bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2021‒08‒29
forty-three papers selected by
Catalina Vasilescu
University of Helsinki
  1. MitoPhen database: a human phenotype ontology-based approach to identify mitochondrial DNA diseases.
  2. Targeted elimination of mutated mitochondrial DNA by a multi-functional conjugate capable of sequence-specific adenine alkylation.
  3. Quality control of protein import into mitochondria.
  4. The mitochondrial coenzyme Q junction and complex III: biochemistry and pathophysiology.
  5. Mitochondrial DNA variants modulate N-formylmethionine, proteostasis and risk of late-onset human diseases.
  6. Mechanism of transcription initiation and primer generation at the mitochondrial replication origin OriL.
  7. Interactions of Mitochondrial Transcription Factor A with DNA Damage: Mechanistic Insights and Functional Implications.
  8. Miro1 functions as an inhibitory regulator of MFN at elevated mitochondrial Ca2+ levels.
  9. Mechano-energetic aspects of Barth Syndrome.
  10. Mitochondria-Induced Immune Response as a Trigger for Neurodegeneration: A Pathogen from Within.
  11. Mitochondrial DNA depletion syndrome with a mutation in SLC25A4 developing epileptic encephalopathy: A case report.
  12. Pathologically Responsive Mitochondrial Gene Therapy in an Allotopic Expression-Independent Manner Cures Leber's Hereditary Optic Neuropathy.
  13. Substrates and interactors of the ClpP protease in the mitochondria.
  14. Pathogenic SLIRP variants as a novel cause of autosomal recessive mitochondrial encephalomyopathy with complex I and IV deficiency.
  15. Two Novel Variants in YARS2 Gene Are Responsible for an Extended MLASA Phenotype with Pancreatic Insufficiency.
  16. Ketogenic Diet for KARS-Related Mitochondrial Dysfunction and Progressive Leukodystrophy.
  17. Serum Fibroblast Growth Factor 21 and Growth Differentiation Factor 15: Two sensitive biomarkers in the diagnosis of mitochondrial disorders.
  18. NAD(H) Regulates the Permeability Transition Pore in Mitochondria through an External Site.
  19. Extracellular vesicle-based interorgan transport of mitochondria from energetically stressed adipocytes.
  20. Miro1 Impairment in a Parkinson's At-Risk Cohort.
  21. N-acetyltaurine and Acetylcarnitine Production for the Mitochondrial Acetyl-CoA Regulation in Skeletal Muscles during Endurance Exercises.
  22. Dynamic control of mitochondria-associated membranes by kinases and phosphatases in health and disease.
  23. Crosstalk between Drp1 phosphorylation sites during mitochondrial remodeling and their impact on metabolic adaptation.
  24. Approaches to monitor ATP levels in living cells: where do we stand?
  25. Qualitative and Quantitative Assessment of the Role of Endocytic Regulatory and/or Rab Proteins on Mitochondrial Fusion and Fission.
  26. Myoclonic Epilepsy with Ragged-red Fibers with Intranuclear Inclusions.
  27. A panoramic view of proteomics and multiomics in precision health.
  28. A Review of Multiple Mitochondrial Dysfunction Syndromes, Syndromes Associated with Defective Fe-S Protein Maturation.
  29. Multidimensional Biomarker Analysis Including Mitochondrial Stress Indicators for Nonalcoholic Fatty Liver Disease.
  30. An optimized protocol for coupling oxygen consumption rates with β-oxidation in isolated mitochondria from mouse soleus.
  31. Mitochondrial Dysfunction in Vascular Wall Cells and Its Role in Atherosclerosis.
  32. Whole exome sequencing reveals a homozygous C1QBP deletion as the cause of progressive external ophthalmoplegia and multiple mtDNA deletions.
  33. Fatty Acyl Availability Modulates Cardiolipin Composition and Alters Mitochondrial Function in HeLa Cells.
  34. SLC-30A9 is required for Zn2+ homeostasis, Zn2+ mobilization, and mitochondrial health.
  35. Quality control in scRNA-Seq can discriminate pacemaker cells: the mtRNA bias.
  36. Effectiveness of clinical exome sequencing in adult patients with difficult-to-diagnose neurological disorders.
  37. Microvesicles transfer mitochondria and increase mitochondrial function in brain endothelial cells.
  38. Cell cycle induction in human cardiomyocytes is dependent on biosynthetic pathway activation.
  39. Determination of Mitochondrial Respiration and Glycolysis in Ex Vivo Retinal Tissue Samples.
  40. GATM and GAMT synthesize creatine locally throughout the mammalian body and within oligodendrocytes of the brain.
  41. MACF1 controls skeletal muscle function through the microtubule-dependent localization of extra-synaptic myonuclei and mitochondria biogenesis.
  42. Electron Transfer Coupled to Conformational Dynamics in Cell Respiration.
  43. Mitochondria control pyroptosis.
  1. Nucleic Acids Res. 2021 Aug 24. pii: gkab726. [Epub ahead of print]
    MitoPhen database: a human phenotype ontology-based approach to identify mitochondrial DNA diseases.
    Thiloka E Ratnaike, Daniel Greene, Wei Wei, Alba Sanchis-Juan, Katherine R Schon, Jelle van den Ameele, Lucy Raymond, Rita Horvath, Ernest Turro, Patrick F Chinnery.
      Diagnosing mitochondrial disorders remains challenging. This is partly because the clinical phenotypes of patients overlap with those of other sporadic and inherited disorders. Although the widespread availability of genetic testing has increased the rate of diagnosis, the combination of phenotypic and genetic heterogeneity still makes it difficult to reach a timely molecular diagnosis with confidence. An objective, systematic method for describing the phenotypic spectra for each variant provides a potential solution to this problem. We curated the clinical phenotypes of 6688 published individuals with 89 pathogenic mitochondrial DNA (mtDNA) mutations, collating 26 348 human phenotype ontology (HPO) terms to establish the MitoPhen database. This enabled a hypothesis-free definition of mtDNA clinical syndromes, an overview of heteroplasmy-phenotype relationships, the identification of under-recognized phenotypes, and provides a publicly available reference dataset for objective clinical comparison with new patients using the HPO. Studying 77 patients with independently confirmed positive mtDNA diagnoses and 1083 confirmed rare disease cases with a non-mitochondrial nuclear genetic diagnosis, we show that HPO-based phenotype similarity scores can distinguish these two classes of rare disease patients with a false discovery rate <10% at a sensitivity of 80%. Enriching the MitoPhen database with more patients will improve predictions for increasingly rare variants.
    DOI:  https://doi.org/10.1093/nar/gkab726
  2. Cell Chem Biol. 2021 Aug 24. pii: S2451-9456(21)00365-2. [Epub ahead of print]
    Targeted elimination of mutated mitochondrial DNA by a multi-functional conjugate capable of sequence-specific adenine alkylation.
    Takuya Hidaka, Kaori Hashiya, Toshikazu Bando, Ganesh N Pandian, Hiroshi Sugiyama.
      Mutations in mitochondrial DNA (mtDNA) cause mitochondrial diseases, characterized by abnormal mitochondrial function. Although eliminating mutated mtDNA has potential to cure mitochondrial diseases, no chemical-based drugs in clinical trials are capable of selective modulation of mtDNA mutations. Here, we construct a class of compounds encompassing pyrrole-imidazole polyamides (PIPs), mitochondria-penetrating peptide, and chlorambucil, an adenine-specific DNA-alkylating reagent. The sequence-selective DNA binding of PIPs allows chlorambucil to alkylate mutant adenine more efficiently than other sites in mtDNA. In vitro DNA alkylation assay shows that our compound 8950A-Chb(Cl/OH) targeting a nonpathogenic point mutation in HeLa S3 cells (m.8950G>A) can specifically alkylate the mutant adenine. Furthermore, the compound reduces the mtDNA possessing the target mutation in cultured HeLa S3 cells. The programmability of PIPs to target different sequences could allow this class of compounds to be developed as designer drugs targeting pathogenic mutations associated with mitochondrial diseases in future studies.
    Keywords:  DNA alkylation; DNA mutation; designer small molecule; heteroplasmy; mitochondria; mitochondrial DNA; mitochondrial disease; pyrrole-imidazole polyamide
    DOI:  https://doi.org/10.1016/j.chembiol.2021.08.003
  3. Biochem J. 2021 Aug 27. 478(16): 3125-3143
    Quality control of protein import into mitochondria.
    Fabian den Brave, Jeannine Engelke, Thomas Becker.
      Mitochondria import about 1000 proteins that are produced as precursors on cytosolic ribosomes. Defects in mitochondrial protein import result in the accumulation of non-imported precursor proteins and proteotoxic stress. The cell is equipped with different quality control mechanisms to monitor protein transport into mitochondria. First, molecular chaperones guide unfolded proteins to mitochondria and deliver non-imported proteins to proteasomal degradation. Second, quality control factors remove translocation stalled precursor proteins from protein translocases. Third, protein translocases monitor protein sorting to mitochondrial subcompartments. Fourth, AAA proteases of the mitochondrial subcompartments remove mislocalized or unassembled proteins. Finally, impaired efficiency of protein transport is an important sensor for mitochondrial dysfunction and causes the induction of cellular stress responses, which could eventually result in the removal of the defective mitochondria by mitophagy. In this review, we summarize our current understanding of quality control mechanisms that govern mitochondrial protein transport.
