bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2022‒01‒23
fifty-two papers selected by
Catalina Vasilescu
University of Helsinki
  1. Brain-derived autophagosome profiling reveals the engulfment of nucleoid-enriched mitochondrial fragments by basal autophagy in neurons.
  2. NAD supplementation improves mitochondrial performance of cardiolipin mutants.
  3. Biallelic Variants in PYROXD2 Cause a Severe Infantile Metabolic Disorder Affecting Mitochondrial Function.
  4. Mitochondrial Membrane Remodeling.
  5. OPA1 Modulates Mitochondrial Ca2+ Uptake Through ER-Mitochondria Coupling.
  6. The Mysterious Multitude: Structural Perspective on the Accessory Subunits of Respiratory Complex I.
  7. Mapping of a N-terminal α-helix domain required for human PINK1 stabilization, Serine228 autophosphorylation and activation in cells.
  8. Assessing Oligomerization Status of Mitochondrial OXPHOS Complexes Via Blue Native Page.
  9. MITOCHONDRIA: Mitochondrial dynamics in the regulation of stem cells.
  10. Dissecting the molecular mechanisms of mitochondrial import and maturation of peroxiredoxins from yeast and mammalian cells.
  11. Mitochondrial transport, partitioning and quality control at the heart of cell proliferation and fate acquisition.
  12. Mitophagy mechanisms in neuronal physiology and pathology during ageing.
  13. Cryo-electron microscopy reveals how acetogenins inhibit mitochondrial respiratory complex I.
  14. Selective localization of Mfn2 near PINK1 enables its preferential ubiquitination by Parkin on mitochondria.
  15. The Role of Mitochondrial DNA Mutations in Cardiovascular Diseases.
  16. Mitoribosomal small subunit maturation involves formation of initiation-like complexes.
  17. Association of mitochondrial DNA copy number with cardiometabolic diseases.
  18. Mitochondrial fusion, fission and mitophagy in cardiac diseases: challenges and therapeutic opportunities.
  19. Therapeutic Strategies Targeting Mitochondrial Calcium Signaling: A New Hope for Neurological Diseases?
  20. Prevalence of primary mutations in Leber hereditary optic neuropathy: A five-year report from a tertiary eye care center in India.
  21. Mitochondrial DNA copy number and disease.
  22. MDH2 produced OAA is a metabolic switch rewiring the fuelling of respiratory chain and TCA cycle.
  23. Enrichment of the exocytosis protein STX4 in skeletal muscle remediates peripheral insulin resistance and alters mitochondrial dynamics via Drp1.
  24. Biomarkers for Drug Development in Propionic and Methylmalonic Acidemias.
  25. Muscle mitochondrial energetics predicts mobility decline in well-functioning older adults: The baltimore longitudinal study of aging.
  26. Pipeline Automation via Snakemake.
  27. StrVCTVRE: A supervised learning method to predict the pathogenicity of human genome structural variants.
  28. Clin.iobio: A Collaborative Diagnostic Workflow to Enable Team-Based Precision Genomics.
  29. The biological clean-ups that could combat age-related disease.
  30. Leukocytes mediate disease pathogenesis in the Ndufs4(KO) mouse model of Leigh syndrome.
  31. Nuclear and mitochondrial DNA editing in human cells with zinc finger deaminases.
  32. Nicotinamide riboside kinase-2 inhibits JNK pathway and limits dilated cardiomyopathy in mice with chronic pressure overload.
  33. FUNDC1 activates the mitochondrial unfolded protein response to preserve mitochondrial quality control in cardiac ischemia/reperfusion injury.
  34. Nonalcoholic Fatty Liver Disease. Reply.
  35. MCU (Mitochondrial Ca2+ Uniporter) makes the calcium go round.
  36. One-Carbon Metabolism: Pulling the Strings behind Aging and Neurodegeneration.
  37. ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines.
  38. Circulating metabolite homeostasis achieved through mass action.
  39. SENP2 regulates mitochondrial function and insulin secretion in pancreatic β cells.
  40. Tau interactome maps synaptic and mitochondrial processes associated with neurodegeneration.
  41. MCAD deficiency caused by compound heterozygous pathogenic variants in ACADM.
  42. Modelling Metabolic Shifts during Cardiomyocyte Differentiation, Iron Deficiency and Transferrin Rescue Using Human Pluripotent Stem Cells.
  43. Cellular senescence: all roads lead to mitochondria.
  44. Idebenone improves motor dysfunction, learning and memory by regulating mitophagy in MPTP-treated mice.
  45. Ageing exacerbates ribosome pausing to disrupt cotranslational proteostasis.
  46. Differential remodelling of mitochondrial subpopulations and mitochondrial dysfunction are a feature of early stage diabetes.
  47. Nonalcoholic Fatty Liver Disease.
  48. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders.
  49. History and development of staining methods for skeletal muscle fiber types.
  50. SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport.
  51. Leber's Hereditary Optic Neuropathy Plus Causing Recurrent Myelopathy due to an MT-DN1 Mutation at G3635A.
  52. The mitochondrial β-oxidation enzyme HADHA restrains hepatic glucagon response by promoting β-hydroxybutyrate production.
  1. Neuron. 2022 Jan 13. pii: S0896-6273(21)01046-1. [Epub ahead of print]
    Brain-derived autophagosome profiling reveals the engulfment of nucleoid-enriched mitochondrial fragments by basal autophagy in neurons.
    Juliet Goldsmith, Alban Ordureau, J Wade Harper, Erika L F Holzbaur.
      Neurons depend on autophagy to maintain cellular homeostasis, and defects in autophagy are pathological hallmarks of neurodegenerative disease. To probe the role of basal autophagy in the maintenance of neuronal health, we isolated autophagic vesicles from mouse brain tissue and used proteomics to identify the major cargos engulfed within autophagosomes, validating our findings in rodent primary and human iPSC-derived neurons. Mitochondrial proteins were identified as a major cargo in the absence of mitophagy adaptors such as OPTN. We found that nucleoid-associated proteins are enriched compared with other mitochondrial components. In the axon, autophagic engulfment of nucleoid-enriched mitochondrial fragments requires the mitochondrial fission machinery Drp1. We proposed that localized Drp1-dependent fission of nucleoid-enriched fragments in proximity to the sites of autophagosome biogenesis enhances their capture. The resulting efficient autophagic turnover of nucleoids may prevent accumulation of mitochondrial DNA in the neuron, thus mitigating activation of proinflammatory pathways that contribute to neurodegeneration.
    Keywords:  Drp1; TFAM; autophagy; mitochondria; mitochondrial division; mitochondrial nucleoids; mitophagy; neurodegeneration; neuronal homeostasis
    DOI:  https://doi.org/10.1016/j.neuron.2021.12.029
  2. Biochim Biophys Acta Mol Cell Biol Lipids. 2022 Jan 17. pii: S1388-1981(21)00222-5. [Epub ahead of print] 159094
    NAD supplementation improves mitochondrial performance of cardiolipin mutants.
    Jiajia Ji, Deena Damschroder, Denise Bessert, Pablo Lazcano, Robert Wessells, Christian A Reynolds, Miriam L Greenberg.
      Cardiolipin (CL) deficiency causes mitochondrial dysfunction and aberrant metabolism that are associated in humans with the severe disease Barth syndrome (BTHS). Several metabolic abnormalities are observed in BTHS patients and model systems, including decreased oxidative phosphorylation, reduced tricarboxylic acid (TCA) cycle flux, and accumulated lactate and D-β-hydroxybutyrate, which strongly suggests that nicotinamide adenine dinucleotide (NAD) redox metabolism may be altered in CL-deficient cells. In this study, we identified abnormal NAD+ metabolism in multiple BTHS model systems and demonstrate that supplementation of NAD+ precursors such as nicotinamide mononucleotide (NMN) improves mitochondrial function. Improved mitochondrial function in the Drosophila model was associated with restored exercise endurance, which suggests a potential therapeutic benefit of NAD+ precursor supplementation in the management of BTHS patients.
    Keywords:  Barth syndrome; Cardiolipin deficiency; Mitochondrial function; NAD(+) precursors; NAD(+) redox; Nicotinamide mononucleotide
    DOI:  https://doi.org/10.1016/j.bbalip.2021.159094
  3. Int J Mol Sci. 2022 Jan 17. pii: 986. [Epub ahead of print]23(2):
    Biallelic Variants in PYROXD2 Cause a Severe Infantile Metabolic Disorder Affecting Mitochondrial Function.
    Nicole J Van Bergen, Daniella H Hock, Lucy Spencer, Sean Massey, Tegan Stait, Zornitza Stark, Sebastian Lunke, Ain Roesley, Heidi Peters, Joy Yaplito Lee, Anna Le Fevre, Oliver Heath, Cristina Mignone, Joseph Yuan-Mou Yang, Monique M Ryan, Colleen D'Arcy, Margot Nash, Sile Smith, Nikeisha J Caruana, David R Thorburn, David A Stroud, Susan M White, John Christodoulou, Natasha J Brown.
      Pyridine Nucleotide-Disulfide Oxidoreductase Domain 2 (PYROXD2; previously called YueF) is a mitochondrial inner membrane/matrix-residing protein and is reported to regulate mitochondrial function. The clinical importance of PYROXD2 has been unclear, and little is known of the protein's precise biological function. In the present paper, we report biallelic variants in PYROXD2 identified by genome sequencing in a patient with suspected mitochondrial disease. The child presented with acute neurological deterioration, unresponsive episodes, and extreme metabolic acidosis, and received rapid genomic testing. He died shortly after. Magnetic resonance imaging (MRI) brain imaging showed changes resembling Leigh syndrome, one of the more common childhood mitochondrial neurological diseases. Functional studies in patient fibroblasts showed a heightened sensitivity to mitochondrial metabolic stress and increased mitochondrial superoxide levels. Quantitative proteomic analysis demonstrated decreased levels of subunits of the mitochondrial respiratory chain complex I, and both the small and large subunits of the mitochondrial ribosome, suggesting a mitoribosomal defect. Our findings support the critical role of PYROXD2 in human cells, and suggest that the biallelic PYROXD2 variants are associated with mitochondrial dysfunction, and can plausibly explain the child's clinical presentation.
    Keywords:  PYROXD2; genome sequencing; mitochondria; mitoribosome; oxidative phosphorylation; reactive oxygen species; ultrarapid genomics
    DOI:  https://doi.org/10.3390/ijms23020986
  4. Front Bioeng Biotechnol. 2021 ;9 786806
    Mitochondrial Membrane Remodeling.
    Ziyun Yang, Liang Wang, Cheng Yang, Shiming Pu, Ziqi Guo, Qiong Wu, Zuping Zhou, Hongxia Zhao.
