCA-Related Encephalopathy: Novel Variants, Phenotype Extension, and Mitochondrial Morphology.
  29. Integration of multi-omics technologies for molecular diagnosis in ataxia patients.
  30. Extracellular vesicle mitochondrial DNA levels are associated with race and mitochondrial DNA haplogroup.
  31. Characterization of Fatigue in Primary Mitochondrial Myopathies: Findings From a Qualitative Interview Study.
  32. Mitochondrial dysfunction in neurodegenerative disorders.
  33. STIGMA: Single-cell tissue-specific gene prioritization using machine learning.
  34. Mitochondrial defects triggered by amg-1 mutation elicit UPRmt and phagocytic clearance during spermatogenesis in C. elegans.
  35. Elevated cholesterol in ATAD3 mutants is a compensatory mechanism that leads to membrane cholesterol aggregation.
  36. Spatial multi-omics: novel tools to study the complexity of cardiovascular diseases.
  37. Neuroimaging changes in the pregeniculate visual pathway and chiasmal enlargement in Leber hereditary optic neuropathy.
  38. Loss of the WDR23 proteostasis impacts mitochondrial homeostasis in the mouse brain.
  39. Nanoarchitectonics with a Membrane-Embedded Electron Shuttle Mimics the Bioenergy Anabolism of Mitochondria.
  40. The potency of mitochondria enlargement for mitochondria-mediated terpenoid production in yeast.
  41. Testing a Hypothesis of 12S rRNA Methylation by Putative METTL17 Methyltransferase.
  42. [Long-term changes in morphological and functional parameters of the optic nerve in patients with various genetic variants of hereditary optic neuropathies].
  43. G-quadruplex in mitochondria as a possible biomarker for mitophagy detection.
  44. Genetically encoded tool for manipulation of ΔΨm identifies the latter as the driver of integrative stress response induced by ATP Synthase dysfunction.
  45. Causality-enriched epigenetic age uncouples damage and adaptation.
  46. Gene therapy for neurotransmitter-related disorders.
  47. Maternally Inherited Essential Hypertension May Be Associated with the Mutations in Mitochondrial tRNAGlu Gene.
  48. Exploring the complexities of 1C metabolism: implications in aging and neurodegenerative diseases.
  49. Glucose-derived glutamate drives neuronal terminal differentiation in vitro.
  50. Unraveling the causes of sarcopenia: Roles of neuromuscular junction impairment and mitochondrial dysfunction.
  51. Using MitER for 3D analysis of mitochondrial morphology and ER contacts.
  52. Obstetric complications in women with mitochondrial disease.
  53. Development of a mouse model expressing a bifunctional glutathione synthesizing enzyme to study glutathione limitation in vivo.
  54. Platelet Mitochondrial Fusion and Function in Vascular Integrity.
  55. Metabolic Bypass Rescues Aberrant S-nitrosylation-Induced TCA Cycle Inhibition and Synapse Loss in Alzheimer's Disease Human Neurons.
  56. Pathogenicity classification of missense mutations based on deep generative model.
  57. Making the connection: How membrane contact sites have changed our view of organelle biology.
  58. Nucleoside modification-based flexizymes with versatile activity for tRNA aminoacylation.
  59. Meet the authors: Yuqiu Sun and Hui Jiang.
  60. Quantum Sensing of Free Radical Generation in Mitochondria of Single Heart Muscle Cells during Hypoxia and Reoxygenation.
  61. Interaction of PINK1 with nucleotides and kinetin.
  62. The impact of bed rest on human skeletal muscle metabolism.
  63. Integrative detection of genome-wide translation using iRibo.
  64. Analysis of α-syn and parkin interaction in mediating neuronal death in Drosophila model of Parkinson's disease.
  65. MITOL deficiency triggers hematopoietic stem cell apoptosis via ER stress response.
  66. Stroke-Like Episodes and Epilepsy in a Patient with COQ8A-Related Coenzyme Q10 Deficiency.
  67. Nanoparticle-based therapeutic strategies for mitochondrial dysfunction in cardiovascular disease.
  68. Does generative AI help academics to do more or less?
  69. mt-tRNAs in the polymerase gamma mutant heart.
  70. An ETFDH-driven metabolon supports OXPHOS efficiency in skeletal muscle by regulating coenzyme Q homeostasis.
  71. Homocysteine and mitochondrial quality control in diabetic retinopathy.
  72. The BCKDH kinase inhibitor BT2 promotes BCAA disposal and mitochondrial proton leak in both insulin-sensitive and insulin-resistant C2C12 myotubes.
  73. Wearable robot helps man with Parkinson's disease to walk.
  1. J Neuromuscul Dis. 2024 Jan 08.
    A Homozygous NDUFS6 Variant Associated with Neuropathy and Optic Atrophy.
    Andrea Gangfuß, Philipp Rating, Tomas Ferreira, Andreas Hentschel, Adela Della Marina, Heike Kölbel, Albert Sickmann, Angela Abicht, Florian Kraft, Tobias Ruck, Johann Böhm, Anne Schänzer, Ulrike Schara-Schmidt, Teresa M Neuhann, Rita Horvath, Andreas Roos.
       BACKGROUND: The NADH dehydrogenase [ubiquinone] iron-sulfur protein 6 (NDUFS6) gene encodes for an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (complex I). Bi-allelic NDUFS6 variants have been linked with a severe disorder mostly reported as a lethal infantile mitochondrial disease (LMID) or Leigh syndrome (LS).
    OBJECTIVE: Here, we identified a homozygous variant (c.309 + 5 G >  A) in NDUFS6 in one male patient with axonal neuropathy accompanied by loss of small fibers in skin biopsy and further complicated by optic atrophy and borderline intellectual disability.
    METHODS: To address the pathogenicity of the variant, biochemical studies (mtDNA copy number quantification, ELISA, Proteomic profiling) of patient-derived leukocytes were performed.
    RESULTS: The analyses revealed loss of NDUFS6 protein associated with a decrease of three further mitochondrial NADH dehydrogenase subunit/assembly proteins (NDUFA12, NDUFS4 and NDUFV1). Mitochondrial copy number is not altered in leukocytes and the mitochondrial biomarker GDF15 is not significantly changed in serum.
    CONCLUSIONS: Hence, our combined clinical and biochemical data strengthen the concept of NDUFS6 being causative for a very rare form of axonal neuropathy associated with optic atrophy and borderline intellectual disability, and thus expand (i) the molecular genetic landscape of neuropathies and (ii) the clinical spectrum of NDUFS6-associated phenotypes.
    Keywords:  Charcot-Marie-Tooth disease; NDUFS6; axonal neuropathy; white blood cell proteomics
    DOI:  https://doi.org/10.3233/JND-230181
  2. Neurotherapeutics. 2023 Dec 19. pii: S1878-7479(23)01940-2. [Epub ahead of print]21(1): e00304
    A clinical approach to diagnosis and management of mitochondrial myopathies.
    Hui-Lin Chin, Poh San Lai, Stacey Kiat Hong Tay.
      This paper provides an overview of the different types of mitochondrial myopathies (MM), associated phenotypes, genotypes as well as a practical clinical approach towards disease diagnosis, surveillance, and management. nDNA-related MM are more common in pediatric-onset disease whilst mtDNA-related MMs are more frequent in adults. Genotype-phenotype correlation in MM is challenging due to clinical and genetic heterogeneity. The multisystemic nature of many MMs adds to the diagnostic challenge. Diagnostic approaches utilizing genetic sequencing with next generation sequencing approaches such as gene panel, exome and genome sequencing are available. This aids molecular diagnosis, heteroplasmy detection in MM patients and furthers knowledge of known mitochondrial genes. Precise disease diagnosis can end the diagnostic odyssey for patients, avoid unnecessary testing, provide prognosis, facilitate anticipatory management, and enable access to available therapies or clinical trials. Adjunctive tests such as functional and exercise testing could aid surveillance of MM patients. Management requires a multi-disciplinary approach, systemic screening for comorbidities, cofactor supplementation, avoidance of substances that inhibit the respiratory chain and exercise training. This update of the current understanding on MMs provides practical perspectives on current diagnostic and management approaches for this complex group of disorders.
    Keywords:  Diagnostic approach; Genetic sequencing; Mitochondrial disease; Mitochondrial disease treatment; Mitochondrial myopathy
    DOI:  https://doi.org/10.1016/j.neurot.2023.11.001
  3. Cell Death Dis. 2024 Jan 17. 15(1): 58
    The mitochondrial ATP-dependent potassium channel (mitoKATP) controls skeletal muscle structure and function.
    Giulia Di Marco, Gaia Gherardi, Agnese De Mario, Ilaria Piazza, Martina Baraldo, Andrea Mattarei, Bert Blaauw, Rosario Rizzuto, Diego De Stefani, Cristina Mammucari.
      MitoKATP is a channel of the inner mitochondrial membrane that controls mitochondrial K+ influx according to ATP availability. Recently, the genes encoding the pore-forming (MITOK) and the regulatory ATP-sensitive (MITOSUR) subunits of mitoKATP were identified, allowing the genetic manipulation of the channel. Here, we analyzed the role of mitoKATP in determining skeletal muscle structure and activity. Mitok-/- muscles were characterized by mitochondrial cristae remodeling and defective oxidative metabolism, with consequent impairment of exercise performance and altered response to damaging muscle contractions. On the other hand, constitutive mitochondrial K+ influx by MITOK overexpression in the skeletal muscle triggered overt mitochondrial dysfunction and energy default, increased protein polyubiquitination, aberrant autophagy flux, and induction of a stress response program. MITOK overexpressing muscles were therefore severely atrophic. Thus, the proper modulation of mitoKATP activity is required for the maintenance of skeletal muscle homeostasis and function.
    DOI:  https://doi.org/10.1038/s41419-024-06426-x
  4. Cell Rep. 2024 Jan 17. pii: S2211-1247(24)00009-3. [Epub ahead of print]43(2): 113681
    Partial loss of MCU mitigates pathology in vivo across a diverse range of neurodegenerative disease models.
    Madeleine J Twyning, Roberta Tufi, Thomas P Gleeson, Kinga M Kolodziej, Susanna Campesan, Ana Terriente-Felix, Lewis Collins, Federica De Lazzari, Flaviano Giorgini, Alexander J Whitworth.
      Mitochondrial calcium (Ca2+) uptake augments metabolic processes and buffers cytosolic Ca2+ levels; however, excessive mitochondrial Ca2+ can cause cell death. Disrupted mitochondrial function and Ca2+ homeostasis are linked to numerous neurodegenerative diseases (NDs), but the impact of mitochondrial Ca2+ disruption is not well understood. Here, we show that Drosophila models of multiple NDs (Parkinson's, Huntington's, Alzheimer's, and frontotemporal dementia) reveal a consistent increase in neuronal mitochondrial Ca2+ levels, as well as reduced mitochondrial Ca2+ buffering capacity, associated with increased mitochondria-endoplasmic reticulum contact sites (MERCs). Importantly, loss of the mitochondrial Ca2+ uptake channel MCU or overexpression of the efflux channel NCLX robustly suppresses key pathological phenotypes across these ND models. Thus, mitochondrial Ca2+ imbalance is a common feature of diverse NDs in vivo and is an important contributor to the disease pathogenesis. The broad beneficial effects from partial loss of MCU across these models presents a common, druggable target for therapeutic intervention.
    Keywords:  Alzheimer's disease; CP: Neuroscience; Drosophila; Huntington's disease; MCU; NCLX; Parkinson's disease; calcium overload; frontotemporal dementia; mitochondrial calcium; neurodegeneration
    DOI:  https://doi.org/10.1016/j.celrep.2024.113681
  5. Cell Death Differ. 2024 Jan 18.
    Activation of Ca2+ phosphatase Calcineurin regulates Parkin translocation to mitochondria and mitophagy in flies.
    Elena Marchesan, Alice Nardin, Sofia Mauri, Greta Bernardo, Vivek Chander, Simone Di Paola, Monica Chinellato, Sophia von Stockum, Joy Chakraborty, Stephanie Herkenne, Valentina Basso, Emilie Schrepfer, Oriano Marin, Laura Cendron, Diego L Medina, Luca Scorrano, Elena Ziviani.
      Selective removal of dysfunctional mitochondria via autophagy is crucial for the maintenance of cellular homeostasis. This event is initiated by the translocation of the E3 ubiquitin ligase Parkin to damaged mitochondria, and it requires the Serine/Threonine-protein kinase PINK1. In a coordinated set of events, PINK1 operates upstream of Parkin in a linear pathway that leads to the phosphorylation of Parkin, Ubiquitin, and Parkin mitochondrial substrates, to promote ubiquitination of outer mitochondrial membrane proteins. Ubiquitin-decorated mitochondria are selectively recruiting autophagy receptors, which are required to terminate the organelle via autophagy. In this work, we show a previously uncharacterized molecular pathway that correlates the activation of the Ca2+-dependent phosphatase Calcineurin to Parkin translocation and Parkin-dependent mitophagy. Calcineurin downregulation or genetic inhibition prevents Parkin translocation to CCCP-treated mitochondria and impairs stress-induced mitophagy, whereas Calcineurin activation promotes Parkin mitochondrial recruitment and basal mitophagy. Calcineurin interacts with Parkin, and promotes Parkin translocation in the absence of PINK1, but requires PINK1 expression to execute mitophagy in MEF cells. Genetic activation of Calcineurin in vivo boosts basal mitophagy in neurons and corrects locomotor dysfunction and mitochondrial respiratory defects of a Drosophila model of impaired mitochondrial functions. Our study identifies Calcineurin as a novel key player in the regulation of Parkin translocation and mitophagy.
    DOI:  https://doi.org/10.1038/s41418-023-01251-9
  6. Acta Naturae. 2023 Oct-Dec;15(4):15(4): 4-22
    Animal Models of Mitochondrial Diseases Associated with Nuclear Gene Mutations.
    O A Averina, S A Kuznetsova, O A Permyakov, P V Sergiev.
      Mitochondrial diseases (MDs) associated with nuclear gene mutations are part of a large group of inherited diseases caused by the suppression of energy metabolism. These diseases are of particular interest, because nuclear genes encode not only most of the structural proteins of the oxidative phosphorylation system (OXPHOS), but also all the proteins involved in the OXPHOS protein import from the cytoplasm and their assembly in mitochondria. Defects in any of these proteins can lead to functional impairment of the respiratory chain, including dysfunction of complex I that plays a central role in cellular respiration and oxidative phosphorylation, which is the most common cause of mitopathologies. Mitochondrial diseases are characterized by an early age of onset and a progressive course and affect primarily energy-consuming tissues and organs. The treatment of MDs should be initiated as soon as possible, but the diagnosis of mitopathologies is extremely difficult because of their heterogeneity and overlapping clinical features. The molecular pathogenesis of mitochondrial diseases is investigated using animal models: i.e. animals carrying mutations causing MD symptoms in humans. The use of mutant animal models opens new opportunities in the study of genes encoding mitochondrial proteins, as well as the molecular mechanisms of mitopathology development, which is necessary for improving diagnosis and developing approaches to drug therapy. In this review, we present the most recent information on mitochondrial diseases associated with nuclear gene mutations and animal models developed to investigate them.