    Keywords:  TIM23 complex; TOM complex; mitochondria; protein sorting; protein transport
    DOI:  https://doi.org/10.1042/BCJ20190584
  4. FEBS J. 2021 Aug 24.
    The mitochondrial coenzyme Q junction and complex III: biochemistry and pathophysiology.
    Rishi Banerjee, Janne Purhonen, Jukka Kallijärvi.
      Coenzyme Q (CoQ, ubiquinone) is the electron-carrying lipid in the mitochondrial electron transport system (ETS). In mammals, it serves as the electron acceptor for nine mitochondrial inner membrane dehydrogenases. These include the NADH-dehydrogenase (complex I, CI) and succinate dehydrogenase (complex II, CII) but also several others that are often omitted in the context of respiratory enzymes: dihydroorotate dehydrogenase, choline dehydrogenase, electron-transferring flavoprotein dehydrogenase, mitochondrial glycerol-3-phosphate dehydrogenase, proline dehydrogenases 1 and 2, and sulfide:quinone oxidoreductase. The metabolic pathways these enzymes are involved in range from amino acid and fatty acid oxidation to nucleotide biosynthesis, methylation, and hydrogen sulfide detoxification, among many others. The CoQ-linked metabolism depends on CoQ re-oxidation by the mitochondrial complex III (cytochrome bc1 complex, CIII). However, the literature is surprisingly limited as for the role of the CoQ-linked metabolism in the pathogenesis of human diseases of oxidative phosphorylation (OXPHOS), in which the CoQ homeostasis is directly or indirectly affected. In this review, we give an introduction to CIII function, and an overview of the pathological consequences of CIII dysfunction in humans and mice and of the CoQ-dependent metabolic processes potentially affected in these pathological states. Finally, we discuss some experimental tools to dissect the various aspects of compromised CoQ oxidation.
    Keywords:  coenzyme Q; complex III; mitochondrial disease; oxidative phosphorylation; ubiquinone
    DOI:  https://doi.org/10.1111/febs.16164
  5. Nat Med. 2021 Aug 23.
    Mitochondrial DNA variants modulate N-formylmethionine, proteostasis and risk of late-onset human diseases.
    Na Cai, Aurora Gomez-Duran, Ekaterina Yonova-Doing, Kousik Kundu, Annette I Burgess, Zoe J Golder, Claudia Calabrese, Marc J Bonder, Marta Camacho, Rachael A Lawson, Lixin Li, Caroline H Williams-Gray, , Emanuele Di Angelantonio, David J Roberts, Nick A Watkins, Willem H Ouwehand, Adam S Butterworth, Isobel D Stewart, Maik Pietzner, Nick J Wareham, Claudia Langenberg, John Danesh, Klaudia Walter, Peter M Rothwell, Joanna M M Howson, Oliver Stegle, Patrick F Chinnery, Nicole Soranzo.
      Mitochondrial DNA (mtDNA) variants influence the risk of late-onset human diseases, but the reasons for this are poorly understood. Undertaking a hypothesis-free analysis of 5,689 blood-derived biomarkers with mtDNA variants in 16,220 healthy donors, here we show that variants defining mtDNA haplogroups Uk and H4 modulate the level of circulating N-formylmethionine (fMet), which initiates mitochondrial protein translation. In human cytoplasmic hybrid (cybrid) lines, fMet modulated both mitochondrial and cytosolic proteins on multiple levels, through transcription, post-translational modification and proteolysis by an N-degron pathway, abolishing known differences between mtDNA haplogroups. In a further 11,966 individuals, fMet levels contributed to all-cause mortality and the disease risk of several common cardiovascular disorders. Together, these findings indicate that fMet plays a key role in common age-related disease through pleiotropic effects on cell proteostasis.
    DOI:  https://doi.org/10.1038/s41591-021-01441-3
  6. EMBO J. 2021 Aug 23. e107988
    Mechanism of transcription initiation and primer generation at the mitochondrial replication origin OriL.
    Azadeh Sarfallah, Angelica Zamudio-Ochoa, Michael Anikin, Dmitry Temiakov.
      The intricate process of human mtDNA replication requires the coordinated action of both transcription and replication machineries. Transcription and replication events at the lagging strand of mtDNA prompt the formation of a stem-loop structure (OriL) and the synthesis of a ∼25 nt RNA primer by mitochondrial RNA polymerase (mtRNAP). The mechanisms by which mtRNAP recognizes OriL, initiates transcription, and transfers the primer to the replisome are poorly understood. We found that transcription initiation at OriL involves slippage of the nascent transcript. The transcript slippage is essential for initiation complex stability and its ability to translocate the mitochondrial DNA polymerase gamma, PolG, which pre-binds to OriL, downstream of the replication origin thus allowing for the primer synthesis. Our data suggest the primosome assembly at OriL-a complex of mtRNAP and PolG-can efficiently generate the primer, transfer it to the replisome, and protect it from degradation by mitochondrial endonucleases.
    Keywords:  POLRMT; PolG; mitochondrial replication; mitochondrial transcription; primosome
    DOI:  https://doi.org/10.15252/embj.2021107988
  7. Genes (Basel). 2021 Aug 15. pii: 1246. [Epub ahead of print]12(8):
    Interactions of Mitochondrial Transcription Factor A with DNA Damage: Mechanistic Insights and Functional Implications.
    Krystie Chew, Linlin Zhao.
      Mitochondria have a plethora of functions in eukaryotic cells, including cell signaling, programmed cell death, protein cofactor synthesis, and various aspects of metabolism. The organelles carry their own genomic DNA, which encodes transfer and ribosomal RNAs and crucial protein subunits in the oxidative phosphorylation system. Mitochondria are vital for cellular and organismal functions, and alterations of mitochondrial DNA (mtDNA) have been linked to mitochondrial disorders and common human diseases. As such, how the cell maintains the integrity of the mitochondrial genome is an important area of study. Interactions of mitochondrial proteins with mtDNA damage are critically important for repairing, regulating, and signaling mtDNA damage. Mitochondrial transcription factor A (TFAM) is a key player in mtDNA transcription, packaging, and maintenance. Due to the extensive contact of TFAM with mtDNA, it is likely to encounter many types of mtDNA damage and secondary structures. This review summarizes recent research on the interaction of human TFAM with different forms of non-canonical DNA structures and discusses the implications on mtDNA repair and packaging.
    Keywords:  DNA modification; DNA packing; DNA-protein interaction; G-quadruplex; epigenetics; nucleoid; post-translational modification
    DOI:  https://doi.org/10.3390/genes12081246
  8. J Cell Biochem. 2021 Aug 25.
    Miro1 functions as an inhibitory regulator of MFN at elevated mitochondrial Ca2+ levels.
    Ferdinand F Fatiga, Li-Jie Wang, Tian Hsu, Jenica Irish Capuno, Chi-Yu Fu.
      Mitochondria function as an integrated network that moves along the microtubules within cells and changes the morphology through membrane fusion and fission events. Mitofusin (MFN) mediates membrane tethering and subsequent fusion of the mitochondrial outer membrane. Understanding the regulatory mechanisms of MFN function is critical to tackling the pathology related to mitochondrial network imbalance. Here, we reveal a novel inhibitory mechanism of MFN-mediated fusion by mitochondrial Rho GTPase (Miro1) in response to elevated mitochondrial Ca2+ concentration ([Ca2+ ]m ). We showed that elevated [Ca2+ ]m prevents the fusion between mitochondria forming the outer membrane tether by ectopically expressing MFN. Lowering [Ca2+ ]m by treating cells with an inhibitor of mitochondrial calcium uniporter or knocking down Miro1/2 induces more fused networks. Miro1 interacts with MFN as supported by co-immunoprecipitation and protein association identified by proximity labeling proteomics. It suggests that Miro1 functions as a Ca2+ -sensor and inhibits MFN function at elevated [Ca2+ ]m. Miro1 EF-hand mutant has a compromised inhibitory effect, which reiterates Ca2+ -modulated regulation. Dysregulated Ca2+ -handling and mitochondrial network imbalance are highly relevant in the pathology of cancers, cardiovascular, and neurodegenerative diseases. Miro1 functions as a coordinated Ca2+ -responder by pausing mitochondrial transport while reducing network fusion and cooperating with Drp1-mediated fission. It likely prevents the detrimental effect of Ca2+ m overload and facilitates mitophagy. Our finding reveals a novel regulation of mitochondrial network dynamics responding to [Ca2+ ]m through the interplay of Miro1 and MFN. Modulation of Miro1 and MFN interaction is a potential intervention to promote network homeostasis.
    Keywords:  mitochondrial Rho GTPase (Miro); mitochondrial calcium; mitochondrial fusion; mitochondrial network homeostasis; mitofusin (MFN)
    DOI:  https://doi.org/10.1002/jcb.30138
  9. J Inherit Metab Dis. 2021 Aug 23.
    Mechano-energetic aspects of Barth Syndrome.
    Jan Dudek, Christoph Maack.
