bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2021–07–18
seventy papers selected by
Catalina Vasilescu, University of Helsinki
  1. The mitochondrial calcium homeostasis orchestra plays its symphony: Skeletal muscle is the guest of honor.
  2. Long-lived mitochondrial cristae proteins in mouse heart and brain.
  3. Tissue-specific expression atlas of murine mitochondrial tRNAs.
  4. Defective Complex III Mitochondrial Respiratory Chain Due to A Novel Variant in CYC1 Gene Masquerades Acute Demyelinating Syndrome or Leber Hereditary Optic Neuropathy.
  5. Mitochondrial Retinopathy.
  6. Mitochondrial Proteostasis Requires Genes Encoded in a Neurodevelopmental Syndrome Locus.
  7. Super-resolution microscopy reveals the arrangement of inner membrane protein complexes in mammalian mitochondria.
  8. Adult-onset mitochondrial movement disorders: a national picture from the Italian Network.
  9. Mitochondrial compartmentalization: emerging themes in structure and function.
  10. Protein Import Assay into Mitochondria Isolated from Human Cells.
  11. ALKBH7-mediated demethylation regulates mitochondrial polycistronic RNA processing.
  12. Nutrition rehabilitation-related complications in primary mitochondrial disorders.
  13. Global kinome profiling reveals DYRK1A as critical activator of the human mitochondrial import machinery.
  14. The Evolutionary Fate of Mitochondrial Aminoacyl-tRNA Synthetases in Amitochondrial Organisms.
  15. SLC25A42-associated mitochondrial encephalomyopathy: Report of additional founder cases and functional characterization of a novel deletion.
  16. Conserved GxxxG and WN motifs of MIC13 are essential for bridging two MICOS subcomplexes.
  17. NMR identification of a conserved Drp1 cardiolipin-binding motif essential for stress-induced mitochondrial fission.
  18. Proteasome activity contributes to pro-survival response upon mild mitochondrial stress in Caenorhabditis elegans.
  19. Glycerol-3-phosphate biosynthesis regenerates cytosolic NAD+ to alleviate mitochondrial disease.
  20. MitoTox: a comprehensive mitochondrial toxicity database.
  21. Mitochondrial haplogroups have a better correlation to insulin requirement than nuclear genetic variants for type 2 diabetes mellitus in Taiwanese individuals.
  22. Mitochondrial Ca2+ and cell cycle regulation.
  23. Human d-lactate dehydrogenase deficiency by LDHD mutation in a patient with neurological manifestations and mitochondrial complex IV deficiency.
  24. Hydrogen sulfide stimulates lipid biogenesis from glutamine that is dependent on the mitochondrial NAD(P)H pool.
  25. On the offense and defense: mitochondrial recovery programs amidst targeted pathogenic assault.
  26. Unravelling the mysteries of mitochondria in health and disease.
  27. Regulation of hepatic coenzyme Q biosynthesis by dietary omega-3 polyunsaturated fatty acids.
  28. Nuclear cGAS: guard or prisoner?
  29. SIRT1 Protects Dopaminergic Neurons in Parkinson's Disease Models via PGC-1α-Mediated Mitochondrial Biogenesis.
  30. SIRT4 is an early regulator of branched-chain amino acid catabolism that promotes adipogenesis.
  31. ATF5, a putative therapeutic target for the mitochondrial DNA 3243A > G mutation-related disease.
  32. Mechanometabolism: Mitochondria promote resilience under pressure.
  33. Prediction and analysis of redox-sensitive cysteines using machine learning and statistical methods.
  34. Circulating Mitochondrial DNA Stimulates Innate Immune Signaling Pathways to Mediate Acute Kidney Injury.
  35. Cell competition acts as a purifying selection to eliminate cells with mitochondrial defects during early mouse development.
  36. OCRbayes: A Bayesian hierarchical modeling framework for Seahorse extracellular flux oxygen consumption rate data analysis.
  37. Mitochondrial calcium homeostasis in hematopoietic stem cell: Molecular regulation of quiescence, function, and differentiation.
  38. In vivo mitochondrial ATP production is improved in older adult skeletal muscle after a single dose of elamipretide in a randomized trial.
  39. Recognizing Subacute Combined Degeneration in Patients With Normal Vitamin B12 Levels.
  40. Deactivation blocks proton pathways in the mitochondrial complex I.
  41. Schwann cells provide iron to axonal mitochondria and its role in nerve regeneration.
  42. Effect of the mitochondrial unfolded protein response on hypoxic death and mitochondrial protein aggregation.
  43. Single-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms in cardiomyocytes.
  44. Effective variant filtering and expected candidate variant yield in studies of rare human disease.
  45. The ARCA Registry: A Collaborative Global Platform for Advancing Trial Readiness in Autosomal Recessive Cerebellar Ataxias.
  46. Analysis of PTRHD1 common and rare variants in European patients with Parkinson's disease.
  47. Genotype and phenotype distribution of 435 patients with Charcot-Marie-Tooth disease from Central South China.
  48. Changes in Key Mitochondrial Lipids Accompany Mitochondrial Dysfunction and Oxidative Stress in NAFLD.
  49. Genetic prediction of complex traits with polygenic scores: a statistical review.
  50. Shadow Electrochemiluminescence Microscopy of Single Mitochondria.
  51. Frequency of carriers for rare recessive Mendelian diseases in a Brazilian cohort of 320 patients.
  52. The regulation of healthspan and lifespan by dietary amino acids.
  53. Mutation spectrum of the OPA1 gene in a large cohort of patients with suspected dominant optic atrophy: Identification and classification of 48 novel variants.
  54. Regulation of muscle and mitochondrial health by the mitochondrial fission protein Drp1 in aged mice.
  55. Outcomes of liver transplantation for mitochondrial respiratory chain disorder in children.
  56. Imaging Patterns Characterizing Mitochondrial Leukodystrophies.
  57. A new phenotype of MT-ND6 gene mutation for Leber's hereditary optic neuropathy.
  58. Stroke-Like Lesion in an m.3243A>G Carrier Presenting as Hyperperfusion and Hypometabolism.
  59. Interorgan Metabolism of Amino Acids in Human Health and Disease.
  60. Mitofusion is required for MOTS-c induced GLUT4 translocation.
  61. Predicting enzymatic reactions with a molecular transformer.
  62. Allosteric Mechanism of Human Mitochondrial Phenylalanyl-tRNA Synthetase: An Atomistic MD Simulation and a Mutual Information-Based Network Study.
  63. Reducing embryonic mtDNA copy number alters epigenetic profile of key hepatic lipolytic genes and causes abnormal lipid accumulation in adult mice.
  64. The Application of an R Language-Based Platform cRacker for Phosphoproteomics Data Analysis.
  65. Molecular and cellular basis of genetically inherited skeletal muscle disorders.
  66. Quick-start infrastructure for untargeted metabolomics analysis in GNPS.
  67. Mitochondrial enrichment in infertile patients: a review of different mitochondrial replacement therapies.
  68. The long and winding road: perspectives of people and parents of children with mitochondrial conditions negotiating management after diagnosis.
  69. Protein-retention expansion microscopy for visualizing subcellular organelles in fixed brain tissue.
  70. A framework for automated gene selection in genomic applications.
  1. Int Rev Cell Mol Biol. 2021 ;pii: S1937-6448(21)00037-X. [Epub ahead of print]362 209-259
    The mitochondrial calcium homeostasis orchestra plays its symphony: Skeletal muscle is the guest of honor.
    Gaia Gherardi, Agnese De Mario, Cristina Mammucari.
      Skeletal muscle mitochondria are placed in close proximity of the sarcoplasmic reticulum (SR), the main intracellular Ca2+ store. During muscle activity, excitation of sarcolemma and of T-tubule triggers the release of Ca2+ from the SR initiating myofiber contraction. The rise in cytosolic Ca2+ determines the opening of the mitochondrial calcium uniporter (MCU), the highly selective channel of the inner mitochondrial membrane (IMM), causing a robust increase in mitochondrial Ca2+ uptake. The Ca2+-dependent activation of TCA cycle enzymes increases the synthesis of ATP required for SERCA activity. Thus, Ca2+ is transported back into the SR and cytosolic [Ca2+] returns to resting levels eventually leading to muscle relaxation. In recent years, thanks to the molecular identification of MCU complex components, the role of mitochondrial Ca2+ uptake in the pathophysiology of skeletal muscle has been uncovered. In this chapter, we will introduce the reader to a general overview of mitochondrial Ca2+ accumulation. We will tackle the key molecular players and the cellular and pathophysiological consequences of mitochondrial Ca2+ dyshomeostasis. In the second part of the chapter, we will discuss novel findings on the physiological role of mitochondrial Ca2+ uptake in skeletal muscle. Finally, we will examine the involvement of mitochondrial Ca2+ signaling in muscle diseases.
    Keywords:  Central core disease; Mitochondrial Ca(2+) uptake; Mitochondrial calcium uniporter; Muscular dystrophy; Skeletal muscle
    DOI:  https://doi.org/10.1016/bs.ircmb.2021.03.005
  2. J Cell Biol. 2021 Sep 06. pii: e202005193. [Epub ahead of print]220(9):
    Long-lived mitochondrial cristae proteins in mouse heart and brain.
    Ewa Bomba-Warczak, Seby L Edassery, Timothy J Hark, Jeffrey N Savas.
      Long-lived proteins (LLPs) have recently emerged as vital components of intracellular structures whose function is coupled to long-term stability. Mitochondria are multifaceted organelles, and their function hinges on efficient proteome renewal and replacement. Here, using metabolic stable isotope labeling of mice combined with mass spectrometry (MS)-based proteomic analysis, we demonstrate remarkable longevity for a subset of the mitochondrial proteome. We discovered that mitochondrial LLPs (mt-LLPs) can persist for months in tissues harboring long-lived cells, such as brain and heart. Our analysis revealed enrichment of mt-LLPs within the inner mitochondrial membrane, specifically in the cristae subcompartment, and demonstrates that the mitochondrial proteome is not turned over in bulk. Pioneering cross-linking experiments revealed that mt-LLPs are spatially restricted and copreserved within protein OXPHOS complexes, with limited subunit exchange throughout their lifetimes. This study provides an explanation for the exceptional mitochondrial protein lifetimes and supports the concept that LLPs provide key structural stability to multiple large and dynamic intracellular structures.
    DOI:  https://doi.org/10.1083/jcb.202005193
  3. J Biol Chem. 2021 Jul 12. pii: S0021-9258(21)00760-2. [Epub ahead of print] 100960
    Tissue-specific expression atlas of murine mitochondrial tRNAs.
    Qiufen He, Xiao He, Yun Xiao, Qiong Zhao, Zhenzhen Ye, Limei Cui, Ye Chen, Min-Xin Guan.
      Mammalian mitochondrial tRNA (mt-tRNA) plays a central role in the synthesis of the 13 subunits of the oxidative phosphorylation complex system (OXPHOS). However, many aspects of the context-dependent expression of mt-tRNAs in mammals remains unknown. To investigate the tissue-specific effects of mt-tRNAs, we performed a comprehensive analysis of mitochondrial tRNA expression across 5 mice tissues (brain, heart, liver, skeletal muscle, and kidney) using Northern blot analysis. Striking differences in the tissue-specific expression of 22 mt-tRNAs were observed, in some cases differing by as much as ten-fold from lowest to highest expression levels among these 5 tissues. Overall, the heart exhibited the highest levels of mt-tRNAs, while the liver displayed markedly lower levels. Variations in the levels of mt-tRNAs showed significant correlations with total mitochondrial DNA (mtDNA) contents in these tissues. However, there were no significant differences observed in the 2-thiouridylation levels of tRNALys, tRNAGlu, and tRNAGln among these tissues. A wide range of aminoacylation levels for 15 mt-tRNAs occurred among these five tissues, with skeletal muscle and kidneys most notably displaying the highest and lowest tRNA aminoacylation levels, respectively. Among these tissues, there was a negative correlation between variations in mt-tRNA aminoacylation levels and corresponding variations in mitochondrial tRNA synthetases (mt-aaRS) expression levels. Furthermore, the variable levels of OXPHOS subunits, as encoded by mtDNA or nuclear genes may reflect differences in relative functional emphasis for mitochondria in each tissue. Our findings provide new insight into the mechanism of mt-tRNA tissue-specific effects on oxidative phosphorylation.
    Keywords:  Mitochondrial tRNA; murine; oxidative phosphorylation; tissue specific expression; translation
    DOI:  https://doi.org/10.1016/j.jbc.2021.100960
  4. Mitochondrion. 2021 Jul 09. pii: S1567-7249(21)00086-6. [Epub ahead of print]
    Defective Complex III Mitochondrial Respiratory Chain Due to A Novel Variant in CYC1 Gene Masquerades Acute Demyelinating Syndrome or Leber Hereditary Optic Neuropathy.
    Erfan Heidari, Maryam Rasoulinezhad, Neda Pak, Mahmoud Reza Ashrafi, Morteza Heidari, Brenda Banwell, Masoud Garshasbi, Ali Reza Tavasoli.