    Keywords:  animal models; mitochondrial diseases; mutations; nDNA
    DOI:  https://doi.org/10.32607/actanaturae.25442
  7. Open Biol. 2024 Jan;14(1): 230279
    Significance of quantitative analyses of the impact of heterogeneity in mitochondrial content and shape on cell differentiation.
    Swati Agarwala, Sukhamoy Dhabal, Kasturi Mitra.
      Mitochondria, classically known as the powerhouse of cells, are unique double membrane-bound multifaceted organelles carrying a genome. Mitochondrial content varies between cell types and precisely doubles within cells during each proliferating cycle. Mitochondrial content also increases to a variable degree during cell differentiation triggered after exit from the proliferating cycle. The mitochondrial content is primarily maintained by the regulation of mitochondrial biogenesis, while damaged mitochondria are eliminated from the cells by mitophagy. In any cell with a given mitochondrial content, the steady-state mitochondrial number and shape are determined by a balance between mitochondrial fission and fusion processes. The increase in mitochondrial content and alteration in mitochondrial fission and fusion are causatively linked with the process of differentiation. Here, we critically review the quantitative aspects in the detection methods of mitochondrial content and shape. Thereafter, we quantitatively link these mitochondrial properties in differentiating cells and highlight the implications of such quantitative link on stem cell functionality. Finally, we discuss an example of cell size regulation predicted from quantitative analysis of mitochondrial shape and content. To highlight the significance of quantitative analyses of these mitochondrial properties, we propose three independent rationale based hypotheses and the relevant experimental designs to test them.
    Keywords:  cell differentiation; cell proliferation; mitochondrial content; mitochondrial heterogeneity; mitochondrial shape; stem cells
    DOI:  https://doi.org/10.1098/rsob.230279
  8. bioRxiv. 2023 Dec 29. pii: 2023.12.29.573615. [Epub ahead of print]
    Identification of SLC25A46 interaction interfaces with mitochondrial membrane fusogens Mfn2 and Opa1.
    Sivakumar Boopathy, Camila Makhlouta Lugo, Bridget E Luce, Julie L McDonald, Pusparanee Hakim, Jackeline Ponce, Beatrix Ueberheide, Luke H Chao.
      Mitochondrial fusion requires the sequential merger of four bilayers to two. The outer-membrane solute carrier protein SLC25A46 interacts with both the outer and inner-membrane dynamin family GTPases Mfn1/2 and Opa1. While SLC25A46 levels are known affect mitochondrial morphology, how SLC25A46 interacts with Mfn1/2 and Opa1 to regulate membrane fusion is not understood. In this study, we use crosslinking mass-spectrometry and AlphaFold 2 modeling to identify interfaces mediating a SLC25A46-Opa1-Mfn1/2 complex. We reveal that the bundle signaling element of Opa1 interacts with SLC25A46, and the helical repeat 1 region of Mfn2 interacts with the SLC25A46 N-terminus. We validate these newly identified interaction interfaces and show that they play a role in mitochondrial network maintenance.
    DOI:  https://doi.org/10.1101/2023.12.29.573615
  9. Nucleic Acids Res. 2024 Jan 16. pii: gkae013. [Epub ahead of print]
    Multifaceted roles of t6A biogenesis in efficiency and fidelity of mitochondrial gene expression.
    Yong Zhang, Jing-Bo Zhou, Yue Yin, En-Duo Wang, Xiao-Long Zhou.
      N 6-Threonylcarbamoyladenosine at A37 (t6A37) of ANN-decoding transfer RNAs (tRNAs) is a universal modification whose functions have been well documented in bacteria and lower eukaryotes; however, its role in organellar translation is not completely understood. In this study, we deleted the mitochondrial t6A37-modifying enzyme OSGEPL1 in HEK293T cells. OSGEPL1 is dispensable for cell viability. t6A37 hypomodification selectively stimulated N1-methyladenosine at A9 (m1A9) and N2-methylguanosine at G10 (m2G10) modifications and caused a substantial reduction in the aminoacylation of mitochondrial tRNAThr and tRNALys, resulting in impaired translation efficiency. Multiple types of amino acid misincorporation due to the misreading of near-cognate codons by t6A37-unmodified tRNAs were detected, indicating a triggered translational infidelity. Accordingly, the alterations in mitochondrial structure, function, and the activated mitochondrial unfolded protein response were observed. Mitochondrial function was efficiently restored by wild-type, but not by tRNA-binding-defective OSGEPL1. Lastly, in Osgepl1 deletion mice, disruption to mitochondrial translation was evident but resulted in no observable deficiency under physiological conditions in heart, which displays the highest Osgepl1 expression. Taken together, our data delineate the multifaceted roles of mitochondrial t6A37 modification in translation efficiency and quality control in mitochondria.
    DOI:  https://doi.org/10.1093/nar/gkae013
  10. Sci Rep. 2024 Jan 19. 14(1): 1729
    Residual Complex I activity and amphidirectional Complex II operation support glutamate catabolism through mtSLP in anoxia.
    Dora Ravasz, David Bui, Sara Nazarian, Gergely Pallag, Noemi Karnok, Jennie Roberts, Bryan P Marzullo, Daniel A Tennant, Bennett Greenwood, Alex Kitayev, Collin Hill, Timea Komlódi, Carolina Doerrier, Kristyna Cunatova, Erika Fernandez-Vizarra, Erich Gnaiger, Michael A Kiebish, Alexandra Raska, Krasimir Kolev, Bence Czumbel, Niven R Narain, Thomas N Seyfried, Christos Chinopoulos.
      Anoxia halts oxidative phosphorylation (OXPHOS) causing an accumulation of reduced compounds in the mitochondrial matrix which impedes dehydrogenases. By simultaneously measuring oxygen concentration, NADH autofluorescence, mitochondrial membrane potential and ubiquinone reduction extent in isolated mitochondria in real-time, we demonstrate that Complex I utilized endogenous quinones to oxidize NADH under acute anoxia. 13C metabolic tracing or untargeted analysis of metabolites extracted during anoxia in the presence or absence of site-specific inhibitors of the electron transfer system showed that NAD+ regenerated by Complex I is reduced by the 2-oxoglutarate dehydrogenase Complex yielding succinyl-CoA supporting mitochondrial substrate-level phosphorylation (mtSLP), releasing succinate. Complex II operated amphidirectionally during the anoxic event, providing quinones to Complex I and reducing fumarate to succinate. Our results highlight the importance of quinone provision to Complex I oxidizing NADH maintaining glutamate catabolism and mtSLP in the absence of OXPHOS.
    DOI:  https://doi.org/10.1038/s41598-024-51365-4
  11. Ann Indian Acad Neurol. 2023 Nov-Dec;26(6):26(6): 977-979
    Mitochondrial Complex I Deficiency Masquerading as Stroke-Like Episode Clinically and as Alexander Disease Radiologically Following Chicken Pox.
    Vykuntaraju K Gowda, Arun Y Bylappa, Uddhav Kinhal, Varunvenkat M Srinivasan, Dhananjaya K Vamyanmane.
      Mitochondrial disorders are a group of metabolic disorders with variable presentation and usually affect organs with high energy requirements like the brain, eye, and heart. Seventeen-month-old girl child presented with right hemiparesis and regression of milestones following chicken pox. Investigations showed elevated lactate, white matter signal changes in both periventricular and subcortical white matter with frontal predominance in the MRI of the brain, cardiomyopathy in the echocardiography, with complex I deficiency in respiratory enzyme assay in the muscle biopsy. A homozygous missense variant c.304C>T (p. Arg102Cys) in exon 5 of NDUFS8 gene (chr11:67800682C>T; NM_002496.4) was detected on whole exome sequencing with positive parental Sanger for the same gene. The child was started on a mitochondrial cocktail, ramipril, and frusemide. Mitochondrial complex deficiency should be considered in cases with stroke-like episodes, and predominant white matter involvement on imaging mimicking classical genetic leukodystrophy like Alexander disease.
    Keywords:  Alexander disease; India; NDUFS8 gene; mitochondrial disorder; stroke-like episodes
    DOI:  https://doi.org/10.4103/aian.aian_339_23
  12. Nat Commun. 2024 Jan 16. 15(1): 546
    NAD+ dependent UPRmt activation underlies intestinal aging caused by mitochondrial DNA mutations.
    Liang Yang, Zifeng Ruan, Xiaobing Lin, Hao Wang, Yanmin Xin, Haite Tang, Zhijuan Hu, Yunhao Zhou, Yi Wu, Junwei Wang, Dajiang Qin, Gang Lu, Kerry M Loomes, Wai-Yee Chan, Xingguo Liu.
      Aging in mammals is accompanied by an imbalance of intestinal homeostasis and accumulation of mitochondrial DNA (mtDNA) mutations. However, little is known about how accumulated mtDNA mutations modulate intestinal homeostasis. We observe the accumulation of mtDNA mutations in the small intestine of aged male mice, suggesting an association with physiological intestinal aging. Using polymerase gamma (POLG) mutator mice and wild-type mice, we generate male mice with progressive mtDNA mutation burdens. Investigation utilizing organoid technology and in vivo intestinal stem cell labeling reveals decreased colony formation efficiency of intestinal crypts and LGR5-expressing intestinal stem cells in response to a threshold mtDNA mutation burden. Mechanistically, increased mtDNA mutation burden exacerbates the aging phenotype of the small intestine through ATF5 dependent mitochondrial unfolded protein response (UPRmt) activation. This aging phenotype is reversed by supplementation with the NAD+ precursor, NMN. Thus, we uncover a NAD+ dependent UPRmt triggered by mtDNA mutations that regulates the intestinal aging.
    DOI:  https://doi.org/10.1038/s41467-024-44808-z
  13. Expert Opin Ther Targets. 2024 Jan 18. 1-3
    Mitochondrial permeability transition pore: a snapshot of a therapeutic target.
    Mario Zoratti, Lucia Biasutto, Sofia Parrasia, Ildikó Szabo.
      
    Keywords:  ATP synthase; Adenine nucleotide translocator; SLC25 transporters; cancer; ischemia reperfusion injury; mitochondria; mitochondrial protein import systems; permeability transition pore
    DOI:  https://doi.org/10.1080/14728222.2024.2306337
  14. Diabetes. 2024 Feb 01. 73(2): 151-161
    Mitochondrial Dynamics, Diabetes, and Cardiovascular Disease.
    Luis Miguel García-Peña, E Dale Abel, Renata O Pereira.
      Mitochondria undergo repeated cycles of fusion and fission that regulate their size and shape by a process known as mitochondrial dynamics. Numerous studies have revealed the importance of this process in maintaining mitochondrial health and cellular homeostasis, particularly in highly metabolically active tissues such as skeletal muscle and the heart. Here, we review the literature on the relationship between mitochondrial dynamics and the pathophysiology of type 2 diabetes and cardiovascular disease (CVD). Importantly, we emphasize divergent outcomes resulting from downregulating distinct mitochondrial dynamics proteins in various tissues. This review underscores compensatory mechanisms and adaptive pathways that offset potentially detrimental effects, resulting instead in improved metabolic health. Finally, we offer a perspective on potential therapeutic implications of modulating mitochondrial dynamics proteins for treatment of diabetes and CVD.
    ARTICLE HIGHLIGHTS:
    DOI:  https://doi.org/10.2337/dbi23-0003
  15. Nat Rev Genet. 2024 Jan 18.
    The expanding diagnostic toolbox for rare genetic diseases.
    Kristin D Kernohan, Kym M Boycott.
      Genomic technologies, such as targeted, exome and short-read genome sequencing approaches, have revolutionized the care of patients with rare genetic diseases. However, more than half of patients remain without a diagnosis. Emerging approaches from research-based settings such as long-read genome sequencing and optical genome mapping hold promise for improving the identification of disease-causal genetic variants. In addition, new omic technologies that measure the transcriptome, epigenome, proteome or metabolome are showing great potential for variant interpretation. As genetic testing options rapidly expand, the clinical community needs to be mindful of their individual strengths and limitations, as well as remaining challenges, to select the appropriate diagnostic test, correctly interpret results and drive innovation to address insufficiencies. If used effectively - through truly integrative multi-omics approaches and data sharing - the resulting large quantities of data from these established and emerging technologies will greatly improve the interpretative power of genetic and genomic diagnostics for rare diseases.
    DOI:  https://doi.org/10.1038/s41576-023-00683-w
  16. Acta Neuropathol. 2024 Jan 19. 147(1): 19
    Multi-level profiling unravels mitochondrial dysfunction in myotonic dystrophy type 2.
    Felix Kleefeld, Rita Horvath, Iago Pinal-Fernandez, Andrew L Mammen, Maria Casal-Dominguez, Denisa Hathazi, Sarah Melchert, Katrin Hahn, Albert Sickmann, Claudia Muselmann-Genschow, Andreas Hentschel, Corinna Preuße, Andreas Roos, Benedikt Schoser, Werner Stenzel.
      Myotonic dystrophy type 2 (DM2) is an autosomal-dominant multisystemic disease with a core manifestation of proximal muscle weakness, muscle atrophy, myotonia, and myalgia. The disease-causing CCTG tetranucleotide expansion within the CNBP gene on chromosome 3 leads to an RNA-dominated spliceopathy, which is currently untreatable. Research exploring the pathophysiological mechanisms in myotonic dystrophy type 1 has resulted in new insights into disease mechanisms and identified mitochondrial dysfunction as a promising therapeutic target. It remains unclear whether similar mechanisms underlie DM2 and, if so, whether these might also serve as potential therapeutic targets. In this cross-sectional study, we studied DM2 skeletal muscle biopsy specimens on proteomic, molecular, and morphological, including ultrastructural levels in two separate patient cohorts consisting of 8 (explorative cohort) and 40 (confirmatory cohort) patients. Seven muscle biopsy specimens from four female and three male DM2 patients underwent proteomic analysis and respiratory chain enzymology. We performed bulk RNA sequencing, immunoblotting of respiratory chain complexes, mitochondrial DNA copy number determination, and long-range PCR (LR-PCR) to study mitochondrial DNA deletions on six biopsies. Proteomic and transcriptomic analyses revealed a downregulation of essential mitochondrial proteins and their respective RNA transcripts, namely of subunits of respiratory chain complexes I, III, and IV (e.g., mt-CO1, mt-ND1, mt-CYB, NDUFB6) and associated translation factors (TACO1). Light microscopy showed mitochondrial abnormalities (e.g., an age-inappropriate amount of COX-deficient fibers, subsarcolemmal accumulation) in most biopsy specimens. Electron microscopy revealed widespread ultrastructural mitochondrial abnormalities, including dysmorphic mitochondria with paracrystalline inclusions. Immunofluorescence studies with co-localization of autophagy (p62, LC-3) and mitochondrial marker proteins (TOM20, COX-IV), as well as immunohistochemistry for mitophagy marker BNIP3 indicated impaired mitophagic flux. Immunoblotting and LR-PCR did not reveal significant differences between patients and controls. In contrast, mtDNA copy number measurement showed a reduction of mtDNA copy numbers in the patient group compared to controls. This first multi-level study of DM2 unravels thus far undescribed functional and structural mitochondrial abnormalities. However, the molecular link between the tetranucleotide expansion and mitochondrial dysfunction needs to be further elucidated.