      Energy-demanding organs like the heart are strongly dependent on oxidative phosphorylation in mitochondria. Oxidative phosphorylation is governed by the respiratory chain located in the inner mitochondrial membrane. The inner mitochondrial membrane is the only cellular membrane with significant amounts of the phospholipid cardiolipin, and cardiolipin was found to directly interact with a number of essential protein complexes, including respiratory chain complexes I to V. An inherited defect in the biogenesis of cardiolipin causes Barth syndrome, which is associated with cardiomyopathy, skeletal myopathy, neutropenia and growth retardation. Energy conversion is dependent on reducing equivalents, which are replenished by oxidative metabolism in the Krebs cycle. Cardiolipin deficiency in Barth syndrome also affects Krebs cycle activity, metabolite transport and mitochondrial morphology. During excitation-contraction coupling, calcium (Ca2+ ) released from the sarcoplasmic reticulum drives sarcomeric contraction. At the same time, Ca2+ influx into mitochondria drives the activation of Krebs cycle dehydrogenases and the regeneration of reducing equivalents. Reducing equivalents are essential not only for energy conversion, but also for maintaining a redox buffer, which is required to detoxify reactive oxygen species (ROS). Defects in CL may also affect Ca2+ uptake into mitochondria and thereby hamper energy supply and demand matching, but also detoxification of ROS. Here, we review the impact of cardiolipin deficiency on mitochondrial function in Barth syndrome and discuss potential therapeutic strategies. This article is protected by copyright. All rights reserved.
    DOI:  https://doi.org/10.1002/jimd.12427
  10. Int J Mol Sci. 2021 Aug 07. pii: 8523. [Epub ahead of print]22(16):
    Mitochondria-Induced Immune Response as a Trigger for Neurodegeneration: A Pathogen from Within.
    Marta Luna-Sánchez, Patrizia Bianchi, Albert Quintana.
      Symbiosis between the mitochondrion and the ancestor of the eukaryotic cell allowed cellular complexity and supported life. Mitochondria have specialized in many key functions ensuring cell homeostasis and survival. Thus, proper communication between mitochondria and cell nucleus is paramount for cellular health. However, due to their archaebacterial origin, mitochondria possess a high immunogenic potential. Indeed, mitochondria have been identified as an intracellular source of molecules that can elicit cellular responses to pathogens. Compromised mitochondrial integrity leads to release of mitochondrial content into the cytosol, which triggers an unwanted cellular immune response. Mitochondrial nucleic acids (mtDNA and mtRNA) can interact with the same cytoplasmic sensors that are specialized in recognizing genetic material from pathogens. High-energy demanding cells, such as neurons, are highly affected by deficits in mitochondrial function. Notably, mitochondrial dysfunction, neurodegeneration, and chronic inflammation are concurrent events in many severe debilitating disorders. Interestingly in this context of pathology, increasing number of studies have detected immune-activating mtDNA and mtRNA that induce an aberrant production of pro-inflammatory cytokines and interferon effectors. Thus, this review provides new insights on mitochondria-driven inflammation as a potential therapeutic target for neurodegenerative and primary mitochondrial diseases.
    Keywords:  antiviral response; inflammation; innate immunity; interferon; mitochondrial disorders; mitochondrial dysfunction; mtDNA; mtRNA; neurodegeneration
    DOI:  https://doi.org/10.3390/ijms22168523
  11. Brain Dev. 2021 Aug 25. pii: S0387-7604(21)00155-8. [Epub ahead of print]
    Mitochondrial DNA depletion syndrome with a mutation in SLC25A4 developing epileptic encephalopathy: A case report.
    Tomoko Kashiki, Jun Kido, Ken Momosaki, Shouichirou Kusunoki, Shiro Ozasa, Keiko Nomura, Atsuko Imai-Okazaki, Tomoko Tsuruoka, Kei Murayama, Yasutoshi Koga, Kimitoshi Nakamura.
      INTRODUCTION: Autosomal dominant mitochondrial DNA depletion syndrome (MTDPS-12A) is characterized by severe hypotonia from birth due to a mutation in the adenine nucleotide translocator 1 (ANT1).CASE REPORT: A 4-year-old female patient diagnosed with neonatal-onset mitochondrial disease, who had good cognitive function while receiving antiepileptic treatment, presented with sudden-onset status epilepticus with facial and limb myoclonus persisting for more than 30 min. Subsequently, she developed epileptic encephalopathy. Brain MRI showed progressive ventricular enlargement and marked white matter atrophy. She was unable to perform verbal communication or make eye contact and fingertip movements. She lacked any signs of cardiomyopathy. Sanger sequencing demonstrated a heterozygous de novo mutation of c.239G>A (p.Arg80His) in SLC25A4. Her right quadriceps muscle tissue showed lowered complexes I, III, and IV activities and mitochondria DNA depletion (mitochondria/nuclear DNA: 14.6 ± 2.2%) through the quantitative polymerase chain reaction. She was definitively diagnosed with MTDPS-12A.
    CONCLUSION: Status epilepticus causes encephalopathy in patients with MTDPS-12A. Reducing the energy requirement on the cardiac muscle and brain may be a treatment strategy for patients with MTDPS-12A. Therefore, seizure management and preventive treatment of status epilepticus are considered to be important for maintaining neurodevelopmental outcomes.
    Keywords:  Encephalopathy; Mitochondrial DNA; SLC25A4; Status epilepticus; c.239G>A
    DOI:  https://doi.org/10.1016/j.braindev.2021.08.005
  12. Adv Mater. 2021 Aug 25. e2103307
    Pathologically Responsive Mitochondrial Gene Therapy in an Allotopic Expression-Independent Manner Cures Leber's Hereditary Optic Neuropathy.
    Yi Wang, Li-Fan Hu, Peng-Fei Cui, Lian-Yu Qi, Lei Xing, Hu-Lin Jiang.
      Leber's hereditary optic neuropathy (LHON) is a rare inherited blindness caused by mutations in the mitochondrial DNA (mtDNA). The disorder is untreatable and tricky, as the existing chemotherapeutic agent Idebenone alleviates symptoms rather than overcoming the underlying cause. Although some studies have made progress on allotopic expression for LHON, in situ mitochondrial gene therapy remains challenging, which may simplify delivery procedures to be a promising therapeutic for LHON. LHON becomes more difficult to manage in the changed mitochondrial microenvironment, including increasing reactive oxygen species (ROS) and decreasing mitochondrial membrane potential (MMP). Herein, a pathologically responsive mitochondrial gene delivery vector named [triphenylphosphine-terminated poly(sulfur-containing thioketal undecafluorohexylamine histamine) and Ide-terminated poly(sulfur-containing thioketal undecafluorohexylamine histamine)] (TISUH) is reported to facilitate commendable in situ mitochondrial gene therapy for LHON. TISUH directly targets diseased mitochondria via triphenylphosphine and fluorination addressing the decreasing MMP. In addition, TISUH can be disassembled by high mitochondrial ROS levels to release functional genes for enhancing gene transfection efficiency and fundamentally correcting genetic abnormalities. In both traditional and gene-mutation-induced LHON mouse models, TISUH-mediated gene therapy shows satisfactory curative effect through the sustained therapeutic protein expression in vivo. This work proposes a novel pathologically responsive in situ mitochondrial delivery platform and provides a promising approach for refractory LHON as well as other mtDNA mutated diseases treatments.
    Keywords:  Idebenone; Leber's hereditary optic neuropathy; fluorination; in situ mitochondrial gene therapy; pathologically responsive polymers
    DOI:  https://doi.org/10.1002/adma.202103307
  13. Curr Opin Chem Biol. 2021 Aug 23. pii: S1367-5931(21)00100-9. [Epub ahead of print]
    Substrates and interactors of the ClpP protease in the mitochondria.
    Mark F Mabanglo, Vaibhav Bhandari, Walid A Houry.
      The ClpP protease is found across eukaryotic and prokaryotic organisms. It is well-characterized in bacteria where its function is important in maintaining protein homeostasis. Along with its ATPase partners, it has been shown to play critical roles in the regulation of enzymes involved in important cellular pathways. In eukaryotes, ClpP is found within cellular organelles. Proteomic studies have begun to characterize the role of this protease in the mitochondria through its interactions. Here, we discuss the proteomic techniques used to identify its interactors and present an atlas of mitochondrial ClpP substrates. The ClpP substrate pool is extensive and consists of proteins involved in essential mitochondrial processes such as the Krebs cycle, oxidative phosphorylation, translation, fatty acid metabolism, and amino acid metabolism. Discoveries of these associations have begun to illustrate the functional significance of ClpP in human health and disease.
    Keywords:  Cancer; ClpP protease; Mitochondria; Mitochondrial diseases; Parkinson's disease; Protein quality control; Proteolysis; Proteomics; Proteostasis
    DOI:  https://doi.org/10.1016/j.cbpa.2021.07.003
  14. Eur J Hum Genet. 2021 Aug 23.
    Pathogenic SLIRP variants as a novel cause of autosomal recessive mitochondrial encephalomyopathy with complex I and IV deficiency.
    Le Guo, Bob P H Engelen, Irene M G M Hemel, Irenaeus F M de Coo, Maaike Vreeburg, Suzanne C E H Sallevelt, Debby M E I Hellebrekers, Ed H Jacobs, Farah Sadeghi-Niaraki, Florence H J van Tienen, Hubert J M Smeets, Mike Gerards.
      In a Dutch non-consanguineous patient having mitochondrial encephalomyopathy with complex I and complex IV deficiency, whole exome sequencing revealed two compound heterozygous variants in SLIRP. SLIRP gene encodes a stem-loop RNA-binding protein that regulates mitochondrial RNA expression and oxidative phosphorylation (OXPHOS). A frameshift and a deep-intronic splicing variant reduced the amount of functional wild-type SLIRP RNA to 5%. Consequently, in patient fibroblasts, MT-ND1, MT-ND6, and MT-CO1 expression was reduced. Lentiviral transduction of wild-type SLIRP cDNA in patient fibroblasts increased MT-ND1, MT-ND6, and MT-CO1 expression (2.5-7.2-fold), whereas mutant cDNAs did not. A fourfold decrease of citrate synthase versus total protein ratio in patient fibroblasts indicated that the resulting reduced mitochondrial mass caused the OXPHOS deficiency. Transduction with wild-type SLIRP cDNA led to a 2.4-fold increase of this ratio and partly restored OXPHOS activity. This confirmed causality of the SLIRP variants. In conclusion, we report SLIRP variants as a novel cause of mitochondrial encephalomyopathy with OXPHOS deficiency.