      Complex III (CIII) is the third out of five mitochondrial respiratory chain complexes residing at the mitochondrial inner membrane. The assembly of 10 subunits encoded by nuclear DNA and one by mitochondrial DNA result in the functional CIII which transfers electrons from ubiquinol to cytochrome c. Deficiencies of CIII are among the least investigated mitochondrial disorders and thus clinical spectrum of patients with mutations in CIII is not well defined. We report on a 10-year-old girl born to consanguineous Iranian parents presenting with recurrent visual loss episodes and optic nerve contrast enhancement in brain imaging reminiscent of an acquired demyelination syndrome (i.e. optic neuritis or multiple sclerosis), who was ultimately confirmed to have a novel homozygous missense variant of unknown significance, c.949C>T; p.(Arg317Trp) in the CYC1 gene, a nuclear DNA subunit of complex III of the mitochondrial chain. Sanger sequencing confirmed the segregation of this variant with disease in the family. The effect of this variant on the protein structure was shown in-silico. Our findings, not only expand the clinical spectrum due to defects in CYC1 gene but also highlight that mitochondrial respiratory chain disorders could be considered as a potential differential diagnosis in children who present with unusual patterns of acquired demyelination syndromes (ADS). In addition, our results support the hypothesis that mitochondrial disorders might have an overlapping presentation with ADS.
    Keywords:  CYC1; acquired demyelinating syndrome; complex III deficiency; mitochondrial leukoencephalopathy
    DOI:  https://doi.org/10.1016/j.mito.2021.07.001
  5. Ophthalmol Retina. 2021 Jul 10. pii: S2468-6530(21)00071-3. [Epub ahead of print]
    Mitochondrial Retinopathy.
    Johannes Birtel, Christina von Landenberg, Martin Gliem, Carla Gliem, Jens Reimann, Wolfram S Kunz, Philipp Herrmann, Christian Betz, Richard Caswell, Victoria Nesbitt, Cornelia Kornblum, Peter Charbel Issa.
       PURPOSE: To report the retinal phenotype and the associated genetic and systemic findings in patients with mitochondrial disease.
    DESIGN: Retrospective case series.
    PARTICIPANTS: Twenty-three patients with retinopathy and mitochondrial disease, including chronic progressive external ophthalmoplegia (CPEO), maternally inherited diabetes and deafness (MIDD), mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS), Kearns-Sayre syndrome, neuropathy, ataxia, and retinitis pigmentosa (NARP) syndrome, and other systemic manifestations.
    METHODS: Review of case notes, retinal imaging, electrophysiologic assessment, molecular genetic testing including protein modeling, and histologic analysis of muscle biopsy.
    MAIN OUTCOME MEASURES: Phenotypic characteristics of mitochondrial retinopathy.
    RESULTS: Genetic testing identified sporadic large-scale mitochondrial DNA deletions and variants in MT-TL1, MT-ATP6, MT-TK, MT-RNR1, or RRM2B. Based on retinal imaging, 3 phenotypes could be differentiated: type 1 with mild, focal pigmentary abnormalities; type 2 characterized by multifocal white-yellowish subretinal deposits and pigment changes limited to the posterior pole; and type 3 with widespread granular pigment alterations. Advanced type 2 and 3 retinopathy presented with chorioretinal atrophy that typically started in the peripapillary and paracentral areas with foveal sparing. Two patients exhibited a different phenotype: 1 revealed an occult retinopathy, and the patient with RRM2B-associated retinopathy showed no foveal sparing, no severe peripapillary involvement, and substantial photoreceptor atrophy before loss of the retinal pigment epithelium. Two patients with type 1 disease showed additional characteristics of mild macular telangiectasia type 2. Patients with type 1 and mild type 2 or 3 disease demonstrated good visual acuity and no symptoms associated with the retinopathy. In contrast, patients with advanced type 2 or 3 disease often reported vision problems in dim light conditions, reduced visual acuity, or both. Short-wavelength autofluorescence usually revealed a distinct pattern, and near-infrared autofluorescence may be severely reduced in type 3 disease. The retinal phenotype was key to suspecting mitochondrial disease in 11 patients, whereas 12 patients were diagnosed before retinal examination.
    CONCLUSIONS: Different types of mitochondrial retinopathy show characteristic features. Even in absence of visual symptoms, their recognition may facilitate the often challenging and delayed diagnosis of mitochondrial disease, in particular in patients with mild or nebulous multisystem disease.
    Keywords:  Autofluorescence; Genetics; Mitochondrial disease; OCT; Retinal imaging
    DOI:  https://doi.org/10.1016/j.oret.2021.02.017
  6. J Neurosci. 2021 Jul 14. pii: JN-RM-2197-20. [Epub ahead of print]
    Mitochondrial Proteostasis Requires Genes Encoded in a Neurodevelopmental Syndrome Locus.
    Avanti Gokhale, Chelsea E Lee, Stephanie A Zlatic, Amanda A H Freeman, Nicole Shearing, Cortnie Hartwig, Oluwaseun Ogunbona, Julia L Bassell, Meghan E Wynne, Erica Werner, Chongchong Xu, Zhexing Wen, Duc Duong, Nicholas T Seyfried, Carrie E Bearden, Viktor János Oláh, Matthew J M Rowan, Jill R Glausier, David A Lewis, Victor Faundez.
      Eukaryotic cells maintain proteostasis through mechanisms that require cytoplasmic and mitochondrial translation. Genetic defects affecting cytoplasmic translation perturb synapse development, neurotransmission, and are causative of neurodevelopmental disorders such as Fragile X syndrome. In contrast, there is little indication that mitochondrial proteostasis, either in the form of mitochondrial protein translation and/or degradation, is required for synapse development and function. Here we focus on two genes deleted in a recurrent copy number variation causing neurodevelopmental disorders, the 22q11.2 microdeletion syndrome. We demonstrate that SLC25A1 and MRPL40, two genes present in the microdeleted segment and whose products localize to mitochondria, interact and are necessary for mitochondrial ribosomal integrity and proteostasis. Our Drosophila studies show that mitochondrial ribosome function is necessary for synapse neurodevelopment, function, and behavior. We propose that mitochondrial proteostasis perturbations, either by genetic or environmental factors, are a pathogenic mechanism for neurodevelopmental disorders.Significance StatementThe balance between cytoplasmic protein synthesis and degradation, or cytoplasmic proteostasis, is required for normal synapse function and neurodevelopment. Cytoplasmic and mitochondrial ribosomes are necessary for two compartmentalized, yet interdependent, forms of proteostasis. Proteostasis dependent on cytoplasmic ribosomes is a well-established target of genetic defects that cause neurodevelopmental disorders such as autism. Here we show that the mitochondrial ribosome is a neurodevelopmentally regulated organelle whose function is required for synapse development and function. We propose that defective mitochondrial proteostasis is a mechanism with the potential to contribute to neurodevelopmental disease.
    DOI:  https://doi.org/10.1523/JNEUROSCI.2197-20.2021
  7. J Cell Sci. 2021 Jul 01. pii: jcs252197. [Epub ahead of print]134(13):
    Super-resolution microscopy reveals the arrangement of inner membrane protein complexes in mammalian mitochondria.
    Catherine S Palmer, Jieqiong Lou, Betty Kouskousis, Elvis Pandzic, Alexander J Anderson, Yilin Kang, Elizabeth Hinde, Diana Stojanovski.
      The mitochondrial inner membrane is a protein-rich environment containing large multimeric complexes, including complexes of the mitochondrial electron transport chain, mitochondrial translocases and quality control machineries. Although the inner membrane is highly proteinaceous, with 40-60% of all mitochondrial proteins localised to this compartment, little is known about the spatial distribution and organisation of complexes in this environment. We set out to survey the arrangement of inner membrane complexes using stochastic optical reconstruction microscopy (STORM). We reveal that subunits of the TIM23 complex, TIM23 and TIM44 (also known as TIMM23 and TIMM44, respectively), and the complex IV subunit COXIV, form organised clusters and show properties distinct from the outer membrane protein TOM20 (also known as TOMM20). Density based cluster analysis indicated a bimodal distribution of TIM44 that is distinct from TIM23, suggesting distinct TIM23 subcomplexes. COXIV is arranged in larger clusters that are disrupted upon disruption of complex IV assembly. Thus, STORM super-resolution microscopy is a powerful tool for examining the nanoscale distribution of mitochondrial inner membrane complexes, providing a 'visual' approach for obtaining pivotal information on how mitochondrial complexes exist in a cellular context.
    Keywords:  COXIV; Mitochondria; Mitochondrial complexes; Nanoscopy; Protein import; STORM; TIM23
    DOI:  https://doi.org/10.1242/jcs.252197
  8. J Neurol. 2021 Jul 14.
    Adult-onset mitochondrial movement disorders: a national picture from the Italian Network.
    V Montano, D Orsucci, V Carelli, C La Morgia, M L Valentino, C Lamperti, S Marchet, O Musumeci, A Toscano, G Primiano, F M Santorelli, C Ticci, M Filosto, A Rubegni, T Mongini, P Tonin, S Servidei, R Ceravolo, G Siciliano, Michelangelo Mancuso.
       INTRODUCTION: Both prevalence and clinical features of the various movement disorders in adults with primary mitochondrial diseases are unknown.
    METHODS: Based on the database of the "Nation-wide Italian Collaborative Network of Mitochondrial Diseases", we reviewed the clinical, genetic, neuroimaging and neurophysiological data of adult patients with primary mitochondrial diseases (n = 764) where ataxia, myoclonus or other movement disorders were part of the clinical phenotype.
    RESULTS: Ataxia, myoclonus and movement disorders were present in 105/764 adults (13.7%), with the onset coinciding or preceding the diagnosis of the mitochondrial disease in 49/105 (46.7%). Ataxia and parkinsonism were the most represented, with an overall prevalence at last follow-up of 59.1% and 30.5%, respectively. Hyperkinetic movement disorders were reported in 15.3% at last follow-up, being the less common reported movement disorders. The pathogenic m.8344A > G and POLG variants were always associated with a movement disorder, while LHON variants and mtDNA single deletions were more commonly found in the subjects who did not present a movement disorder. The most common neuroimaging features were cortical and/or cerebellar atrophy, white matter hyperintensities, basal ganglia abnormalities and nigro-striatal degeneration. Almost 70% of patients with parkinsonism responded to dopaminergic therapy, mainly levodopa, and 50% with myoclonus were successfully treated with levetiracetam.
    CONCLUSION: Movement disorders, mainly ataxia and parkinsonism, are important findings in adult primary mitochondrial diseases. This study underlies the importance of looking for a mitochondrial etiology in the diagnostic flowchart of a movement disorder and may help direct genetic screening in daily practice.
    Keywords:  Ataxia; Mitochondrial disorders; Movement disorders; Parkinsonism
    DOI:  https://doi.org/10.1007/s00415-021-10697-1
  9. Trends Biochem Sci. 2021 Jul 06. pii: S0968-0004(21)00121-3. [Epub ahead of print]
    Mitochondrial compartmentalization: emerging themes in structure and function.
    Joseph C Iovine, Steven M Claypool, Nathan N Alder.
      Within cellular structures, compartmentalization is the concept of spatial segregation of macromolecules, metabolites, and biochemical pathways. Therefore, this concept bridges organellar structure and function. Mitochondria are morphologically complex, partitioned into several subcompartments by a topologically elaborate two-membrane system. They are also dynamically polymorphic, undergoing morphogenesis events with an extent and frequency that is only now being appreciated. Thus, mitochondrial compartmentalization is something that must be considered both spatially and temporally. Here, we review new developments in how mitochondrial structure is established and regulated, the factors that underpin the distribution of lipids and proteins, and how they spatially demarcate locations of myriad mitochondrial processes. Consistent with its pre-eminence, disturbed mitochondrial compartmentalization contributes to the dysfunction associated with heritable and aging-related diseases.
    Keywords:  bioenergetics; cristae; macromolecular trafficking; mitochondria; morphogenesis; ultrastructure
    DOI:  https://doi.org/10.1016/j.tibs.2021.06.003
  10. Bio Protoc. 2021 Jun 20. 11(12): e4057
    Protein Import Assay into Mitochondria Isolated from Human Cells.
    Lena M Murschall, Esra Peker, Thomas MacVicar, Thomas Langer, Jan Riemer.
      Mitochondria are essential organelles containing approximately 1,500 proteins. Only approximately 1% of these proteins are synthesized inside mitochondria, whereas the remaining 99% are synthesized as precursors on cytosolic ribosomes and imported into the organelle. Various tools and techniques to analyze the import process have been developed. Among them, in vitro reconstituted import systems are of importance to study these processes in detail. These experiments monitor the import reaction of mitochondrial precursors that were previously radiolabeled in a cell-free environment. However, the methods described have been mostly performed in mitochondria isolated from S. cerevisiae. Here, we describe the adaptation of this powerful assay to import proteins into crude mitochondria isolated from human tissue culture cells. Graphic abstract: Overview of the assay to monitor protein import into mitochondria isolated from human cells.