    Keywords:  Mitochondrial dysfunction; Myotonic dystrophy type 2; Proximal myotonic myopathy
    DOI:  https://doi.org/10.1007/s00401-023-02673-y
  17. EMBO J. 2024 Jan 15.
    In situ architecture of Opa1-dependent mitochondrial cristae remodeling.
    Michelle Y Fry, Paula P Navarro, Pusparanee Hakim, Virly Y Ananda, Xingping Qin, Juan C Landoni, Sneha Rath, Zintis Inde, Camila Makhlouta Lugo, Bridget E Luce, Yifan Ge, Julie L McDonald, Ilzat Ali, Leillani L Ha, Benjamin P Kleinstiver, David C Chan, Kristopher A Sarosiek, Luke H Chao.
      Cristae membrane state plays a central role in regulating mitochondrial function and cellular metabolism. The protein Optic atrophy 1 (Opa1) is an important crista remodeler that exists as two forms in the mitochondrion, a membrane-anchored long form (l-Opa1) and a processed short form (s-Opa1). The mechanisms for how Opa1 influences cristae shape have remained unclear due to lack of native three-dimensional views of cristae. We perform in situ cryo-electron tomography of cryo-focused ion beam milled mouse embryonic fibroblasts with defined Opa1 states to understand how each form of Opa1 influences cristae architecture. In our tomograms, we observe a variety of cristae shapes with distinct trends dependent on s-Opa1:l-Opa1 balance. Increased l-Opa1 levels promote cristae stacking and elongated mitochondria, while increased s-Opa1 levels correlated with irregular cristae packing and round mitochondria shape. Functional assays indicate a role for l-Opa1 in wild-type apoptotic and calcium handling responses, and show a compromised respiratory function under Opa1 imbalance. In summary, we provide three-dimensional visualization of cristae architecture to reveal relationships between mitochondrial ultrastructure and cellular function dependent on Opa1-mediated membrane remodeling.
    Keywords:  Cristae Remodeling; Cryo-Electron Tomography; Cryo-Focused Ion Beam Milling; Mitochondrial Biology
    DOI:  https://doi.org/10.1038/s44318-024-00027-2
  18. Vestn Oftalmol. 2023 ;139(6): 166-174
    [Rare pathogenic nucleotide variants of mitochondrial DNA associated with Leber's hereditary optic neuropathy].
    N A Andreeva, Yu K Murakhovskaya, T D Krylova, P G Tsygankova, N L Sheremet.
      Patients with Leber Hereditary Optic Neuropathy (LHON) in most cases have one of the three most common mutations: m.11778G>A in the ND4 gene, m.3460G>A in the ND1 gene, or m.14484T>C in the ND6 gene. According to the international Mitomap database, in addition to these three most common mutations, there are 16 other primary mutations that are even more rare. There are nucleotide substitutions that are classified as candidate or conditionally pathogenic mutations. Their involvement in the disease development is not proven due to insufficient research. Moreover, in many publications, the authors describe new primary and potential mitochondrial DNA mutations associated with LHON, which are not yet included in the genetic data bases. This makes it possible to expand the diagnostic spectrum during genetic testing in the future. The advancements in genetic diagnostic technologies allow confirmation of the clinical diagnosis of LHON. The importance of genetic verification of the disease is determined by the existing problem of differential diagnosis of hereditary optic neuropathies with optic neuropathies of a different origin.
    Keywords:  Leber hereditary optic neuropathy; mitochondrial DNA mutations; optic neuropathy; sequencing
    DOI:  https://doi.org/10.17116/oftalma2023139061166
  19. Lab Invest. 2024 Jan 16. pii: S0023-6837(24)00007-2. [Epub ahead of print] 100329
    Nuclear NAD+ deficiency by NMNAT1 deletion impaired hepatic insulin signaling, mitochondrial function and hepatokine expression in mice fed a high-fat diet.
    Haibo Dong, Wei Guo, Ruichao Yue, Xinguo Sun, Zhanxiang Zhou.
      Metabolic syndrome (MetS) is a worldwide challenge that is closely associated with obesity, non-alcoholic liver disease, insulin resistance, and type 2 diabetes. Boosting nicotinamide adenine dinucleotide (NAD+) presents a great potential in preventing MetS. However, the function of nuclear NAD+ in the development of MetS remains poorly understood. In this study, hepatocyte-specific Nmnat1 knockout (KO) mice were used to determine a possible link between nuclear NAD+ and high-fat diet (HFD)-induced MetS. We found that Nmnat1 knockout significantly reduced hepatic nuclear NAD+ levels but did not exacerbate high-fat diet (HFD)-induced obesity and hepatic triglycerides (TG) accumulation. Interestingly, loss of Nmnat1 caused insulin resistance. Further analysis revealed that Nmnat1 deletion promoted gluconeogenesis but inhibited glycogen synthesis in the liver. Moreover, Nmnat1 deficiency induced mitochondrial dysfunction by decreasing mitochondrial DNA (mtDNA)-encoded complexes Ⅰ and Ⅳ, suppressing mtDNA replication and mtRNA transcription as well as reducing mtDNA copy number. In addition, Nmnat1 depletion affected the expression of hepatokines in the liver, particularly downregulating the expression of follistatin (Fst). These findings highlight the importance of nuclear NAD+ in maintaining insulin sensitivity and provide insights into the mechanisms underlying HFD-induced insulin resistance.
    DOI:  https://doi.org/10.1016/j.labinv.2024.100329
  20. J Cell Physiol. 2024 Jan 14.
    Angiogenic activity of mitochondria; beyond the sole bioenergetic organelle.
    Fatemeh Sadeghsoltani, Parisa Hassanpour, Mir-Meghdad Safari, Sanya Haiaty, Reza Rahbarghazi, Mohamad Rahmati, Ali Mota.
      Angiogenesis is a complex process that involves the expansion of the pre-existing vascular plexus to enhance oxygen and nutrient delivery and is stimulated by various factors, including hypoxia. Since the process of angiogenesis requires a lot of energy, mitochondria play an important role in regulating and promoting this phenomenon. Besides their roles as an oxidative metabolism base, mitochondria are potential bioenergetics organelles to maintain cellular homeostasis via sensing alteration in oxygen levels. Under hypoxic conditions, mitochondria can regulate angiogenesis through different factors. It has been indicated that unidirectional and bidirectional exchange of mitochondria or their related byproducts between the cells is orchestrated via different intercellular mechanisms such as tunneling nanotubes, extracellular vesicles, and gap junctions to maintain the cell homeostasis. Even though, the transfer of mitochondria is one possible mechanism by which cells can promote and regulate the process of angiogenesis under reperfusion/ischemia injury. Despite the existence of a close relationship between mitochondrial donation and angiogenic response in different cell types, the precise molecular mechanisms associated with this phenomenon remain unclear. Here, we aimed to highlight the possible role of mitochondria concerning angiogenesis, especially the role of mitochondrial transport and the possible relation of this transfer with autophagy, the housekeeping phenomenon of cells, and angiogenesis.
    Keywords:  Phosphatase and Tensin Homolog; angiogenesis; autophagy; endothelial cells; exosomes; mitochondrial donation; tunneling nanotubes
    DOI:  https://doi.org/10.1002/jcp.31185
  21. Nat Metab. 2024 Jan 19.
    Optimizing metabolism is a complex issue.
    Jerry Vockley.
      
    DOI:  https://doi.org/10.1038/s42255-023-00965-x
  22. J Transl Med. 2024 Jan 16. 22(1): 59
    Intracellular delivery of Parkin-RING0-based fragments corrects Parkin-induced mitochondrial dysfunction through interaction with SLP-2.
    Alessandra Zanon, Marianna Guida, Alexandros A Lavdas, Corrado Corti, Maria Paulina Castelo Rueda, Alessandro Negro, Peter P Pramstaller, Francisco S Domingues, Andrew A Hicks, Irene Pichler.
       BACKGROUND: Loss-of-function mutations in the PRKN gene, encoding Parkin, are the most common cause of autosomal recessive Parkinson's disease (PD). We have previously identified mitoch ondrial Stomatin-like protein 2 (SLP-2), which functions in the assembly of respiratory chain proteins, as a Parkin-binding protein. Selective knockdown of either Parkin or SLP-2 led to reduced mitochondrial and neuronal function in neuronal cells and Drosophila, where a double knockdown led to a further worsening of Parkin-deficiency phenotypes. Here, we investigated the minimal Parkin region involved in the Parkin-SLP-2 interaction and explored the ability of Parkin-fragments and peptides from this minimal region to restore mitochondrial function.
    METHODS: In fibroblasts, human induced pluripotent stem cell (hiPSC)-derived neurons, and neuroblastoma cells the interaction between Parkin and SLP-2 was investigated, and the Parkin domain responsible for the binding to SLP-2 was mapped. High resolution respirometry, immunofluorescence analysis and live imaging were used to analyze mitochondrial function.
    RESULTS: Using a proximity ligation assay, we quantitatively assessed the Parkin-SLP-2 interaction in skin fibroblasts and hiPSC-derived neurons. When PD-associated PRKN mutations were present, we detected a significantly reduced interaction between the two proteins. We found a preferential binding of SLP-2 to the N-terminal part of Parkin, with a highest affinity for the RING0 domain. Computational modeling based on the crystal structure of Parkin protein predicted several potential binding sites for SLP-2 within the Parkin RING0 domain. Amongst these, three binding sites were observed to overlap with natural PD-causing missense mutations, which we demonstrated interfere substantially with the binding of Parkin to SLP-2. Finally, delivery of the isolated Parkin RING0 domain and a Parkin mini-peptide, conjugated to cell-permeant and mitochondrial transporters, rescued compromised mitochondrial function in Parkin-deficient neuroblastoma cells and hiPSC-derived neurons with endogenous, disease causing PRKN mutations.
    CONCLUSIONS: These findings place further emphasis on the importance of the protein-protein interaction between Parkin and SLP-2 for the maintenance of optimal mitochondrial function. The possibility of restoring an abolished binding to SLP-2 by delivering the Parkin RING0 domain or the Parkin mini-peptide involved in this specific protein-protein interaction into cells might represent a novel organelle-specific therapeutic approach for correcting mitochondrial dysfunction in Parkin-linked PD.
    Keywords:  Mitochondria; Parkin; Parkin mini-peptide; Parkinson′s disease; SLP-2
    DOI:  https://doi.org/10.1186/s12967-024-04850-3
  23. J Parkinsons Dis. 2024 Jan 09.
    Parkinson's Disease Is Predominantly an Environmental Disease.
    E Ray Dorsey, Bastiaan R Bloem.
      Parkinson's disease is the world's fastest growing brain disorder, and exposure to environmental toxicants is the principal reason. In this paper, we consider alternative, but unsatisfactory, explanations for its rise, including improved diagnostic skills, aging populations, and genetic causes. We then detail three environmental toxicants that are likely among the main causes of Parkinson's disease- certain pesticides, the solvent trichloroethylene, and air pollution. All three environmental toxicants are ubiquitous, many affect mitochondrial functioning, and all can access humans via various routes, including inhalation and ingestion. We reach the hopeful conclusion that most of Parkinson's disease is thus preventable and that we can help to create a world where Parkinson's disease is increasingly rare.
    Keywords:  Parkinson disease; genetics; indoor air pollution; mitochondria; pesticides; primary prevention; solvents; tetrachloroethylene; trichloroethylene; water pollution
    DOI:  https://doi.org/10.3233/JPD-230357
  24. Mol Neurobiol. 2024 Jan 15.
    Cellular and Molecular Responses to Mitochondrial DNA Deletions in Kearns-Sayre Syndrome: Some Underlying Mechanisms.
    Mazyar Yazdani.
      Kearns-Sayre syndrome (KSS) is a rare multisystem mitochondrial disorder. It is caused by mitochondrial DNA (mtDNA) rearrangements, mostly large-scale deletions of 1.1-10 kb. These deletions primarily affect energy supply through impaired oxidative phosphorylation and reduced ATP production. This impairment gives rise to dysfunction of several tissues, in particular those with high energy demand like brain and muscles. Over the past decades, changes in respiratory chain complexes and energy metabolism have been emphasized, whereas little attention has been paid to other reports on ROS overproduction, protein synthesis inhibition, myelin vacuolation, demyelination, autophagy, apoptosis, and involvement of lipid raft and oligodendrocytes in KSS. Therefore, this paper draws attention towards these relatively underemphasized findings that might further clarify the pathologic cascades following deletions in the mtDNA.
    Keywords:  Apoptosis; Autophagy; Lipid raft; Myelin Vacuolation; Oligodendrocyte; Reactive Oxygen Species (ROS)
    DOI:  https://doi.org/10.1007/s12035-024-03938-7
  25. Cell Death Dis. 2024 Jan 15. 15(1): 52
    USP30 inhibition induces mitophagy and reduces oxidative stress in parkin-deficient human neurons.
    Justyna Okarmus, Jette Bach Agergaard, Tina C Stummann, Henriette Haukedal, Malene Ambjørn, Kristine K Freude, Karina Fog, Morten Meyer.
      Ubiquitination of mitochondrial proteins plays an important role in the cellular regulation of mitophagy. The E3 ubiquitin ligase parkin (encoded by PARK2) and the ubiquitin-specific protease 30 (USP30) have both been reported to regulate the ubiquitination of outer mitochondrial proteins and thereby mitophagy. Loss of E3 ligase activity is thought to be pathogenic in both sporadic and inherited Parkinson's disease (PD), with loss-of-function mutations in PARK2 being the most frequent cause of autosomal recessive PD. The aim of the present study was to evaluate whether mitophagy induced by USP30 inhibition provides a functional rescue in isogenic human induced pluripotent stem cell-derived dopaminergic neurons with and without PARK2 knockout (KO). Our data show that healthy neurons responded to CCCP-induced mitochondrial damage by clearing the impaired mitochondria and that this process was accelerated by USP30 inhibition. Parkin-deficient neurons showed an impaired mitophagic response to the CCCP challenge, although mitochondrial ubiquitination was enhanced. USP30 inhibition promoted mitophagy in PARK2 KO neurons, independently of whether left in basal conditions or treated with CCCP. In PARK2 KO, as in control neurons, USP30 inhibition balanced oxidative stress levels by reducing excessive production of reactive oxygen species. Interestingly, non-dopaminergic neurons were the main driver of the beneficial effects of USP30 inhibition. Our findings demonstrate that USP30 inhibition is a promising approach to boost mitophagy and improve cellular health, also in parkin-deficient cells, and support the potential relevance of USP30 inhibitors as a novel therapeutic approach in diseases with a need to combat neuronal stress mediated by impaired mitochondria.