      Mitochondria are key regulators of many important cellular processes and their dysfunction has been implicated in a large number of human disorders. Importantly, mitochondrial function is tightly linked to their ultrastructure, which possesses an intricate membrane architecture defining specific submitochondrial compartments. In particular, the mitochondrial inner membrane is highly folded into membrane invaginations that are essential for oxidative phosphorylation. Furthermore, mitochondrial membranes are highly dynamic and undergo constant membrane remodeling during mitochondrial fusion and fission. It has remained enigmatic how these membrane curvatures are generated and maintained, and specific factors involved in these processes are largely unknown. This review focuses on the current understanding of the molecular mechanism of mitochondrial membrane architectural organization and factors critical for mitochondrial morphogenesis, as well as their functional link to human diseases.
    Keywords:  Mitochondrial disease; cardiolipin; crista junctions; cristae; membrane curvature; mitochondrial dynamics; mitochondrial fission; mitochondrial fusion
    DOI:  https://doi.org/10.3389/fbioe.2021.786806
  5. Front Cell Dev Biol. 2021 ;9 774108
    OPA1 Modulates Mitochondrial Ca2+ Uptake Through ER-Mitochondria Coupling.
    Benjamín Cartes-Saavedra, Josefa Macuada, Daniel Lagos, Duxan Arancibia, María E Andrés, Patrick Yu-Wai-Man, György Hajnóczky, Verónica Eisner.
      Autosomal Dominant Optic Atrophy (ADOA), a disease that causes blindness and other neurological disorders, is linked to OPA1 mutations. OPA1, dependent on its GTPase and GED domains, governs inner mitochondrial membrane (IMM) fusion and cristae organization, which are central to oxidative metabolism. Mitochondrial dynamics and IMM organization have also been implicated in Ca2+ homeostasis and signaling but the specific involvements of OPA1 in Ca2+ dynamics remain to be established. Here we studied the possible outcomes of OPA1 and its ADOA-linked mutations in Ca2+ homeostasis using rescue and overexpression strategies in Opa1-deficient and wild-type murine embryonic fibroblasts (MEFs), respectively and in human ADOA-derived fibroblasts. MEFs lacking Opa1 required less Ca2+ mobilization from the endoplasmic reticulum (ER) to induce a mitochondrial matrix [Ca2+] rise ([Ca2+]mito). This was associated with closer ER-mitochondria contacts and no significant changes in the mitochondrial calcium uniporter complex. Patient cells carrying OPA1 GTPase or GED domain mutations also exhibited altered Ca2+ homeostasis, and the mutations associated with lower OPA1 levels displayed closer ER-mitochondria gaps. Furthermore, in Opa1 -/- MEF background, we found that acute expression of OPA1 GTPase mutants but no GED mutants, partially restored cytosolic [Ca2+] ([Ca2+]cyto) needed for a prompt [Ca2+]mito rise. Finally, OPA1 mutants' overexpression in WT MEFs disrupted Ca2+ homeostasis, partially recapitulating the observations in ADOA patient cells. Thus, OPA1 modulates functional ER-mitochondria coupling likely through the OPA1 GED domain in Opa1 -/- MEFs. However, the co-existence of WT and mutant forms of OPA1 in patients promotes an imbalance of Ca2+ homeostasis without a domain-specific effect, likely contributing to the overall ADOA progress.
    Keywords:  ADOA; OPA1; calcium; endoplasmic reticulum; mitochondria
    DOI:  https://doi.org/10.3389/fcell.2021.774108
  6. Front Mol Biosci. 2021 ;8 798353
    The Mysterious Multitude: Structural Perspective on the Accessory Subunits of Respiratory Complex I.
    Abhilash Padavannil, Maria G Ayala-Hernandez, Eimy A Castellanos-Silva, James A Letts.
      Complex I (CI) is the largest protein complex in the mitochondrial oxidative phosphorylation electron transport chain of the inner mitochondrial membrane and plays a key role in the transport of electrons from reduced substrates to molecular oxygen. CI is composed of 14 core subunits that are conserved across species and an increasing number of accessory subunits from bacteria to mammals. The fact that adding accessory subunits incurs costs of protein production and import suggests that these subunits play important physiological roles. Accordingly, knockout studies have demonstrated that accessory subunits are essential for CI assembly and function. Furthermore, clinical studies have shown that amino acid substitutions in accessory subunits lead to several debilitating and fatal CI deficiencies. Nevertheless, the specific roles of CI's accessory subunits have remained mysterious. In this review, we explore the possible roles of each of mammalian CI's 31 accessory subunits by integrating recent high-resolution CI structures with knockout, assembly, and clinical studies. Thus, we develop a framework of experimentally testable hypotheses for the function of the accessory subunits. We believe that this framework will provide inroads towards the complete understanding of mitochondrial CI physiology and help to develop strategies for the treatment of CI deficiencies.
    Keywords:  accessory subunits; electron transport chain; mitochondrial complex I; mitochondrial diseases; oxidative phosphorylation (OXPHOS)
    DOI:  https://doi.org/10.3389/fmolb.2021.798353
  7. Open Biol. 2022 Jan;12(1): 210264
    Mapping of a N-terminal α-helix domain required for human PINK1 stabilization, Serine228 autophosphorylation and activation in cells.
    Poonam Kakade, Hina Ojha, Olawale G Raimi, Andrew Shaw, Andrew D Waddell, James R Ault, Sophie Burel, Kathrin Brockmann, Atul Kumar, Mohd Syed Ahangar, Ewelina M Krysztofinska, Thomas Macartney, Richard Bayliss, Julia C Fitzgerald, Miratul M K Muqit.
      Autosomal recessive mutations in the PINK1 gene are causal for Parkinson's disease (PD). PINK1 encodes a mitochondrial localized protein kinase that is a master-regulator of mitochondrial quality control pathways. Structural studies to date have elaborated the mechanism of how mutations located within the kinase domain disrupt PINK1 function; however, the molecular mechanism of PINK1 mutations located upstream and downstream of the kinase domain is unknown. We have employed mutagenesis studies to define the minimal region of human PINK1 required for optimal ubiquitin phosphorylation, beginning at residue Ile111. Inspection of the AlphaFold human PINK1 structure model predicts a conserved N-terminal α-helical extension (NTE) domain forming an intramolecular interaction with the C-terminal extension (CTE), which we corroborate using hydrogen/deuterium exchange mass spectrometry of recombinant insect PINK1 protein. Cell-based analysis of human PINK1 reveals that PD-associated mutations (e.g. Q126P), located within the NTE : CTE interface, markedly inhibit stabilization of PINK1; autophosphorylation at Serine228 (Ser228) and Ubiquitin Serine65 (Ser65) phosphorylation. Furthermore, we provide evidence that NTE and CTE domain mutants disrupt PINK1 stabilization at the mitochondrial Translocase of outer membrane complex. The clinical relevance of our findings is supported by the demonstration of defective stabilization and activation of endogenous PINK1 in human fibroblasts of a patient with early-onset PD due to homozygous PINK1 Q126P mutations. Overall, we define a functional role of the NTE : CTE interface towards PINK1 stabilization and activation and show that loss of NTE : CTE interactions is a major mechanism of PINK1-associated mutations linked to PD.
    Keywords:  PINK1; Parkinson's disease; kinase; mitochondria; phosphorylation; translocase
    DOI:  https://doi.org/10.1098/rsob.210264
  8. Methods Mol Biol. 2022 ;2413 55-62
    Assessing Oligomerization Status of Mitochondrial OXPHOS Complexes Via Blue Native Page.
    Jordan Woytash, Joseph R Inigo, Dhyan Chandra.
      Mitochondrial metabolism plays key roles in pathologies such as cancer. The five complexes of the oxidative phosphorylation (OXPHOS) system are crucial for producing ATP and maintaining cellular functions and are particularly exploited in cancer cells. Understanding the oligomeric state of these OXPHOS complexes will help elucidate their function (or dysfunction) in cancer cells and can be used as a mechanistic tool for anticancer agents that target mitochondria. Here we describe a protocol to observe the oligomeric state of the five OXPHOS complexes by isolating mitochondrial-enriched fractions followed by assessing their oligomeric state by nondenaturing blue native page electrophoresis.
    Keywords:  Mitochondria; Native page; OXPHOS complexes; Oxidative phosphorylation
    DOI:  https://doi.org/10.1007/978-1-0716-1896-7_7
  9. Int J Biochem Cell Biol. 2022 Jan 18. pii: S1357-2725(22)00003-6. [Epub ahead of print] 106158
    MITOCHONDRIA: Mitochondrial dynamics in the regulation of stem cells.
    Steven Wade, Mireille Khacho.
      Mitochondria are considered the metabolic hubs within a cell. These organelles are highly dynamic and continuously undergo cycles of fission and fusion events. The balance in the dynamic state of mitochondria is critical for maintaining key physiological events within cells. Here we discuss the emerging role of mitochondrial dynamics in regulating stem cell function and highlight the crosstalk between mitochondrial shape and intracellular signaling cascades within the context of stem cells.
    DOI:  https://doi.org/10.1016/j.biocel.2022.106158
  10. Biophys Rev. 2021 Dec;13(6): 983-994
    Dissecting the molecular mechanisms of mitochondrial import and maturation of peroxiredoxins from yeast and mammalian cells.
    Fernando Gomes, Helena Turano, Angélica Ramos, Mário Henrique de Barros, Luciana A Haddad, Luis E S Netto.
      Peroxiredoxins (Prxs) are cysteine-based peroxidases that play a central role in keeping the H2O2 at physiological levels. Eukaryotic cells express different Prxs isoforms, which differ in their subcellular locations and substrate specificities. Mitochondrial Prxs are synthesized in the cytosol as precursor proteins containing N-terminal cleavable presequences that act as mitochondrial targeting signals. Due to the fact that presequence controls the import of the vast majority of mitochondrial matrix proteins, the mitochondrial Prxs were initially predicted to be localized exclusively in the matrix. However, recent studies showed that mitochondrial Prxs are also targeted to the intermembrane space by mechanisms that remain poorly understood. While in yeast the IMP complex can translocate Prx1 to the intermembrane space, the maturation of yeast Prx1 and mammalian Prdx3 and Prdx5 in the matrix has been associated with sequential cleavages of the presequence by MPP and Oct1/MIP proteases. In this review, we describe the state of the art of the molecular mechanisms that control the mitochondrial import and maturation of Prxs of yeast and human cells. Once mitochondria are considered the major intracellular source of H2O2, understanding the mitochondrial Prx biogenesis pathways is essential to increase our knowledge about the H2O2-dependent cellular signaling, which is relevant to the pathophysiology of some human diseases.