    Keywords:  Cell-free protein synthesis; Human tissue culture cells; In organello import ; Isolated mitochondria; Radiolabeled proteins
    DOI:  https://doi.org/10.21769/BioProtoc.4057
  11. Nat Cell Biol. 2021 Jul;23(7): 684-691
    ALKBH7-mediated demethylation regulates mitochondrial polycistronic RNA processing.
    Li-Sheng Zhang, Qing-Ping Xiong, Sonia Peña Perez, Chang Liu, Jiangbo Wei, Cassy Le, Linda Zhang, Bryan T Harada, Qing Dai, Xinran Feng, Ziyang Hao, Yuru Wang, Xueyang Dong, Lulu Hu, En-Duo Wang, Tao Pan, Arne Klungland, Ru-Juan Liu, Chuan He.
      Members of the mammalian AlkB family are known to mediate nucleic acid demethylation1,2. ALKBH7, a mammalian AlkB homologue, localizes in mitochondria and affects metabolism3, but its function and mechanism of action are unknown. Here we report an approach to site-specifically detect N1-methyladenosine (m1A), N3-methylcytidine (m3C), N1-methylguanosine (m1G) and N2,N2-dimethylguanosine (m22G) modifications simultaneously within all cellular RNAs, and discovered that human ALKBH7 demethylates m22G and m1A within mitochondrial Ile and Leu1 pre-tRNA regions, respectively, in nascent polycistronic mitochondrial RNA4-6. We further show that ALKBH7 regulates the processing and structural dynamics of polycistronic mitochondrial RNAs. Depletion of ALKBH7 leads to increased polycistronic mitochondrial RNA processing, reduced steady-state mitochondria-encoded tRNA levels and protein translation, and notably decreased mitochondrial activity. Thus, we identify ALKBH7 as an RNA demethylase that controls nascent mitochondrial RNA processing and mitochondrial activity.
    DOI:  https://doi.org/10.1038/s41556-021-00709-7
  12. Nutr Clin Pract. 2021 Jul 16.
    Nutrition rehabilitation-related complications in primary mitochondrial disorders.
    Tamir Diamond, Donna DiVito, Melanie Savoca, Maria Mascarenhas, Amy Goldstein.
      Primary mitochondrial disorders (PMDs) comprise a group of hundreds of individual genetic diseases affecting mitochondrial function, including oxidative phosphorylation and energy production. The estimated prevalence of these disorders ranges from 2.9 to 20 cases per 100,000. PMDs are commonly associated with malnutrition and growth failure. There is a paucity of literature regarding nutrition assessment and long-term data in the PMD population. We present three patients with various PMDs who presented complications related to malnutrition: (1) a 16-year-old male with Kearns-Sayre syndrome developed type 2 insulin-requiring diabetes mellitus after the initiation of high-calorie nutrition rehabilitation via gastrostomy tube (G-tube); (2) an 11-year-old female with myoclonic epilepsy associated with ragged red fibers developed diarrhea with metabolic decompensation and profound neurological and respiratory deterioration during nutrition rehabilitation after surgical G-tube placement; and (3) a 19-year-old male with a WARS2-associated PMD manifesting with developmental delay and severe parkinsonism presented complications related to poor wound healing after gastrojejunostomy tube placement. The last patient required prolonged hospitalization in the intensive care unit. Clinicians should be vigilant in monitoring these possible complications, as no standards of care exist for the initiation of enteral nutrition for this unique population.
    Keywords:  enteral nutrition; inborn genetic diseases; mitochondrial diseases; nutrition support
    DOI:  https://doi.org/10.1002/ncp.10739
  13. Nat Commun. 2021 07 13. 12(1): 4284
    Global kinome profiling reveals DYRK1A as critical activator of the human mitochondrial import machinery.
    Corvin Walter, Adinarayana Marada, Tamara Suhm, Ralf Ernsberger, Vera Muders, Cansu Kücükköse, Pablo Sánchez-Martín, Zehan Hu, Abhishek Aich, Stefan Loroch, Fiorella Andrea Solari, Daniel Poveda-Huertes, Alexandra Schwierzok, Henrike Pommerening, Stanka Matic, Jan Brix, Albert Sickmann, Claudine Kraft, Jörn Dengjel, Sven Dennerlein, Tilman Brummer, F-Nora Vögtle, Chris Meisinger.
      The translocase of the outer mitochondrial membrane TOM constitutes the organellar entry gate for nearly all precursor proteins synthesized on cytosolic ribosomes. Thus, TOM presents the ideal target to adjust the mitochondrial proteome upon changing cellular demands. Here, we identify that the import receptor TOM70 is targeted by the kinase DYRK1A and that this modification plays a critical role in the activation of the carrier import pathway. Phosphorylation of TOM70Ser91 by DYRK1A stimulates interaction of TOM70 with the core TOM translocase. This enables transfer of receptor-bound precursors to the translocation pore and initiates their import. Consequently, loss of TOM70Ser91 phosphorylation results in a strong decrease in import capacity of metabolite carriers. Inhibition of DYRK1A impairs mitochondrial structure and function and elicits a protective transcriptional response to maintain a functional import machinery. The DYRK1A-TOM70 axis will enable insights into disease mechanisms caused by dysfunctional DYRK1A, including autism spectrum disorder, microcephaly and Down syndrome.
    DOI:  https://doi.org/10.1038/s41467-021-24426-9
  14. J Mol Evol. 2021 Jul 12.
    The Evolutionary Fate of Mitochondrial Aminoacyl-tRNA Synthetases in Amitochondrial Organisms.
    Gabor L Igloi.
      During the endosymbiotic evolution of mitochondria, the genes for aminoacyl-tRNA synthetases were transferred to the ancestral nucleus. A further reduction of mitochondrial function resulted in mitochondrion-related organisms (MRO) with a loss of the organelle genome. The fate of the now redundant ancestral mitochondrial aminoacyl-tRNA synthetase genes is uncertain. The derived protein sequence for arginyl-tRNA synthetase from thirty mitosomal organisms have been classified as originating from the ancestral nuclear or mitochondrial gene and compared to the identity element at position 20 of the cognate tRNA that distinguishes the two enzyme forms. The evolutionary choice between loss and retention of the ancestral mitochondrial gene for arginyl-tRNA synthetase reflects the coevolution of arginyl-tRNA synthetase and tRNA identity elements.
    Keywords:  Aminoacyl-tRNA synthetase; Amitochondrial; Arginyl-tRNA; Identity elements; Mitosome; Protozoa
    DOI:  https://doi.org/10.1007/s00239-021-10019-z
  15. JIMD Rep. 2021 Jul;60(1): 75-87
    SLC25A42-associated mitochondrial encephalomyopathy: Report of additional founder cases and functional characterization of a novel deletion.
    Mazhor Aldosary, Shahad Baselm, Maha Abdulrahim, Rawan Almass, Maysoon Alsagob, Zainab AlMasseri, Rozeena Huma, Laila AlQuait, Tarfa Al-Shidi, Eman Al-Obeid, Albandary AlBakheet, Basma Alahideb, Lujane Alahaidib, Alya Qari, Robert W Taylor, Dilek Colak, Moeenaldeen D AlSayed, Namik Kaya.
      SLC25A42 is the main transporter of coenzyme A (CoA) into mitochondria. To date, 15 individuals have been reported to have one of two bi-allelic homozygous missense variants in the SLC25A42 as the cause of mitochondrial encephalomyopathy, of which 14 of them were of Saudi origin and share the same founder variant, c.871A > G:p.Asn291Asp. The other subject was of German origin with a variant at canonical splice site, c.380 + 2 T > A. Here, we describe the clinical manifestations and the disease course in additional six Saudi patients from four unrelated consanguineous families. While five patients have the Saudi founder p.Asn291Asp variant, one subject has a novel deletion. Functional analyses on fibroblasts obtained from this patient revealed that the deletion causes significant decrease in mitochondrial oxygen consumption and ATP production compared to healthy individuals. Moreover, extracellular acidification rate revealed significantly reduced glycolysis, glycolytic capacity, and glycolytic reserve as compared to control individuals. There were no changes in the mitochondrial DNA (mtDNA) content of patient fibroblasts. Immunoblotting experiments revealed significantly diminished protein expression due to the deletion. In conclusion, we report additional patients with SLC25A42-associated mitochondrial encephalomyopathy. Our study expands the molecular spectrum of this condition and provides further evidence of mitochondrial dysfunction as a central cause of pathology. We therefore propose that this disorder should be included in the differential diagnosis of any patient with an unexplained motor and speech delay, recurrent encephalopathy with metabolic acidosis, intermittent or persistent dystonia, lactic acidosis, basal ganglia lesions and, especially, of Arab ethnicity. Finally, deep brain stimulation should be considered in the management of patients with life altering dystonia.
    Keywords:  ATP production; SLC25A42; deep brain stimulation; mitochondrial oxygen consumption; truncation
    DOI:  https://doi.org/10.1002/jmd2.12218
  16. Biochim Biophys Acta Biomembr. 2021 Jul 13. pii: S0005-2736(21)00133-4. [Epub ahead of print] 183683
    Conserved GxxxG and WN motifs of MIC13 are essential for bridging two MICOS subcomplexes.
    Jennifer Urbach, Arun Kumar Kondadi, Céline David, Ritam Naha, Kim Deinert, Andreas S Reichert, Ruchika Anand.
      Mitochondrial ultrastructure is highly adaptable and undergoes dynamic changes upon physiological and energetic cues. MICOS (mitochondrial contact site and cristae organizing system), a large oligomeric protein complex, maintains mitochondrial ultrastructure as it is required for formation of crista junctions (CJs) and contact sites. MIC13 acts as a critical bridge between two MICOS subcomplexes. Deletion of MIC13 causes loss of CJs resulting in cristae accumulating as concentric rings and specific destabilization of the MIC10-subcomplex. Mutations in MIC13 are associated with infantile lethal mitochondrial hepato-encephalopathy, yet functional regions within MIC13 were not known. To identify and characterize such regions, we systemically generated 20 amino-acids deletion variants across the length of MIC13. While deletion of many of these regions of MIC13 is dispensable for its stability, the N-terminal region and a stretch between amino acid residues 84 and 103 are necessary for the stability and functionality of MIC13. We could further locate conserved motifs within these regions and found that a GxxxG motif in the N-terminal transmembrane segment and an internal WN motif are essential for stability of MIC13, formation of the MIC10-subcomplex, interaction with MIC10- and MIC60-subcomplexes and maintenance of cristae morphology. The GxxxG motif is required for membrane insertion of MIC13. Overall, we systematically found important conserved residues of MIC13 that are required to perform the bridging between the two MICOS subcomplexes. The study improves our understanding of the basic molecular function of MIC13 and has implications for its role in the pathogenesis of a severe mitochondrial disease.
    Keywords:  Conserved motifs; Crista junction; Cristae; MICOS; Mitochondrial disease
    DOI:  https://doi.org/10.1016/j.bbamem.2021.183683
  17. Proc Natl Acad Sci U S A. 2021 Jul 20. pii: e2023079118. [Epub ahead of print]118(29):
    NMR identification of a conserved Drp1 cardiolipin-binding motif essential for stress-induced mitochondrial fission.
    Mukesh Mahajan, Nikhil Bharambe, Yutong Shang, Bin Lu, Abhishek Mandal, Pooja Madan Mohan, Rihua Wang, Jennifer C Boatz, Juan Manuel Martinez Galvez, Anna V Shnyrova, Xin Qi, Matthias Buck, Patrick C A van der Wel, Rajesh Ramachandran.
      Mitochondria form tubular networks that undergo coordinated cycles of fission and fusion. Emerging evidence suggests that a direct yet unresolved interaction of the mechanoenzymatic GTPase dynamin-related protein 1 (Drp1) with mitochondrial outer membrane-localized cardiolipin (CL), externalized under stress conditions including mitophagy, catalyzes essential mitochondrial hyperfragmentation. Here, using a comprehensive set of structural, biophysical, and cell biological tools, we have uncovered a CL-binding motif (CBM) conserved between the Drp1 variable domain (VD) and the unrelated ADP/ATP carrier (AAC/ANT) that intercalates into the membrane core to effect specific CL interactions. CBM mutations that weaken VD-CL interactions manifestly impair Drp1-dependent fission under stress conditions and induce "donut" mitochondria formation. Importantly, VD membrane insertion and GTP-dependent conformational rearrangements mediate only transient CL nonbilayer topological forays and high local membrane constriction, indicating that Drp1-CL interactions alone are insufficient for fission. Our studies establish the structural and mechanistic bases of Drp1-CL interactions in stress-induced mitochondrial fission.
    Keywords:  NMR; cardiolipin; dynamin; intrinsically disordered; mitochondria
    DOI:  https://doi.org/10.1073/pnas.2023079118
  18. PLoS Biol. 2021 Jul;19(7): e3001302
    Proteasome activity contributes to pro-survival response upon mild mitochondrial stress in Caenorhabditis elegans.