    DOI:  https://doi.org/10.1038/s41431-021-00947-1
  15. J Clin Med. 2021 Aug 05. pii: 3471. [Epub ahead of print]10(16):
    Two Novel Variants in YARS2 Gene Are Responsible for an Extended MLASA Phenotype with Pancreatic Insufficiency.
    Lidia Carreño-Gago, Diana Luz Juárez-Flores, Josep Maria Grau, Javier Ramón, Ester Lozano, Ferran Vila-Julià, Ramon Martí, Glòria Garrabou, Elena Garcia-Arumí.
      Pathogenic variants in the mitochondrial tyrosyl-tRNA synthetase gene (YARS2) were associated with myopathy, lactic acidosis, and sideroblastic anemia (MLASA). However, patients can present mitochondrial myopathy, with exercise intolerance and muscle weakness, leading from mild to lethal phenotypes. Genes implicated in mtDNA replication were studied by Next Generation Sequencing (NGS) and whole exome sequence with the TruSeq Rapid Exome kit (Illumina, San Diego, CA, USA). Mitochondrial protein translation was studied following the Sasarman and Shoubridge protocol and oxygen consumption rates with Agilent Seahorse XF24 Analyzer Mitostress Test, (Agilent, Santa Clara, CA, USA). We report two siblings with two novel compound heterozygous pathogenic variants in YARS2 gene: a single nucleotide deletion in exon 1, c.314delG (p.(Gly105Alafs*4)), which creates a premature stop codon in the amino acid 109, and a single nucleotide change in exon 5 c.1391T>C (p.(Ile464Thr)), that cause a missense variant in amino acid 464. We demonstrate the pathogenicity of these new variants associated with reduced YARS2 mRNA transcript, reduced mitochondrial protein translation and dysfunctional organelle function. These pathogenic variants are responsible for late onset MLASA, herein accompanied by pancreatic insufficiency, observed in both brothers, clinically considered as Pearson's syndrome. Molecular study of YARS2 gene should be considered in patients presenting Pearson's syndrome characteristics and MLASA related phenotypes.
    Keywords:  Pearson’s syndrome; mitochondrial aminocyl-tRNA synthetase; novel pathogenic variant
    DOI:  https://doi.org/10.3390/jcm10163471
  16. Neuropediatrics. 2021 Aug 26.
    Ketogenic Diet for KARS-Related Mitochondrial Dysfunction and Progressive Leukodystrophy.
    Yuka Murofushi, Itaru Hayakawa, Yuichi Abe, Tatsuyuki Ohto, Kei Murayama, Hisato Suzuki, Toshiki Takenouchi, Kenjiro Kosaki, Masaya Kubota.
      KARS encodes lysyl-tRNA synthetase, which is essential for protein translation. KARS mutations sometimes cause impairment of cytoplasmic and mitochondrial protein synthesis, and sometimes lead to progressive leukodystrophies with mitochondrial signature and psychomotor regression, and follow a rapid regressive course to premature death. There has been no disease-modifying therapy beyond supportive treatment. We present a 5-year-old male patient with an asymmetrical leukodystrophy who showed overt evidence of mitochondrial dysfunction, including elevation of lactate on brain MR spectroscopy and low oxygen consumption rate in fibroblasts. We diagnosed this patient's condition as KARS-related leukodystrophy with cerebral calcification, congenital deafness, and evidence of mitochondrial dysfunction. We employed a ketogenic diet as well as multiple vitamin supplementation with the intention to alleviate mitochondrial dysfunction. The patient showed alleviation of his psychomotor regression and even partial restoration of his abilities within 4 months. This is an early report of a potential disease-modifying therapy for KARS-related progressive leukodystrophy without appreciable adverse effects.
    DOI:  https://doi.org/10.1055/s-0041-1732446
  17. Mitochondrion. 2021 Aug 19. pii: S1567-7249(21)00112-4. [Epub ahead of print]
    Serum Fibroblast Growth Factor 21 and Growth Differentiation Factor 15: Two sensitive biomarkers in the diagnosis of mitochondrial disorders.
    Akshata Huddar, Periyasamy Govindaraj, Shwetha Chiplunkar, Sekar Deepha, J N Jessiena Ponmalar, Mariyamma Philip, Madhu Nagappa, Gayathri Narayanappa, Anita Mahadevan, Sanjib Sinha, Arun B Taly, Bindu Parayil Sankaran.
      Mitochondrial disorders are often difficult to diagnose because of diverse clinical phenotypes. FGF-21 and GDF-15 are metabolic hormones and promising biomarkers for the diagnosis of these disorders. This study has systematically evaluated serum FGF-21 and GDF-15 levels by ELISA in a well-defined cohort of patients with definite mitochondrial disorders (n=30), neuromuscular disease controls (n=36) and healthy controls (n=36) and aimed to ascertain their utility in the diagnosis of mitochondrial disorders. Both serum GDF-15 and FGF-21 were significantly elevated in patients with mitochondrial disorders, especially in those with muscle involvement. The levels were higher in patients with mitochondrial deletions (both single and multiple) and translation disorders compared to respiratory chain subunit or assembly factor defects.
    Keywords:  FGF-21; GDF-15; Mitochondrial disease; RBF; RRF; biomarker
    DOI:  https://doi.org/10.1016/j.mito.2021.08.011
  18. Int J Mol Sci. 2021 Aug 09. pii: 8560. [Epub ahead of print]22(16):
    NAD(H) Regulates the Permeability Transition Pore in Mitochondria through an External Site.
    Ekaterina Kharechkina, Anna Nikiforova, Alexey Kruglov.
      The opening of the permeability transition pore (mPTP) in mitochondria initiates cell death in numerous diseases. The regulation of mPTP by NAD(H) in the mitochondrial matrix is well established; however, the role of extramitochondrial (cytosolic) NAD(H) is still unclear. We studied the effect of added NADH and NAD+ on: (1) the Ca2+-retention capacity (CRC) of isolated rat liver, heart, and brain mitochondria; (2) the Ca2+-dependent mitochondrial swelling in media whose particles can (KCl) or cannot (sucrose) be extruded from the matrix by mitochondrial carriers; (3) the Ca2+-dependent mitochondrial depolarization and the release of entrapped calcein from mitochondria of permeabilized hepatocytes; and (4) the Ca2+-dependent mitochondrial depolarization and subsequent repolarization. NADH and NAD+ increased the CRC of liver, heart, and brain mitochondria 1.5-2.5 times, insignificantly affecting the rate of Ca2+-uptake and the free Ca2+ concentration in the medium. NAD(H) suppressed the Ca2+-dependent mitochondrial swelling both in KCl- and sucrose-based media but did not induce the contraction and repolarization of swollen mitochondria. By contrast, EGTA caused mitochondrial repolarization in both media and the contraction in KCl-based medium only. NAD(H) delayed the Ca2+-dependent depolarization and the release of calcein from individual mitochondria in hepatocytes. These data unambiguously demonstrate the existence of an external NAD(H)-dependent site of mPTP regulation.
    Keywords:  NAD+; NADH; calcium retention capacity; cytosolic; external regulatory site; permeability transition pore; pore closure
    DOI:  https://doi.org/10.3390/ijms22168560
  19. Cell Metab. 2021 Aug 17. pii: S1550-4131(21)00365-X. [Epub ahead of print]
    Extracellular vesicle-based interorgan transport of mitochondria from energetically stressed adipocytes.
    Clair Crewe, Jan-Bernd Funcke, Shujuan Li, Nolwenn Joffin, Christy M Gliniak, Alexandra L Ghaben, Yu A An, Hesham A Sadek, Ruth Gordillo, Yucel Akgul, Shiuhwei Chen, Dmitri Samovski, Pamela Fischer-Posovszky, Christine M Kusminski, Samuel Klein, Philipp E Scherer.
      Adipocytes undergo intense energetic stress in obesity resulting in loss of mitochondrial mass and function. We have found that adipocytes respond to mitochondrial stress by rapidly and robustly releasing small extracellular vesicles (sEVs). These sEVs contain respiration-competent, but oxidatively damaged mitochondrial particles, which enter circulation and are taken up by cardiomyocytes, where they trigger a burst of ROS. The result is compensatory antioxidant signaling in the heart that protects cardiomyocytes from acute oxidative stress, consistent with a preconditioning paradigm. As such, a single injection of sEVs from energetically stressed adipocytes limits cardiac ischemia/reperfusion injury in mice. This study provides the first description of functional mitochondrial transfer between tissues and the first vertebrate example of "inter-organ mitohormesis." Thus, these seemingly toxic adipocyte sEVs may provide a physiological avenue of potent cardio-protection against the inevitable lipotoxic or ischemic stresses elicited by obesity.
    Keywords:  adipocyte; cardiovascular disease; diabetes; exosomes; extracellular vesicles; mitochondria; mitochondrial dysfunction; mitohormesis; obesity; stress response
    DOI:  https://doi.org/10.1016/j.cmet.2021.08.002
  20. Front Mol Neurosci. 2021 ;14 734273
    Miro1 Impairment in a Parkinson's At-Risk Cohort.