    Keywords:  H2O2; Intermembrane space; Matrix; Mitochondria; Peroxiredoxin; Presequence
    DOI:  https://doi.org/10.1007/s12551-021-00899-2
  11. Am J Physiol Cell Physiol. 2022 Jan 19.
    Mitochondrial transport, partitioning and quality control at the heart of cell proliferation and fate acquisition.
    Rakesh Kumar Sharma, Abderrahman Chafik, Giulia Bertolin.
      Mitochondria are essential to cell homeostasis, and alterations in mitochondrial distribution, segregation or turnover have been linked to complex pathologies such as neurodegenerative diseases or cancer. Understanding how these functions are coordinated in specific cell types is a major challenge to discover how mitochondria globally shape cell functionality. In this review, we will first describe how mitochondrial transport and dynamics are regulated throughout the cell cycle in yeast and in mammals. Second, we will explore the functional consequences of mitochondrial transport and partitioning on cell proliferation, fate acquisition, stemness, and on the way cells adapt their metabolism. Last, we will focus on how mitochondrial clearance programs represent a further layer of complexity for cell differentiation, or in the maintenance of stemness. Defining how mitochondrial transport, dynamics and clearance are mutually orchestrated in specific cell types may help our understanding of how cells can transition from a physiological to a pathological state.
    Keywords:  dynamics; fate acquisition; mitochondria; mitophagy; transport
    DOI:  https://doi.org/10.1152/ajpcell.00256.2021
  12. Biophys Rev. 2021 Dec;13(6): 955-965
    Mitophagy mechanisms in neuronal physiology and pathology during ageing.
    Maria Markaki, Dikaia Tsagkari, Nektarios Tavernarakis.
      Ageing in diverse species ranging from the simple nematode Caenorhabditis elegans to humans is associated with a marked decrease of neuronal function and increased susceptibility to neurodegeneration. Accumulating findings also indicate that alterations in neuronal functionality with age are associated with a decline in mitochondrial integrity and function. The rate at which a mitochondrial population is refreshed is determined by the coordination of mitochondrial biogenesis with mitophagy, a selective type of autophagy targeting damaged or superfluous mitochondria for degradation. Coupling of these opposing processes is crucial for maintaining cellular energy homeostasis, which eventually contributes to health span. Here, we focus on the role of mitophagy in nervous system function in the context of normal physiology and disease. First, we consider the progress that has been made over the last decade in elucidating the mechanisms that govern and regulate mitophagy, placing emphasis on the PINK1/Parkin-mediated mitophagy. We further discuss the contribution of mitophagy to the maintenance of neuronal homeostasis and health as well as recent findings implicating impaired mitophagy in age-related decline of the nervous system function and consequently in the pathogenesis of neurodegenerative diseases.
    Keywords:  Ageing; Energy homeostasis; Mitophagy; Neurodegeneration; Neuron; Neuronal health
    DOI:  https://doi.org/10.1007/s12551-021-00894-7
  13. J Biol Chem. 2022 Jan 18. pii: S0021-9258(22)00042-4. [Epub ahead of print] 101602
    Cryo-electron microscopy reveals how acetogenins inhibit mitochondrial respiratory complex I.
    Daniel N Grba, James N Blaza, Hannah R Bridges, Ahmed-Noor A Agip, Zhan Yin, Masatoshi Murai, Hideto Miyoshi, Judy Hirst.
      Mitochondrial complex I (NADH:ubiquinone oxidoreductase), a crucial enzyme in energy metabolism, captures the redox potential energy from NADH oxidation and ubiquinone reduction to create the proton motive force used to drive ATP synthesis in oxidative phosphorylation. Recent high-resolution cryo-EM analyses have provided detailed structural knowledge of the catalytic machinery of complex I, but not of the molecular principles of its energy transduction mechanism. Although ubiquinone is considered to bind in a long channel at the interface of the membrane-embedded and hydrophilic domains, and channel residues are likely involved in coupling substrate reduction to proton translocation, no structures with the channel fully occupied have yet been described. Here, we report the cryo-EM structure of mouse complex I with an extremely tight-binding natural-product acetogenin inhibitor, which resembles the native substrate, bound along the full length of the expected ubiquinone-binding channel. Our structure reveals the mode of acetogenin binding and the molecular basis for structure-activity relationships within the acetogenin family. It also shows that acetogenins are such potent inhibitors because they are highly hydrophobic molecules that contain two specific hydrophilic moieties ideally spaced to lock into two hydrophilic regions of the otherwise hydrophobic channel. The central hydrophilic section of the channel does not favor binding of the isoprenoid chain when the native substrate is fully bound, but stabilises the ubiquinone/ubiquinol headgroup as it transits to/from the active site. Therefore, the amphipathic nature of the channel supports both tight binding of the amphipathic inhibitor and rapid exchange of the ubiquinone/ubiquinol substrate and product.
    Keywords:  acetogenin; binding site; complex I; cryo-electron microscopy; inhibitor-bound structure
    DOI:  https://doi.org/10.1016/j.jbc.2022.101602
  14. Open Biol. 2022 Jan;12(1): 210255
    Selective localization of Mfn2 near PINK1 enables its preferential ubiquitination by Parkin on mitochondria.
    Marta Vranas, Yang Lu, Shafqat Rasool, Nathalie Croteau, Jonathan D Krett, Véronique Sauvé, Kalle Gehring, Edward A Fon, Thomas M Durcan, Jean-François Trempe.
      Mutations in Parkin and PINK1 cause early-onset familial Parkinson's disease. Parkin is a RING-In-Between-RING E3 ligase that transfers ubiquitin from an E2 enzyme to a substrate in two steps: (i) thioester intermediate formation on Parkin and (ii) acyl transfer to a substrate lysine. The process is triggered by PINK1, which phosphorylates ubiquitin on damaged mitochondria, which in turn recruits and activates Parkin. This leads to the ubiquitination of outer mitochondrial membrane proteins and clearance of the organelle. While the targets of Parkin on mitochondria are known, the factors determining substrate selectivity remain unclear. To investigate this, we examined how Parkin catalyses ubiquitin transfer to substrates. We found that His433 in the RING2 domain contributes to the catalysis of acyl transfer. In cells, the mutation of His433 impairs mitophagy. In vitro ubiquitination assays with isolated mitochondria show that Mfn2 is a kinetically preferred substrate. Using proximity-ligation assays, we show that Mfn2 specifically co-localizes with PINK1 and phospho-ubiquitin (pUb) in U2OS cells upon mitochondrial depolarization. We propose a model whereby ubiquitination of Mfn2 is efficient by virtue of its localization near PINK1, which leads to the recruitment and activation of Parkin via pUb at these sites.
    Keywords:  Mfn2; PINK1; Parkin; mitochondria; ubiquitin
    DOI:  https://doi.org/10.1098/rsob.210255
  15. Int J Mol Sci. 2022 Jan 16. pii: 952. [Epub ahead of print]23(2):
    The Role of Mitochondrial DNA Mutations in Cardiovascular Diseases.
    Siarhei A Dabravolski, Victoria A Khotina, Vasily N Sukhorukov, Vladislav A Kalmykov, Liudmila M Mikhaleva, Alexander N Orekhov.
      Cardiovascular diseases (CVD) are one of the leading causes of morbidity and mortality worldwide. mtDNA (mitochondrial DNA) mutations are known to participate in the development and progression of some CVD. Moreover, specific types of mitochondria-mediated CVD have been discovered, such as MIEH (maternally inherited essential hypertension) and maternally inherited CHD (coronary heart disease). Maternally inherited mitochondrial CVD is caused by certain mutations in the mtDNA, which encode structural mitochondrial proteins and mitochondrial tRNA. In this review, we focus on recently identified mtDNA mutations associated with CVD (coronary artery disease and hypertension). Additionally, new data suggest the role of mtDNA mutations in Brugada syndrome and ischemic stroke, which before were considered only as a result of mutations in nuclear genes. Moreover, we discuss the molecular mechanisms of mtDNA involvement in the development of the disease.
    Keywords:  Brugada syndrome; atherosclerosis; cardiovascular diseases; coronary artery disease; hypertension; ischemic stroke; mitochondria
    DOI:  https://doi.org/10.3390/ijms23020952
  16. Proc Natl Acad Sci U S A. 2022 Jan 18. pii: e2114710118. [Epub ahead of print]119(3):
    Mitoribosomal small subunit maturation involves formation of initiation-like complexes.
    Tea Lenarčič, Moritz Niemann, David J F Ramrath, Salvatore Calderaro, Timo Flügel, Martin Saurer, Marc Leibundgut, Daniel Boehringer, Céline Prange, Elke K Horn, André Schneider, Nenad Ban.
      Mitochondrial ribosomes (mitoribosomes) play a central role in synthesizing mitochondrial inner membrane proteins responsible for oxidative phosphorylation. Although mitoribosomes from different organisms exhibit considerable structural variations, recent insights into mitoribosome assembly suggest that mitoribosome maturation follows common principles and involves a number of conserved assembly factors. To investigate the steps involved in the assembly of the mitoribosomal small subunit (mt-SSU) we determined the cryoelectron microscopy structures of middle and late assembly intermediates of the Trypanosoma brucei mitochondrial small subunit (mt-SSU) at 3.6- and 3.7-Å resolution, respectively. We identified five additional assembly factors that together with the mitochondrial initiation factor 2 (mt-IF-2) specifically interact with functionally important regions of the rRNA, including the decoding center, thereby preventing premature mRNA or large subunit binding. Structural comparison of assembly intermediates with mature mt-SSU combined with RNAi experiments suggests a noncanonical role of mt-IF-2 and a stepwise assembly process, where modular exchange of ribosomal proteins and assembly factors together with mt-IF-2 ensure proper 9S rRNA folding and protein maturation during the final steps of assembly.
    Keywords:  mitochondria; ribosome assembly; structural biology; translation
    DOI:  https://doi.org/10.1073/pnas.2114710118
  17. Cell Genom. 2021 Oct 13. pii: 100006. [Epub ahead of print]1(1):
    Association of mitochondrial DNA copy number with cardiometabolic diseases.
    TOPMed mtDNA Working Group in NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium
      Mitochondrial DNA (mtDNA) is present in multiple copies in human cells. We evaluated cross-sectional associations of whole blood mtDNA copy number (CN) with several cardiometabolic disease traits in 408,361 participants of multiple ancestries in TOPMed and UK Biobank. Age showed a threshold association with mtDNA CN: among younger participants (<65 years of age), each additional 10 years of age was associated with 0.03 standard deviation (s.d.) higher level of mtDNA CN (P = 0.0014) versus a 0.14 s.d. lower level of mtDNA CN (P = 1.82 × 10-13) among older participants (≥65 years). At lower mtDNA CN levels, we found age-independent associations with increased odds of obesity (P = 5.6 × 10-238), hypertension (P = 2.8 × 10-50), diabetes (P = 3.6 × 10-7), and hyperlipidemia (P = 6.3 × 10-5). The observed decline in mtDNA CN after 65 years of age may be a key to understanding age-related diseases.