    Maria Sladowska, Michał Turek, Min-Ji Kim, Krzysztof Drabikowski, Ben Hur Marins Mussulini, Karthik Mohanraj, Remigiusz A Serwa, Ulrike Topf, Agnieszka Chacinska.
      Defects in mitochondrial function activate compensatory responses in the cell. Mitochondrial stress that is caused by unfolded proteins inside the organelle induces a transcriptional response (termed the "mitochondrial unfolded protein response" [UPRmt]) that is mediated by activating transcription factor associated with stress 1 (ATFS-1). The UPRmt increases mitochondrial protein quality control. Mitochondrial dysfunction frequently causes defects in the import of proteins, resulting in the accumulation of mitochondrial proteins outside the organelle. In yeast, cells respond to mistargeted mitochondrial proteins by increasing activity of the proteasome in the cytosol (termed the "unfolded protein response activated by mistargeting of proteins" [UPRam]). The presence and relevance of this response in higher eukaryotes is unclear. Here, we demonstrate that defects in mitochondrial protein import in Caenorhabditis elegans lead to proteasome activation and life span extension. Both proteasome activation and life span prolongation partially depend on ATFS-1, despite its lack of influence on proteasomal gene transcription. Importantly, life span prolongation depends on the fully assembled proteasome. Our data provide a link between mitochondrial dysfunction and proteasomal activity and demonstrate its direct relevance to mechanisms that promote longevity.
    DOI:  https://doi.org/10.1371/journal.pbio.3001302
  19. Cell Metab. 2021 Jul 08. pii: S1550-4131(21)00283-7. [Epub ahead of print]
    Glycerol-3-phosphate biosynthesis regenerates cytosolic NAD+ to alleviate mitochondrial disease.
    Shanshan Liu, Song Fu, Guodong Wang, Yu Cao, Lanlan Li, Xuemei Li, Jun Yang, Ning Li, Yabing Shan, Yang Cao, Yan Ma, Mengqiu Dong, Qinghua Liu, Hui Jiang.
      Electron transport chain (ETC) dysfunction or hypoxia causes toxic NADH accumulation. How cells regenerate NAD+ under such conditions remains elusive. Here, integrating bioinformatic analysis and experimental validation, we identify glycerol-3-phosphate (Gro3P) biosynthesis as an endogenous NAD+-regeneration pathway. Under genetic or pharmacological ETC inhibition, disrupting Gro3P synthesis inhibits yeast proliferation, shortens lifespan of C. elegans, impairs growth of cancer cells in culture and in xenografts, and causes metabolic derangements in mouse liver. Moreover, the Gro3P shuttle selectively regenerates cytosolic NAD+ under mitochondrial complex I inhibition; enhancing Gro3P synthesis promotes shuttle activity to restore proliferation of complex I-impaired cells. Mouse brain has much lower levels of Gro3P synthesis enzymes as compared with other organs. Strikingly, enhancing Gro3P synthesis suppresses neuroinflammation and extends lifespan in the Ndufs4-/- mice. Collectively, our results reveal Gro3P biosynthesis as an evolutionarily conserved coordinator of NADH/NAD+ redox homeostasis and present a therapeutic target for mitochondrial complex I diseases.
    Keywords:  ETC dysfunction and hypoxia; NAD(+) regeneration; glycerol-3-phosphate biosynthesis; mitochondrial complex I disease
    DOI:  https://doi.org/10.1016/j.cmet.2021.06.013
  20. BMC Bioinformatics. 2021 Jul 15. 22(Suppl 10): 369
    MitoTox: a comprehensive mitochondrial toxicity database.
    Yu-Te Lin, Ko-Hong Lin, Chi-Jung Huang, An-Chi Wei.
       BACKGROUND: Mitochondria play essential roles in regulating cellular functions. Some drug treatments and molecular interventions have been reported to have off-target effects damaging mitochondria and causing severe side effects. The development of a database for the management of mitochondrial toxicity-related molecules and their targets is important for further analyses.
    RESULTS: To correlate chemical, biological and mechanistic information on clinically relevant mitochondria-related toxicity, a comprehensive mitochondrial toxicity database (MitoTox) was developed. MitoTox is an electronic repository that integrates comprehensive information about mitochondria-related toxins and their targets. Information and data related to mitochondrial toxicity originate from various sources, including scientific journals and other electronic databases. These resources were manually verified and extracted into MitoTox. The database currently contains over 1400 small-molecule compounds, 870 mitochondrial targets, and more than 4100  mitochondrial toxin-target associations. Each MitoTox data record contains over 30 fields, including biochemical properties, therapeutic classification, target proteins, toxicological data, mechanistic information, clinical side effects, and references.
    CONCLUSIONS: MitoTox provides a fully searchable database with links to references and other databases. Potential applications of MitoTox include toxicity classification, prediction, reference and education. MitoTox is available online at http://www.mitotox.org .
    Keywords:  Database; Mitochondria; Mitochondrial toxicity; Toxin-target association
    DOI:  https://doi.org/10.1186/s12859-021-04285-3
  21. J Diabetes Investig. 2021 Jul 13.
    Mitochondrial haplogroups have a better correlation to insulin requirement than nuclear genetic variants for type 2 diabetes mellitus in Taiwanese individuals.
    Feng-Chih Shen, Shao-Wen Weng, Meng-Han Tsai, Yu-Jih Su, Sung-Chou Li, Shun-Jen Chang, Jung-Fu Chen, Yen-Hsiang Chang, Chia-Wei Liou, Tsu-Kung Lin, Jiin-Haur Chuang, Ching-Yi Lin, Pei-Wen Wang.
       AIMS/INTRODUCTION: Identifying the diabetes-susceptible genetic variants will help to provide the personalized therapy for management of type 2 diabetes. Previous studies have reported a genetic risk score (GRS), computed by the sum of nuclear DNA (nDNA) risk alleles, may predict the future requirement of insulin therapy. Although mitochondrial dysfunction has close association with insulin resistance (IR), there are few studies investigate whether genetic variants of mitochondrial DNA (mtDNA) will affect the clinical characteristics of type 2 diabetes.
    MATERIALS AND METHODS: We determined mitochondrial haplogroups using mtDNA whole genome next generation sequencing and 13 single nucleotide polymorphisms (SNPs) in nDNA susceptibility loci of 13 genes in 604 Taiwanese subjects with type 2 diabetes. A GRS of nDNA was computed by summation of the number of risk alleles. The correlation between mtDNA haplogroup and the clinical characteristics of type 2 diabetes was assessed by logistic regression analysis. The results were compared with the GRS subgroups for the risk of insulin requirement.
    RESULTS: Mitochondrial haplogroups modulate the clinical characteristics of type 2 diabetes, in which patients harboring haplogroup D4, as compared to those harboring non-D4 haplotypes were less prone to require insulin treatment, after adjusting for age, gender and diabetes duration. However, there was no association between insulin requirement and GRS calculated from nuclear genetic variants.
    CONCLUSIONS: Mitochondrial haplogroups, but not nuclear genetic variants, have a better association with the insulin requirement. Our results highlight the role of mitochondria in the management of common metabolic diseases.
    Keywords:  diabetes; insulin; mitochondria
    DOI:  https://doi.org/10.1111/jdi.13629
  22. Int Rev Cell Mol Biol. 2021 ;pii: S1937-6448(21)00020-4. [Epub ahead of print]362 171-207
    Mitochondrial Ca2+ and cell cycle regulation.
    Haixin Zhao, Xin Pan.
      It has been demonstrated for more than 40 years that intracellular calcium (Ca2+) controls a variety of cellular functions, including mitochondrial metabolism and cell proliferation. Cytosolic Ca2+ fluctuation during key stages of the cell cycle can lead to mitochondrial Ca2+ uptake and subsequent activation of mitochondrial oxidative phosphorylation and a range of signaling. However, the relationship between mitochondrial Ca2+ and cell cycle progression has long been neglected because the molecule responsible for Ca2+ uptake has been unknown. Recently, the identification of the mitochondrial Ca2+ uniporter (MCU) has led to key advances. With improved Ca2+ imaging and detection, effects of MCU-mediated mitochondrial Ca2+ have been observed at different stages of the cell cycle. Elevated Ca2+ signaling boosts ATP and ROS production, remodels cytosolic Ca2+ pathways and reprograms cell fate-determining networks. These findings suggest that manipulating mitochondrial Ca2+ signaling may serve as a potential strategy in the control of many crucial biological events, such as tumor development and cell division in hematopoietic stem cells (HSCs). In this review, we summarize the current understanding of the role of mitochondrial Ca2+ signaling during different stages of the cell cycle and highlight the potential physiological and pathological significance of mitochondrial Ca2+ signaling.
    Keywords:  Cell cycle; MCU; Metabolism; Mitochondrial Ca(2+)
    DOI:  https://doi.org/10.1016/bs.ircmb.2021.02.015
  23. JIMD Rep. 2021 Jul;60(1): 15-22
    Human d-lactate dehydrogenase deficiency by LDHD mutation in a patient with neurological manifestations and mitochondrial complex IV deficiency.
    Anna Ka-Yee Kwong, Sheila Suet-Na Wong, Richard J T Rodenburg, Jan Smeitink, Godfrey Chi Fung Chan, Cheuk-Wing Fung.
       Background: d-lactate, one of the isomers of lactate, exists in a low concentration in healthy individuals and it can be oxidized to pyruvate catalyzed by d-lactate dehydrogenase. Excessive amount of d-lactate causes d-lactate acidosis associated with neurological manifestations.
    Methods and Results: We report here a patient with developmental delay, cerebellar ataxia, and transient hepatomegaly. Enzyme analysis in the patient's skin fibroblast showed decreased mitochondrial complex IV activity. Using whole exome sequencing, we identified compound heterozygous variants in the LDHD gene, which encodes the d-lactate dehydrogenase, consisting of a splice site variant c.469+1dupG and a missense variant c.752C>T, p.(Thr251Met) which are pathogenic and likely pathogenic respectively according to the American College of Medical Genetics and Genomics (ACMG) classification. The serum d-lactate level was subsequently detected to be elevated (0.61 mmol/L, reference value: 0-0.25 mmol/L).
    Conclusion: This is the third report on LDHD mutations associated with d-lactate elevation and was first reported to have decreased mitochondrial complex IV activity. The study provides more information on this rare metabolic condition but the association of LDHD deficiency with the clinical presentations requires further investigations.
    Keywords:  LDHD; ataxia; complex IV deficiency; developmental delay; d‐lactate dehydrogenase; neurological
    DOI:  https://doi.org/10.1002/jmd2.12220
  24. J Biol Chem. 2021 Jul 09. pii: S0021-9258(21)00750-X. [Epub ahead of print] 100950
    Hydrogen sulfide stimulates lipid biogenesis from glutamine that is dependent on the mitochondrial NAD(P)H pool.
    Sebastian Carballal, Victor Vitvitsky, Roshan Kumar, David A Hanna, Marouane Libiad, Aditi Gupta, Jace W Jones, Ruma Banerjee.
      Mammalian cells synthesize H2S from sulfur containing amino acids and are also exposed to exogenous sources of this signaling molecule, notably from gut microbes. As an inhibitor of complex IV in the electron transport chain, H2S can have a profound impact on metabolism, suggesting the hypothesis that metabolic reprogramming is a primary mechanism by which H2S signals. In this study, we report that H2S increases lipogenesis in many cell types, using carbon derived from glutamine rather than from glucose. H2S-stimulated lipid synthesis is sensitive to the mitochondrial NAD(P)H pools and is enabled by reductive carboxylation of α-ketoglutarate. Lipidomics analysis revealed that H2S elicits time-dependent changes across several lipid classes, e.g., upregulating triglycerides while down regulating phosphatidylcholine. Direct analysis of triglyceride concentration revealed that H2S induces a net increase in the size of this lipid pool. These results provide a mechanistic framework for understanding the effects of H2S on increasing lipid droplets in adipocytes and population studies that have pointed to a positive correlation between cysteine (a substrate for H2S synthesis) and fat mass.
    DOI:  https://doi.org/10.1016/j.jbc.2021.100950
  25. FEBS J. 2021 Jul 16.
    On the offense and defense: mitochondrial recovery programs amidst targeted pathogenic assault.
    Siraje A Mahmud, Mohammed A Qureshi, Mark W Pellegrino.
      Bacterial pathogens employ a variety of tactics to persist in their host and promote infection. Pathogens often target host organelles in order to benefit their survival, either through manipulation or subversion of their function. Mitochondria are regularly targeted by bacterial pathogens owing to their diverse cellular roles, including energy production and regulation of programmed cell death. However, disruption of normal mitochondrial function during infection can be detrimental to cell viability because of their essential nature. In response, cells use multiple quality control programs to mitigate mitochondrial dysfunction and promote recovery. In this review, we will provide an overview of mitochondrial recovery programs including mitochondrial dynamics, the mitochondrial unfolded protein response (UPRmt ), and mitophagy. We will then discuss the various approaches used by bacterial pathogens to target mitochondria which result in mitochondrial dysfunction. Lastly, we will discuss how cells leverage mitochondrial recovery programs beyond their role in organelle repair, to promote host defense against pathogen infection.