    David Nguyen, Vinita Bharat, Devon M Conradson, Pawan Nandakishore, Xinnan Wang.
      There is a lack of reliable molecular markers for Parkinson's disease (PD) patients and at-risk individuals. The detection of the pre-symptomatic population of PD will empower more effective clinical intervention to delay or prevent disease onset. We have previously found that the mitochondrial protein Miro1 is resistant to mitochondrial depolarization-induced degradation in fibroblasts from a large number of PD patients and several at-risk individuals. Therefore, Miro1 has the potential to molecularly label PD populations. In order to determine whether Miro1 could serve as a molecular marker for the risk of PD, here we examine the Miro1 response to mitochondrial depolarization by biochemical approaches in induced pluripotent stem cells from a cohort of at-risk individuals. Our results show that the Miro1 phenotype is significantly associated with PD risk. We propose that Miro1 is a promising molecular marker for detecting both PD and at-risk populations. Tracking this Miro1 marker could aid in diagnosis and Miro1-based drug discoveries.
    Keywords:  IPSC; Miro1; Parkinson’s disease; mitophagy; risk
    DOI:  https://doi.org/10.3389/fnmol.2021.734273
  21. Metabolites. 2021 Aug 06. pii: 522. [Epub ahead of print]11(8):
    N-acetyltaurine and Acetylcarnitine Production for the Mitochondrial Acetyl-CoA Regulation in Skeletal Muscles during Endurance Exercises.
    Teruo Miyazaki, Yuho Nakamura-Shinya, Kei Ebina, Shoichi Komine, Song-Gyu Ra, Keisuke Ishikura, Hajime Ohmori, Akira Honda.
      During endurance exercises, a large amount of mitochondrial acetyl-CoA is produced in skeletal muscles from lipids, and the excess acetyl-CoA suppresses the metabolic flux from glycolysis to the TCA cycle. This study evaluated the hypothesis that taurine and carnitine act as a buffer of the acetyl moiety of mitochondrial acetyl-CoA derived from the short- and long-chain fatty acids of skeletal muscles during endurance exercises. In human subjects, the serum concentrations of acetylated forms of taurine (NAT) and carnitine (ACT), which are the metabolites of acetyl-CoA buffering, significantly increased after a full marathon. In the culture medium of primary human skeletal muscle cells, NAT and ACT concentrations significantly increased when they were cultured with taurine and acetate or with carnitine and palmitic acid, respectively. The increase in the mitochondrial acetyl-CoA/free CoA ratio induced by acetate and palmitic acid was suppressed by taurine and carnitine, respectively. Elevations of NAT and ACT in the blood of humans during endurance exercises might serve the buffering of the acetyl-moiety in mitochondria by taurine and carnitine, respectively. The results suggest that blood levels of NAT and ACT indicate energy production status from fatty acids in the skeletal muscles of humans undergoing endurance exercise.
    Keywords:  ACT; NAT; acetyl-CoA; carnitine; endurance exercise; mitochondria; skeletal muscle; taurine
    DOI:  https://doi.org/10.3390/metabo11080522
  22. Cell Mol Life Sci. 2021 Aug 27.
    Dynamic control of mitochondria-associated membranes by kinases and phosphatases in health and disease.
    Monika Pichla, Flore Sneyers, Kinga B Stopa, Geert Bultynck, Martijn Kerkhofs.
      Membrane-contact sites are getting more and more credit for their indispensable role in maintenance of cell function and homeostasis. In the last decades, the ER-mitochondrial contact sites in particular received a lot of attention. While our knowledge of ER-mitochondrial contact sites increases steadily, the focus often lies on a static exploration of their functions. However, it is increasingly clear that these contact sites are very dynamic. In this review, we highlight the dynamic nature of ER-mitochondrial contact sites and the role of kinases and phosphatases therein with a focus on recent findings. Phosphorylation events allow for rapid integration of information on the protein level, impacting protein function, localization and interaction at ER-mitochondrial contact sites. To illustrate the importance of these events and to put them in a broader perspective, we connect them to pathologies like diabetes type II, Parkinson's disease and cancer.
    Keywords:  Ca2+ signalling; Insulin signalling; Mitochondria-associated membranes; Mitochondrial dynamics; Mitophagy
    DOI:  https://doi.org/10.1007/s00018-021-03920-9
  23. Cell Rep. 2021 Aug 24. pii: S2211-1247(21)00999-2. [Epub ahead of print]36(8): 109565
    Crosstalk between Drp1 phosphorylation sites during mitochondrial remodeling and their impact on metabolic adaptation.
    Miriam Valera-Alberni, Magali Joffraud, Joan Miro-Blanch, Jordi Capellades, Alexandra Junza, Loïc Dayon, Antonio Núñez Galindo, Jose L Sanchez-Garcia, Armand Valsesia, Angelique Cercillieux, Flavia Söllner, Andreas G Ladurner, Oscar Yanes, Carles Cantó.
      Mitochondria constantly undergo fusion and fission events, referred as mitochondrial dynamics, which determine mitochondrial architecture and bioenergetics. Cultured cell studies demonstrate that mitochondrial dynamics are acutely regulated by phosphorylation of the mitochondrial fission orchestrator dynamin-related protein 1 (Drp1) at S579 or S600. However, the physiological impact and crosstalk of these phosphorylation sites is poorly understood. Here, we describe the functional interrelation between S579 and S600 phosphorylation sites in vivo and their role on mitochondrial remodeling. Mice carrying a homozygous Drp1 S600A knockin (Drp1 KI) mutation display larger mitochondria and enhanced lipid oxidation and respiratory capacities, granting improved glucose tolerance and thermogenic response upon high-fat feeding. Housing mice at thermoneutrality blunts these differences, suggesting a role for the brown adipose tissue in the protection of Drp1 KI mice against metabolic damage. Overall, we demonstrate crosstalk between Drp1 phosphorylation sites and provide evidence that their modulation could be used in the treatment and prevention of metabolic diseases.
    Keywords:  Drp1; brown adipose tissue; insulin resistance; metabolic syndrome; mitochondrial dynamics; mitochondrial respiration; phosphorylation; thermoneutrality
    DOI:  https://doi.org/10.1016/j.celrep.2021.109565
  24. FEBS J. 2021 Aug 26.
    Approaches to monitor ATP levels in living cells: where do we stand?
    Seyta Ley-Ngardigal, Giulia Bertolin.
      ATP is the most universal and essential energy molecule in cells. This is due to its ability to store cellular energy in form of high energy phosphate bonds, which are extremely stable and readily usable by the cell. This energy is key for a variety of biological functions such as cell growth and division, metabolism, signaling, and for the turnover of biomolecules. Understanding how ATP is produced and hydrolyzed with a spatiotemporal resolution is necessary to understand its functions both in physiological and pathological contexts. In this review, we will first describe the organization of the electron transport chain and ATP synthase, the main molecular motor for ATP production in mitochondria. Second, we will review the biochemical assays currently available to estimate ATP quantities in cells, and we will compare their readouts, strengths and weaknesses. Finally, we will explore the palette of genetically-encoded biosensors designed for microscopy-based approaches, and show how their spatiotemporal resolution opened up the possibility to follow ATP levels in living cells.
    Keywords:  ATP; ATP synthase; biochemical assays; fluorescence-based tools; mitochondria
    DOI:  https://doi.org/10.1111/febs.16169
  25. Methods Mol Biol. 2021 ;2293 213-227
    Qualitative and Quantitative Assessment of the Role of Endocytic Regulatory and/or Rab Proteins on Mitochondrial Fusion and Fission.
    Trey Farmer, Steve Caplan.
      Mitochondria are the major energy generating organelle in the cell; accordingly mitochondrial homeostasis is key to mitochondrial function. In recent years, new paradigms have uncovered roles for endocytic regulatory proteins in the control of mitochondrial fusion and fission, thus highlighting the utility of techniques for the study of mitochondrial morphology. Herein we detail methods to qualitatively and quantitatively measure the impact of select proteins on mitochondrial fusion and fission in human retinal pigmented epithelial (RPE1) cells. We demonstrate how commercially available small interfering RNA (siRNA) can be used to target various endocytic regulatory proteins, and freely available software can be used to evaluate the impact of these proteins on mitochondria by quantifying their effect on mitochondrial morphology. It is our goal to provide simple protocols that may prove useful for researchers new to the realm of endocytic regulatory proteins and mitochondrial homeostasis.
    Keywords:  Endocytic regulatory proteins; Fission/fusion; Homeostasis; ImageJ/FIJI; Mito-Morphology plug-in; Mitochondria
    DOI:  https://doi.org/10.1007/978-1-0716-1346-7_15
  26. Intern Med. 2021 Aug 24.
    Myoclonic Epilepsy with Ragged-red Fibers with Intranuclear Inclusions.
    Tomoya Kawazoe, Shinsuke Tobisawa, Keizo Sugaya, Akinori Uruha, Kazuhito Miyamoto, Takashi Komori, Yu-Ichi Goto, Ichizo Nishino, Hiroshi Yoshihashi, Takeshi Mizuguchi, Naomichi Matsumoto, Naohiro Egawa, Akihiro Kawata, Eiji Isozaki.