    DOI:  https://doi.org/10.1016/j.xgen.2021.100006
  18. Antioxid Redox Signal. 2022 Jan 19.
    Mitochondrial fusion, fission and mitophagy in cardiac diseases: challenges and therapeutic opportunities.
    Débora da Luz Scheffer, Adriana Ann Garcia, Lucia Lee, Daria Mochly-Rosen, Julio Cesar Batista Ferreira.
      SIGNIFICANCE: Mitochondria play a critical role in the physiology of the heart by controlling cardiac metabolism, function, and remodeling. Accumulation of fragmented and damaged mitochondria is a hallmark of cardiac diseases. Recent Advances: Disruption of quality control systems that maintain mitochondrial number, size, and shape through fission-fusion balance and mitophagy results in dysfunctional mitochondria, defective mitochondrial segregation, impaired cardiac bioenergetics, and excessive oxidative stress.CRITICAL ISSUES: Pharmacological tools that improve the cardiac pool of healthy mitochondria through inhibition of excessive mitochondrial fission, boosting mitochondrial fusion, or increasing the clearance of damaged mitochondria have emerged as promising approaches to improve the prognosis of heart diseases.
    FUTURE DIRECTIONS: There is a reasonable amount of pre-clinical evidence supporting the effectiveness of molecules targeting mitochondrial fission and fusion to treat cardiac diseases. The current and future challenges are turning these lead molecules into treatments. Clinical studies focusing on acute (i.e., myocardial infarction) and chronic (i.e., heart failure) cardiac diseases are needed to validate the effectiveness of such strategies in improving mitochondrial morphology, metabolism, and cardiac function.
    DOI:  https://doi.org/10.1089/ars.2021.0145
  19. Antioxidants (Basel). 2022 Jan 15. pii: 165. [Epub ahead of print]11(1):
    Therapeutic Strategies Targeting Mitochondrial Calcium Signaling: A New Hope for Neurological Diseases?
    Laura R Rodríguez, Tamara Lapeña-Luzón, Noelia Benetó, Vicent Beltran-Beltran, Federico V Pallardó, Pilar Gonzalez-Cabo, Juan Antonio Navarro.
      Calcium (Ca2+) is a versatile secondary messenger involved in the regulation of a plethora of different signaling pathways for cell maintenance. Specifically, intracellular Ca2+ homeostasis is mainly regulated by the endoplasmic reticulum and the mitochondria, whose Ca2+ exchange is mediated by appositions, termed endoplasmic reticulum-mitochondria-associated membranes (MAMs), formed by proteins resident in both compartments. These tethers are essential to manage the mitochondrial Ca2+ influx that regulates the mitochondrial function of bioenergetics, mitochondrial dynamics, cell death, and oxidative stress. However, alterations of these pathways lead to the development of multiple human diseases, including neurological disorders, such as amyotrophic lateral sclerosis, Friedreich's ataxia, and Charcot-Marie-Tooth. A common hallmark in these disorders is mitochondrial dysfunction, associated with abnormal mitochondrial Ca2+ handling that contributes to neurodegeneration. In this work, we highlight the importance of Ca2+ signaling in mitochondria and how the mechanism of communication in MAMs is pivotal for mitochondrial maintenance and cell homeostasis. Lately, we outstand potential targets located in MAMs by addressing different therapeutic strategies focused on restoring mitochondrial Ca2+ uptake as an emergent approach for neurological diseases.
    Keywords:  Charcot–Marie–Tooth; Friedreich’s ataxia; amyotrophic lateral sclerosis; calcium; endoplasmic reticulum; mitochondria; mitochondrial calcium uniporter; neurological; sigma-1 receptor
    DOI:  https://doi.org/10.3390/antiox11010165
  20. Mol Vis. 2021 ;27 718-724
    Prevalence of primary mutations in Leber hereditary optic neuropathy: A five-year report from a tertiary eye care center in India.
    Srilekha Sundaramurthy, Ambika Selvakumar, Vidhya Dharani, Nagasamy Soumittra, Jayaprakash Mani, Karthiyayini Thirumalai, Porkodi Periyasamy, Sinnakaruppan Mathavan, Sarangapani Sripriya.
      Purpose: Genetic testing for primary mutations m.3460G>A, m.11778G>A, and m.14484T>C in ND1, ND4, and ND6 genes of mitochondrial DNA is the recommended assay for Leber hereditary optic neuropathy (LHON; OMIM 535000). This report discusses the outcome of molecular genetic screening for these three primary mutations in suspected LHON cases in India.Methods: Two hundred and seventy-eight unrelated presumed LHON patients who were seen at the neuro-ophthalmology clinic of a tertiary eye care center from 2014-2018 were analyzed. They were genotyped for the three common variants by polymerase chain reaction-based direct sequencing, and their plasmy status was also determined by restriction enzyme digestion.
    Results: Eighty two of 278 patients were positive for one of the 3 common mutations with m.11778G>A in ND4 gene more frequently distributed (N=72) in homoplasmic state (N=59/82). The mean onset age of visual loss was 21.1years (SD, 9.8 years; range, 5-58 years) in patients harboring the primary mutation. The most common clinical presentation was bilateral sequential painless vision loss with central and cecocentral scotomas in the visual field due to optic disc atrophy.
    Conclusions: The study subjects are a sample of a much larger number of suspected LHON cases tested for primary mutations in India. (N= 278) and 29.4% (82/278) of patients harbour one of the 3 common mutations. Screening the entire mitochondrial genome and the other nuclear genes encoding mitochondrial protein, would probably aid in identifying the other less common mtDNA mutations causing LHON in Indian population.
  21. Nat Rev Genet. 2022 Jan 21.
    Mitochondrial DNA copy number and disease.
    Dorothy Clyde.
      
    DOI:  https://doi.org/10.1038/s41576-022-00451-2
  22. Biochim Biophys Acta Bioenerg. 2022 Jan 18. pii: S0005-2728(22)00001-9. [Epub ahead of print] 148532
    MDH2 produced OAA is a metabolic switch rewiring the fuelling of respiratory chain and TCA cycle.
    Thibaut Molinié, Elodie Cougouilles, Claudine David, Edern Cahoreau, Jean-Charles Portais, Arnaud Mourier.
      The mitochondrial respiratory chain (RC) enables many metabolic processes by regenerating both mitochondrial and cytosolic NAD+ and ATP. The oxidation by the RC of the NADH metabolically produced in the cytosol involves redox shuttles as the malate-aspartate shuttle (MAS) and is of paramount importance for cell fate. However, the specific metabolic regulations allowing mitochondrial respiration to prioritize NADH oxidation in response to high NADH/NAD+ redox stress have not been elucidated. The recent discovery that complex I (NADH dehydrogenase), and not complex II (Succinate dehydrogenase), can assemble with other respiratory chain (RC) complexes to form functional entities called respirasomes, led to the assumption that this supramolecular organization would favour NADH oxidation. Unexpectedly, characterization of heart and liver mitochondria demonstrates that the RC systematically favours electrons provided by the 'respirasome free' complex II. Our results demonstrate that the preferential succinate driven respiration is tightly controlled by OAA levels, and that OAA feedback inhibition of complex II rewires RC fuelling increasing NADH oxidation capacity. This new regulatory mechanism synergistically increases RC's NADH oxidative capacity and rewires MDH2 driven anaplerosis of the TCA, preventing malate production from succinate to favour oxidation of cytosolic malate. This regulatory mechanism synergistically adjusts RC and TCA fuelling in response to extramitochondrial malate produced by the MAS.
    Keywords:  Bioenergetics; MDH2; Malate aspartate shuttle; Mitochondria; NADH redox homeostasis; Oxaloacetate; Respirasomes; Respiratory chain supercomplexes
    DOI:  https://doi.org/10.1016/j.bbabio.2022.148532
  23. Nat Commun. 2022 Jan 20. 13(1): 424
    Enrichment of the exocytosis protein STX4 in skeletal muscle remediates peripheral insulin resistance and alters mitochondrial dynamics via Drp1.
    Karla E Merz, Jinhee Hwang, Chunxue Zhou, Rajakrishnan Veluthakal, Erika M McCown, Angelica Hamilton, Eunjin Oh, Wenting Dai, Patrick T Fueger, Lei Jiang, Janice M Huss, Debbie C Thurmond.
      Mitochondrial dysfunction is implicated in skeletal muscle insulin resistance. Syntaxin 4 (STX4) levels are reduced in human diabetic skeletal muscle, and global transgenic enrichment of STX4 expression improves insulin sensitivity in mice. Here, we show that transgenic skeletal muscle-specific STX4 enrichment (skmSTX4tg) in mice reverses established insulin resistance and improves mitochondrial function in the context of diabetogenic stress. Specifically, skmSTX4tg reversed insulin resistance caused by high-fat diet (HFD) without altering body weight or food consumption. Electron microscopy of wild-type mouse muscle revealed STX4 localisation at or proximal to the mitochondrial membrane. STX4 enrichment prevented HFD-induced mitochondrial fragmentation and dysfunction through a mechanism involving STX4-Drp1 interaction and elevated AMPK-mediated phosphorylation at Drp1 S637, which favors fusion. Our findings challenge the dogma that STX4 acts solely at the plasma membrane, revealing that STX4 localises at/proximal to and regulates the function of mitochondria in muscle. These results establish skeletal muscle STX4 enrichment as a candidate therapeutic strategy to reverse peripheral insulin resistance.
    DOI:  https://doi.org/10.1038/s41467-022-28061-w
  24. J Inherit Metab Dis. 2022 Jan 17.
    Biomarkers for Drug Development in Propionic and Methylmalonic Acidemias.
    Nicola Longo, Jörn Oliver Sass, Agnieszka Jurecka, Jerry Vockley.
      There is an unmet need for the development and validation of biomarkers and surrogate endpoints for clinical trials in propionic acidemia (PA) and methylmalonic acidemia (MMA). This review examines the pathophysiology and clinical consequences of PA and MMA that could form the basis for potential biomarkers and surrogate endpoints. Changes in primary metabolites such as methylcitric acid (MCA), MCA:citric acid ratio, oxidation of 13 C-propionate (exhaled 13 CO2 ), and propionylcarnitine (C3) have demonstrated clinical relevance in patients with PA or MMA. Methylmalonic acid, another primary metabolite, is a potential biomarker, but only in patients with MMA. Other potential biomarkers in patients with either PA and MMA include secondary metabolites, such as ammonium, or the mitochondrial disease marker, fibroblast growth factor 21. Additional research is needed to validate these biomarkers as surrogate endpoints, and to determine whether other metabolites or markers of organ damage could also be useful biomarkers for clinical trials of investigational drug treatments in patients with PA or MMA. This article is protected by copyright. All rights reserved.