    Keywords:  UPRmt; defense; infection; mitochondria; mitochondrial dynamics; mitochondrial fission; mitochondrial fusion; mitophagy; pathogen
    DOI:  https://doi.org/10.1111/febs.16126
  26. J Physiol. 2021 Jul;599(14): 3447-3448
    Unravelling the mysteries of mitochondria in health and disease.
    Livia C Hool.
      
    Keywords:  calcium; cardiomyopathy; diabetes; exercise; mitochondria; protein synthesis
    DOI:  https://doi.org/10.1113/JP281833
  27. Redox Biol. 2021 Jul 03. pii: S2213-2317(21)00220-2. [Epub ahead of print]46 102061
    Regulation of hepatic coenzyme Q biosynthesis by dietary omega-3 polyunsaturated fatty acids.
    Lucía Fernández-Del-Río, Sandra Rodríguez-López, Elena Gutiérrez-Casado, José Antonio González-Reyes, Catherine F Clarke, María Isabel Burón, José Manuel Villalba.
      Dietary fats are important for human health, yet it is not fully understood how different fats affect various health problems. Although polyunsaturated fatty acids (PUFAs) are generally considered as highly oxidizable, those of the n-3 series can ameliorate the risk of many age-related disorders. Coenzyme Q (CoQ) is both an essential component of the mitochondrial electron transport chain and the only lipid-soluble antioxidant that animal cells can synthesize. Previous work has documented the protective antioxidant properties of CoQ against the autoxidation products of PUFAs. Here, we have explored in vitro and in vivo models to better understand the regulation of CoQ biosynthesis by dietary fats. In mouse liver, PUFAs increased CoQ content, and PUFAs of the n-3 series increased preferentially CoQ10. This response was recapitulated in hepatic cells cultured in the presence of lipid emulsions, where we additionally demonstrated a role for n-3 PUFAs as regulators of CoQ biosynthesis via the upregulation of several COQ proteins and farnesyl pyrophosphate levels. In both models, n-3 PUFAs altered the mitochondrial network without changing the overall mitochondrial mass. Furthermore, in cellular systems, n-3 PUFAs favored the synthesis of CoQ10 over CoQ9, thus altering the ratio between CoQ isoforms through a mechanism that involved downregulation of farnesyl diphosphate synthase activity. This effect was recapitulated by both siRNA silencing and by pharmacological inhibition of farnesyl diphosphate synthase with zoledronic acid. We highlight here the ability of n-3 PUFAs to regulate CoQ biosynthesis, CoQ content, and the ratio between its isoforms, which might be relevant to better understand the health benefits associated with this type of fat. Additionally, we identify for the first time zoledronic acid as a drug that inhibits CoQ biosynthesis, which must be also considered with respect to its biological effects on patients.
    Keywords:  Coenzyme Q; Farnesyl diphosphate synthase; MUFAs; Mevalonate pathway; PUFAs; Zoledronic acid
    DOI:  https://doi.org/10.1016/j.redox.2021.102061
  28. EMBO J. 2021 Jul 12. e108293
    Nuclear cGAS: guard or prisoner?
    Carina C de Oliveira Mann, Karl-Peter Hopfner.
      cGAS, an innate immune sensor of cellular stress, recognizes double-stranded DNA mislocalized in the cytosol upon infection, mitochondrial stress, DNA damage, or malignancy. Early models suggested that cytosolic localization of cGAS prevents autoreactivity to nuclear and mitochondrial self-DNA, but this paradigm has shifted in light of recent findings of cGAS as a predominantly nuclear protein tightly bound to chromatin. This has raised the question how nuclear cGAS is kept inactive while being surrounded by chromatin, and what function nuclear localization of cGAS may serve in the first place? Cryo-EM structures have revealed that cGAS interacts with nucleosomes, the minimal units of chromatin, mainly via histones H2A/H2B, and that these protein-protein interactions block cGAS from DNA binding and thus prevent autoreactivity. Here, we discuss the biological implications of nuclear cGAS and its interaction with chromatin, including various mechanisms for nuclear cGAS inhibition, release of chromatin-bound cGAS, regulation of different cGAS pools in the cell, and chromatin structure/chromatin protein effects on cGAS activation leading to cGAS-induced autoimmunity.
    Keywords:  DNA sensing; chromatin; cyclic GMP-AMP synthase; innate immunity; nucleosome
    DOI:  https://doi.org/10.15252/embj.2021108293
  29. Neurotox Res. 2021 Jul 12.
    SIRT1 Protects Dopaminergic Neurons in Parkinson's Disease Models via PGC-1α-Mediated Mitochondrial Biogenesis.
    Yu Chen, Yuhui Jiang, Yinuo Yang, Xinzhong Huang, Cheng Sun.
      SIRT1 is a deacetylase with multiple physiological functions by targeting histones and non-histone proteins. It has been shown that SIRT1 activation is involved in neuroprotection in Parkinson's disease (PD) models. In the present study, we provided direct evidences showing the neuroprotective roles of SIRT1 in dopaminergic neurons. Our data showed that increased expression of SIRT1 plays beneficial roles against MPP+ insults in SH-SY5Y cells and primary dopaminergic neurons, including increased cell viability, reduced LDH release, improved the mitochondrial membrane potential (MMP), and attenuated cell apoptosis. On the contrary, knockdown of SIRT1 further aggravated cell injuries induced by MPP+. Moreover, mutated SIRT1 without deacetylase activity (SIRT1 H363Y) failed to protect dopaminergic neurons from MPP+ injuries. Mechanistically, SIRT1 improved PGC-1α expression and mitochondrial biogenesis. Knockdown of PGC-1α almost completely abolished the neuroprotective roles of SIRT1 in SH-SY5Y cells. Collectively, our data indicate that SIRT1 has neuroprotective roles in dopaminergic neurons, which is dependent upon PGC-1α-mediated mitochondrial biogenesis. These findings suggest that SIRT1 may hold great therapeutic potentials for treating dopaminergic neuron loss associated disorders such as PD.
    Keywords:  Dopaminergic neurons; Mitochondrial biogenesis; PGC-1α; Parkinson’s disease; SIRT1
    DOI:  https://doi.org/10.1007/s12640-021-00392-4
  30. Cell Rep. 2021 Jul 13. pii: S2211-1247(21)00721-X. [Epub ahead of print]36(2): 109345
    SIRT4 is an early regulator of branched-chain amino acid catabolism that promotes adipogenesis.
    Elma Zaganjor, Haejin Yoon, Jessica B Spinelli, Elizabeth R Nunn, Gaëlle Laurent, Paulina Keskinidis, Suganja Sivaloganathan, Shakchhi Joshi, Giulia Notarangelo, Stacy Mulei, Mathew T Chvasta, Sarah A Tucker, Krystle Kalafut, Robert A H van de Ven, Clary B Clish, Marcia C Haigis.
      Upon nutrient stimulation, pre-adipocytes undergo differentiation to transform into mature adipocytes capable of storing nutrients as fat. We profiled cellular metabolite consumption to identify early metabolic drivers of adipocyte differentiation. We find that adipocyte differentiation raises the uptake and consumption of numerous amino acids. In particular, branched-chain amino acid (BCAA) catabolism precedes and promotes peroxisome proliferator-activated receptor gamma (PPARγ), a key regulator of adipogenesis. In early adipogenesis, the mitochondrial sirtuin SIRT4 elevates BCAA catabolism through the activation of methylcrotonyl-coenzyme A (CoA) carboxylase (MCCC). MCCC supports leucine oxidation by catalyzing the carboxylation of 3-methylcrotonyl-CoA to 3-methylglutaconyl-CoA. Sirtuin 4 (SIRT4) expression is decreased in adipose tissue of numerous diabetic mouse models, and its expression is most correlated with BCAA enzymes, suggesting a potential role for SIRT4 in adipose pathology through the alteration of BCAA metabolism. In summary, this work provides a temporal analysis of adipocyte differentiation and uncovers early metabolic events that stimulate transcriptional reprogramming.
    Keywords:  BCAA catabolism; MCCC; PPARg; SIRT4; adipogenesis; amino acids; differentiation; sirtuin
    DOI:  https://doi.org/10.1016/j.celrep.2021.109345
  31. Cell Death Dis. 2021 Jul 14. 12(7): 701
    ATF5, a putative therapeutic target for the mitochondrial DNA 3243A > G mutation-related disease.
    Xinpei Gao, Zhixin Jiang, Xinfeng Yan, Jiping Liu, Fengwen Li, Peng Liu, Jialu Li, Yuehua Wei, Yi Eve Sun, Yinan Zhang, Congrong Wang.
      The mitochondrial DNA m.3243A > G mutation is well-known to cause a variety of clinical phenotypes, including diabetes, deafness, and osteoporosis. Here, we report isolation and expansion of urine-derived stem cells (USCs) from patients carrying the m.3243A > G mutation, which demonstrate bimodal heteroplasmy. USCs with high levels of m.3243A > G mutation displayed abnormal mitochondrial morphology and function, as well as elevated ATF5-dependent mitochondrial unfolded protein response (UPRmt), together with reduced Wnt/β-catenin signaling and osteogenic potentials. Knockdown of ATF5 in mutant USCs suppressed UPRmt, improved mitochondrial function, restored expression of GSK3B and WNT7B, and rescued osteogenic potentials. These results suggest that ATF5-dependent UPRmt could be a core disease mechanism underlying mitochondrial dysfunction and osteoporosis related to the m.3243A > G mutation, and therefore could be a novel putative therapeutic target for this genetic disorder.
    DOI:  https://doi.org/10.1038/s41419-021-03993-1
  32. Curr Biol. 2021 Jul 12. pii: S0960-9822(21)00763-6. [Epub ahead of print]31(13): R859-R861
    Mechanometabolism: Mitochondria promote resilience under pressure.
    Thomas MacVicar, Thomas Langer.
      Mechanical forces regulate metabolism in healthy and cancerous tissue. A new study reveals that extracellular matrix stiffness modulates mitochondrial shape and function. The mechanical reprogramming of mitochondria confers resistance to oxidative stress and promotes survival.
    DOI:  https://doi.org/10.1016/j.cub.2021.05.065
  33. Biol Chem. 2021 Jul 27. 402(8): 925-935
    Prediction and analysis of redox-sensitive cysteines using machine learning and statistical methods.
    Marcus Keßler, Ilka Wittig, Jörg Ackermann, Ina Koch.
      Reactive oxygen species are produced by a number of stimuli and can lead both to irreversible intracellular damage and signaling through reversible post-translational modification. It is unclear which factors contribute to the sensitivity of cysteines to redox modification. Here, we used statistical and machine learning methods to investigate the influence of different structural and sequence features on the modifiability of cysteines. We found several strong structural predictors for redox modification. Sensitive cysteines tend to be characterized by higher exposure, a lack of secondary structure elements, and a high number of positively charged amino acids in their close environment. Our results indicate that modified cysteines tend to occur close to other post-translational modifications, such as phosphorylated serines. We used these features to create models and predict the presence of redox-modifiable cysteines in human mitochondrial complex I as well as make novel predictions regarding redox-sensitive cysteines in proteins.
    Keywords:  cysteine; human mitochondrial complex I; machine learning; post-translational modification; proteomics; redox
    DOI:  https://doi.org/10.1515/hsz-2020-0321
  34. Front Immunol. 2021 ;12 680648
    Circulating Mitochondrial DNA Stimulates Innate Immune Signaling Pathways to Mediate Acute Kidney Injury.
    Jiaye Liu, Zhanjun Jia, Wei Gong.
      Mitochondrial dysfunction is increasingly considered as a critical contributor to the occurrence and progression of acute kidney injury (AKI). However, the mechanisms by which damaged mitochondria mediate AKI progression are multifactorial and complicated. Mitochondrial DNA (mtDNA) released from damaged mitochondria could serve as a danger-associated molecular pattern (DAMP) and activate the innate immune system through STING, TLR9, NLRP3, and some other adaptors, and further mediate tubular cell inflammation and apoptosis. Accumulating evidence has demonstrated the important role of circulating mtDNA and its related pathways in the progression of AKI, and regulating the proteins involved in these pathways may be an effective strategy to reduce renal tubular injury and alleviate AKI. Here, we aim to provide a comprehensive overview of recent studies on mtDNA-mediated renal pathological events to provide new insights in the setting of AKI.
    Keywords:  NLRP3; STING; TLR9; acute kidney injury; mitochondrial DNA
    DOI:  https://doi.org/10.3389/fimmu.2021.680648
  35. Nat Metab. 2021 Jul 12.
    Cell competition acts as a purifying selection to eliminate cells with mitochondrial defects during early mouse development.