    DOI:  https://doi.org/10.1038/s41419-024-06439-6
  26. Cell Death Dis. 2024 Jan 15. 15(1): 51
    Mitochondrial stress activates YAP/TAZ through RhoA oxidation to promote liver injury.
    Ari Kwon, Na Young Lee, Jae-Hyun Yu, Myeung Gi Choi, Jeongwoo Park, Ja Hyun Koo.
      Yes-associated protein (YAP) and WW domain-containing transcription regulator protein 1 (WWTR1; also known as TAZ) are the main effectors of the Hippo pathway and their dysregulation contributes to diseases in tissues including the liver. Although mitochondria are capable of transmitting signals to change transcriptomic landscape of diseased hepatocytes, such retrograde signaling and the related nuclear machinery are largely unknown. Here, we show that increased YAP activity is associated with mitochondrial stress during liver injury; and this is required for secondary inflammation, promoting hepatocyte death. Mitochondrial stress inducers robustly promoted YAP/TAZ dephosphorylation, nuclear accumulation, and target gene transcription. RNA sequencing revealed that the majority of mitochondrial stress transcripts required YAP/TAZ. Mechanistically, direct oxidation of RhoA by mitochondrial superoxide was responsible for PP2A-mediated YAP/TAZ dephosphorylation providing a novel physiological input for the Hippo pathway. Hepatocyte-specific Yap/Taz ablation suppressed acetaminophen-induced liver injury and blunted transcriptomic changes associated with the pathology. Our observations uncover unappreciated pathway of mitochondrial stress signaling and reveal YAP/TAZ activation as the mechanistic basis for liver injury progression.
    DOI:  https://doi.org/10.1038/s41419-024-06448-5
  27. Glob Med Genet. 2024 Jan;11(1): 25-28
    A Pair of Compound Heterozygous IARS2 Variants Manifesting West Syndrome and Electrolyte Disorders in a Chinese Patient.
    Feiyu Zhou, Gui Yi, Xiangyu Liu, Wenchao Sheng, Jianbo Shu, Dong Li, Chunquan Cai.
      Background  Aminoacyl-tRNA synthetases (ARSs) are evolutionarily conserved enzymes that ensure the accuracy of the translation process. Isoleucyl-tRNA synthetase 2 ( IARS2 ) gene is a type of ARS that encodes mitochondrial isoleucine-tRNA synthetase. Pathogenic variants in the IARS2 gene are associated with mitochondrial disease which involves several patients presenting broad clinical phenotypes. These clinical phenotypes include West syndrome, Leigh syndrome, and Cataract, growth hormone deficiency, sensory neuropathy, sensorineural hearing loss, and skeletal dysplasia syndrome. Only 29 cases have been reported worldwide. The patient manifested recurrent convulsions, and specific clinical manifestations included electrolyte disorders and recurrent infections. Methods  Whole-exome sequencing was performed on the child with West syndrome. Three-dimensional structure reconstruction and thermodynamic stability prediction were performed to further analyze the relationship between variation and phenotype. Conclusion  This study further expands the clinical spectrum of IARS2 pathogenic variants. The case summaries help raise clinical awareness of IARS2 -associated disease and reduce misdiagnosis. Result  In this report, a 13-month-old girl was diagnosed with West syndrome and Leigh syndrome for 7 months. Compound heterozygous variants in the IARS2 gene (NM_018060.4), c.2450G>A (Arg817His) and copy number variation (NC_000001. 11: g. (220267549_220284289) del), were detected by WES. This study further expands the clinical spectrum of IARS2 pathogenic variants. The case summaries help raise clinical awareness of IARS2-associated disease and reduce misdiagnosis.
    Keywords:  CAGSSS; West syndrome; aminoacyl-tRNA synthetases
    DOI:  https://doi.org/10.1055/s-0043-1778091
  28. Neurol Genet. 2023 Dec;9(6): e200106
    PMPCA-Related Encephalopathy: Novel Variants, Phenotype Extension, and Mitochondrial Morphology.
    Vibhuti Rambani, Miriam Kolnikova, Michal Cagalinec, Martina Skopkova, Daniela Gasperikova.
       Objectives: The PMPCA gene encodes the α-subunit of mitochondrial processing peptidase (α-MPP), an enzyme responsible for cleavage of nuclear-encoded mitochondrial precursor proteins after their import into mitochondria. Mutations in this gene have been described in patients with nonprogressive or slow progressive cerebellar ataxia, with variable age at onset and severity. Cerebellar atrophy and striatum changes were found in severe cases.
    Methods: The patient was diagnosed using whole exome sequencing. Skin fibroblasts were used for confirmation of α-MPP levels using western blot and mitochondrial morphology assessment of immunofluorescent confocal microscopy images.
    Results: Two novel compound heterozygous variants in the PMPCA gene (p.Tyr241Ser and p.Met251Val) were identified in an 8-year-old proband with progressive spastic quadriparesis, delayed psychomotor development, and intellectual disability, with onset at 13 months. The brain imaging showed cortical and cerebellar atrophy, reduced volume of basal ganglia with striatum hyperintensity, and periventricular white matter changes. The patient's fibroblasts showed a decreased α-MPP level and reduced and fragmented mitochondria.
    Discussion: The described case contributes to the number of patients with progressive PMPCA-related disease with a severe intermediate phenotype. Moreover, we extend the phenotype to Leigh-like white matter changes that have not been described in previously reported cases.
    DOI:  https://doi.org/10.1212/NXG.0000000000200106
  29. Front Genet. 2023 ;14 1304711
    Integration of multi-omics technologies for molecular diagnosis in ataxia patients.
    Sebastien Audet, Valerie Triassi, Myriam Gelinas, Nab Legault-Cadieux, Vincent Ferraro, Antoine Duquette, Martine Tetreault.
      Background: Episodic ataxias are rare neurological disorders characterized by recurring episodes of imbalance and coordination difficulties. Obtaining definitive molecular diagnoses poses challenges, as clinical presentation is highly heterogeneous, and literature on the underlying genetics is limited. While the advent of high-throughput sequencing technologies has significantly contributed to Mendelian disorders genetics, interpretation of variants of uncertain significance and other limitations inherent to individual methods still leaves many patients undiagnosed. This study aimed to investigate the utility of multi-omics for the identification and validation of molecular candidates in a cohort of complex cases of ataxia with episodic presentation. Methods: Eight patients lacking molecular diagnosis despite extensive clinical examination were recruited following standard genetic testing. Whole genome and RNA sequencing were performed on samples isolated from peripheral blood mononuclear cells. Integration of expression and splicing data facilitated genomic variants prioritization. Subsequently, long-read sequencing played a crucial role in the validation of those candidate variants. Results: Whole genome sequencing uncovered pathogenic variants in four genes (SPG7, ATXN2, ELOVL4, PMPCB). A missense and a nonsense variant, both previously reported as likely pathogenic, configured in trans in individual #1 (SPG7: c.2228T>C/p.I743T, c.1861C>T/p.Q621*). An ATXN2 microsatellite expansion (CAG32) in another late-onset case. In two separate individuals, intronic variants near splice sites (ELOVL4: c.541 + 5G>A; PMPCB: c.1154 + 5G>C) were predicted to induce loss-of-function splicing, but had never been reported as disease-causing. Long-read sequencing confirmed the compound heterozygous variants configuration, repeat expansion length, as well as splicing landscape for those pathogenic variants. A potential genetic modifier of the ATXN2 expansion was discovered in ZFYVE26 (c.3022C>T/p.R1008*). Conclusion: Despite failure to identify pathogenic variants through clinical genetic testing, the multi-omics approach enabled the molecular diagnosis in 50% of patients, also giving valuable insights for variant prioritization in remaining cases. The findings demonstrate the value of long-read sequencing for the validation of candidate variants in various scenarios. Our study demonstrates the effectiveness of leveraging complementary omics technologies to unravel the underlying genetics in patients with unresolved rare diseases such as ataxia. Molecular diagnoses not only hold significant promise in improving patient care management, but also alleviates the burden of diagnostic odysseys, more broadly enhancing quality of life.
    Keywords:  RNA sequencing (RNAseq); ataxia; genomics; long-read sequencing (LRS); multi-omics; transcriptomics; variant of uncertain significance (VUS); whole genome sequencing (WGS)
    DOI:  https://doi.org/10.3389/fgene.2023.1304711
  30. iScience. 2024 Jan 19. 27(1): 108724
    Extracellular vesicle mitochondrial DNA levels are associated with race and mitochondrial DNA haplogroup.
    Anjali M Byappanahalli, Victor Omoniyi, Nicole Noren Hooten, Jessica T Smith, Nicolle A Mode, Ngozi Ezike, Alan B Zonderman, Michele K Evans.
      Circulating cell-free mitochondrial DNA (ccf-mtDNA) acts as a damage-associated molecular pattern molecule and may be cargo within extracellular vesicles (EVs). ccf-mtDNA and select mitochondrial DNA (mtDNA) haplogroups are associated with cardiovascular disease. We hypothesized that ccf-mtDNA and plasma EV mtDNA would be associated with hypertension, sex, self-identified race, and mtDNA haplogroup ancestry. Participants were normotensive (n = 107) and hypertensive (n = 108) African American and White adults from the Healthy Aging in Neighborhoods of Diversity across the Life Span study. ccf-mtDNA levels were higher in African American participants compared with White participants in both plasma and EVs, but ccf-mtDNA levels were not related to hypertension. EV mtDNA levels were highest in African American participants with African mtDNA haplogroup. Circulating inflammatory protein levels were altered with mtDNA haplogroup, race, and EV mtDNA. Our findings highlight that race is a social construct and that ancestry is crucial when examining health and biomarker differences between groups.
    Keywords:  Biochemistry; Biological sciences; Cell biology; Immunology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2023.108724
  31. Neurol Clin Pract. 2024 Feb;14(1): e200229
    Characterization of Fatigue in Primary Mitochondrial Myopathies: Findings From a Qualitative Interview Study.
    Amel Karaa, Nathan Johnson, Ian Clarkson, Wendy Newman, Alejandro Dorenbaum, Bruce H Cohen.
       Background and Objectives: Primary mitochondrial myopathies are genetic disorders that primarily affect peripheral skeletal muscles. Patients with primary mitochondrial myopathies often experience muscle weakness, fatigue, and other significant impacts on health-related quality of life. The aim of this noninterventional qualitative study was to collect the most bothersome fatigue-related symptoms and impacts reported by patients with primary mitochondrial myopathies and determine whether the questions included in an existing patient-reported outcome measure, the Modified Fatigue Impact Scale, are relevant and interpretable for this population.
    Methods: The interviews contained a concept elicitation exercise to understand the most bothersome primary mitochondrial myopathies symptoms and impacts and a cognitive debriefing section to review the questions included in the Modified Fatigue Impact Scale for relevance and interpretability. Transcripts were coded using ATLAS.ti software.
    Results: Interviews were conducted with 16 patients who were aged 16 years and older with a genetically confirmed and clinical diagnosis of symptomatic primary mitochondrial myopathies. Concept elicitation interviews established that while patients with mitochondrial myopathies reported a wide variety of symptoms and impacts, one of the most impactful symptoms discussed was fatigue. Cognitive debriefing interview results confirmed that the Modified Fatigue Impact Scale items were relevant, were interpretable, and largely captured patients' experience with fatigue.
    Discussion: Fatigue was one of the most widely discussed experiences discussed by participants and was considered the most important symptom/impact to treat by most of the participants. The Modified Fatigue Impact Scale could be used in future clinical trials to measure treatment benefit in fatigue-related impacts.
    DOI:  https://doi.org/10.1212/CPJ.0000000000200229
  32. Neurotherapeutics. 2023 Dec 19. pii: S1878-7479(23)01900-1. [Epub ahead of print]21(1): e00292
    Mitochondrial dysfunction in neurodegenerative disorders.
    Madelyn M Klemmensen, Seth H Borrowman, Colin Pearce, Benjamin Pyles, Bharatendu Chandra.
      Recent advances in understanding the role of mitochondrial dysfunction in neurodegenerative diseases have expanded the opportunities for neurotherapeutics targeting mitochondria to alleviate symptoms and slow disease progression. In this review, we offer a historical account of advances in mitochondrial biology and neurodegenerative disease. Additionally, we summarize current knowledge of the normal physiology of mitochondria and the pathogenesis of mitochondrial dysfunction, the role of mitochondrial dysfunction in neurodegenerative disease, current therapeutics and recent therapeutic advances, as well as future directions for neurotherapeutics targeting mitochondrial function. A focus is placed on reactive oxygen species and their role in the disruption of telomeres and their effects on the epigenome. The effects of mitochondrial dysfunction in the etiology and progression of Alzheimer's disease, amyotrophic lateral sclerosis, Parkinson's disease, and Huntington's disease are discussed in depth. Current clinical trials for mitochondria-targeting neurotherapeutics are discussed.
    Keywords:  Aging; Bioenergetics; Mitochondria; Neurodegeneration; Reactive oxygen species (ROS)
    DOI:  https://doi.org/10.1016/j.neurot.2023.10.002
  33. Am J Hum Genet. 2024 Jan 08. pii: S0002-9297(23)00443-3. [Epub ahead of print]
    STIGMA: Single-cell tissue-specific gene prioritization using machine learning.
    Saranya Balachandran, Cesar A Prada-Medina, Martin A Mensah, Naseebullah Kakar, Inga Nagel, Jelena Pozojevic, Enrique Audain, Marc-Phillip Hitz, Martin Kircher, Varun K A Sreenivasan, Malte Spielmann.
      Clinical exome and genome sequencing have revolutionized the understanding of human disease genetics. Yet many genes remain functionally uncharacterized, complicating the establishment of causal disease links for genetic variants. While several scoring methods have been devised to prioritize these candidate genes, these methods fall short of capturing the expression heterogeneity across cell subpopulations within tissues. Here, we introduce single-cell tissue-specific gene prioritization using machine learning (STIGMA), an approach that leverages single-cell RNA-seq (scRNA-seq) data to prioritize candidate genes associated with rare congenital diseases. STIGMA prioritizes genes by learning the temporal dynamics of gene expression across cell types during healthy organogenesis. To assess the efficacy of our framework, we applied STIGMA to mouse limb and human fetal heart scRNA-seq datasets. In a cohort of individuals with congenital limb malformation, STIGMA prioritized 469 variants in 345 genes, with UBA2 as a notable example. For congenital heart defects, we detected 34 genes harboring nonsynonymous de novo variants (nsDNVs) in two or more individuals from a set of 7,958 individuals, including the ortholog of Prdm1, which is associated with hypoplastic left ventricle and hypoplastic aortic arch. Overall, our findings demonstrate that STIGMA effectively prioritizes tissue-specific candidate genes by utilizing single-cell transcriptome data. The ability to capture the heterogeneity of gene expression across cell populations makes STIGMA a powerful tool for the discovery of disease-associated genes and facilitates the identification of causal variants underlying human genetic disorders.