    DOI:  https://doi.org/10.1002/jimd.12478
  25. Aging Cell. 2022 Jan 20. e13552
    Muscle mitochondrial energetics predicts mobility decline in well-functioning older adults: The baltimore longitudinal study of aging.
    Qu Tian, Brendan A Mitchell, Marta Zampino, Kenneth W Fishbein, Richard G Spencer, Luigi Ferrucci.
      BACKGROUND: Muscle mitochondrial dysfunction is associated with poor mobility in aging. Whether mitochondrial dysfunction predicts subsequent mobility decline is unknown.METHODS: We examined 380 cognitively normal participants aged 60 and older (53%women, 22%Black) who were well-functioning (gait speed ≥ 1.0 m/s) and free of Parkinson's disease and stroke at baseline and had data on baseline skeletal muscle oxidative capacity and one or more mobility assessments during an average 2.5 years. Muscle oxidative capacity was measured by phosphorus magnetic resonance spectroscopy as the post-exercise recovery rate of phosphocreatine (kPCr ). Mobility was measured by four walking tests. Associations of baseline kPCr with mobility changes were examined using linear mixed-effects models, adjusted for covariates. In a subset, we examined whether changes in muscle strength and mass affected these associations by adjusting for longitudinal muscle strength, lean mass, and fat mass.
    RESULTS: Lower baseline kPCr was associated with greater decline in all four mobility measures (β, p-value: (0.036, 0.020) 6-m usual gait speed; (0.029, 0.038) 2.5-min usual gait speed; (0.034, 0.011) 6-m rapid gait speed; (-0.042, <0.001) 400-m time). In the subset, further adjustment for longitudinal muscle strength, lean mass, and fat mass attenuated longitudinal associations with changes in mobility (Δβ reduced 26-63%).
    CONCLUSION: Among initially well-functioning older adults, worse muscle mitochondrial function predicts mobility decline, and part of this longitudinal association is explained by decline in muscle strength and mass. Our findings suggest that worse mitochondrial function contributes to mobility decline with aging. These findings need to be verified in studies correlating longitudinal changes in mitochondrial function, muscle, and mobility performance.
    Keywords:  magnetic resonance spectroscopy; mitochondrial energetics; mobility decline; skeletal muscle; walking speed
    DOI:  https://doi.org/10.1111/acel.13552
  26. Methods Mol Biol. 2022 ;2443 181-196
    Pipeline Automation via Snakemake.
    Jakob Petereit.
      With third generation DNA sequencing and a general reduction of sequencing costs, the production of bioinformatic data has become easier than ever. Several pipeline automation tools have emerged to ease data processing through a multitude of steps. Here, we describe the setup and use of Snakemake, a pipeline automation tool derived from GNU MAKE.
    Keywords:  Bioinformatics; Bowtie2 alignments; Pipeline; Snakemake; Trimming; fastQC
    DOI:  https://doi.org/10.1007/978-1-0716-2067-0_9
  27. Am J Hum Genet. 2022 Jan 11. pii: S0002-9297(21)00462-6. [Epub ahead of print]
    StrVCTVRE: A supervised learning method to predict the pathogenicity of human genome structural variants.
    Andrew G Sharo, Zhiqiang Hu, Shamil R Sunyaev, Steven E Brenner.
      Whole-genome sequencing resolves many clinical cases where standard diagnostic methods have failed. However, at least half of these cases remain unresolved after whole-genome sequencing. Structural variants (SVs; genomic variants larger than 50 base pairs) of uncertain significance are the genetic cause of a portion of these unresolved cases. As sequencing methods using long or linked reads become more accessible and SV detection algorithms improve, clinicians and researchers are gaining access to thousands of reliable SVs of unknown disease relevance. Methods to predict the pathogenicity of these SVs are required to realize the full diagnostic potential of long-read sequencing. To address this emerging need, we developed StrVCTVRE to distinguish pathogenic SVs from benign SVs that overlap exons. In a random forest classifier, we integrated features that capture gene importance, coding region, conservation, expression, and exon structure. We found that features such as expression and conservation are important but are absent from SV classification guidelines. We leveraged multiple resources to construct a size-matched training set of rare, putatively benign and pathogenic SVs. StrVCTVRE performs accurately across a wide SV size range on independent test sets, which will allow clinicians and researchers to eliminate about half of SVs from consideration while retaining a 90% sensitivity. We anticipate clinicians and researchers will use StrVCTVRE to prioritize SVs in probands where no SV is immediately compelling, empowering deeper investigation into novel SVs to resolve cases and understand new mechanisms of disease. StrVCTVRE runs rapidly and is publicly available.
    Keywords:  copy-number variant; machine learning; random forest; rare disease; structural variant; variant interpretation
    DOI:  https://doi.org/10.1016/j.ajhg.2021.12.007
  28. J Pers Med. 2022 Jan 08. pii: 73. [Epub ahead of print]12(1):
    Clin.iobio: A Collaborative Diagnostic Workflow to Enable Team-Based Precision Genomics.
    Alistair Ward, Matt Velinder, Tonya Di Sera, Aditya Ekawade, Sabrina Malone Jenkins, Barry Moore, Rong Mao, Pinar Bayrak-Toydemir, Gabor Marth.
      The primary goal of precision genomics is the identification of causative genetic variants in targeted or whole-genome sequencing data. The ultimate clinical hope is that these findings lead to an efficacious change in treatment for the patient. In current clinical practice, these findings are typically returned by expert analysts as static, text-based reports. Ideally, these reports summarize the quality of the data obtained, integrate known gene-phenotype associations, follow allele segregation and affected status within the sequenced samples, and weigh computational evidence of pathogenicity. These findings are used to prioritize the variant(s) most likely to cause the given patient's phenotypes. In most diagnostic settings, a team of experts contribute to these reports, including bioinformaticians, clinicians, and genetic counselors, among others. However, these experts often do not have the necessary tools to review genomic findings, test genetic hypotheses, or query specific gene and variant information. Additionally, team members often rely on different tools and methods based on their given expertise, resulting in further difficulties in communicating and discussing genomic findings. Here, we present clin.iobio-a web-based solution to collaborative genomic analysis that enables diagnostic team members to focus on their area of expertise within the diagnostic process, while allowing them to easily review and contribute to all steps of the diagnostic process. Clin.iobio integrates tools from the popular iobio genomic visualization suite into a comprehensive diagnostic workflow, encompassing (1) genomic data quality review, (2) dynamic phenotype-driven gene prioritization, (3) variant prioritization using a comprehensive set of knowledge bases and annotations, (4) and an exportable findings summary. In conclusion, clin.iobio is a comprehensive solution to team-based precision genomics, the findings of which stand to inform genomic considerations in clinical practice.
    Keywords:  NICU; clinical; collaboration; diagnostics; genetics; genomics; rapid sequencing; reanalysis; software; undiagnosed disease; visualization
    DOI:  https://doi.org/10.3390/jpm12010073
  29. Nature. 2022 Jan;601(7893): S15-S17
    The biological clean-ups that could combat age-related disease.
    Elie Dolgin.
      
    Keywords:  Ageing; Biotechnology; Drug discovery
    DOI:  https://doi.org/10.1038/d41586-022-00075-w
  30. JCI Insight. 2022 Jan 20. pii: e156522. [Epub ahead of print]
    Leukocytes mediate disease pathogenesis in the Ndufs4(KO) mouse model of Leigh syndrome.
    Julia C Stokes, Rebecca L Bornstein, Katerina James, Kyung Yeon Park, Kira A Spencer, Katie Vo, John C Snell, Brittany M Johnson, Philip G Morgan, Margaret M Sedensky, Nathan A Baertsch, Simon C Johnson.
      Symmetric, progressive, necrotizing lesions in the brainstem are a defining feature of Leigh syndrome (LS). A mechanistic understanding of the pathogenesis of these lesions has been elusive. Here, we report that leukocyte proliferation is causally involved in the pathogenesis of LS. Depleting leukocytes with a colony-stimulating factor 1 receptor inhibitor disrupts disease progression, including suppression of CNS lesion formation and a substantial extension of survival. Leukocyte depletion rescues diverse symptoms including seizures, respiratory center function, hyperlactemia, and neurologic sequelae. These data reveal a mechanistic explanation for the beneficial effects of mTOR inhibition. More importantly, these findings dramatically alter our understanding of the pathogenesis of LS, demonstrating that immune involvement is causal in disease. This work has significant implications for the mechanisms of mitochondrial disease and may lead to novel therapeutic strategies.
    Keywords:  Genetic diseases; Inflammation; Mitochondria; Mouse models; Neuroscience
    DOI:  https://doi.org/10.1172/jci.insight.156522
  31. Nat Commun. 2022 Jan 18. 13(1): 366
    Nuclear and mitochondrial DNA editing in human cells with zinc finger deaminases.
    Kayeong Lim, Sung-Ik Cho, Jin-Soo Kim.
      Base editing in nuclear DNA and mitochondrial DNA (mtDNA) is broadly useful for biomedical research, medicine, and biotechnology. Here, we present a base editing platform, termed zinc finger deaminases (ZFDs), composed of custom-designed zinc-finger DNA-binding proteins, the split interbacterial toxin deaminase DddAtox, and a uracil glycosylase inhibitor (UGI), which catalyze targeted C-to-T base conversions without inducing unwanted small insertions and deletions (indels) in human cells. We assemble plasmids encoding ZFDs using publicly available zinc finger resources to achieve base editing at frequencies of up to 60% in nuclear DNA and 30% in mtDNA. Because ZFDs, unlike CRISPR-derived base editors, do not cleave DNA to yield single- or double-strand breaks, no unwanted indels caused by error-prone non-homologous end joining are produced at target sites. Furthermore, recombinant ZFD proteins, expressed in and purified from E. coli, penetrate cultured human cells spontaneously to induce targeted base conversions, demonstrating the proof-of-principle of gene-free gene therapy.
    DOI:  https://doi.org/10.1038/s41467-022-27962-0
  32. Clin Sci (Lond). 2022 Jan 20. pii: CS20210964. [Epub ahead of print]
    Nicotinamide riboside kinase-2 inhibits JNK pathway and limits dilated cardiomyopathy in mice with chronic pressure overload.