      We herein report a case of myoclonic epilepsy with ragged-red fibers (MERRF) harboring a novel variant in mitochondrial cysteine transfer RNA (MT-TC). A 68-year-old woman presented with progressive myoclonic epilepsy with optic atrophy and peripheral neuropathy. A skin biopsy revealed p62-positive intranuclear inclusions. No mutations were found in the causative genes for diseases known to be related to intranuclear inclusions; however, a novel variant in MT-TC was found. The association between intranuclear inclusions and this newly identified MERRF-associated variant is unclear; however, the rare complication of intranuclear inclusions in a patient with typical MERRF symptoms should be noted for future studies.
    Keywords:  Epilepsies; Intranuclear Inclusions; Mitochondrial Diseases; Myoclonic; Optic Atrophy; Peripheral Neuropathies
    DOI:  https://doi.org/10.2169/internalmedicine.7767-21
  27. iScience. 2021 Aug 20. 24(8): 102925
    A panoramic view of proteomics and multiomics in precision health.
    Mara Zilocchi, Cheng Wang, Mohan Babu, Jingjing Li.
      Health is often qualitatively defined as a status free from disease and its quantitative definition requires finding the boundary separating health from pathological conditions. Since many complex diseases have a strong genetic component, substantial efforts have been made to sequence large-scale personal genomes; however, we are not yet able to effectively quantify health status from personal genomes. Since mutational impacts are ultimately manifested at the protein level, we envision that introducing a panoramic proteomic view of complex diseases will allow us to mechanistically understand the molecular etiologies of human diseases. In this perspective article, we will highlight key proteomic approaches to identify pathogenic mutations and map their convergent pathways underlying disease pathogenesis and the integration of omics data at multiple levels to define the borderline between health and disease.
    Keywords:  Genomics; Machine learning; Proteomics; Systems biology
    DOI:  https://doi.org/10.1016/j.isci.2021.102925
  28. Biomedicines. 2021 Aug 10. pii: 989. [Epub ahead of print]9(8):
    A Review of Multiple Mitochondrial Dysfunction Syndromes, Syndromes Associated with Defective Fe-S Protein Maturation.
    Elise Lebigot, Manuel Schiff, Marie-Pierre Golinelli-Cohen.
      Mitochondrial proteins carrying iron-sulfur (Fe-S) clusters are involved in essential cellular pathways such as oxidative phosphorylation, lipoic acid synthesis, and iron metabolism. NFU1, BOLA3, IBA57, ISCA2, and ISCA1 are involved in the last steps of the maturation of mitochondrial [4Fe-4S]-containing proteins. Since 2011, mutations in their genes leading to five multiple mitochondrial dysfunction syndromes (MMDS types 1 to 5) were reported. The aim of this systematic review is to describe all reported MMDS-patients. Their clinical, biological, and radiological data and associated genotype will be compared to each other. Despite certain specific clinical elements such as pulmonary hypertension or dilated cardiomyopathy in MMDS type 1 or 2, respectively, nearly all of the patients with MMDS presented with severe and early onset leukoencephalopathy. Diagnosis could be suggested by high lactate, pyruvate, and glycine levels in body fluids. Genetic analysis including large gene panels (Next Generation Sequencing) or whole exome sequencing is needed to confirm diagnosis.
    Keywords:  BOLA3; Fe-S proteins; IBA57; ISCA1; ISCA2; MMDS; NFU1
    DOI:  https://doi.org/10.3390/biomedicines9080989
  29. Gut Liver. 2021 Aug 24.
    Multidimensional Biomarker Analysis Including Mitochondrial Stress Indicators for Nonalcoholic Fatty Liver Disease.
    Eunha Chang, Jae Seung Chang, In Deok Kong, Soon Koo Baik, Moon Young Kim, Kyu-Sang Park.
      Nonalcoholic fatty liver disease (NAFLD) is accompanied by a complex and multifactorial pathogenesis with sequential progressions from inflammation to fibrosis and then to cancer. This heterogeneity interferes with the development of precise diagnostic and prognostic strategies for NAFLD. The current approach for the diagnosis of simple steatosis, steatohepatitis, and cirrhosis mainly consists of ultrasonography, magnetic resonance imaging, elastography, and various serological analyses. However, individual dry and wet biomarkers have limitations demanding an integrative approach for the assessment of disease progression. Here, we review diagnostic strategies for simple steatosis, steatohepatitis and hepatic fibrosis, followed by potential biomarkers associated with fat accumulation and mitochondrial stress. For mitochondrial stress indicators, we focused on fibroblast growth factor 21 (FGF21), growth differentiation factor 15 (GDF15), angiopoietin-related growth factor and mitochondrial-derived peptides. Each biomarker may not strongly indicate the severity of steatosis or steatohepatitis. Instead, multidimensional analysis of different groups of biomarkers based on pathogenic mechanisms may provide decisive diagnostic/prognostic information to develop a therapeutic plan for patients with NAFLD. For this purpose, mitochondrial stress indicators, such as FGF21 or GDF15, could be an important component in the multiplexed and contextual interpretation of NAFLD. Further validation of the integrative evaluation of mitochondrial stress indicators combined with other biomarkers is needed in the diagnosis/prognosis of NAFLD.
    Keywords:  Biomarkers; Fibroblast growth factor 21; Growth differentiation factor 15; Mitochondrial stress; Non-alcoholic fatty liver disease
    DOI:  https://doi.org/10.5009/gnl210106
  30. STAR Protoc. 2021 Sep 17. 2(3): 100735
    An optimized protocol for coupling oxygen consumption rates with β-oxidation in isolated mitochondria from mouse soleus.
    Cristina Sánchez-González, Laura Formentini.
      Depending on metabolic requirements, skeletal muscle mitochondria integrate O2 consumption and ATP production with lipid, glucose, or amino acid metabolism. Free fatty acids (FFAs) are the main source of energy during rest and mild-intensity exercise. We present a detailed protocol for measuring FFA-β-oxidation coupled with O2 respiration by a Clark-type electrode in isolated mitochondria from mouse soleus oxidative muscle. We optimized the procedure, including buffer composition, protease treatment, and quantifiable parameters (P/O, Phosphate/Oxygen Ratio; OCR, Oxygen Consumption Rate; RCR,Respiration Control Rate; OSR, Oligomycin Sensitive Respiration). For complete details on the use and execution of this protocol, please refer to Sanchez-Gonzalez et al. (2020).
    Keywords:  cell biology; cell isolation; cell membrane; cell separation/fractionation; metabolism
    DOI:  https://doi.org/10.1016/j.xpro.2021.100735
  31. Int J Mol Sci. 2021 Aug 20. pii: 8990. [Epub ahead of print]22(16):
    Mitochondrial Dysfunction in Vascular Wall Cells and Its Role in Atherosclerosis.
    Diana Salnikova, Varvara Orekhova, Andrey Grechko, Antonina Starodubova, Evgeny Bezsonov, Tatyana Popkova, Alexander Orekhov.
      Altered mitochondrial function is currently recognized as an important factor in atherosclerosis initiation and progression. Mitochondrial dysfunction can be caused by mitochondrial DNA (mtDNA) mutations, which can be inherited or spontaneously acquired in various organs and tissues, having more or less profound effects depending on the tissue energy status. Arterial wall cells are among the most vulnerable to mitochondrial dysfunction due to their barrier and metabolic functions. In atherosclerosis, mitochondria cause alteration of cellular metabolism and respiration and are known to produce excessive amounts of reactive oxygen species (ROS) resulting in oxidative stress. These processes are involved in vascular disease and chronic inflammation associated with atherosclerosis. Currently, the list of known mtDNA mutations associated with human pathologies is growing, and many of the identified mtDNA variants are being tested as disease markers. Alleviation of oxidative stress and inflammation appears to be promising for atherosclerosis treatment. In this review, we discuss the role of mitochondrial dysfunction in atherosclerosis development, focusing on the key cell types of the arterial wall involved in the pathological processes. Accumulation of mtDNA mutations in isolated arterial wall cells, such as endothelial cells, may contribute to the development of local inflammatory process that helps explaining the focal distribution of atherosclerotic plaques on the arterial wall surface. We also discuss antioxidant and anti-inflammatory approaches that can potentially reduce the impact of mitochondrial dysfunction.
    Keywords:  atherosclerosis; inflammation; mitochondrial DNA; mitochondrion; oxidative stress
    DOI:  https://doi.org/10.3390/ijms22168990
  32. Neuromuscul Disord. 2021 Jul 04. pii: S0960-8966(21)00176-0. [Epub ahead of print]
    Whole exome sequencing reveals a homozygous C1QBP deletion as the cause of progressive external ophthalmoplegia and multiple mtDNA deletions.
    Le Guo, Periyasamy Govindaraj, Mariëlle Kievit, Irenaeus F M de Coo, Mike Gerards, Debby M E I Hellebrekers, Alphons P M Stassen, Narayanappa Gayathri, Arun B Taly, Bindu Parayil Sankaran, Hubert J M Smeets.
      Whole exome sequencing (WES), analyzed with GENESIS and WeGET, revealed a homozygous deletion in the C1QBP gene in a patient with progressive external ophthalmoplegia (PEO) and multiple mtDNA deletions. The gene encodes the mitochondria-located complementary 1 Q subcomponent-binding protein, involved in mitochondrial homeostasis. Biallelic mutations in C1QBP cause mitochondrial cardiomyopathy and/or PEO with variable age of onset. Our patient showed only late-onset PEO-plus syndrome without overt cardiac involvement. Available data suggest that early-onset cardiomyopathy variants localize in important structural domains and PEO-plus variants in the coiled-coil region. Our patient demonstrates that C1QBP mutations should be considered in individuals with PEO with or without cardiomyopathy.