    Keywords:  gene prioritzation, single-cell sequencing, congenital limb malformations, congenital heart disease, pseudotime, gene expression, congenital diseases
    DOI:  https://doi.org/10.1016/j.ajhg.2023.12.011
  34. Development. 2024 Jan 12. pii: dev.202165. [Epub ahead of print]
    Mitochondrial defects triggered by amg-1 mutation elicit UPRmt and phagocytic clearance during spermatogenesis in C. elegans.
    Peng Wang, Lianwan Chen, Ning Wang, Long Miao, Yanmei Zhao.
      Mitochondria are the powerhouses of many biological processes. During spermatogenesis, post-transcriptional regulation of mitochondrial gene expression is mediated by nuclear-encoded mitochondrial RNA-binding proteins (mtRBPs). We identified AMG-1 as an mtRBP required for reproductive success in C. elegans. amg-1 mutation led to defects in mitochondrial structure and sperm budding, resulting in mitochondria being discarded into residual bodies (RBs), which ultimately delayed spermatogenesis in the proximal gonad. In addition, mitochondrial defects triggered the gonadal mitochondrial unfolded protein response and phagocytic clearance to ensure spermatogenesis but ultimately failed to rescue hermaphroditic fertility. These findings reveal a previously undiscovered role for AMG-1 in regulating C. elegans spermatogenesis, in which mitochondrial-damaged sperm prevented the transmission of defective mitochondria to mature sperm by budding and phagocytic clearance, which may also exist in the reproductive systems of higher organisms.
    Keywords:   Caenorhabditis elegans ; Mitochondria; Mitochondrial unfolded protein response; Phagocytic clearance; Sperm
    DOI:  https://doi.org/10.1242/dev.202165
  35. Brain. 2024 Jan 18. pii: awae018. [Epub ahead of print]
    Elevated cholesterol in ATAD3 mutants is a compensatory mechanism that leads to membrane cholesterol aggregation.
    Mikel Muñoz-Oreja, Abigail Sandoval, Ove Bruland, Diego Perez-Rodriguez, Uxoa Fernandez-Pelayo, Amaia Lopez de Arbina, Marina Villar-Fernandez, Haizea Hernández-Eguiazu, Ixiar Hernández, Yohan Park, Leire Goicoechea, Nerea Pascual-Frías, Carmen Garcia-Ruiz, Jose Fernandez-Checa, Itxaso Martí-Carrera, Francisco Javier Gil-Bea, Mazahir T Hasan, Matthew E Gegg, Cecilie Bredrup, Per-Morten Knappskog, Gorka Gereñu-Lopetegui, Kristin N Varhaug, Laurence A Bindoff, Antonella Spinazzola, Wan Hee Yoon, Ian J Holt.
      Aberrant cholesterol metabolism causes neurological disease and neurodegeneration, and mitochondria have been linked to perturbed cholesterol homeostasis via the study of pathological mutations in the ATAD3 gene cluster. However, whether the cholesterol changes were compensatory or contributory to the disorder was unclear, nor were the effects on cell membranes or the wider cell known. Using patient-derived cells we show that cholesterol perturbation is a conserved feature of pathological ATAD3 variants that is accompanied by an expanded lysosome population containing membrane whorls characteristic of lysosomal storage diseases. Lysosomes are also more numerous in Drosophila neural progenitor cells expressing mutant Atad3, which exhibit abundant membrane-bound cholesterol aggregates, many of which co-localize with lysosomes. Using nutrient restriction and cholesterol supplementation, we show that the Drosophila Atad3 mutant displays heightened cholesterol dependence. Collectively, these findings suggest elevated cholesterol enhances tolerance to pathological ATAD3 variants, at a cost of inducing cholesterol aggregation in membranes, which lysosomal clearance only partly mitigates.
    Keywords:  AAA+ ATPase; ATAD3; cholesterol disorders; lysosomal storage disorders; lysosomes; mitochondrial disease
    DOI:  https://doi.org/10.1093/brain/awae018
  36. Genome Med. 2024 Jan 18. 16(1): 14
    Spatial multi-omics: novel tools to study the complexity of cardiovascular diseases.
    Paul Kiessling, Christoph Kuppe.
      Spatial multi-omic studies have emerged as a promising approach to comprehensively analyze cells in tissues, enabling the joint analysis of multiple data modalities like transcriptome, epigenome, proteome, and metabolome in parallel or even the same tissue section. This review focuses on the recent advancements in spatial multi-omics technologies, including novel data modalities and computational approaches. We discuss the advancements in low-resolution and high-resolution spatial multi-omics methods which can resolve up to 10,000 of individual molecules at subcellular level. By applying and integrating these techniques, researchers have recently gained valuable insights into the molecular circuits and mechanisms which govern cell biology along the cardiovascular disease spectrum. We provide an overview of current data analysis approaches, with a focus on data integration of multi-omic datasets, highlighting strengths and weaknesses of various computational pipelines. These tools play a crucial role in analyzing and interpreting spatial multi-omics datasets, facilitating the discovery of new findings, and enhancing translational cardiovascular research. Despite nontrivial challenges, such as the need for standardization of experimental setups, data analysis, and improved computational tools, the application of spatial multi-omics holds tremendous potential in revolutionizing our understanding of human disease processes and the identification of novel biomarkers and therapeutic targets. Exciting opportunities lie ahead for the spatial multi-omics field and will likely contribute to the advancement of personalized medicine for cardiovascular diseases.
    Keywords:  Data integration; In situ sequencing; MALDI; Multiplex in situ FISH; Spatial multi-omics; Spatial neighborhood analysis; Spatial proteomics; Spatial transcriptomics
    DOI:  https://doi.org/10.1186/s13073-024-01282-y
  37. Br J Ophthalmol. 2024 Jan 17. pii: bjo-2023-324628. [Epub ahead of print]
    Neuroimaging changes in the pregeniculate visual pathway and chiasmal enlargement in Leber hereditary optic neuropathy.
    Xintong Xu, Huanfen Zhou, Mingming Sun, Yuyu Li, Biyue Chen, Xiyun Chen, Quangang Xu, Patrick Yu-Wai-Man, Shihui Wei.
       PURPOSE: To describe the pattern of MRI changes in the pregeniculate visual pathway in Leber hereditary optic neuropathy (LHON).
    METHOD: This retrospective observational study enrolled 60 patients with LHON between January 2015 and December 2021. The abnormal MRI features seen in the pregeniculate visual pathway were investigated, and then correlated with the causative mitochondrial DNA (mtDNA) mutation, the distribution of the MRI lesions and the duration of vision loss.
    RESULT: The cohort included 48 (80%) males and 53 (88%) had bilateral vision loss. The median age of onset was 17.0 years (range 4.0-58.0). 28 (47%) patients had the m.11778G>A mutation. 34 (57%) patients had T2 hyperintensity (HS) in the pregeniculate visual pathway and 13 (22%) patients with chiasmal enlargement. 20 patients (71%) carrying the m.11778G>A mutation had T2 HS, significantly more than the 14 patients (44%) with T2 HS in the other LHON mutation groups (p=0.039). Furthermore, significantly more patients in the m.11778G>A group (16 patients (57%)) had T2 HS in optic chiasm (OCh)/optic tract (OTr) than the other LHON mutation groups (7 patients (22%), p=0.005). Optic chiasmal enlargement was more common in patients with vision loss duration <3 months compared with those ≥3 months (p=0.028).
    CONCLUSION: T2 HS in the pregeniculate visual pathway is a frequent finding in LHON. Signal changes in the OCh/OTr and chiasmal enlargement, in particular within the first 3 months of visual loss, were more commonly seen in patients carrying the m.11778G>A mtDNA mutation, which may be of diagnostic significance.
    Keywords:  imaging; optic nerve; visual pathway
    DOI:  https://doi.org/10.1136/bjo-2023-324628
  38. Cell Signal. 2024 Jan 17. pii: S0898-6568(24)00029-9. [Epub ahead of print] 111061
    Loss of the WDR23 proteostasis impacts mitochondrial homeostasis in the mouse brain.
    Chatrawee Duangjan, Ronald W Irwin, Sean P Curran.
      Mitochondrial adaptation is important for stress resistance throughout life. Here we show that WDR23 loss results in an enrichment for genes regulated by nuclear respiratory factor 1 (NRF1), which coordinates mitochondrial biogenesis and respiratory functions, and an increased steady state level of several nuclear coded mitochondrial resident proteins in the brain. Wdr23KO also increases the endogenous levels of insulin degrading enzyme (IDE) and the relaxin-3 peptide (RLN3), both of which have established roles in mediating mitochondrial metabolic and oxidative stress responses. Taken together, these studies reveal an important role for WDR23 as a component of the mitochondrial homeostat in the murine brain.
    Keywords:  Complex I; Homeostasis; Mitochondria; Wdr23; hippocampus
    DOI:  https://doi.org/10.1016/j.cellsig.2024.111061
  39. Angew Chem Int Ed Engl. 2024 Jan 16. e202319116
    Nanoarchitectonics with a Membrane-Embedded Electron Shuttle Mimics the Bioenergy Anabolism of Mitochondria.
    Tonghui Wang, Jinbo Fei, Zhenzhen Dong, Fanchen Yu, Junbai Li.
      Enhanced bioenergy anabolism through transmembrane redox reactions in artificial systems remains a great challenge. Here, we explore synthetic electron shuttle to activate transmembrane chemo-enzymatic cascade reactions in a mitochondria-like nanoarchitecture for augmenting bioenergy anabolism. In this nanoarchitecture, dendritic mesoporous silica microparticle as inner compartment possesses higher load capacity of NADH as proton source and allows faster mass transfer. In addition, it permits the stability of the outer compartment ATP synthase-reconstituted proteoliposomes. Like natural enzymes in mitochondrion respiratory chain, small synthetic electron shuttle embedded in lipid bilayer, facilely mediates transmembrane redox reactions to convert NADH into NAD+ and proton. These facilitate enhanced outward proton gradient to drive ATP synthase to rotate for catalytic ATP synthesis with improved performance in a sustainable manner. This present work opens a new avenue to achieve enhanced bioenergy anabolism by utilizing synthetic electron shuttle and tuning inner nanostructures, holding great promise in wide-range ATP-powered bioapplications.
    Keywords:  Biomaterials; mitochondria; nanoarchitectonics; oxidative phosphorylation; supramolecular assembly
    DOI:  https://doi.org/10.1002/anie.202319116
  40. Appl Microbiol Biotechnol. 2024 Dec;108(1): 110
    The potency of mitochondria enlargement for mitochondria-mediated terpenoid production in yeast.
    So Yanagibashi, Takahiro Bamba, Takayoshi Kirisako, Akihiko Kondo, Tomohisa Hasunuma.
      Terpenoids are widely used in the food, beverage, cosmetics, and pharmaceutical industries. Microorganisms have been extensively studied for terpenoid production. In yeast, the introduction of the mevalonate (MVA) pathway in organelles in addition to the augmentation of its own MVA pathway have been challenging. Introduction of the MVA pathway into mitochondria is considered a promising approach for terpenoid production because acetyl-CoA, the starting molecule of the MVA pathway, is abundant in mitochondria. However, mitochondria comprise only a small percentage of the entire cell. Therefore, we hypothesized that increasing the total mitochondrial volume per cell would increase terpenoid production. First, we ascertained that the amounts of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), the final molecules of the MVA pathway, were 15-fold higher of the strain expressing the MVA pathway in mitochondria than in the wild-type yeast strain. Second, we found that different deletion mutants induced different mitochondrial volumes by measuring the mitochondrial volume in various deletion mutants affecting mitochondrial morphology; for example,Δmdm32 increased mitochondrial volume, and Δfzo1 decreased it. Finally, the effects of mitochondrial volume on amounts of IPP/DMAPP and terpenoids (squalene or β-carotene) were investigated using mutants harboring large or small mitochondria expressing the MVA pathway in mitochondria. Amounts of IPP/DMAPP and terpenoids (squalene or β-carotene) increased when the mitochondrial volume expanded. Introducing the MVA pathway into mitochondria for terpenoid production in yeast may become more attractive by enlarging the mitochondrial volume. KEY POINTS: • IPP/DMAPP content increased in the strain expressing the MVA pathway in mitochondria • IPP/DMAPP and terpenoid contents are positively correlated with mitochondrial volume • Enlarging the mitochondria may improve mitochondria-mediated terpenoid production.
    Keywords:  Mevalonate pathway; Mitochondria; Squalene; Terpenoid; Yeast; β-carotene
    DOI:  https://doi.org/10.1007/s00253-023-12922-5
  41. Acta Naturae. 2023 Oct-Dec;15(4):15(4): 75-82
    Testing a Hypothesis of 12S rRNA Methylation by Putative METTL17 Methyltransferase.
    A V Mashkovskaia, S S Mariasina, M V Serebryakova, M P Rubtsova, O A Dontsova, P V Sergiev.
      Mitochondrial ribosome assembly is a complex multi-step process involving many additional factors. Ribosome formation differs in various groups of organisms. However, there are universal steps of assembly and conservative factors that have been retained in evolutionarily distant taxa. METTL17, the object of the current study, is one of these conservative factors involved in mitochondrial ribosome assembly. It is present in both bacteria and the mitochondria of eukaryotes, in particular mice and humans. In this study, we tested a hypothesis of putative METTL17 methyltransferase activity. MALDI-TOF mass spectrometry was used to evaluate the methylation of a putative METTL17 target - a 12S rRNA region interacting with METTL17 during mitochondrial ribosome assembly. The investigation of METTL17 and other mitochondrial ribosome assembly factors is of both fundamental and practical significance, because defects in mitochondrial ribosome assembly are often associated with human mitochondrial diseases.
    Keywords:  MALDI-TOF mass spectrometry; RNA methylation; methyltransferases; mitochondrial ribosome; ribosome assembly factors
    DOI:  https://doi.org/10.32607/actanaturae.25441
  42. Vestn Oftalmol. 2023 ;139(6): 77-86
    [Long-term changes in morphological and functional parameters of the optic nerve in patients with various genetic variants of hereditary optic neuropathies].
    Yu K Murakhovskaya, N A Andreeva, P G Tsygankova, T D Krylova, N L Sheremet.
      Leber's hereditary optic neuropathy (LHON) and autosomal recessive optic neuropathy (ARON) are degenerative diseases of the optic nerve caused by mutations in nuclear or mitochondrial DNA (nDNA, mtDNA). The clinical picture of these diseases is similar, but there are some differences in how the visual functions change in patients with different molecular genetic variants of hereditary optic neuropathies (HON).
    PURPOSE: This study evaluates the long-term changes in morphological and functional parameters in patients with different genetic variants of HON.
    MATERIAL AND METHODS: The study included 84 patients (165 eyes) with a genetically confirmed LHON or ARON diagnosis. The patients underwent best-corrected visual acuity (VA) test, color vision (CV) examination, computerized perimetry using the program for low vision assessment, optical coherence tomography (OCT).