    Syeda Kiran Shahzadi, Hezlin Marzook, Rizwan Qaisar, Firdos Ahmad.
      Nicotinamide riboside kinase-2 (NRK-2) has recently emerged as a critical regulator of cardiac remodeling however, underlying molecular mechanisms is largely unknown. To explore the same, NRK2 knockout (KO) and littermate control mice were subjected to trans-aortic constriction (TAC) or sham surgeries and cardiac function was assessed by serial M-mode echocardiography. A mild cardiac contractile dysfunction was observed in the KOs at the early adaptive phase of remodeling followed by a significant deterioration during the maladaptive cardiac remodeling phase. Consistently, NRK2 KO hearts displayed increased cardiac hypertrophy and heart failure reflected by morphometric parameters as well as increased fetal genes ANP and BNP expressions. Histological assessment revealed an extensive left ventricular (LV) chamber dilatation accompanied by elevated cardiomyopathy and fibrosis in the KO hearts post-TAC. In a gain-of-function model, NRK-2 overexpressing in AC16 cardiomyocytes displayed significantly attenuated fetal genes ANP and BNP expression. Consistently, NRK-2 overexpression attenuated angiotensin II- induced cardiomyocyte death. Mechanistically, we identified NRK-2 as a regulator of JNK MAP kinase and mitochondrial function where NRK-2 overexpression in human cardiomyocytes markedly suppressed the angiotensin II- induced JNK activation and mitochondrial depolarization. Thus, our results demonstrate that NRK-2 plays protective roles in pressure overload- induced dilatative cardiac remodeling and, genetic ablation exacerbates dilated cardiomyopathy, interstitial collagen deposition, and cardiac dysfunction post-TAC due, in part, to increased JNK activation and mitochondrial dysfunction.
    Keywords:  Dilated cardiomyopathy; JNK MAP Kinases; MIBP; Mitochondrial dysfunction; NMRK-2; Pressure Overload
    DOI:  https://doi.org/10.1042/CS20210964
  33. Cell Signal. 2022 Jan 17. pii: S0898-6568(22)00009-2. [Epub ahead of print] 110249
    FUNDC1 activates the mitochondrial unfolded protein response to preserve mitochondrial quality control in cardiac ischemia/reperfusion injury.
    Haizhe Ji, Jin Wang, David Muid, Wei Song, Yinong Jiang, Hao Zhou.
      The mitochondrial unfolded protein response (UPRmt) is an adaptive transcriptional response involving the activation of proteases, chaperones, and antioxidant enzymes and serves to degrade abnormal or unfolded proteins and restore mitochondrial function. Although the cardioprotective action of the UPRmt has been verified in myocardial ischemia/reperfusion (I/R) injuries, the upstream signals involved remain unclear. Here, we explored the regulatory mechanisms underlying UPRmt in the reperfused mouse heart. UPRmt was slightly activated by I/R injury. UPRmt activation (using oligomycin) and inhibition (with the protease inhibitor AEBSF) respectively alleviated and augmented the reperfusion-mediated myocardial damage. Gene expression analysis demonstrated that oxidative stress was partly inhibited by UPRmt through upregulation of mitochondria-localized, not cytoplasmic, antioxidant enzymes. Contributing to cardiomyocyte survival under I/R, the transcription of pro-apoptotic proteins Bcl2 and c-IAP was also stimulated by UPRmt. Moreover, UPRmt upregulated mitochondrial fusion-related, but not fission-related, genes and stimulated the expression of mitochondrial biogenesis markers in reperfused hearts. Finally, we found that FUN14 domain containing 1 (FUNDC1)-mediated mitophagy induces the mitochondrial DNA decrease, triggering UPRmt. These results demonstrate that FUNDC1 functions upstream of the UPRmt to maintain mitochondrial quality control during myocardial I/R injury.
    Keywords:  Cardiomyocyte; FUNDC1; Mitochondrial unfolded protein response; Mitophagy; Myocardial I/R injury
    DOI:  https://doi.org/10.1016/j.cellsig.2022.110249
  34. N Engl J Med. 2022 01 20. pii: 10.1056/NEJMc2118255#sa4. [Epub ahead of print]386(3): 295-296
    Nonalcoholic Fatty Liver Disease. Reply.
    Sven M Francque, Pierre Bedossa, Manal F Abdelmalek.
      
    DOI:  https://doi.org/10.1056/NEJMc2118255
  35. J Biol Chem. 2022 Jan 17. pii: S0021-9258(22)00044-8. [Epub ahead of print] 101604
    MCU (Mitochondrial Ca2+ Uniporter) makes the calcium go round.
    Grant C Walters, Yuriy M Usachev.
      Store-operated Ca2+ entry (SOCE) is a major mechanism controlling Ca2+ signaling and Ca2+-dependent functions and has been implicated in immunity, cancer, and organ development. SOCE-dependent cytosolic Ca2+ signals are affected by mitochondrial Ca2+ transport through several competing mechanisms. However, how these mechanisms interact in shaping Ca2+ dynamics and regulating Ca2+-dependent functions remains unclear. In a recent issue, Yoast and colleagues shed light on these questions by defining multiple roles of the mitochondrial Ca2+ uniporter (MCU) in regulating SOCE, Ca2+ dynamics, transcription, and lymphocyte activation.
    DOI:  https://doi.org/10.1016/j.jbc.2022.101604
  36. Cells. 2022 Jan 09. pii: 214. [Epub ahead of print]11(2):
    One-Carbon Metabolism: Pulling the Strings behind Aging and Neurodegeneration.
    Eirini Lionaki, Christina Ploumi, Nektarios Tavernarakis.
      One-carbon metabolism (OCM) is a network of biochemical reactions delivering one-carbon units to various biosynthetic pathways. The folate cycle and methionine cycle are the two key modules of this network that regulate purine and thymidine synthesis, amino acid homeostasis, and epigenetic mechanisms. Intersection with the transsulfuration pathway supports glutathione production and regulation of the cellular redox state. Dietary intake of micronutrients, such as folates and amino acids, directly contributes to OCM, thereby adapting the cellular metabolic state to environmental inputs. The contribution of OCM to cellular proliferation during development and in adult proliferative tissues is well established. Nevertheless, accumulating evidence reveals the pivotal role of OCM in cellular homeostasis of non-proliferative tissues and in coordination of signaling cascades that regulate energy homeostasis and longevity. In this review, we summarize the current knowledge on OCM and related pathways and discuss how this metabolic network may impact longevity and neurodegeneration across species.
    Keywords:  Alzheimer’s disease; Parkinson disease; aging; diet; folate; metabolism; methionine; mitochondria; neurodegeneration; one-carbon vitamins
    DOI:  https://doi.org/10.3390/cells11020214
  37. Genome Med. 2022 Jan 18. 14(1): 6
    ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines.
    Clinical Genome Resource (ClinGen)
      BACKGROUND: Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments in next-generation sequencing technologies. However, the infrastructure and accessible comprehensive curation tools necessary for analyzing an individual patient genome and interpreting genetic variants to inform healthcare management have been lacking.RESULTS: Here we present the ClinGen Variant Curation Interface (VCI), a global open-source variant classification platform for supporting the application of evidence criteria and classification of variants based on the ACMG/AMP variant classification guidelines. The VCI is among a suite of tools developed by the NIH-funded Clinical Genome Resource (ClinGen) Consortium and supports an FDA-recognized human variant curation process. Essential to this is the ability to enable collaboration and peer review across ClinGen Expert Panels supporting users in comprehensively identifying, annotating, and sharing relevant evidence while making variant pathogenicity assertions. To facilitate evidence-based improvements in human variant classification, the VCI is publicly available to the genomics community. Navigation workflows support users providing guidance to comprehensively apply the ACMG/AMP evidence criteria and document provenance for asserting variant classifications.
    CONCLUSIONS: The VCI offers a central platform for clinical variant classification that fills a gap in the learning healthcare system, facilitates widespread adoption of standards for clinical curation, and is available at https://curation.clinicalgenome.org.
    Keywords:  Clinical Genome Resource Consortium; Clinical genetics; Precision medicine; Variant curation
    DOI:  https://doi.org/10.1186/s13073-021-01004-8
  38. Nat Metab. 2022 Jan 20.
    Circulating metabolite homeostasis achieved through mass action.
    Xiaoxuan Li, Sheng Hui, Emily T Mirek, William O Jonsson, Tracy G Anthony, Won Dong Lee, Xianfeng Zeng, Cholsoon Jang, Joshua D Rabinowitz.
      Homeostasis maintains serum metabolites within physiological ranges. For glucose, this requires insulin, which suppresses glucose production while accelerating its consumption. For other circulating metabolites, a comparable master regulator has yet to be discovered. Here we show that, in mice, many circulating metabolites are cleared via the tricarboxylic acid cycle (TCA) cycle in linear proportionality to their circulating concentration. Abundant circulating metabolites (essential amino acids, serine, alanine, citrate, 3-hydroxybutyrate) were administered intravenously in perturbative amounts and their fluxes were measured using isotope labelling. The increased circulating concentrations induced by the perturbative infusions hardly altered production fluxes while linearly enhancing consumption fluxes and TCA contributions. The same mass action relationship between concentration and consumption flux largely held across feeding, fasting and high- and low-protein diets, with amino acid homeostasis during fasting further supported by enhanced endogenous protein catabolism. Thus, despite the copious regulatory machinery in mammals, circulating metabolite homeostasis is achieved substantially through mass action-driven oxidation.
    DOI:  https://doi.org/10.1038/s42255-021-00517-1
  39. Exp Mol Med. 2022 Jan 21.
    SENP2 regulates mitochondrial function and insulin secretion in pancreatic β cells.
    Jinyan Nan, Ji Seon Lee, Joon Ho Moon, Seung-Ah Lee, Young Joo Park, Dong-Sup Lee, Sung Soo Chung, Kyong Soo Park.
      Increasing evidence has shown that small ubiquitin-like modifier (SUMO) modification plays an important role in metabolic regulation. We previously demonstrated that SUMO-specific protease 2 (SENP2) is involved in lipid metabolism in skeletal muscle and adipogenesis. In this study, we investigated the function of SENP2 in pancreatic β cells by generating a β cell-specific knockout (Senp2-βKO) mouse model. Glucose tolerance and insulin secretion were significantly impaired in the Senp2-βKO mice. In addition, glucose-stimulated insulin secretion (GSIS) was decreased in the islets of the Senp2-βKO mice without a significant change in insulin synthesis. Furthermore, islets of the Senp2-βKO mice exhibited enlarged mitochondria and lower oxygen consumption rates, accompanied by lower levels of S616 phosphorylated DRP1 (an active form of DRP1), a mitochondrial fission protein. Using a cell culture system of NIT-1, an islet β cell line, we found that increased SUMO2/3 conjugation to DRP1 due to SENP2 deficiency suppresses the phosphorylation of DRP1, which possibly induces mitochondrial dysfunction. In addition, SENP2 overexpression restored GSIS impairment induced by DRP1 knockdown and increased DRP1 phosphorylation. Furthermore, palmitate treatment decreased phosphorylated DRP1 and GSIS in β cells, which was rescued by SENP2 overexpression. These results suggest that SENP2 regulates mitochondrial function and insulin secretion at least in part by modulating the phosphorylation of DRP1 in pancreatic β cells.