    Ana Lima, Gabriele Lubatti, Jörg Burgstaller, Di Hu, Alistair P Green, Aida Di Gregorio, Tamzin Zawadzki, Barbara Pernaute, Elmir Mahammadov, Salvador Perez-Montero, Marian Dore, Juan Miguel Sanchez, Sarah Bowling, Margarida Sancho, Thomas Kolbe, Mohammad M Karimi, David Carling, Nick Jones, Shankar Srinivas, Antonio Scialdone, Tristan A Rodriguez.
      Cell competition is emerging as a quality-control mechanism that eliminates unfit cells in a wide range of settings from development to the adult. However, the nature of the cells normally eliminated by cell competition and what triggers their elimination remains poorly understood. In mice, 35% of epiblast cells are eliminated before gastrulation. Here we show that cells with mitochondrial defects are eliminated by cell competition during early mouse development. Using single-cell transcriptional profiling of eliminated mouse epiblast cells, we identify hallmarks of cell competition and mitochondrial defects. We demonstrate that mitochondrial defects are common to a range of different loser cell types and that manipulating mitochondrial function triggers cell competition. Moreover, we show that in the mouse embryo, cell competition eliminates cells with sequence changes in mt-Rnr1 and mt-Rnr2, and that even non-pathological changes in mitochondrial DNA sequences can induce cell competition. Our results suggest that cell competition is a purifying selection that optimizes mitochondrial performance before gastrulation.
    DOI:  https://doi.org/10.1038/s42255-021-00422-7
  36. PLoS One. 2021 ;16(7): e0253926
    OCRbayes: A Bayesian hierarchical modeling framework for Seahorse extracellular flux oxygen consumption rate data analysis.
    Xiang Zhang, Taolin Yuan, Jaap Keijer, Vincent C J de Boer.
       BACKGROUND: Mitochondrial dysfunction is involved in many complex diseases. Efficient and accurate evaluation of mitochondrial functionality is crucial for understanding pathology as well as facilitating novel therapeutic developments. As a popular platform, Seahorse extracellular flux (XF) analyzer is widely used for measuring mitochondrial oxygen consumption rate (OCR) in living cells. A hidden feature of Seahorse XF OCR data is that it has a complex data structure, caused by nesting and crossing between measurement cycles, wells and plates. Surprisingly, statistical analysis of Seahorse XF data has not received sufficient attention, and current methods completely ignore the complex data structure, impairing the robustness of statistical inference.
    RESULTS: To rigorously incorporate the complex structure into data analysis, here we developed a Bayesian hierarchical modeling framework, OCRbayes, and demonstrated its applicability based on analysis of published data sets.
    CONCLUSIONS: We showed that OCRbayes can analyze Seahorse XF OCR experimental data derived from either single or multiple plates. Moreover, OCRbayes has potential to be used for diagnosing patients with mitochondrial diseases.
    DOI:  https://doi.org/10.1371/journal.pone.0253926
  37. Int Rev Cell Mol Biol. 2021 ;pii: S1937-6448(21)00062-9. [Epub ahead of print]362 111-140
    Mitochondrial calcium homeostasis in hematopoietic stem cell: Molecular regulation of quiescence, function, and differentiation.
    Massimo Bonora, Asrat Kahsay, Paolo Pinton.
      Hematopoiesis is based on the existence of hematopoietic stem cells (HSC) with the capacity to self-proliferate and self-renew or to differentiate into specialized cells. The hematopoietic niche is the essential microenvironment where stem cells reside and integrate various stimuli to determine their fate. Recent studies have identified niche containing high level of calcium (Ca2+) suggesting that HSCs are sensitive to Ca2+. This is a highly versatile and ubiquitous second messenger that regulates a wide variety of cellular functions. Advanced methods for measuring its concentrations, genetic experiments, cell fate tracing data, single-cell imaging, and transcriptomics studies provide information into its specific roles to integrate signaling into an array of mechanisms that determine HSC identity, lineage potential, maintenance, and self-renewal. Accumulating and contrasting evidence, are revealing Ca2+ as a previously unacknowledged feature of HSC, involved in functional maintenance, by regulating multiple actors including transcription and epigenetic factors, Ca2+-dependent kinases and mitochondrial physiology. Mitochondria are significant participants in HSC functions and their responsiveness to cellular demands is controlled to a significant extent via Ca2+ signals. Recent reports indicate that mitochondrial Ca2+ uptake also controls HSC fate. These observations reveal a physiological feature of hematopoietic stem cells that can be harnessed to improve HSC-related disease. In this review, we discuss the current knowledge Ca2+ in hematopoietic stem cell focusing on its potential involvement in proliferation, self-renewal and maintenance of HSC and discuss future research directions.
    Keywords:  AML; Ca(2+); Hematopoietic stem cell; MDS; Mitochondria; Preleukemia; Self-renewal
    DOI:  https://doi.org/10.1016/bs.ircmb.2021.05.003
  38. PLoS One. 2021 ;16(7): e0253849
    In vivo mitochondrial ATP production is improved in older adult skeletal muscle after a single dose of elamipretide in a randomized trial.
    Baback Roshanravan, Sophia Z Liu, Amir S Ali, Eric G Shankland, Chessa Goss, John K Amory, H Thomas Robertson, David J Marcinek, Kevin E Conley.
       BACKGROUND: Loss of mitochondrial function contributes to fatigue, exercise intolerance and muscle weakness, and is a key factor in the disability that develops with age and a wide variety of chronic disorders. Here, we describe the impact of a first-in-class cardiolipin-binding compound that is targeted to mitochondria and improves oxidative phosphorylation capacity (Elamipretide, ELAM) in a randomized, double-blind, placebo-controlled clinical trial.
    METHODS: Non-invasive magnetic resonance and optical spectroscopy provided measures of mitochondrial capacity (ATPmax) with exercise and mitochondrial coupling (ATP supply per O2 uptake; P/O) at rest. The first dorsal interosseous (FDI) muscle was studied in 39 healthy older adult subjects (60 to 85 yrs of age; 46% female) who were enrolled based on the presence of poorly functioning mitochondria. We measured volitional fatigue resistance by force-time integral over repetitive muscle contractions.
    RESULTS: A single ELAM dose elevated mitochondrial energetic capacity in vivo relative to placebo (ΔATPmax; P = 0.055, %ΔATPmax; P = 0.045) immediately after a 2-hour infusion. No difference was found on day 7 after treatment, which is consistent with the half-life of ELAM in human blood. No significant changes were found in resting muscle mitochondrial coupling. Despite the increase in ATPmax there was no significant effect of treatment on fatigue resistance in the FDI.
    CONCLUSIONS: These results highlight that ELAM rapidly and reversibly elevates mitochondrial capacity after a single dose. This response represents the first demonstration of a pharmacological intervention that can reverse mitochondrial dysfunction in vivo immediately after treatment in aging human muscle.
    DOI:  https://doi.org/10.1371/journal.pone.0253849
  39. Cureus. 2021 Jun;13(6): e15429
    Recognizing Subacute Combined Degeneration in Patients With Normal Vitamin B12 Levels.
    Brianna Burlock, Jason P Williams.
      Vitamin B12 deficiency is commonly associated with dementia in patients over the age of 65 years; however, it can affect people of all ages. Recognizing the clinical sequelae of subacute combined degeneration is essential for the timely diagnosis and treatment of vitamin B12 deficiency. In this report, we describe a case of a young man presenting with several months of neuropathy, depression, and abdominal symptoms. His initial vitamin B12 levels were within normal limits, but an elevated methylmalonic acid level and subacute combined degeneration of his spine on MRI confirmed the diagnosis of vitamin B12 deficiency. The patient later tested positive for autoantibodies associated with pernicious anemia. His symptoms improved with intramuscular injections of cyanocobalamin. This case highlights the importance of recognizing vitamin B12 deficiency in patients of all age groups even in the setting of apparently "normal" B12 levels.
    Keywords:  cobalamin deficiency; methylmalonic acid; pernicious-anemia; serum vitamin b12; subacute combined degeneration
    DOI:  https://doi.org/10.7759/cureus.15429
  40. Proc Natl Acad Sci U S A. 2021 Jul 20. pii: e2019498118. [Epub ahead of print]118(29):
    Deactivation blocks proton pathways in the mitochondrial complex I.
    Michael Röpke, Daniel Riepl, Patricia Saura, Andrea Di Luca, Max E Mühlbauer, Alexander Jussupow, Ana P Gamiz-Hernandez, Ville R I Kaila.
      Cellular respiration is powered by membrane-bound redox enzymes that convert chemical energy into an electrochemical proton gradient and drive the energy metabolism. By combining large-scale classical and quantum mechanical simulations with cryo-electron microscopy data, we resolve here molecular details of conformational changes linked to proton pumping in the mammalian complex I. Our data suggest that complex I deactivation blocks water-mediated proton transfer between a membrane-bound quinone site and proton-pumping modules, decoupling the energy-transduction machinery. We identify a putative gating region at the interface between membrane domain subunits ND1 and ND3/ND4L/ND6 that modulates the proton transfer by conformational changes in transmembrane helices and bulky residues. The region is perturbed by mutations linked to human mitochondrial disorders and is suggested to also undergo conformational changes during catalysis of simpler complex I variants that lack the "active"-to-"deactive" transition. Our findings suggest that conformational changes in transmembrane helices modulate the proton transfer dynamics by wetting/dewetting transitions and provide important functional insight into the mammalian respiratory complex I.
    Keywords:  QM/MM; bioenergetics; cell respiration; cryoEM; molecular simulations
    DOI:  https://doi.org/10.1073/pnas.2019498118
  41. J Neurosci. 2021 Jul 16. pii: JN-RM-0900-21. [Epub ahead of print]
    Schwann cells provide iron to axonal mitochondria and its role in nerve regeneration.
    Bruno Siqueira Mietto, Priya Jhelum, Katrin Schulz, Samuel David.
      Iron is an essential co-factor for several metabolic processes, including the generation of adenosine triphosphate (ATP) in mitochondria, which is required for axonal function and regeneration. However, it is not known how mitochondria in long axons, such as those in sciatic nerves, acquire iron in vivo Due to their close proximity to axons, Schwann cells (SCs) are a likely source of iron for axonal mitochondria in the peripheral nervous system. Here we demonstrate the critical role of iron in promoting neurite growth in vitro using iron chelation. We also show that SCs express the molecular machinery to release iron, namely, the iron exporter, ferroportin (Fpn) and the ferroxidase ceruloplasmin (Cp). In Cp knockout (KO) mice, SCs accumulate iron, because Fpn requires to partner with Cp to export iron. Axons and SCs also express the iron importer transferrin receptor 1 (TfR1), indicating their ability for iron uptake. In teased nerve fibers, Fpn and TfR1 are predominantly localized at the nodes of Ranvier (NR) and Schmidt-Lanterman incisures (SLIs), axonal sites that are in close contact with SC cytoplasm. We also show that lack of iron export from SCs in Cp KO mice reduces mitochondrial iron in axons as detected by reduction in mitochondrial ferritin, affects localization of axonal mitochondria at the NR and SLIs, and impairs axonal regeneration following sciatic nerve injury. These finding suggest that SCs contribute to the delivery of iron to axonal mitochondria, required for proper nerve repair.Significance StatementThis work addresses how and where mitochondria in long axons in peripheral nerves acquire iron. We show that Schwann cells (SCs) are a likely source as they express the molecular machinery to import iron (transferrin receptor 1), and to export iron (ferroportin and ceruloplasmin (Cp)) to the axonal compartment at the nodes of Ranvier (NR) and Schmidt-Lanterman incisures (SLIs). Cp knockout (CpKO) mice, which cannot export iron from SC, show reduced iron content in axonal mitochondria, along with increased localization of axonal mitochondria at SLIs and NR, and impaired sciatic nerve regeneration. Iron chelation in vitro also drastically reduces neurite growth. These data suggest that SC are likely to contribute iron to axonal mitochondria needed for axon growth and regeneration.
    DOI:  https://doi.org/10.1523/JNEUROSCI.0900-21.2021
  42. Cell Death Dis. 2021 Jul 15. 12(7): 711
    Effect of the mitochondrial unfolded protein response on hypoxic death and mitochondrial protein aggregation.
    Junyi Yan, Chun-Ling Sun, Seokyung Shin, Marc Van Gilst, C Michael Crowder.
      Mitochondria are the main oxygen consumers in cells and as such are the primary organelle affected by hypoxia. All hypoxia pathology presumably derives from the initial mitochondrial dysfunction. An early event in hypoxic pathology in C. elegans is disruption of mitochondrial proteostasis with induction of the mitochondrial unfolded protein response (UPRmt) and mitochondrial protein aggregation. Here in C. elegans, we screen through RNAis and mutants that confer either strong resistance to hypoxic cell death or strong induction of the UPRmt to determine the relationship between hypoxic cell death, UPRmt activation, and hypoxia-induced mitochondrial protein aggregation (HIMPA). We find that resistance to hypoxic cell death invariantly mitigated HIMPA. We also find that UPRmt activation invariantly mitigated HIMPA. However, UPRmt activation was neither necessary nor sufficient for resistance to hypoxic death and vice versa. We conclude that UPRmt is not necessarily hypoxia protective against cell death but does protect from mitochondrial protein aggregation, one of the early hypoxic pathologies in C. elegans.