    RESULTS: Over the course of the follow-up (60 months or longer) HON patients were revealed to have higher VA in c.152A>G and m.14484T>C mutations compared to mutations m.11778G>A and m.3460G>A. The final VA 0.5 or higher in patients with c.152A>G and m.14484T>C mutations in 54 and 71% of cases, and only in 6 and 13% of cases - with m.11778G>A and m.3460G>A mutations. Direct correlation was determined between minimal VA in the first year after disease onset and the final VA (K=0.67; p<0.001). In all patients with the investigated mutations CV recovered slightly quicker than VA.
    CONCLUSION: HON associated with c.152A>G and m.14484T>C mutations have better prognosis compared to LHON caused by m.11778G>A and m.3460G>A mutations. Vision recovery prognosis is worse in patients who had significant decrease of visual acuity at the disease onset. OCT findings reveal preservation of visual functions in all mutations.
    Keywords:  Leber’s hereditary optic neuropathy; autosomal recessive optic neuropathy; mitochondrial optic neuropathies; vision recovery
    DOI:  https://doi.org/10.17116/oftalma202313906177
  43. Int J Biol Macromol. 2024 Jan 11. pii: S0141-8130(24)00140-5. [Epub ahead of print]259(Pt 2): 129337
    G-quadruplex in mitochondria as a possible biomarker for mitophagy detection.
    Boyang Zhang, Ranran Sun, Ruiyang Bai, Zhicheng Sun, Ruping Liu, Wenchao Li, Li Yao, Hongxia Sun, Yalin Tang.
      Mitochondrial autophagy (mitophagy) is a key physiological process that maintains the homeostasis of mitochondrial quality and quantity. Monitoring mitophagy is of great significance for detecting cellular abnormalities and developing therapeutic drugs. However, there are still very few biomarkers specifically developed for monitoring mitophagy. Here, we propose for the first time that mitochondrial G-quadruplex may serve as a biomarker for mitophagy detection, and develope a fluorescent light-up probe AMTC to monitor mitophagy in live cells. During mitophagy, AMTC fluorescence is significantly enhanced, but once mitophagy is inhibited, its fluorescence immediately decreases. The fluorescence behavior of AMTC implicates an increase in the formation of mitochondrial G-quadruplex during mitophagy. This inference has also been supported by the other two G-quadruplex probes. Taken together, this work provides a new possible biomarker and detection tool for the study of mitophagy.
    Keywords:  Biomarker; Mitochondrial G-quadruplex; Mitophagy monitoring
    DOI:  https://doi.org/10.1016/j.ijbiomac.2024.129337
  44. bioRxiv. 2023 Dec 27. pii: 2023.12.27.573435. [Epub ahead of print]
    Genetically encoded tool for manipulation of ΔΨm identifies the latter as the driver of integrative stress response induced by ATP Synthase dysfunction.
    Mangyu Choe, Denis V Titov.
      Mitochondrial membrane potential (ΔΨm) is one of the key parameters controlling cellular bioenergetics. Investigation of the role of ΔΨm in live cells is complicated by a lack of tools for its direct manipulation without off-target effects. Here, we adopted the uncoupling protein UCP1 from brown adipocytes as a genetically encoded tool for direct manipulation of ΔΨm. We validated the ability of exogenously expressed UCP1 to induce uncoupled respiration and lower ΔΨm in mammalian cells. UCP1 expression lowered ΔΨm to the same extent as chemical uncouplers but did not inhibit cell proliferation, suggesting that it manipulates ΔΨm without the off-target effects of chemical uncouplers. Using UCP1, we revealed that elevated ΔΨm is the driver of the Integrated Stress Response induced by ATP synthase inhibition in mammalian cells.
    DOI:  https://doi.org/10.1101/2023.12.27.573435
  45. Nat Aging. 2024 Jan 19.
    Causality-enriched epigenetic age uncouples damage and adaptation.
    Kejun Ying, Hanna Liu, Andrei E Tarkhov, Marie C Sadler, Ake T Lu, Mahdi Moqri, Steve Horvath, Zoltán Kutalik, Xia Shen, Vadim N Gladyshev.
      Machine learning models based on DNA methylation data can predict biological age but often lack causal insights. By harnessing large-scale genetic data through epigenome-wide Mendelian randomization, we identified CpG sites potentially causal for aging-related traits. Neither the existing epigenetic clocks nor age-related differential DNA methylation are enriched in these sites. These CpGs include sites that contribute to aging and protect against it, yet their combined contribution negatively affects age-related traits. We established a new framework to introduce causal information into epigenetic clocks, resulting in DamAge and AdaptAge-clocks that track detrimental and adaptive methylation changes, respectively. DamAge correlates with adverse outcomes, including mortality, while AdaptAge is associated with beneficial adaptations. These causality-enriched clocks exhibit sensitivity to short-term interventions. Our findings provide a detailed landscape of CpG sites with putative causal links to lifespan and healthspan, facilitating the development of aging biomarkers, assessing interventions, and studying reversibility of age-associated changes.
    DOI:  https://doi.org/10.1038/s43587-023-00557-0
  46. J Inherit Metab Dis. 2024 Jan;47(1): 176-191
    Gene therapy for neurotransmitter-related disorders.
    Wing Sum Chu, Joanne Ng, Simon N Waddington, Manju A Kurian.
      Inborn errors of neurotransmitter (NT) metabolism are a group of rare, heterogenous diseases with predominant neurological features, such as movement disorders, autonomic dysfunction, and developmental delay. Clinical overlap with other disorders has led to delayed diagnosis and treatment, and some conditions are refractory to oral pharmacotherapies. Gene therapies have been developed and translated to clinics for paediatric inborn errors of metabolism, with 38 interventional clinical trials ongoing to date. Furthermore, efforts in restoring dopamine synthesis and neurotransmission through viral gene therapy have been developed for Parkinson's disease. Along with the recent European Medicines Agency (EMA) and Medicines and Healthcare Products Regulatory Agency (MHRA) approval of an AAV2 gene supplementation therapy for AADC deficiency, promising efficacy and safety profiles can be achieved in this group of diseases. In this review, we present preclinical and clinical advances to address NT-related diseases, and summarise potential challenges that require careful considerations for NT gene therapy studies.
    Keywords:  AADC deficiency; DTDS; Gene therapy; inborn errors of neurotransmission; neurotransmitter disease
    DOI:  https://doi.org/10.1002/jimd.12697
  47. Pharmgenomics Pers Med. 2024 ;17 13-26
    Maternally Inherited Essential Hypertension May Be Associated with the Mutations in Mitochondrial tRNAGlu Gene.
    Chun Wang, Xin Deng, Lei Li, Mei Li.
       Background: Mitochondrial DNA (mtDNA) mutations are associated with essential hypertension (EH), but the molecular mechanism remains largely unknown.
    Objective: The aim of this study is to explore the association between mtDNA mutations and EH.
    Methods: Two maternally inherited families with EH are underwent clinical, genetic and biochemical assessments. mtDNA mutations are screened by PCR-Sanger sequencing and phylogenetic, and bioinformatics analyses are performed to evaluate the pathogenicity of mtDNA mutations. We also generate cytoplasmic hybrid (cybrid) cell lines to analysis mitochondrial functions.
    Results: Matrilineal relatives exhibit variable degree of clinical phenotypes. Molecular analysis reveals the presence of m.A14693G and m.A14696G mutations in two pedigrees. Notably, the m.A14693G mutation occurs at position 54 in the TψC loop of tRNAGlu, a position which is critical for post-transcriptionally modification of tRNAGlu. While the m.A14696G mutation creates a novel base-pairing (51C-64G). Bioinformatic analysis shows that these mutations alter tRNAGlu secondary structure. Additionally, patients with tRNAGlu mutations exhibit markedly decreased in mtDNA copy number, mitochondrial membrane potential (MMP) and ATP, whereas the levels of reactive oxygen species (ROS) increase significantly.
    Conclusion: The m.A14696G and m.A14693G mutations lead to failure in tRNAGlu metabolism and cause mitochondrial dysfunction that is responsible for EH.
    Keywords:  Chinese families; EH; mitochondrial dysfunction; mt-tRNAGlu m.A14693G m.A14696G
    DOI:  https://doi.org/10.2147/PGPM.S436235
  48. Front Aging Neurosci. 2023 ;15 1322419
    Exploring the complexities of 1C metabolism: implications in aging and neurodegenerative diseases.
    Ayman Bou Ghanem, Yaman Hussayni, Raghid Kadbey, Yara Ratel, Shereen Yehya, Lara Khouzami, Hilda E Ghadieh, Amjad Kanaan, Sami Azar, Frederic Harb.
      The intricate interplay of one-carbon metabolism (OCM) with various cellular processes has garnered substantial attention due to its fundamental implications in several biological processes. OCM serves as a pivotal hub for methyl group donation in vital biochemical reactions, influencing DNA methylation, protein synthesis, and redox balance. In the context of aging, OCM dysregulation can contribute to epigenetic modifications and aberrant redox states, accentuating cellular senescence and age-associated pathologies. Furthermore, OCM's intricate involvement in cancer progression is evident through its capacity to provide essential one-carbon units crucial for nucleotide synthesis and DNA methylation, thereby fueling uncontrolled cell proliferation and tumor development. In neurodegenerative disorders like Alzheimer's and Parkinson's, perturbations in OCM pathways are implicated in the dysregulation of neurotransmitter synthesis and mitochondrial dysfunction, contributing to disease pathophysiology. This review underscores the profound impact of OCM in diverse disease contexts, reinforcing the need for a comprehensive understanding of its molecular complexities to pave the way for targeted therapeutic interventions across inflammation, aging and neurodegenerative disorders.
    Keywords:  Alzheimer’s disease; Parkinson disease; aging; folate; mitochondrial dysfuntion; neurodegenerative disease; one carbon metabolism
    DOI:  https://doi.org/10.3389/fnagi.2023.1322419
  49. EMBO Rep. 2024 Jan 19.
    Glucose-derived glutamate drives neuronal terminal differentiation in vitro.
    Laura D'Andrea, Matteo Audano, Silvia Pedretti, Silvia Pelucchi, Ramona Stringhi, Gabriele Imperato, Giulia De Cesare, Clara Cambria, Marine H Laporte, Nicola Zamboni, Flavia Antonucci, Monica Di Luca, Nico Mitro, Elena Marcello.
      Neuronal maturation is the phase during which neurons acquire their final characteristics in terms of morphology, electrical activity, and metabolism. However, little is known about the metabolic pathways governing neuronal maturation. Here, we investigate the contribution of the main metabolic pathways, namely glucose, glutamine, and fatty acid oxidation, during the maturation of primary rat hippocampal neurons. Blunting glucose oxidation through the genetic and chemical inhibition of the mitochondrial pyruvate transporter reveals that this protein is critical for the production of glutamate, which is required for neuronal arborization, proper dendritic elongation, and spine formation. Glutamate supplementation in the early phase of differentiation restores morphological defects and synaptic function in mitochondrial pyruvate transporter-inhibited cells. Furthermore, the selective activation of metabotropic glutamate receptors restores the impairment of neuronal differentiation due to the reduced generation of glucose-derived glutamate and rescues synaptic local translation. Fatty acid oxidation does not impact neuronal maturation. Whereas glutamine metabolism is important for mitochondria, it is not for endogenous glutamate production. Our results provide insights into the role of glucose-derived glutamate as a key player in neuronal terminal differentiation.
    Keywords:  Glutamate; Local Protein Translation in Neurons; Metabolism; Mitochondrial Pyruvate Carrier
    DOI:  https://doi.org/10.1038/s44319-023-00048-8
  50. Physiol Rep. 2024 Jan;12(1): e15917
    Unraveling the causes of sarcopenia: Roles of neuromuscular junction impairment and mitochondrial dysfunction.
    Yanmei Miao, Leiyu Xie, Jiamei Song, Xing Cai, Jinghe Yang, Xinglong Ma, Shaolin Chen, Peng Xie.
      Sarcopenia is a systemic skeletal muscle disease characterized by a decline in skeletal muscle mass and function. Originally defined as an age-associated condition, sarcopenia presently also encompasses muscular atrophy due to various pathological factors, such as intensive care unit-acquired weakness, inactivity, and malnutrition. The exact pathogenesis of sarcopenia is still unknown; herein, we review the pathological roles of the neuromuscular junction and mitochondria in this condition. Sarcopenia is caused by complex and interdependent pathophysiological mechanisms, including aging, neuromuscular junction impairment, mitochondrial dysfunction, insulin resistance, lipotoxicity, endocrine factors, oxidative stress, and inflammation. Among these, neuromuscular junction instability and mitochondrial dysfunction are particularly significant. Dysfunction in neuromuscular junction can lead to muscle weakness or paralysis. Mitochondria, which are plentiful in neurons and muscle fibers, play an important role in neuromuscular junction transmission. Therefore, impairments in both mitochondria and neuromuscular junction may be one of the key pathophysiological mechanisms leading to sarcopenia. Moreover, this article explores the structural and functional alterations in the neuromuscular junction and mitochondria in sarcopenia, suggesting that a deeper understanding of these changes could provide valuable insights for the prevention or treatment of sarcopenia.
    Keywords:  Sarcopenia; mitochondrion; neuromuscular junction
    DOI:  https://doi.org/10.14814/phy2.15917
  51. Cell Rep Methods. 2024 Jan 11. pii: S2667-2375(23)00378-8. [Epub ahead of print] 100692
    Using MitER for 3D analysis of mitochondrial morphology and ER contacts.
    Therese Kichuk, Satyen Dhamankar, Saurabh Malani, William A Hofstadter, Scott A Wegner, Ileana M Cristea, José L Avalos.
      We have developed an open-source workflow that allows for quantitative single-cell analysis of organelle morphology, distribution, and inter-organelle contacts with an emphasis on the analysis of mitochondria and mitochondria-endoplasmic reticulum (mito-ER) contact sites. As the importance of inter-organelle contacts becomes more widely recognized, there is a concomitant increase in demand for tools to analyze subcellular architecture. Here, we describe a workflow we call MitER (pronounced "mightier"), which allows for automated calculation of organelle morphology, distribution, and inter-organelle contacts from 3D renderings by employing the animation software Blender. We then use MitER to quantify the variations in the mito-ER networks of Saccharomyces cerevisiae, revealing significantly more mito-ER contacts within respiring cells compared to fermenting cells. We then demonstrate how this workflow can be applied to mammalian systems and used to monitor mitochondrial dynamics and inter-organelle contact in time-lapse studies.
    Keywords:  CP: Imaging; Saccharomyces cerevisea; image analysis; imaging; inter-organelle contact; mitochondrial-ER contact; organelle distribution; organelle morphology
    DOI:  https://doi.org/10.1016/j.crmeth.2023.100692
  52. Acta Diabetol. 2024 Jan 18.
    Obstetric complications in women with mitochondrial disease.