    DOI:  https://doi.org/10.1038/s12276-021-00723-7
  40. Cell. 2022 Jan 14. pii: S0092-8674(21)01563-4. [Epub ahead of print]
    Tau interactome maps synaptic and mitochondrial processes associated with neurodegeneration.
    Tara E Tracy, Jesus Madero-Pérez, Danielle L Swaney, Timothy S Chang, Michelle Moritz, Csaba Konrad, Michael E Ward, Erica Stevenson, Ruth Hüttenhain, Grant Kauwe, Maria Mercedes, Lauren Sweetland-Martin, Xu Chen, Sue-Ann Mok, Man Ying Wong, Maria Telpoukhovskaia, Sang-Won Min, Chao Wang, Peter Dongmin Sohn, Jordie Martin, Yungui Zhou, Wenjie Luo, John Q Trojanowski, Virginia M Y Lee, Shiaoching Gong, Giovanni Manfredi, Giovanni Coppola, Nevan J Krogan, Daniel H Geschwind, Li Gan.
      Tau (MAPT) drives neuronal dysfunction in Alzheimer disease (AD) and other tauopathies. To dissect the underlying mechanisms, we combined an engineered ascorbic acid peroxidase (APEX) approach with quantitative affinity purification mass spectrometry (AP-MS) followed by proximity ligation assay (PLA) to characterize Tau interactomes modified by neuronal activity and mutations that cause frontotemporal dementia (FTD) in human induced pluripotent stem cell (iPSC)-derived neurons. We established interactions of Tau with presynaptic vesicle proteins during activity-dependent Tau secretion and mapped the Tau-binding sites to the cytosolic domains of integral synaptic vesicle proteins. We showed that FTD mutations impair bioenergetics and markedly diminished Tau's interaction with mitochondria proteins, which were downregulated in AD brains of multiple cohorts and correlated with disease severity. These multimodal and dynamic Tau interactomes with exquisite spatial resolution shed light on Tau's role in neuronal function and disease and highlight potential therapeutic targets to block Tau-mediated pathogenesis.
    Keywords:  APEX; Tau; Tau secretion; affinity purification mass spectrometry; interactome; mitochondria; neurodegeneration; protein-protein interaction; synapse; tauopathies
    DOI:  https://doi.org/10.1016/j.cell.2021.12.041
  41. Hum Genome Var. 2022 Jan 17. 9(1): 2
    MCAD deficiency caused by compound heterozygous pathogenic variants in ACADM.
    Fumikatsu Nohara, Go Tajima, Hideo Sasai, Yoshio Makita.
      Medium-chain acyl-coenzyme A dehydrogenase (MCAD) deficiency is an autosomal recessive disease caused by biallelic pathogenic ACADM variants. We report a case of an asymptomatic Japanese girl with MCAD deficiency caused by compound heterozygous pathogenic variants (NM_000016.5:c.1040G > T (p.Gly347Val) and c.449_452delCTGA (p.Thr150ArgfsTer4)). Because the MCAD residual activity in lymphocytes of the patient was below the limit of quantification, both variants are likely to cause complete loss of MCAD enzymatic activity.
    DOI:  https://doi.org/10.1038/s41439-021-00177-3
  42. Metabolites. 2021 Dec 22. pii: 9. [Epub ahead of print]12(1):
    Modelling Metabolic Shifts during Cardiomyocyte Differentiation, Iron Deficiency and Transferrin Rescue Using Human Pluripotent Stem Cells.
    Benjamin B Johnson, Johannes Reinhold, Terri L Holmes, Jamie A Moore, Verity Cowell, Andreia S Bernardo, Stuart A Rushworth, Vassilios Vassiliou, James G W Smith.
      Cardiomyocytes rely on specialised metabolism to meet the high energy demand of the heart. During heart development, metabolism matures and shifts from the predominant utilisation of glycolysis and glutamine oxidation towards lactate and fatty acid oxidation. Iron deficiency (ID) leads to cellular metabolism perturbations. However, the exact alterations in substrate metabolism during ID are poorly defined. Using human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM), the present study investigated changes in major metabolic substrate utilisation in the context of ID or upon transferrin rescue. Typically, during hiPSC-CM differentiation, the greatest increase in total metabolic output and rate was seen in fatty acid metabolism. When ID was induced, hiPSC-CMs displayed increased reliance on glycolytic metabolism, and six TCA cycle, five amino acid, and four fatty acid substrates were significantly impaired. Transferrin rescue was able to improve TCA cycle substrate metabolism, but the amino acid and fatty acid metabolism remained perturbed. Replenishing iron stores partially reverses the adverse metabolic changes that occur during ID. Understanding the changes in metabolic substrate utilisation and their modification may provide potential for discovery of new biomarkers and therapeutic targets in cardiovascular diseases.
    Keywords:  cardiomyocytes; iron deficiency; pluripotent stem cells
    DOI:  https://doi.org/10.3390/metabo12010009
  43. FEBS J. 2022 Jan 20.
    Cellular senescence: all roads lead to mitochondria.
    Hélène Martini, João F Passos.
      Senescence is a multi-functional cell fate, characterized by an irreversible cell-cycle arrest and a pro-inflammatory phenotype, commonly known as the Senescence-Associated secretory Phenotype (SASP). Emerging evidence indicates that accumulation of senescent cells in multiple tissues, drives tissue dysfunction and several age-related conditions. This has spurred the academic community and industry to identify new therapeutic interventions targeting this process. Mitochondrial dysfunction is an often-unappreciated hallmark of cellular senescence which plays important roles not only in the senescence growth arrest but also in the development of the SASP and resistance to cell-death. Here, we review the evidence that supports a role for mitochondria in the development of senescence and describe the underlying mechanisms. Finally, we propose that a detailed road map of mitochondrial biology in senescence will be crucial to guide the future development of senotherapies.
    Keywords:  Mitochondria; SASP; aging; senescence
    DOI:  https://doi.org/10.1111/febs.16361
  44. Cell Death Discov. 2022 Jan 17. 8(1): 28
    Idebenone improves motor dysfunction, learning and memory by regulating mitophagy in MPTP-treated mice.
    Junqiang Yan, Wenjie Sun, Mengmeng Shen, Yongjiang Zhang, Menghan Jiang, Anran Liu, Hongxia Ma, Xiaoyi Lai, Jiannan Wu.
      The progression of Parkinson's disease (PD) is often accompanied by the loss of substantia nigra dopaminergic neurons, mitophagy damage, learning, and memory impairment. Idebenone is a therapeutic drug that targets the mitochondria of neurodegenerative diseases, but its role in Parkinson's disease and its pathological mechanism are still unclear. The purpose of this study was to investigate whether idebenone could improve behavioral disorders, especially motor, learning, and memory disorders, in mouse PD models and to explore its molecular mechanism. In the present study, C57BL-6 mice underwent intraperitoneal injection of MPTP (30 mg/kg) once a day for five consecutive days. Then, a 200 mg/kg dose was given as a single daily gavage of idebenone dissolved in water for 21 days after the successful establishment of the subacute MPTP model. Motor, learning, and memory were measured by a water maze and a rotarod test. Our results showed that idebenone could reduce MPTP-induced dopaminergic neuron damage and improve movement disorders, memory, and learning ability, which may be associated with upregulating mitochondrial autophagy-related outer membrane proteins VDAC1 and BNIP3 and activating the Parkin/PINK1 mitochondrial autophagy pathway. To confirm whether idebenone promotes the smooth progression of autophagy, we used eGFP-mCherry-LC3 mice to construct a subacute model of Parkinson's disease and found that idebenone can increase autophagy in dopaminergic neurons in Parkinson's disease. In summary, our results confirm that idebenone can regulate the expression of the mitochondrial outer membrane proteins VDAC1 and BNIP3, activate Parkin/PINK1 mitophagy, promote the degradation of damaged mitochondria, reduce dopaminergic neuron damage, and improve behavioral disorders in Parkinson's disease mice.
    DOI:  https://doi.org/10.1038/s41420-022-00826-8
  45. Nature. 2022 Jan 19.
    Ageing exacerbates ribosome pausing to disrupt cotranslational proteostasis.
    Kevin C Stein, Fabián Morales-Polanco, Joris van der Lienden, T Kelly Rainbolt, Judith Frydman.
      Ageing is accompanied by a decline in cellular proteostasis, which underlies many age-related protein misfolding diseases1,2. Yet, how ageing impairs proteostasis remains unclear. As nascent polypeptides represent a substantial burden on the proteostasis network3, we hypothesized that altered translational efficiency during ageing could help to drive the collapse of proteostasis. Here we show that ageing alters the kinetics of translation elongation in both Caenorhabditis elegans and Saccharomyces cerevisiae. Ribosome pausing was exacerbated at specific positions in aged yeast and worms, including polybasic stretches, leading to increased ribosome collisions known to trigger ribosome-associated quality control (RQC)4-6. Notably, aged yeast cells exhibited impaired clearance and increased aggregation of RQC substrates, indicating that ageing overwhelms this pathway. Indeed, long-lived yeast mutants reduced age-dependent ribosome pausing, and extended lifespan correlated with greater flux through the RQC pathway. Further linking altered translation to proteostasis collapse, we found that nascent polypeptides exhibiting age-dependent ribosome pausing in C. elegans were strongly enriched among age-dependent protein aggregates. Notably, ageing increased the pausing and aggregation of many components of proteostasis, which could initiate a cycle of proteostasis collapse. We propose that increased ribosome pausing, leading to RQC overload and nascent polypeptide aggregation, critically contributes to proteostasis impairment and systemic decline during ageing.
    DOI:  https://doi.org/10.1038/s41586-021-04295-4
  46. Sci Rep. 2022 Jan 19. 12(1): 978
    Differential remodelling of mitochondrial subpopulations and mitochondrial dysfunction are a feature of early stage diabetes.