    Keywords:  C1QBP gene; Multiple mtDNA deletions; Progressive external ophthalmoplegia; Whole exome sequencing
    DOI:  https://doi.org/10.1016/j.nmd.2021.06.014
  33. J Lipid Res. 2021 Aug 24. pii: S0022-2275(21)00093-6. [Epub ahead of print] 100111
    Fatty Acyl Availability Modulates Cardiolipin Composition and Alters Mitochondrial Function in HeLa Cells.
    Gregor Oemer, Marie-Luise Edenhofer, Yvonne Wohlfarter, Katharina Lackner, Geraldine Leman, Jakob Koch, Luiza H D Cardoso, Herbert H Lindner, Erich Gnaiger, Sandrine Dubrac, Johannes Zschocke, Markus A Keller.
      The molecular assembly of cells depends not only on the balance between anabolism and catabolism, but to a large degree on the building blocks available in the environment. For cultured mammalian cells, this is largely determined by the composition of the applied growth medium. Here we study the impact of lipids in the medium on mitochondrial membrane architecture and function by combining LC-MS/MS lipidomics and functional tests with lipid supplementation experiments in an otherwise serum- and lipid-free cell culture model. We demonstrate that the composition of mitochondrial cardiolipins strongly depends on the lipid environment in cultured cells and favours the incorporation of essential linoleic acid over other fatty acids. Simultaneously, the mitochondrial respiratory Complex I activity was altered, whereas the matrix-localized enzyme citrate synthase was unaffected. This raises the question on a link between membrane composition and respiratory control. In summary, we found a strong dependency of central mitochondrial features on the type of lipids contained in the growth medium. This underlines the importance of considering these factors when using and establishing cell culture models in biomedical research.
    Keywords:  Cardiolipin; Fatty acids; Lipids; Mass spectroscopy; Mitochondria
    DOI:  https://doi.org/10.1016/j.jlr.2021.100111
  34. Proc Natl Acad Sci U S A. 2021 Aug 31. pii: e2023909118. [Epub ahead of print]118(35):
    SLC-30A9 is required for Zn2+ homeostasis, Zn2+ mobilization, and mitochondrial health.
    Huichao Deng, Xinhua Qiao, Ting Xie, Wenfeng Fu, Hang Li, Yanmei Zhao, Miaomiao Guo, Yaqian Feng, Ligong Chen, Yan Zhao, Long Miao, Chang Chen, Kang Shen, Xiangming Wang.
      The trace element zinc is essential for many aspects of physiology. The mitochondrion is a major Zn2+ store, and excessive mitochondrial Zn2+ is linked to neurodegeneration. How mitochondria maintain their Zn2+ homeostasis is unknown. Here, we find that the SLC-30A9 transporter localizes on mitochondria and is required for export of Zn2+ from mitochondria in both Caenorhabditis elegans and human cells. Loss of slc-30a9 leads to elevated Zn2+ levels in mitochondria, a severely swollen mitochondrial matrix in many tissues, compromised mitochondrial metabolic function, reductive stress, and induction of the mitochondrial stress response. SLC-30A9 is also essential for organismal fertility and sperm activation in C. elegans, during which Zn2+ exits from mitochondria and acts as an activation signal. In slc-30a9-deficient neurons, misshapen mitochondria show reduced distribution in axons and dendrites, providing a potential mechanism for the Birk-Landau-Perez cerebrorenal syndrome where an SLC30A9 mutation was found.
    Keywords:  Birk–Landau–Perez cerebrorenal syndrome; SLC-30A9; Zn2+ transporters; mitochondria
    DOI:  https://doi.org/10.1073/pnas.2023909118
  35. Cell Mol Life Sci. 2021 Aug 24.
    Quality control in scRNA-Seq can discriminate pacemaker cells: the mtRNA bias.
    Anne-Marie Galow, Sophie Kussauer, Markus Wolfien, Ronald M Brunner, Tom Goldammer, Robert David, Andreas Hoeflich.
      Single-cell RNA-sequencing (scRNA-seq) provides high-resolution insights into complex tissues. Cardiac tissue, however, poses a major challenge due to the delicate isolation process and the large size of mature cardiomyocytes. Regardless of the experimental technique, captured cells are often impaired and some capture sites may contain multiple or no cells at all. All this refers to "low quality" potentially leading to data misinterpretation. Common standard quality control parameters involve the number of detected genes, transcripts per cell, and the fraction of transcripts from mitochondrial genes. While cutoffs for transcripts and genes per cell are usually user-defined for each experiment or individually calculated, a fixed threshold of 5% mitochondrial transcripts is standard and often set as default in scRNA-seq software. However, this parameter is highly dependent on the tissue type. In the heart, mitochondrial transcripts comprise almost 30% of total mRNA due to high energy demands. Here, we demonstrate that a 5%-threshold not only causes an unacceptable exclusion of cardiomyocytes but also introduces a bias that particularly discriminates pacemaker cells. This effect is apparent for our in vitro generated induced-sinoatrial-bodies (iSABs; highly enriched physiologically functional pacemaker cells), and also evident in a public data set of cells isolated from embryonal murine sinoatrial node tissue (Goodyer William et al. in Circ Res 125:379-397, 2019). Taken together, we recommend omitting this filtering parameter for scRNA-seq in cardiovascular applications whenever possible.
    Keywords:  Cardiomyocytes; Cluster analysis; Conduction system; Mitochondrial transcripts; Single-cell RNA-sequencing; Sinoatrial node; iSABs
    DOI:  https://doi.org/10.1007/s00018-021-03916-5
  36. Acta Neurol Scand. 2021 Aug 21.
    Effectiveness of clinical exome sequencing in adult patients with difficult-to-diagnose neurological disorders.
    Markus T Sainio, Juho Aaltio, Virva Hyttinen, Mika Kortelainen, Simo Ojanen, Anders Paetau, Pentti Tienari, Emil Ylikallio, Mari Auranen, Henna Tyynismaa.
      OBJECTIVES: Clinical diagnostics in adults with hereditary neurological diseases is complicated by clinical and genetic heterogeneity, as well as lifestyle effects. Here, we evaluate the effectiveness of exome sequencing and clinical costs in our difficult-to-diagnose adult patient cohort. Additionally, we expand the phenotypic and genetic spectrum of hereditary neurological disorders in Finland.METHODS: We performed clinical exome sequencing (CES) to 100 adult patients from Finland with neurological symptoms of suspected genetic cause. The patients were classified as myopathy (n = 57), peripheral neuropathy (n = 16), ataxia (n = 15), spastic paraplegia (n = 4), Parkinsonism (n = 3), and mixed (n = 5). In addition, we gathered the costs of prior diagnostic work-up to retrospectively assess the cost-effectiveness of CES as a first-line diagnostic tool.
    RESULTS: The overall diagnostic yield of CES was 27%. Pathogenic variants were found for 14 patients (in genes ANO5, CHCHD10, CLCN1, DES, DOK7, FKBP14, POLG, PYROXD1, SCN4A, TUBB3, and TTN) and likely pathogenic previously undescribed variants for 13 patients (in genes ABCD1, AFG3L2, ATL1, CACNA1A, COL6A1, DYSF, IRF2BPL, KCNA1, MT-ATP6, SAMD9L, SGCB, and TPM2). Age of onset below 40 years increased the probability of finding a genetic cause. Our cost evaluation of prior diagnostic work-up suggested that early CES would be cost-effective in this patient group, in which diagnostic costs increase linearly with prolonged investigations.
    CONCLUSIONS: Based on our results, CES is a cost-effective, powerful first-line diagnostic tool in establishing the molecular diagnosis in adult neurological patients with variable symptoms. Importantly, CES can markedly shorten the diagnostic odysseys of about one third of patients.
    Keywords:  clinical exome sequencing; cost analysis; diagnostics; neurological disease
    DOI:  https://doi.org/10.1111/ane.13522
  37. J Control Release. 2021 Aug 24. pii: S0168-3659(21)00444-2. [Epub ahead of print]
    Microvesicles transfer mitochondria and increase mitochondrial function in brain endothelial cells.
    Anisha D'Souza, Amelia Burch, Kandarp M Dave, Aravind Sreeram, Michael J Reynolds, Duncan X Dobbins, Yashika S Kamte, Wanzhu Zhao, Courtney Sabatelle, Gina M Joy, Vishal Soman, Uma R Chandran, Sruti S Shiva, Nidia Quillinan, Paco S Herson, Devika S Manickam.
      We have demonstrated, for the first time that microvesicles, a sub-type of extracellular vesicles (EVs) derived from hCMEC/D3: a human brain endothelial cell (BEC) line transfer polarized mitochondria to recipient BECs in culture and to neurons in mice acute brain cortical and hippocampal slices. This mitochondrial transfer increased ATP levels by 100 to 200-fold (relative to untreated cells) in the recipient BECs exposed to oxygen-glucose deprivation, an in vitro model of cerebral ischemia. We have also demonstrated that transfer of microvesicles, the larger EV fraction, but not exosomes resulted in increased mitochondrial function in hypoxic endothelial cultures. Gene ontology and pathway enrichment analysis of EVs revealed a very high association to glycolysis-related processes. In comparison to heterotypic macrophage-derived EVs, BEC-derived EVs demonstrated a greater selectivity to transfer mitochondria and increase endothelial cell survival under ischemic conditions.