    DOI:  https://doi.org/10.1038/s41419-021-03979-z
  43. Nat Commun. 2021 07 09. 12(1): 4203
    Single-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms in cardiomyocytes.
    Chenchen Zhu, Jingyan Wu, Han Sun, Francesca Briganti, Benjamin Meder, Wu Wei, Lars M Steinmetz.
      Alternative splicing generates differing RNA isoforms that govern phenotypic complexity of eukaryotes. Its malfunction underlies many diseases, including cancer and cardiovascular diseases. Comparative analysis of RNA isoforms at the genome-wide scale has been difficult. Here, we establish an experimental and computational pipeline that performs de novo transcript annotation and accurately quantifies transcript isoforms from cDNA sequences with a full-length isoform detection accuracy of 97.6%. We generate a searchable, quantitative human transcriptome annotation with 31,025 known and 5,740 novel transcript isoforms ( http://steinmetzlab.embl.de/iBrowser/ ). By analyzing the isoforms in the presence of RNA Binding Motif Protein 20 (RBM20) mutations associated with aggressive dilated cardiomyopathy (DCM), we identify 121 differentially expressed transcript isoforms in 107 cardiac genes. Our approach enables quantitative dissection of complex transcript architecture instead of mere identification of inclusion or exclusion of individual exons, as exemplified by the discovery of IMMT isoforms mis-spliced by RBM20 mutations. Thereby we achieve a path to direct differential expression testing independent of an existing annotation of transcript isoforms, providing more immediate biological interpretation and higher resolution transcriptome comparisons.
    DOI:  https://doi.org/10.1038/s41467-021-24484-z
  44. NPJ Genom Med. 2021 Jul 15. 6(1): 60
    Effective variant filtering and expected candidate variant yield in studies of rare human disease.
    Brent S Pedersen, Joe M Brown, Harriet Dashnow, Amelia D Wallace, Matt Velinder, Martin Tristani-Firouzi, Joshua D Schiffman, Tatiana Tvrdik, Rong Mao, D Hunter Best, Pinar Bayrak-Toydemir, Aaron R Quinlan.
      In studies of families with rare disease, it is common to screen for de novo mutations, as well as recessive or dominant variants that explain the phenotype. However, the filtering strategies and software used to prioritize high-confidence variants vary from study to study. In an effort to establish recommendations for rare disease research, we explore effective guidelines for variant (SNP and INDEL) filtering and report the expected number of candidates for de novo dominant, recessive, and autosomal dominant modes of inheritance. We derived these guidelines using two large family-based cohorts that underwent whole-genome sequencing, as well as two family cohorts with whole-exome sequencing. The filters are applied to common attributes, including genotype-quality, sequencing depth, allele balance, and population allele frequency. The resulting guidelines yield ~10 candidate SNP and INDEL variants per exome, and 18 per genome for recessive and de novo dominant modes of inheritance, with substantially more candidates for autosomal dominant inheritance. For family-based, whole-genome sequencing studies, this number includes an average of three de novo, ten compound heterozygous, one autosomal recessive, four X-linked variants, and roughly 100 candidate variants following autosomal dominant inheritance. The slivar software we developed to establish and rapidly apply these filters to VCF files is available at https://github.com/brentp/slivar under an MIT license, and includes documentation and recommendations for best practices for rare disease analysis.
    DOI:  https://doi.org/10.1038/s41525-021-00227-3
  45. Front Neurol. 2021 ;12 677551
    The ARCA Registry: A Collaborative Global Platform for Advancing Trial Readiness in Autosomal Recessive Cerebellar Ataxias.
    PREPARE Consortium
      Autosomal recessive cerebellar ataxias (ARCAs) form an ultrarare yet expanding group of neurodegenerative multisystemic diseases affecting the cerebellum and other neurological or non-neurological systems. With the advent of targeted therapies for ARCAs, disease registries have become a precious source of real-world quantitative and qualitative data complementing knowledge from preclinical studies and clinical trials. Here, we review the ARCA Registry, a global collaborative multicenter platform (>15 countries, >30 sites) with the overarching goal to advance trial readiness in ARCAs. It presents a good clinical practice (GCP)- and general data protection regulation (GDPR)-compliant professional-reported registry for multicenter web-based capture of cross-center standardized longitudinal data. Modular electronic case report forms (eCRFs) with core, extended, and optional datasets allow data capture tailored to the participating site's variable interests and resources. The eCRFs cover all key data elements required by regulatory authorities [European Medicines Agency (EMA)] and the European Rare Disease (ERD) platform. They capture genotype, phenotype, and progression and include demographic data, biomarkers, comorbidity, medication, magnetic resonance imaging (MRI), and longitudinal clinician- or patient-reported ratings of ataxia severity, non-ataxia features, disease stage, activities of daily living, and (mental) health status. Moreover, they are aligned to major autosomal-dominant spinocerebellar ataxia (SCA) and sporadic ataxia (SPORTAX) registries in the field, thus allowing for joint and comparative analyses not only across ARCAs but also with SCAs and sporadic ataxias. The registry is at the core of a systematic multi-component ARCA database cluster with a linked biobank and an evolving study database for digital outcome measures. Currently, the registry contains more than 800 patients with almost 1,500 visits representing all ages and disease stages; 65% of patients with established genetic diagnoses capture all the main ARCA genes, and 35% with unsolved diagnoses are targets for advanced next-generation sequencing. The ARCA Registry serves as the backbone of many major European and transatlantic consortia, such as PREPARE, PROSPAX, and the Ataxia Global Initiative, with additional data input from SPORTAX. It has thus become the largest global trial-readiness registry in the ARCA field.
    Keywords:  ataxia; natural history; network; registry; trial readiness
    DOI:  https://doi.org/10.3389/fneur.2021.677551
  46. Neurobiol Aging. 2021 Jun 16. pii: S0197-4580(21)00198-6. [Epub ahead of print]
    Analysis of PTRHD1 common and rare variants in European patients with Parkinson's disease.
    IPDGC
      Three studies in Iranian and African families identified three different variants in the peptidyl-tRNA hydrolase domain containing 1 gene (PTRHD1) in patients affected by parkinsonism with intellectual impairment. In the current study, our objective was to investigate whether PTRHD1 variants are associated with Parkinson's disease (PD) risk and age at onset (AAO). To evaluate the association between PTRHD1 and PD risk, we analyzed whole genome sequencing data of 1647 PD cases and 1050 healthy controls, as well as genome-wide imputed genotyping data on 14,671 PD cases and 17,667 controls, all of European ancestry. Furthermore, we examined the association of PTRHD1 with PD risk and AAO using summary statistics data from the most recent PD genome-wide association study meta-analyses. Our results show no association between PTRHD1 and PD risk or AAO. We conclude that PTRHD1 does not play a major role in PD in the European population. Further large-scale studies including subjects with different ancestry and family trios are required.
    Keywords:  Burden test; Familial parkinsonism; GWAS; PTRHD1; Parkinson's disease; SKATO
    DOI:  https://doi.org/10.1016/j.neurobiolaging.2021.06.005
  47. Eur J Neurol. 2021 Jul 13.
    Genotype and phenotype distribution of 435 patients with Charcot-Marie-Tooth disease from Central South China.
    Yongzhi Xie, Zhiqiang Lin, Lei Liu, Xiaobo Li, Shunxiang Huang, Huadong Zhao, Wang Binghao, Sen Zeng, Wanqian Cao, Lu Li, Xiying Zhu, Siwei Huang, Honglan Yang, Mengli Wang, Zhengmao Hu, Junling Wang, Jifeng Guo, Lu Shen, Hong Jiang, Stephan Zuchner, Beisha Tang, Ruxu Zhang.
       OBJECTIVE: To provide an overview of genotype and phenotype distribution in a cohort of patients with Charcot-Marie-Tooth disease (CMT) and related disorders from Central South China.
    METHODS: We enrolled 435 patients and collected detailed clinical data. Multiplex ligation-dependent probe amplification for PMP22 duplication/deletion and CMT multi-gene panels sequencing were performed. Whole-exome sequencing was further applied in the remaining patients who failed to achieve molecular diagnosis.
    RESULTS: Among the 435 patients, 216 had CMT1, 14 had HNPP, 178 had CMT2, 24 had dHMN and 3 had HSAN. The overall molecular diagnosis rate was 70%: 75.7% in CMT1, 100% in HNPP, 64.6% in CMT2, 41.7% in dHMN, and 33.3% in HSAN. The most common four genotypes accounted for 68.9% of molecular diagnosed patients. Relatively frequent causes were missense changes in PMP22 (4.6%) and SH3TC2 (2.3%) in CMT1; and GDAP1 (5.1%), IGHMBP2 (4.5%) and MORC2 (3.9%) in CMT2. Twenty out of 160 detected pathogenic variants and the associated phenotypes were not previously reported. Broad phenotype spectra were observed in six genes, among which the pathogenic variants in BAG3 and SPTLC1 were detected in two sporadic patients presenting with CMT2 phenotype.
    CONCLUSIONS: Our results provided a unique genotypic and phenotypic landscape of patients with CMT and related disorders from Central South China, including relatively high proportion of CMT2 and lower occurrence of PMP22 duplication. The broad phenotype spectra in certain genes advanced our understanding of CMT.
    Keywords:  Charcot-Marie-Tooth disease; genotype-phenotype distribution; onset age analysis; phenotype spectra
    DOI:  https://doi.org/10.1111/ene.15024
  48. Oxid Med Cell Longev. 2021 ;2021 9986299
    Changes in Key Mitochondrial Lipids Accompany Mitochondrial Dysfunction and Oxidative Stress in NAFLD.
    Manon Durand, Marine Coué, Mikaël Croyal, Thomas Moyon, Angela Tesse, Florian Atger, Khadija Ouguerram, David Jacobi.
      Nonalcoholic fatty liver disease (NAFLD) is a dysmetabolic hepatic damage of increasing severity: simple fat accumulation (steatosis), nonalcoholic steatohepatitis (NASH), and hepatic fibrosis. Oxidative stress is considered an important factor in producing hepatocyte injury associated with NAFLD progression. Studies also suggest a link between the accumulation of specific hepatic lipid species, mitochondrial dysfunction, and the progression of NAFLD. However, it is unclear whether mitochondrial lipid modifications are involved in NAFLD progression. To gain insight into the relationship between mitochondrial lipids and disease progression through different stages of NAFLD, we performed lipidomic analyses on mouse livers at different stages of western diet-induced NAFLD, with or without hepatic fibrosis. After organelle separation, we studied separately the mitochondrial and the "nonmitochondrial" hepatic lipidomes. We identified 719 lipid species from 16 lipid families. Remarkably, the western diet triggered time-dependent changes in the mitochondrial lipidome, whereas the "nonmitochondrial" lipidome showed little difference with levels of hepatic steatosis or the presence of fibrosis. In mitochondria, the changes in the lipidome preceded hepatic fibrosis. In particular, two critical phospholipids, phosphatidic acid (PA) and cardiolipin (CL), displayed opposite responses in mitochondria. Decrease in CL and increase in PA were concurrent with an increase of coenzyme Q. Electron paramagnetic resonance spectroscopy superoxide spin trapping and Cu2+ measurement showed the progressive increase in oxidative stress in the liver. Overall, these results suggest mitochondrial lipid modifications could act as an early event in mitochondrial dysfunction and NAFLD progression.
    DOI:  https://doi.org/10.1155/2021/9986299
  49. Trends Genet. 2021 Jul 06. pii: S0168-9525(21)00145-1. [Epub ahead of print]
    Genetic prediction of complex traits with polygenic scores: a statistical review.
    Ying Ma, Xiang Zhou.
      Accurate genetic prediction of complex traits can facilitate disease screening, improve early intervention, and aid in the development of personalized medicine. Genetic prediction of complex traits requires the development of statistical methods that can properly model polygenic architecture and construct a polygenic score (PGS). We present a comprehensive review of 46 methods for PGS construction. We connect the majority of these methods through a multiple linear regression framework which can be instrumental for understanding their prediction performance for traits with distinct genetic architectures. We discuss the practical considerations of PGS analysis as well as challenges and future directions of PGS method development. We hope our review serves as a useful reference both for statistical geneticists who develop PGS methods and for data analysts who perform PGS analysis.
    Keywords:  complex traits; genetic prediction; genome-wide association studies; polygenic risk scores; polygenic scores; statistical methods
    DOI:  https://doi.org/10.1016/j.tig.2021.06.004
  50. Angew Chem Int Ed Engl. 2021 Jun 11.
    Shadow Electrochemiluminescence Microscopy of Single Mitochondria.
    Yumeng Ma, Camille Colin, Julie Descamps, Stéphane Arbault, Neso Sojic.