    Bodour S Rajab, Sarah Kassab, Connor D Stonall, Hussam Daghistani, Stephen Gibbons, Mamas Mamas, David Smith, Aleksandr Mironov, Zainab AlBalawi, Yin Hua Zhang, Florence Baudoin, Min Zi, Sukhpal Prehar, Elizabeth J Cartwright, Ashraf Kitmitto.
      Mitochondrial dysfunction is a feature of type I and type II diabetes, but there is a lack of consistency between reports and links to disease development. We aimed to investigate if mitochondrial structure-function remodelling occurs in the early stages of diabetes by employing a mouse model (GENA348) of Maturity Onset Diabetes in the Young, exhibiting hyperglycemia, but not hyperinsulinemia, with mild left ventricular dysfunction. Employing 3-D electron microscopy (SBF-SEM) we determined that compared to wild-type, WT, the GENA348 subsarcolemma mitochondria (SSM) are ~ 2-fold larger, consistent with up-regulation of fusion proteins Mfn1, Mfn2 and Opa1. Further, in comparison, GENA348 mitochondria are more irregular in shape, have more tubular projections with SSM projections being longer and wider. Mitochondrial density is also increased in the GENA348 myocardium consistent with up-regulation of PGC1-α and stalled mitophagy (down-regulation of PINK1, Parkin and Miro1). GENA348 mitochondria have more irregular cristae arrangements but cristae dimensions and density are similar to WT. GENA348 Complex activity (I, II, IV, V) activity is decreased but the OCR is increased, potentially linked to a shift towards fatty acid oxidation due to impaired glycolysis. These novel data reveal that dysregulated mitochondrial morphology, dynamics and function develop in the early stages of diabetes.
    DOI:  https://doi.org/10.1038/s41598-022-04929-1
  47. N Engl J Med. 2022 01 20. pii: 10.1056/NEJMc2118255#sa2. [Epub ahead of print]386(3): 294-295
    Nonalcoholic Fatty Liver Disease.
    Mao-Li Xia, Hai Wang.
      
    DOI:  https://doi.org/10.1056/NEJMc2118255
  48. HGG Adv. 2022 Jan 13. 3(1): 100075
    Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders.
    Michael A Levy, Haley McConkey, Jennifer Kerkhof, Mouna Barat-Houari, Sara Bargiacchi, Elisa Biamino, María Palomares Bralo, Gerarda Cappuccio, Andrea Ciolfi, Angus Clarke, Barbara R DuPont, Mariet W Elting, Laurence Faivre, Timothy Fee, Robin S Fletcher, Florian Cherik, Aidin Foroutan, Michael J Friez, Cristina Gervasini, Sadegheh Haghshenas, Benjamin A Hilton, Zandra Jenkins, Simranpreet Kaur, Suzanne Lewis, Raymond J Louie, Silvia Maitz, Donatella Milani, Angela T Morgan, Renske Oegema, Elsebet Østergaard, Nathalie Ruiz Pallares, Maria Piccione, Simone Pizzi, Astrid S Plomp, Cathryn Poulton, Jack Reilly, Raissa Relator, Rocio Rius, Stephen Robertson, Kathleen Rooney, Justine Rousseau, Gijs W E Santen, Fernando Santos-Simarro, Josephine Schijns, Gabriella Maria Squeo, Miya St John, Christel Thauvin-Robinet, Giovanna Traficante, Pleuntje J van der Sluijs, Samantha A Vergano, Niels Vos, Kellie K Walden, Dimitar Azmanov, Tugce Balci, Siddharth Banka, Jozef Gecz, Peter Henneman, Jennifer A Lee, Marcel M A M Mannens, Tony Roscioli, Victoria Siu, David J Amor, Gareth Baynam, Eric G Bend, Kym Boycott, Nicola Brunetti-Pierri, Philippe M Campeau, John Christodoulou, David Dyment, Natacha Esber, Jill A Fahrner, Mark D Fleming, David Genevieve, Kristin D Kerrnohan, Alisdair McNeill, Leonie A Menke, Giuseppe Merla, Paolo Prontera, Cheryl Rockman-Greenberg, Charles Schwartz, Steven A Skinner, Roger E Stevenson, Antonio Vitobello, Marco Tartaglia, Marielle Alders, Matthew L Tedder, Bekim Sadikovic.
      Overlapping clinical phenotypes and an expanding breadth and complexity of genomic associations are a growing challenge in the diagnosis and clinical management of Mendelian disorders. The functional consequences and clinical impacts of genomic variation may involve unique, disorder-specific, genomic DNA methylation episignatures. In this study, we describe 19 novel episignature disorders and compare the findings alongside 38 previously established episignatures for a total of 57 episignatures associated with 65 genetic syndromes. We demonstrate increasing resolution and specificity ranging from protein complex, gene, sub-gene, protein domain, and even single nucleotide-level Mendelian episignatures. We show the power of multiclass modeling to develop highly accurate and disease-specific diagnostic classifiers. This study significantly expands the number and spectrum of disorders with detectable DNA methylation episignatures, improves the clinical diagnostic capabilities through the resolution of unsolved cases and the reclassification of variants of unknown clinical significance, and provides further insight into the molecular etiology of Mendelian conditions.
    Keywords:  Clinical diagnostics; DNA methylation; Epigenetics; Episignatures; Neurodevelopmental disorders
    DOI:  https://doi.org/10.1016/j.xhgg.2021.100075
  49. Histol Histopathol. 2022 Jan 19. 18422
    History and development of staining methods for skeletal muscle fiber types.
    Shoko Sawano, Wataru Mizunoya.
      The contractile and metabolic properties of skeletal muscles depend on the composition of muscle fibers. There are two major fiber types: type 1 and type 2. Type 2 fibers are further subdivided into type 2A, 2X, and 2B fibers. Muscle fiber type composition is an important property that affects sports performance and metabolic ability in humans, and meat quality in domestic animals. In this review, we summarize the history of muscle fiber type classification based on various staining methods for skeletal muscle sections. The history illustrates the development of an experimental method to detect myosin heavy chain (MyHC) proteins, which are the most common marker molecules for muscle fiber type. Metabolic enzymes, such as nicotinamide adenine dinucleotide-tetrazolium reductase and succinate dehydrogenase are also described for histochemical staining combined with myosin ATPase staining. We found an improvement in the quality of antibodies used for immunostaining of MyHC, from polyclonal antibodies to monoclonal antibodies (mAbs) and then to mAbs produced by synthetic peptides as antigens. We believe that the information presented herein will assist researchers in selecting optimal staining methods, dependent on the experimental conditions and purposes.
    DOI:  https://doi.org/10.14670/HH-18-422
  50. J Comput Biol. 2022 Jan;29(1): 3-18
    SCOT: Single-Cell Multi-Omics Alignment with Optimal Transport.
    Pinar Demetci, Rebecca Santorella, Björn Sandstede, William Stafford Noble, Ritambhara Singh.
      Recent advances in sequencing technologies have allowed us to capture various aspects of the genome at single-cell resolution. However, with the exception of a few of co-assaying technologies, it is not possible to simultaneously apply different sequencing assays on the same single cell. In this scenario, computational integration of multi-omic measurements is crucial to enable joint analyses. This integration task is particularly challenging due to the lack of sample-wise or feature-wise correspondences. We present single-cell alignment with optimal transport (SCOT), an unsupervised algorithm that uses the Gromov-Wasserstein optimal transport to align single-cell multi-omics data sets. SCOT performs on par with the current state-of-the-art unsupervised alignment methods, is faster, and requires tuning of fewer hyperparameters. More importantly, SCOT uses a self-tuning heuristic to guide hyperparameter selection based on the Gromov-Wasserstein distance. Thus, in the fully unsupervised setting, SCOT aligns single-cell data sets better than the existing methods without requiring any orthogonal correspondence information.
    Keywords:  data integration; manifold alignment; multi-omics; optimal transport; single-cell genomics
    DOI:  https://doi.org/10.1089/cmb.2021.0446
  51. Case Rep Neurol Med. 2022 ;2022 1628892
    Leber's Hereditary Optic Neuropathy Plus Causing Recurrent Myelopathy due to an MT-DN1 Mutation at G3635A.
    Elijah Lackey, Ariel Lefland, Christopher Eckstein.
      A 51-year-old man with known Leber's hereditary optic neuropathy (LHON) presented with worsening lower extremity weakness and numbness. Following an episode of myelopathy two years before, he had been ambulating with a walker but over two weeks became wheelchair bound. He also developed a sensory level below the T4 dermatome to light touch, pinprick, and vibration. MRI of his cervical and thoracic spine showed a nonenhancing T2 hyperintense lesion extending from C2 to T12. At his presentation two years earlier, he was found to have a longitudinally extensive myelopathy attributed to his LHON. Genetic testing revealed a 3635 guanine to adenine mutation. MRI at that presentation demonstrated a C1-T10 lesion involving the central and posterior cord but, unlike the new lesion, did not involve the ventral and lateral horns. Given the similarity to his prior presentation and a negative evaluation for alternative etiologies, he was thought to have recurrent myelopathy secondary to Leber's Plus. To our knowledge, recurrent myelopathy due specifically to the G3635A mutation in Leber's Plus has not been reported previously.
    DOI:  https://doi.org/10.1155/2022/1628892
  52. Nat Commun. 2022 Jan 19. 13(1): 386
    The mitochondrial β-oxidation enzyme HADHA restrains hepatic glucagon response by promoting β-hydroxybutyrate production.
    An Pan, Xiao-Meng Sun, Feng-Qing Huang, Jin-Feng Liu, Yuan-Yuan Cai, Xin Wu, Raphael N Alolga, Ping Li, Bao-Lin Liu, Qun Liu, Lian-Wen Qi.
      Disordered hepatic glucagon response contributes to hyperglycemia in diabetes. The regulators involved in glucagon response are less understood. This work aims to investigate the roles of mitochondrial β-oxidation enzyme HADHA and its downstream ketone bodies in hepatic glucagon response. Here we show that glucagon challenge impairs expression of HADHA. Liver-specific HADHA overexpression reversed hepatic gluconeogenesis in mice, while HADHA knockdown augmented glucagon response. Stable isotope tracing shows that HADHA promotes ketone body production via β-oxidation. The ketone body β-hydroxybutyrate (BHB) but not acetoacetate suppresses gluconeogenesis by selectively inhibiting HDAC7 activity via interaction with Glu543 site to facilitate FOXO1 nuclear exclusion. In HFD-fed mice, HADHA overexpression improved metabolic disorders, and these effects are abrogated by knockdown of BHB-producing enzyme. In conclusion, BHB is responsible for the inhibitory effect of HADHA on hepatic glucagon response, suggesting that HADHA activation or BHB elevation by pharmacological intervention hold promise in treating diabetes.
    DOI:  https://doi.org/10.1038/s41467-022-28044-x
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