    M M Byrne, B Sanchez-Lechuga, N Ng, B Byrne.
      
    DOI:  https://doi.org/10.1007/s00592-023-02225-6
  53. J Biol Chem. 2024 Jan 11. pii: S0021-9258(24)00021-8. [Epub ahead of print] 105645
    Development of a mouse model expressing a bifunctional glutathione synthesizing enzyme to study glutathione limitation in vivo.
    Rebecca C Timson, Artem Khan, Beste Uygur, Marwa Saad, Hsi-Wen Yeh, Nicole L DelGaudio, Ross Weber, Hanan Alwaseem, Jing Gao, Chingwen Yang, Kıvanç Birsoy.
      Glutathione (GSH) is a highly abundant tripeptide thiol that performs diverse protective and biosynthetic functions in cells. While changes in GSH availability are associated with inborn errors of metabolism, cancer and neurodegenerative disorders, studying the limiting role of GSH in physiology and disease has been challenging due to its tight regulation. To address this, we generated cell and mouse models that express a bifunctional glutathione-synthesizing enzyme from Streptococcus thermophilus (GshF), which possesses both glutamate-cysteine ligase and glutathione synthase activities. GshF expression allows efficient production of GSH in the cytosol and mitochondria and prevents cell death in response to GSH depletion, but not ferroptosis induction, indicating that GSH is not a limiting factor under lipid peroxidation. CRISPR screens using engineered enzymes further revealed genes required for cell proliferation under cellular and mitochondrial GSH depletion. Among these, we identified the glutamate-cysteine ligase modifier subunit, Gclm, as a requirement for cellular sensitivity to buthionine sulfoximne, a glutathione synthesis inhibitor. Finally, GshF expression in mice is embryonically lethal but sustains postnatal viability when restricted to adulthood. Overall, our work identifies a conditional mouse model to investigate the limiting role of GSH in physiology and disease.
    DOI:  https://doi.org/10.1016/j.jbc.2024.105645
  54. Circ Res. 2024 Jan 19. 134(2): 162-164
    Platelet Mitochondrial Fusion and Function in Vascular Integrity.
    Tarun Tyagi, Timur O Yarovinsky, E Vincent S Faustino, John Hwa.
      
    Keywords:  Editorials; blood platelets; hemostasis; lipids; megakaryocytes; mitochondria
    DOI:  https://doi.org/10.1161/CIRCRESAHA.123.323867
  55. Adv Sci (Weinh). 2024 Jan 18. e2306469
    Metabolic Bypass Rescues Aberrant S-nitrosylation-Induced TCA Cycle Inhibition and Synapse Loss in Alzheimer's Disease Human Neurons.
    Alexander Y Andreyev, Hongmei Yang, Paschalis-Thomas Doulias, Nima Dolatabadi, Xu Zhang, Melissa Luevanos, Mayra Blanco, Christine Baal, Ivan Putra, Tomohiro Nakamura, Harry Ischiropoulos, Steven R Tannenbaum, Stuart A Lipton.
      In Alzheimer's disease (AD), dysfunctional mitochondrial metabolism is associated with synaptic loss, the major pathological correlate of cognitive decline. Mechanistic insight for this relationship, however, is still lacking. Here, comparing isogenic wild-type and AD mutant human induced pluripotent stem cell (hiPSC)-derived cerebrocortical neurons (hiN), evidence is found for compromised mitochondrial energy in AD using the Seahorse platform to analyze glycolysis and oxidative phosphorylation (OXPHOS). Isotope-labeled metabolic flux experiments revealed a major block in activity in the tricarboxylic acid (TCA) cycle at the α-ketoglutarate dehydrogenase (αKGDH)/succinyl coenzyme-A synthetase step, metabolizing α-ketoglutarate to succinate. Associated with this block, aberrant protein S-nitrosylation of αKGDH subunits inhibited their enzyme function. This aberrant S-nitrosylation is documented not only in AD-hiN but also in postmortem human AD brains versus controls, as assessed by two separate unbiased mass spectrometry platforms using both SNOTRAP identification of S-nitrosothiols and chemoselective-enrichment of S-nitrosoproteins. Treatment with dimethyl succinate, a cell-permeable derivative of a TCA substrate downstream to the block, resulted in partial rescue of mitochondrial bioenergetic function as well as reversal of synapse loss in AD-hiN. These findings have therapeutic implications that rescue of mitochondrial energy metabolism can ameliorate synaptic loss in hiPSC-based models of AD.
    Keywords:  Alzheimer's diseases; S-nitrosylation; tricarboxylic acid cycles
    DOI:  https://doi.org/10.1002/advs.202306469
  56. Comput Biol Med. 2024 Jan 13. pii: S0010-4825(24)00064-7. [Epub ahead of print]170 107980
    Pathogenicity classification of missense mutations based on deep generative model.
    Ke Bai, Lu Yang, Jian Xue, Lin Zhao, Fanchang Hao.
      Missense mutations affect the function of human proteins and are closely associated with multiple acute and chronic diseases. The identification of disease-associated missense mutations and their classification for pathogenicity can provide insights into the genetic basis of disease and protein function. This paper proposes MLAE (Method based on LSTM-Ladder AutoEncoder), a deep learning classification model for identifying disease-associated missense mutations and classifying their pathogenicity based on the Variational AutoEncoder (VAE) framework. MLAE overcomes the limitations of the VAE framework by introducing the Ladder structure, combined with LSTM networks. This reduces the loss of original information during the transmission process, thereby making the model more effective in learning. In the experiment, MLAE classified all 27572 possible missense variants of the three input proteins with an average classification AUC of 0.941. This result provides evidence that MLAE is effective in predicting pathogenicity. Additionally, MLAE provides results for multi-label classification, with an average Hamming loss of 0.196, supporting the classification of complex variants. The proposed MLAE method provides an insightful approach to effectively capture amino acid sequence information and accurately predict the pathogenicity of mutations, thereby providing an analytical basis for the study and prevention of related diseases.
    Keywords:  Deep generation model; Multiple label classification; Pathogenicity classification; Single amino acid variation; Variational autoencoder
    DOI:  https://doi.org/10.1016/j.compbiomed.2024.107980
  57. Cell. 2024 Jan 18. pii: S0092-8674(23)01328-4. [Epub ahead of print]187(2): 257-270
    Making the connection: How membrane contact sites have changed our view of organelle biology.
    G K Voeltz, E M Sawyer, G Hajnóczky, W A Prinz.
      The view of organelles and how they operate together has changed dramatically over the last two decades. The textbook view of organelles was that they operated largely independently and were connected by vesicular trafficking and the diffusion of signals through the cytoplasm. We now know that all organelles make functional close contacts with one another, often called membrane contact sites. The study of these sites has moved to center stage in cell biology as it has become clear that they play critical roles in healthy and developing cells and during cell stress and disease states. Contact sites have important roles in intracellular signaling, lipid metabolism, motor-protein-mediated membrane dynamics, organelle division, and organelle biogenesis. Here, we summarize the major conceptual changes that have occurred in cell biology as we have come to appreciate how contact sites integrate the activities of organelles.
    DOI:  https://doi.org/10.1016/j.cell.2023.11.040
  58. Chem Commun (Camb). 2024 Jan 17.
    Nucleoside modification-based flexizymes with versatile activity for tRNA aminoacylation.
    Xin-Dan Zhang, Yi-Shen Wang, Hua Xiang, Li-Wen Bai, Peng Cheng, Kai Li, Rong Huang, Xiaolei Wang, Xinxiang Lei.
      Extensive research has focused on genetic code reprogramming using flexizymes (Fxs), ribozymes enabling diverse tRNA acylation. Here we describe a nucleoside-modification strategy for the preparation of flexizyme variants derived from 2'-OMe, 2'-F, and 2'-MOE modifications with unique and versatile activities, enabling the charging of tRNAs with a broad range of substrates. This innovative strategy holds promise for synthetic biology applications, offering a robust pathway to expand the genetic code for diverse substrate incorporation.
    DOI:  https://doi.org/10.1039/d3cc05673b
  59. Mol Cell. 2024 Jan 18. pii: S1097-2765(23)01076-6. [Epub ahead of print]84(2): 183-185
    Meet the authors: Yuqiu Sun and Hui Jiang.
    Yuqiu Sun, Hui Jiang.
      We talk to first author Yuqiu Sun and corresponding author Hui Jiang about their paths in science, mentorship, and the exciting moments in the journey towards their paper "A mitophagy sensor PPTC7 controls BNIP3 and NIX degradation to regulate mitochondrial mass" (this issue of Molecular Cell).
    DOI:  https://doi.org/10.1016/j.molcel.2023.12.030
  60. ACS Nano. 2024 Jan 18.
    Quantum Sensing of Free Radical Generation in Mitochondria of Single Heart Muscle Cells during Hypoxia and Reoxygenation.
    Siyu Fan, Han Gao, Yue Zhang, Linyan Nie, Raquel Bártolo, Reinier Bron, Hélder A Santos, Romana Schirhagl.
      Cells are damaged during hypoxia (blood supply deprivation) and reoxygenation (oxygen return). This damage occurs in conditions such as cardiovascular diseases, cancer, and organ transplantation, potentially harming the tissue and organs. The role of free radicals in cellular metabolic reprogramming under hypoxia is under debate, but their measurement is challenging due to their short lifespan and limited diffusion range. In this study, we employed a quantum sensing technique to measure the real-time production of free radicals at the subcellular level. We utilize fluorescent nanodiamonds (FNDs) that exhibit changes in their optical properties based on the surrounding magnetic noise. This way, we were able to detect the presence of free radicals. To specifically monitor radical generation near mitochondria, we coated the FNDs with an antibody targeting voltage-dependent anion channel 2 (anti-VDAC2), which is located in the outer membrane of mitochondria. We observed a significant increase in the radical load on the mitochondrial membrane when cells were exposed to hypoxia. Subsequently, during reoxygenation, the levels of radicals gradually decreased back to the normoxia state. Overall, by applying a quantum sensing technique, the connections among hypoxia, free radicals, and the cellular redox status has been revealed.
    Keywords:  NV centers; diamonds; hypoxia; nanodiamonds; quantum sensing
    DOI:  https://doi.org/10.1021/acsnano.3c07959
  61. Sci Adv. 2024 Jan 19. 10(3): eadj7408
    Interaction of PINK1 with nucleotides and kinetin.
    Zhong Yan Gan, Sylvie Callegari, Thanh N Nguyen, Nicholas S Kirk, Andrew Leis, Michael Lazarou, Grant Dewson, David Komander.
      The ubiquitin kinase PINK1 accumulates on damaged mitochondria to trigger mitophagy, and PINK1 loss-of-function mutations cause early onset Parkinson's disease. Nucleotide analogs such as kinetin triphosphate (KTP) were reported to enhance PINK1 activity and may represent a therapeutic strategy for the treatment of Parkinson's disease. Here, we investigate the interaction of PINK1 with nucleotides, including KTP. We establish a cryo-EM platform exploiting the dodecamer assembly of Pediculus humanus corporis (Ph) PINK1 and determine PINK1 structures bound to AMP-PNP and ADP, revealing conformational changes in the kinase N-lobe that help establish PINK1's ubiquitin binding site. Notably, we find that KTP is unable to bind PhPINK1 or human (Hs) PINK1 due to a steric clash with the kinase "gatekeeper" methionine residue, and mutation to Ala or Gly is required for PINK1 to bind and use KTP as a phosphate donor in ubiquitin phosphorylation and mitophagy. HsPINK1 M318G can be used to conditionally uncouple PINK1 stabilization and activity on mitochondria.
    DOI:  https://doi.org/10.1126/sciadv.adj7408
  62. Cell Rep Med. 2024 Jan 16. pii: S2666-3791(23)00601-8. [Epub ahead of print]5(1): 101372
    The impact of bed rest on human skeletal muscle metabolism.
    Moritz Eggelbusch, Braeden T Charlton, Alessandra Bosutti, Bergita Ganse, Ifigenia Giakoumaki, Anita E Grootemaat, Paul W Hendrickse, Yorrick Jaspers, Stephan Kemp, Tom J Kerkhoff, Wendy Noort, Michel van Weeghel, Nicole N van der Wel, Julia R Wesseling, Petra Frings-Meuthen, Jörn Rittweger, Edwin R Mulder, Richard T Jaspers, Hans Degens, Rob C I Wüst.
      Insulin sensitivity and metabolic flexibility decrease in response to bed rest, but the temporal and causal adaptations in human skeletal muscle metabolism are not fully defined. Here, we use an integrative approach to assess human skeletal muscle metabolism during bed rest and provide a multi-system analysis of how skeletal muscle and the circulatory system adapt to short- and long-term bed rest (German Clinical Trials: DRKS00015677). We uncover that intracellular glycogen accumulation after short-term bed rest accompanies a rapid reduction in systemic insulin sensitivity and less GLUT4 localization at the muscle cell membrane, preventing further intracellular glycogen deposition after long-term bed rest. We provide evidence of a temporal link between the accumulation of intracellular triglycerides, lipotoxic ceramides, and sphingomyelins and an altered skeletal muscle mitochondrial structure and function after long-term bed rest. An intracellular nutrient overload therefore represents a crucial determinant for rapid skeletal muscle insulin insensitivity and mitochondrial alterations after prolonged bed rest.
    Keywords:  GLUT4; bed rest; insulin sensitivity; lipotoxicity; metabolism; mitochondria; nutrient overload; physical inactivity; skeletal muscle
    DOI:  https://doi.org/10.1016/j.xcrm.2023.101372
  63. STAR Protoc. 2024 Jan 12. pii: S2666-1667(23)00793-1. [Epub ahead of print]5(1): 102826
    Integrative detection of genome-wide translation using iRibo.
    Alistair Turcan, Jiwon Lee, Aaron Wacholder, Anne-Ruxandra Carvunis.
      Ribosome profiling is a sequencing technique that provides a global picture of translation across a genome. Here, we present iRibo, a software program for integrating any number of ribosome profiling samples to obtain sensitive inference of annotated or unannotated translated open reading frames. We describe the process of using iRibo to generate a species' translatome from a set of ribosome profiling samples using S. cerevisiae as an example. For complete details on the use and execution of this protocol, please refer to Wacholder et al. (2023).1.
    Keywords:  Bioinformatics; Genomics; Model Organisms; Sequence analysis
    DOI:  https://doi.org/10.1016/j.xpro.2023.102826
  64. Front Cell Neurosci. 2023 ;17 1295805
    Analysis of α-syn and parkin interaction in mediating neuronal death in Drosophila model of Parkinson's disease.
    Sonia Narwal, Amit Singh, Meghana Tare.