    Keywords:  BBB protection; Exosomes; Extracellular vesicles; Ischemic stroke; Microvesicles; Mitochondrial function; Mitochondrial transfer
    DOI:  https://doi.org/10.1016/j.jconrel.2021.08.038
  38. Redox Biol. 2021 Aug 05. pii: S2213-2317(21)00253-6. [Epub ahead of print]46 102094
    Cell cycle induction in human cardiomyocytes is dependent on biosynthetic pathway activation.
    Riham R E Abouleisa, Lindsey McNally, Abou Bakr M Salama, Sally K Hammad, Qinghui Ou, Collin Wells, Pawel K Lorkiewicz, Roberto Bolli, Tamer M A Mohamed, Bradford G Hill.
      AIMS: The coordinated gene and metabolic programs that facilitate cardiomyocyte entry and progression in the cell cycle are poorly understood. The purpose of this study was to identify the metabolic changes that influence myocyte proliferation.METHODS AND RESULTS: In adult mouse cardiomyocytes and human induced pluripotent stem cell cardiomyocytes (hiPS-CMs), cell cycle initiation by ectopic expression of Cyclin B1, Cyclin D1, CDK1, and CDK4 (termed 4F) downregulated oxidative phosphorylation genes and upregulated genes that regulate ancillary biosynthetic pathways of glucose metabolism. Results from metabolic analyses and stable isotope tracing experiments indicate that 4F-mediated cell cycle induction in hiPS-CMs decreases glucose oxidation and oxidative phosphorylation and augments NAD+, glycogen, hexosamine, phospholipid, and serine biosynthetic pathway activity. Interventions that diminish NAD+ synthesis, serine synthesis, or protein O-GlcNAcylation decreased 4F-mediated cell cycle entry. In a gain of function approach, we overexpressed phosphoenolpyruvate carboxykinase 2 (PCK2), which can drive carbon from the Krebs cycle to the glycolytic intermediate pool, and found that PCK2 augments 4F-mediated cell cycle entry.
    CONCLUSIONS: These findings suggest that a metabolic shift from catabolic to anabolic activity is a critical step for cardiomyocyte cell cycle entry and is required to facilitate proliferation.
    DOI:  https://doi.org/10.1016/j.redox.2021.102094
  39. J Vis Exp. 2021 Aug 04.
    Determination of Mitochondrial Respiration and Glycolysis in Ex Vivo Retinal Tissue Samples.
    Ke Jiang, Jacob Nellissery, Anand Swaroop.
      Mitochondrial respiration is a critical energy-generating pathway in all cells, especially retinal photoreceptors that possess a highly active metabolism. In addition, photoreceptors also exhibit high aerobic glycolysis like cancer cells. Precise measurements of these metabolic activities can provide valuable insights into cellular homeostasis under physiological conditions and in disease states. High throughput microplate-based assays have been developed to measure mitochondrial respiration and various metabolic activities in live cells. However, a vast majority of these are developed for cultured cells and have not been optimized for intact tissue samples and for application ex vivo. Described here is a detailed step-by-step protocol, using microplate-based fluorescence technology, to directly measure oxygen consumption rate (OCR) as an indicator of mitochondrial respiration, as well as extracellular acidification rate (ECAR) as an indicator of glycolysis, in intact ex vivo retinal tissue. This method has been used to successfully assess metabolic activities in adult mouse retina and demonstrate its application in investigating cellular mechanisms of aging and disease.
    DOI:  https://doi.org/10.3791/62914
  40. Brain Res. 2021 Aug 19. pii: S0006-8993(21)00484-4. [Epub ahead of print]1770 147627
    GATM and GAMT synthesize creatine locally throughout the mammalian body and within oligodendrocytes of the brain.
    Steven Andrew Baker, Chandresh R Gajera, Adam M Wawro, M Ryan Corces, Thomas J Montine.
      The enzymes glycine amidinotransferase, mitochondrial (GATM also known as AGAT) and guanidinoacetate N-methyltransferase (GAMT) function together to synthesize creatine from arginine, glycine, and S-Adenosyl methionine. Deficiency in either enzyme or the creatine transporter, CT1, results in a devastating neurological disorder, Cerebral Creatine Deficiency Syndrome (CCDS). To better understand the pathophysiology of CCDS, we mapped the distribution of GATM and GAMT at single cell resolution, leveraging RNA sequencing analysis combined with in vivo immunofluorescence (IF). Using the mouse as a model system, we find that GATM and GAMT are coexpressed in several tissues with distinct and overlapping cellular sources, implicating local synthesis as an important mechanism of creatine metabolism in numerous organs. Extending previous findings at the RNA level, our analysis demonstrates that oligodendrocytes express the highest level of Gatm and Gamt of any cell type in the body. We confirm this finding in the mouse brain by IF, where GATM localizes to the mitochondria of oligodendrocytes, whereas both oligodendrocytes and cerebral cortical neurons express GAMT. Interestingly, the latter is devoid of GATM. Single nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq) analysis of 4 brain regions highlights a similar primacy of oligodendrocytes in the expression of GATM and GAMT in the human central nervous system. Importantly, an active putative regulatory element within intron 2 of human GATM is detected in oligodendrocytes but not neurons.
    Keywords:  AGAT; Creatine metabolism; GAMT; GATM; Neuron; Oligodendrocyte
    DOI:  https://doi.org/10.1016/j.brainres.2021.147627
  41. Elife. 2021 Aug 27. pii: e70490. [Epub ahead of print]10
    MACF1 controls skeletal muscle function through the microtubule-dependent localization of extra-synaptic myonuclei and mitochondria biogenesis.
    Alireza Ghasemizadeh, Emilie Christin, Alexandre Guiraud, Nathalie Couturier, Marie Abitbol, Valerie Risson, Emmanuelle Girard, Krzysztof Jagla, Cedric Soler, Lilia Laddada, Colline Sanchez, Francisco-Ignacio Jaque-Fernandez, Vincent Jacquemond, Jean-Luc Thomas, Marine Lanfranchi, Julien Courchet, Julien Gondin, Laurent Schaeffer, Vincent Gache.
      Skeletal muscles are composed of hundreds of multinucleated muscle fibers (myofibers) whose myonuclei are regularly positioned all along the myofiber's periphery except the few ones clustered underneath the neuromuscular junction (NMJ) at the synaptic zone. This precise myonuclei organization is altered in different types of muscle disease, including centronuclear myopathies (CNMs). However, the molecular machinery regulating myonuclei position and organization in mature myofibers remains largely unknown. Conversely, it is also unclear how peripheral myonuclei positioning is lost in the related muscle diseases. Here, we describe the microtubule-associated protein, MACF1, as an essential and evolutionary conserved regulator of myonuclei positioning and maintenance, in cultured mammalian myotubes, in Drosophila muscle, and in adult mammalian muscle using a conditional muscle-specific knockout mouse model. In vitro, we show that MACF1 controls microtubules dynamics and contributes to microtubule stabilization during myofiber's maturation. In addition, we demonstrate that MACF1 regulates the microtubules density specifically around myonuclei, and, as a consequence, governs myonuclei motion. Our in vivo studies show that MACF1 deficiency is associated with alteration of extra-synaptic myonuclei positioning and microtubules network organization, both preceding NMJ fragmentation. Accordingly, MACF1 deficiency results in reduced muscle excitability and disorganized triads, leaving voltage-activated sarcoplasmic reticulum Ca2+ release and maximal muscle force unchanged. Finally, adult MACF1-KO mice present an improved resistance to fatigue correlated with a strong increase in mitochondria biogenesis.
    Keywords:  D. melanogaster; cell biology; developmental biology; mouse
    DOI:  https://doi.org/10.7554/eLife.70490
  42. Front Mol Biosci. 2021 ;8 711436
    Electron Transfer Coupled to Conformational Dynamics in Cell Respiration.
    Marco Reidelbach, Christoph Zimmer, Brigitte Meunier, Peter R Rich, Vivek Sharma.
      Cellular respiration is a fundamental process required for energy production in many organisms. The terminal electron transfer complex in mitochondrial and many bacterial respiratory chains is cytochrome c oxidase (CcO). This converts the energy released in the cytochrome c/oxygen redox reaction into a transmembrane proton electrochemical gradient that is used subsequently to power ATP synthesis. Despite detailed knowledge of electron and proton transfer paths, a central question remains as to whether the coupling between electron and proton transfer in mammalian mitochondrial forms of CcO is mechanistically equivalent to its bacterial counterparts. Here, we focus on the conserved span between H376 and G384 of transmembrane helix (TMH) X of subunit I. This conformationally-dynamic section has been suggested to link the redox activity with the putative H pathway of proton transfer in mammalian CcO. The two helix X mutants, Val380Met (V380M) and Gly384Asp (G384D), generated in the genetically-tractable yeast CcO, resulted in a respiratory-deficient phenotype caused by the inhibition of intra-protein electron transfer and CcO turnover. Molecular aspects of these variants were studied by long timescale atomistic molecular dynamics simulations performed on wild-type and mutant bovine and yeast CcOs. We identified redox- and mutation-state dependent conformational changes in this span of TMH X of bovine and yeast CcOs which strongly suggests that this dynamic module plays a key role in optimizing intra-protein electron transfers.
    Keywords:  density functional theory; mitochondrial respiration; molecular dynamics simulations; proton pumping; yeast bioenergetics
    DOI:  https://doi.org/10.3389/fmolb.2021.711436
  43. Nat Immunol. 2021 09;22(9): 1071
    Mitochondria control pyroptosis.
    Nicholas J Bernard.
      
    DOI:  https://doi.org/10.1038/s41590-021-01017-w
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