      One of the hallmarks of Parkinson's Disease (PD) is aggregation of incorrectly folded α-synuclein (SNCA) protein resulting in selective death of dopaminergic neurons. Another form of PD is characterized by the loss-of-function of an E3-ubiquitin ligase, parkin. Mutations in SNCA and parkin result in impaired mitochondrial morphology, causing loss of dopaminergic neurons. Despite extensive research on the individual effects of SNCA and parkin, their interactions in dopaminergic neurons remain understudied. Here we employ Drosophila model to study the effect of collective overexpression of SNCA along with the downregulation of parkin in the dopaminergic neurons of the posterior brain. We found that overexpression of SNCA along with downregulation of parkin causes a reduction in the number of dopaminergic neuronal clusters in the posterior region of the adult brain, which is manifested as progressive locomotor dysfunction. Overexpression of SNCA and downregulation of parkin collectively results in altered mitochondrial morphology in a cluster-specific manner, only in a subset of dopaminergic neurons of the brain. Further, we found that SNCA overexpression causes transcriptional downregulation of parkin. However, this downregulation is not further enhanced upon collective SNCA overexpression and parkin downregulation. This suggests that the interactions of SNCA and parkin may not be additive. Our study thus provides insights into a potential link between α-synuclein and parkin interactions. These interactions result in altered mitochondrial morphology in a cluster-specific manner for dopaminergic neurons over a time, thus unraveling the molecular interactions involved in the etiology of Parkinson's Disease.
    Keywords:  Drosophila melanogaster; Parkinson's disease; dopaminergic neurons; mitochondrial morphology; parkin; tyrosine hydroxylase; α-synuclein
    DOI:  https://doi.org/10.3389/fncel.2023.1295805
  65. EMBO J. 2024 Jan 18.
    MITOL deficiency triggers hematopoietic stem cell apoptosis via ER stress response.
    Wenjuan Ma, Shah Adil Ishtiyaq Ahmad, Michihiro Hashimoto, Ahad Khalilnezhad, Miho Kataoka, Yuichiro Arima, Yosuke Tanaka, Shigeru Yanagi, Terumasa Umemoto, Toshio Suda.
      Hematopoietic stem cell (HSC) divisional fate and function are determined by cellular metabolism, yet the contribution of specific cellular organelles and metabolic pathways to blood maintenance and stress-induced responses in the bone marrow remains poorly understood. The outer mitochondrial membrane-localized E3 ubiquitin ligase MITOL/MARCHF5 (encoded by the Mitol gene) is known to regulate mitochondrial and endoplasmic reticulum (ER) interaction and to promote cell survival. Here, we investigated the functional involvement of MITOL in HSC maintenance by generating MX1-cre inducible Mitol knockout mice. MITOL deletion in the bone marrow resulted in HSC exhaustion and impairment of bone marrow reconstitution capability in vivo. Interestingly, MITOL loss did not induce major mitochondrial dysfunction in hematopoietic stem and progenitor cells. In contrast, MITOL deletion induced prolonged ER stress in HSCs, which triggered cellular apoptosis regulated by IRE1α. In line, dampening of ER stress signaling by IRE1α inihibitor KIRA6 partially rescued apoptosis of long-term-reconstituting HSC. In summary, our observations indicate that MITOL is a principal regulator of hematopoietic homeostasis and protects blood stem cells from cell death through its function in ER stress signaling.
    Keywords:  Apoptosis; Cell Cycle; ER Stress Response; IRE1; MITOL
    DOI:  https://doi.org/10.1038/s44318-024-00029-0
  66. Ann Indian Acad Neurol. 2023 Nov-Dec;26(6):26(6): 980-982
    Stroke-Like Episodes and Epilepsy in a Patient with COQ8A-Related Coenzyme Q10 Deficiency.
    Rithvik Ramesh, Sundar Hariharan, Latha Sundar.
      Coenzyme q10 (CoQ10) deficiency is an extremely uncommon disease that has very rarely been reported in adulthood. This case describes an elderly male with ataxia since adolescence, and visual disturbance since 40, presenting with recurrent episodes of seizures. Imaging revealed stroke-like episodes, with other immune and infective evaluations being negative. He was eventually diagnosed to have Primary CoQ10 deficiency secondary to CoQ8A mutation. This account highlights the challenges in diagnosing and managing primary Coenzyme Q10 deficiency, especially when it presents later in life with atypical features such as stroke-like episodes.
    Keywords:  Mitochondrial diseases; primary CoQ deficiency; stroke like episode
    DOI:  https://doi.org/10.4103/aian.aian_511_23
  67. J Biomed Mater Res A. 2024 Jan 12.
    Nanoparticle-based therapeutic strategies for mitochondrial dysfunction in cardiovascular disease.
    Isabella Suzuki, Huihua Xing, Joshua Giblin, Anisa Ashraf, Eun Ji Chung.
      Although cardiovascular diseases (CVD) are the leading cause of global mortality, there is a lack of therapies that target and revert underlying pathological processes. Mitochondrial dysfunction is involved in the pathophysiology of CVD, and thus is a potential target for therapeutic development. To target the mitochondria and improve therapeutic efficacy, nanoparticle-based delivery systems have been proposed as promising strategies for the delivery of therapeutic agents to the mitochondria. This review will first discuss how mitochondrial dysfunction is related to the progression of several CVD and then delineate recent progress in mitochondrial targeting using nanoparticle-based delivery systems including peptide-based nanosystems, polymeric nanoparticles, liposomes, and lipid nanoparticles. In addition, we summarize the advantages of these nanocarriers and remaining challenges in targeting the mitochondria as a therapeutic strategy for CVD treatment.
    Keywords:  cardiovascular disease; drug delivery; mitochondria; nanoparticles
    DOI:  https://doi.org/10.1002/jbm.a.37668
  68. Nature. 2024 Jan;625(7995): 450
    Does generative AI help academics to do more or less?
    Richard Watermeyer, Donna Lanclos, Lawrie Phipps.
      
    Keywords:  Machine learning; Research management
    DOI:  https://doi.org/10.1038/d41586-024-00115-7
  69. J Cardiovasc Aging. 2023 Oct;pii: 41. [Epub ahead of print]3(4):
    mt-tRNAs in the polymerase gamma mutant heart.
    M Bilal Bayazit, Ashley Francois, Erin McGrail, Federica Accornero, Matthew S Stratton.
       Introduction: Mice harboring a D257A mutation in the proofreading domain of the mitochondrial DNA polymerase, Polymerase Gamma (POLG), experience severe metabolic dysfunction and display hallmarks of accelerated aging. We previously reported a mitochondrial unfolded protein response (UPTmt) - like (UPRmt-like) gene and protein expression pattern in the right ventricular tissue of POLG mutant mice.
    Aim: We sought to determine if POLG mutation altered the expression of genes encoded by the mitochondria in a way that might also reduce proteotoxic stress.
    Methods and Results: The expression of genes encoded by the mitochondrial DNA was interrogated via RNA-seq and northern blot analysis. A striking, location-dependent effect was seen in the expression of mitochondrial-encoded tRNAs in the POLG mutant as assayed by RNA-seq. These expression changes were negatively correlated with the tRNA partner amino acid's amyloidogenic potential. Direct measurement by northern blot was conducted on candidate mt-tRNAs identified from the RNA-seq. This analysis confirmed reduced expression of MT-TY in the POLG mutant but failed to show increased expression of MT-TP, which was dramatically increased in the RNA-seq data.
    Conclusion: We conclude that reduced expression of amyloid-associated mt-tRNAs is another indication of adaptive response to severe mitochondrial dysfunction in the POLG mutant. Incongruence between RNA-seq and northern blot measurement of MT-TP expression points towards the existence of mt-tRNA post-transcriptional modification regulation in the POLG mutant that alters either polyA capture or cDNA synthesis in RNA-seq library generation. Together, these data suggest that 1) evolution has distributed mt-tRNAs across the circular mitochondrial genome to allow chromosomal location-dependent mt-tRNA regulation (either by expression or PTM) and 2) this regulation is cognizant of the tRNA partner amino acid's amyloidogenic properties.
    Keywords:  Cardiac aging; POLG; UPRMT; mt-tRNA
    DOI:  https://doi.org/10.20517/jca.2023.26
  70. Nat Metab. 2024 Jan 19.
    An ETFDH-driven metabolon supports OXPHOS efficiency in skeletal muscle by regulating coenzyme Q homeostasis.
    Juan Cruz Herrero Martín, Beñat Salegi Ansa, Gerardo Álvarez-Rivera, Sonia Domínguez-Zorita, Pilar Rodríguez-Pombo, Belén Pérez, Enrique Calvo, Alberto Paradela, David G Miguez, Alejandro Cifuentes, José M Cuezva, Laura Formentini.
      Coenzyme Q (Q) is a key lipid electron transporter, but several aspects of its biosynthesis and redox homeostasis remain undefined. Various flavoproteins reduce ubiquinone (oxidized form of Q) to ubiquinol (QH2); however, in eukaryotes, only oxidative phosphorylation (OXPHOS) complex III (CIII) oxidizes QH2 to Q. The mechanism of action of CIII is still debated. Herein, we show that the Q reductase electron-transfer flavoprotein dehydrogenase (ETFDH) is essential for CIII activity in skeletal muscle. We identify a complex (comprising ETFDH, CIII and the Q-biosynthesis regulator COQ2) that directs electrons from lipid substrates to the respiratory chain, thereby reducing electron leaks and reactive oxygen species production. This metabolon maintains total Q levels, minimizes QH2-reductive stress and improves OXPHOS efficiency. Muscle-specific Etfdh-/- mice develop myopathy due to CIII dysfunction, indicating that ETFDH is a required OXPHOS component and a potential therapeutic target for mitochondrial redox medicine.
    DOI:  https://doi.org/10.1038/s42255-023-00956-y
  71. Eye Vis (Lond). 2024 Jan 16. 11(1): 5
    Homocysteine and mitochondrial quality control in diabetic retinopathy.
    Pooja Malaviya, Renu A Kowluru.
       BACKGROUND: Diabetic retinopathy is a progressive disease, and one of the key metabolic abnormalities in the pathogenesis of diabetic retinopathy, mitochondrial damage, is also influenced by the duration of hyperglycemia. Mitochondrial quality control involves a coordination of mitochondrial dynamics, biogenesis and removal of the damaged mitochondria. In diabetes, these processes are impaired, and the damaged mitochondria continue to produce free radicals. Diabetic patients also have high homocysteine and reduced levels of hydrogen sulfide, and hyperhomocysteinemia is shown to exacerbate diabetes-induced mitochondrial damage and worsen their dynamics. This study aims to investigate the temporal relationship between hyperhomocysteinemia and retinal mitochondrial quality control in diabetic retinopathy.
    METHODS: Human retinal endothelial cells incubated in 20 mM D-glucose for 24 to 96 h, in the absence or presence of 100 µM homocysteine, with/without a hydrogen sulfide donor GYY4137, were analyzed for mitochondrial ROS (MitoSox fluorescence), DNA damage (transcripts of mtDNA-encoded ND6 and CytB), copy numbers, oxygen consumption rate (Seahorse XF analyzer) and mitophagy (mitophagosomes immunofluorescence labeling and flow cytometry). Results were confirmed in the retina from mice genetically manipulated for hyperhomocysteinemia (cystathionine β-synthase deficient mice, Cbs+/-), streptozotocin-induced diabetic for 8 to 24 weeks. At 24 weeks of diabetes, vascular health was evaluated by counting acellular capillaries in the trypsin digested retinal vasculature and by fluorescein angiography.
    RESULTS: Homocysteine, in high glucose medium, exacerbated mitochondrial ROS production, mtDNA damage and impaired mitochondrial respiration within 24 h, and slowed down/worsened mitochondrial biogenesis and mitophagy, as compared to 48 to 96 h in high glucose alone. GYY4137 supplementation ameliorated homocysteine + high glucose-induced mitochondrial damage and impairment in biogenesis and mitophagy. Similar results were obtained from Cbs+/- mice-mitochondrial ROS, mtDNA damage and decline in biogenesis and mitophagy were observed within eight weeks of diabetes vs. 16 to 24 weeks of diabetes in Cbs+/+ mice, and at 24 weeks of diabetes, Cbs+/- mice had significantly higher acellular capillaries and vascular leakage.
    CONCLUSIONS: Hyperhomocysteinemia, in a hyperglycemic environment, overwhelms the mitochondria, accelerating and exacerbating their dysfunction, and also delays/worsens their removal, augmenting the development of diabetic retinopathy. Thus, our results strengthen the importance of maintaining homocysteine-hydrogen sulfide balance during the early stages of diabetes for a patient to prevent/retard vision loss.
    Keywords:  Diabetic retinopathy; Homocysteine; Hydrogen sulfide; Mitochondria; Mitophagy; Retina
    DOI:  https://doi.org/10.1186/s40662-023-00362-1
  72. J Cell Biochem. 2024 Jan 16.
    The BCKDH kinase inhibitor BT2 promotes BCAA disposal and mitochondrial proton leak in both insulin-sensitive and insulin-resistant C2C12 myotubes.
    Caroline N Rivera, Carly E Smith, Lillian V Draper, Madison E Kee, Norah E Cook, Macey R McGovern, Rachel M Watne, Andrew J Wommack, Roger A Vaughan.
      Elevated circulating branched-chain amino acids (BCAAs) have been correlated with the severity of insulin resistance, leading to recent investigations that stimulate BCAA metabolism for the potential benefit of metabolic diseases. BT2 (3,6-dichlorobenzo[b]thiophene-2-carboxylic acid), an inhibitor of branched-chain ketoacid dehydrogenase kinase, promotes BCAA metabolism by enhancing BCKDH complex activity. The purpose of this report was to investigate the effects of BT2 on mitochondrial and glycolytic metabolism, insulin sensitivity, and de novo lipogenesis both with and without insulin resistance. C2C12 myotubes were treated with or without low or moderate levels of BT2 with or without insulin resistance. Western blot and quantitative real-time polymerase chain reaction were used to assess protein and gene expression, respectively. Mitochondrial, nuclei, and lipid content were measured using fluorescent staining and microscopy. Cell metabolism was assessed via oxygen consumption and extracellular acidification rate. Liquid chromatography-mass spectrometry was used to quantify BCAA media content. BT2 treatment consistently promoted mitochondrial uncoupling following 24-h treatment, which occurred largely independent of changes in expressional profiles associated with mitochondrial biogenesis, mitochondrial dynamics, BCAA catabolism, insulin sensitivity, or lipogenesis. Acute metabolic studies revealed a significant and dose-dependent effect of BT2 on mitochondrial proton leak, suggesting BT2 functions as a small-molecule uncoupler. Additionally, BT2 treatment consistently and dose-dependently reduced extracellular BCAA levels without altering expression of BCAA catabolic enzymes or pBCKDHa activation. BT2 appears to act as a small-molecule mitochondrial uncoupler that promotes BCAA utilization, though the interplay between these two observations requires further investigation.
    Keywords:  diabetes; insulin resistance; isoleucine; leucine; pAkt/Akt; skeletal muscle; valine
    DOI:  https://doi.org/10.1002/jcb.30520
  73. Nat Med. 2024 Jan 15.
    Wearable robot helps man with Parkinson's disease to walk.
      
    DOI:  https://doi.org/10.1038/s41591-023-02756-z
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