      Mitochondria are the subcellular bioenergetic organelles. The analysis of their morphology and topology is essential to provide useful information on their activity and metabolism. Herein, we report a label-free shadow electrochemiluminescence (ECL) microscopy based on the spatial confinement of the ECL-emitting reactive layer to image single living mitochondria deposited on the electrode surface. The ECL mechanism of the freely-diffusing [Ru(bpy)3 ]2+ dye with the sacrificial tri-n-propylamine coreactant restrains the light-emitting region to a micrometric thickness allowing to visualize individual mitochondria with a remarkable sharp negative optical contrast. The imaging approach named "shadow ECL" (SECL) reflects the negative imprint of the local diffusional hindrance of the ECL reagents by each mitochondrion. The statistical analysis of the colocalization of the shadow ECL spots with the functional mitochondria revealed by classical fluorescent biomarkers, MitoTracker Deep Red and the endogenous intramitochondrial NADH, validates the reported methodology. The versatility and extreme sensitivity of the approach are further demonstrated by visualizing single mitochondria, which remain hardly detectable with the usual biomarkers. Finally, by alleviating problems of photobleaching and phototoxicity associated with conventional microscopy methods, SECL microscopy should find promising applications in the imaging of subcellular structures.
    Keywords:  bioelectrochemistry; electrochemiluminescence; mechanism; microscopy; mitochondria
    DOI:  https://doi.org/10.1002/anie.202105867
  51. Am J Med Genet C Semin Med Genet. 2021 Jul 16.
    Frequency of carriers for rare recessive Mendelian diseases in a Brazilian cohort of 320 patients.
    Caio Robledo D'Angioli Costa Quaio, Christine Hsiaoyun Chung, Sandro Felix Perazzio, Aurelio Pimenta Dutra, Caroline Monaco Moreira, Gil Monteiro Novo Filho, Patricia Rossi Sacramento-Bobotis, Michele Groenner Penna, Rafaela Rogerio Floriano de Souza, Vivian Pedigone Cintra, Juliana Emilia Prior Carnavalli, Rafael Alves da Silva, Daniele Paixão, Wagner Antonio da Rosa Baratela, Caroline Olivati, Gustavo Marquezani Spolador, Monize Nakamoto Provisor Santos, Maria Carolina Pintao, Alexandre Ricardo Dos Santos Fornari, Matheus Burger, Rodrigo Fernandes Ramalho, Otavio Jose Eulalio Pereira, Elisa Napolitano E Ferreira, Miguel Mitne-Neto, Chong Ae Kim.
      Several Mendelian disorders follow an autosomal recessive inheritance pattern. Epidemiological information on many inherited disorders may be useful to guide health policies for rare diseases, but it is often inadequate, particularly in developing countries. We aimed to calculate the carrier frequencies of rare autosomal recessive Mendelian diseases in a cohort of Brazilian patients using whole exome sequencing (WES). We reviewed the molecular findings of WES from 320 symptomatic patients who had carrier status for recessive diseases. Using the Hardy-Weinberg equation, we estimated recessive disease frequencies (q2 ) considering the respective carrier frequencies (2pq) observed in our study. We calculated the sensitivity of carrier screening tests based on lists of genes from five different clinical laboratories that offer them in Brazil. A total of 425 occurrences of 351 rare variants were reported in 278 different genes from 230 patients (71.9%). Almost half (48.8%) were carriers of at least one heterozygous pathogenic/likely pathogenic variant for rare metabolic disorders, while 25.9% of epilepsy, 18.1% of intellectual disabilities, 15.6% of skeletal disorders, 10.9% immune disorders, and 9.1% of hearing loss. We estimated that an average of 67% of the variants would not have been detected by carrier screening panels. The combined frequencies of autosomal recessive diseases were estimated to be 26.39/10,000 (or ~0.26%). This study shows the potential research utility of WES to determine carrier status, which may be a possible strategy to evaluate the clinical and social burden of recessive diseases at the population level and guide the optimization of carrier screening panels.
    Keywords:  carrier; carrier frequency; next-generation sequencing; rare diseases; recessive Mendelian diseases; whole exome sequencing
    DOI:  https://doi.org/10.1002/ajmg.c.31932
  52. Transl Med Aging. 2021 ;5 17-30
    The regulation of healthspan and lifespan by dietary amino acids.
    Reji Babygirija, Dudley W Lamming.
      As a key macronutrient and source of essential macromolecules, dietary protein plays a significant role in health. For many years, protein-rich diets have been recommended as healthy due to the satiety-inducing and muscle-building effects of protein, as well as the ability of protein calories to displace allegedly unhealthy calories from fats and carbohydrates. However, clinical studies find that consumption of dietary protein is associated with an increased risk of multiple diseases, especially diabetes, while studies in rodents have demonstrated that protein restriction can promote metabolic health and even lifespan. Emerging evidence suggests that the effects of dietary protein on health and longevity are not mediated simply by protein quantity but are instead mediated by protein quality - the specific amino acid composition of the diet. Here, we discuss how dietary protein and specific amino acids including methionine, the branched chain amino acids (leucine, isoleucine, and valine), tryptophan and glycine regulate metabolic health, healthspan, and aging, with attention to the specific molecular mechanisms that may participate in these effects. Finally, we discuss the potential applicability of these findings to promoting healthy aging in humans.
    Keywords:  aging; amino acids; branched-chain amino acids; methionine; protein restriction
    DOI:  https://doi.org/10.1016/j.tma.2021.05.001
  53. PLoS One. 2021 ;16(7): e0253987
    Mutation spectrum of the OPA1 gene in a large cohort of patients with suspected dominant optic atrophy: Identification and classification of 48 novel variants.
    Nicole Weisschuh, Simone Schimpf-Linzenbold, Pascale Mazzola, Sinja Kieninger, Ting Xiao, Ulrich Kellner, Teresa Neuhann, Carina Kelbsch, Felix Tonagel, Helmut Wilhelm, Susanne Kohl, Bernd Wissinger.
      Autosomal dominant optic atrophy is one of the most common inherited optic neuropathies. This disease is genetically heterogeneous, but most cases are due to pathogenic variants in the OPA1 gene: depending on the population studied, 32-90% of cases harbor pathogenic variants in this gene. The aim of this study was to provide a comprehensive overview of the entire spectrum of likely pathogenic variants in the OPA1 gene in a large cohort of patients. Over a period of 20 years, 755 unrelated probands with a diagnosis of bilateral optic atrophy were referred to our laboratory for molecular genetic investigation. Genetic testing of the OPA1 gene was initially performed by a combined analysis using either single-strand conformation polymorphism or denaturing high performance liquid chromatography followed by Sanger sequencing to validate aberrant bands or melting profiles. The presence of copy number variations was assessed using multiplex ligation-dependent probe amplification. Since 2012, genetic testing was based on next-generation sequencing platforms. Genetic screening of the OPA1 gene revealed putatively pathogenic variants in 278 unrelated probands which represent 36.8% of the entire cohort. A total of 156 unique variants were identified, 78% of which can be considered null alleles. Variant c.2708_2711del/p.(V903Gfs*3) was found to constitute 14% of all disease-causing alleles. Special emphasis was placed on the validation of splice variants either by analyzing cDNA derived from patients´ blood samples or by heterologous splice assays using minigenes. Splicing analysis revealed different aberrant splicing events, including exon skipping, activation of exonic or intronic cryptic splice sites, and the inclusion of pseudoexons. Forty-eight variants that we identified were novel. Nine of them were classified as pathogenic, 34 as likely pathogenic and five as variant of uncertain significance. Our study adds a significant number of novel variants to the mutation spectrum of the OPA1 gene and will thereby facilitate genetic diagnostics of patients with suspected dominant optic atrophy.
    DOI:  https://doi.org/10.1371/journal.pone.0253987
  54. J Physiol. 2021 Jul 16.
    Regulation of muscle and mitochondrial health by the mitochondrial fission protein Drp1 in aged mice.
    Maude Dulac, Jean-Philippe Leduc-Gaudet, Marina Cefis, Marie-Belle Ayoub, Olivier Reynaud, Anwar Shams, Alaa Moamer, Marcos Francisco Nery Ferreira, Sabah Na Hussain, Gilles Gouspillou.
       KEY POINTS: The maintenance of mitochondrial integrity is critical for skeletal muscle health. Mitochondrial dynamics play key roles in mitochondrial quality control; however, the exact role that mitochondrial fission plays in the muscle aging process remains unclear. Here we report that both Drp1 knockdown and overexpression late in life in mice is detrimental to skeletal muscle function and mitochondrial health. Drp1 knockdown in 18-month-old mice resulted in severe skeletal muscle atrophy, mitochondrial dysfunction, muscle degeneration/regeneration, oxidative stress, and impaired autophagy. Overexpressing Drp1 in 18-month-old mice resulted in mild skeletal muscle atrophy and decreased mitochondrial quality. Our data indicate that silencing or overexpressing Drp1 late in life is detrimental to skeletal muscle integrity. We conclude that modulating Drp1 expression is unlikely to be a viable approach to counter the muscle aging process.
    ABSTRACT: Sarcopenia, the aging-related loss of skeletal muscle mass and function, is a debilitating process negatively impacting s the quality of life of afflicted individuals. Although the mechanisms underlying sarcopenia are still only partly understood, impairments in mitochondrial dynamics, and specifically mitochondrial fission, have been proposed as an underlying mechanism. Importantly, conflicting data exist in the field and both excessive and insufficient mitochondrial fission were proposed to contribute to sarcopenia. In D. Melanogaster, enhancing mitochondrial fission in midlife through overexpression of dynamin-1-like protein (Drp1) extended lifespan and attenuated several key hallmarks of muscle aging. Whether a similar outcome of Drp1 overexpression is observed in mammalian muscles remains unknown. In this study, we investigated the impact of knocking down and overexpressing Drp1 protein for 4 months in skeletal muscles of late middle-aged (18 months) mice using intra-muscular injections of adeno-associated viruses expressing shRNA targeting Drp1 or full Drp1 cDNA. We report that knocking down Drp1 expression late in life triggers severe muscle atrophy, mitochondrial dysfunctions, degeneration/regeneration, oxidative stress and impaired autophagy. Drp1 overexpression late in life triggered mild muscle atrophy and decreased mitochondrial quality. Taken altogether, our results indicate that both overexpression or silencing Drp1 in late middle-aged mice negatively impact skeletal muscle mass and mitochondrial health. These data suggest that Drp1 content must remain within a narrow physiological range to preserve muscle and mitochondrial integrity during aging. Altering Drp1 expression is therefore unlikely to be a viable target to counter sarcopenia. This article is protected by copyright. All rights reserved.
    Keywords:  autophagy; mitochondrial dynamics; mitochondrial fission; myopathic phenotype; oxidative stress; skeletal muscle aging; skeletal muscle atrophy
    DOI:  https://doi.org/10.1113/JP281752
  55. Pediatr Transplant. 2021 Jul 15. e14091
    Outcomes of liver transplantation for mitochondrial respiratory chain disorder in children.
    Hajime Uchida, Seisuke Sakamoto, Seiichi Shimizu, Yusuke Yanagi, Akinari Fukuda, Reiko Horikawa, Reiko Ito, Ayako Matsunaga, Kei Murayama, Mureo Kasahara.
       AIM: Mitochondrial respiratory chain disorder (MRCD) can cause acute liver failure (ALF), which may necessitate liver transplantation (LT). However, MRCD is often difficult to diagnose before LT and the indications of LT are controversial due to the likelihood of progressive neurological disease. The present study further characterized the patient population and described the outcomes.
    METHODS: Thirteen patients who underwent LT for MRCD from November 2005 to May 2020 were enrolled in this study.
    RESULTS: Six of 13 MRCD patients were diagnosed with a mitochondrial inner membrane protein 17-related mitochondrial DNA depletion syndrome (MTDPS). Overall, nine survived with a median follow-up of 1.8 years (IQR, 1.3-5.1 years); four died within 2 years. In the long-term, seven survivors showed no progression of hypotonia after LT and attended a normal kindergarten or primary school. Neurological abnormalities were observed in two survivors, including vison loss related to Leber's hereditary optic neuropathy in one patient and psychomotor retardation related to Leigh syndrome in the other. Three non-survivors after LT were diagnosed with MTDPS and died of severe pulmonary hypertension, which had developed at 8, 9, and 18 months after LT (n=1 each). The remaining patient died of postoperative respiratory infection with respiratory syncytial virus.
    CONCLUSION: The long-term results support the performance of LT in patients with MRCD, although a genetic diagnosis is preferable for determining the accurate indications for LT in these patients. Furthermore, care should be taken to avoid complications due to mitochondrial dysfunction during the long-term follow-up.
    Keywords:  acute liver failure; mitochondrial respiratory chain disorder; pediatric liver transplantation
    DOI:  https://doi.org/10.1111/petr.14091
  56. AJNR Am J Neuroradiol. 2021 Jul;42(7): 1334-1340
    Imaging Patterns Characterizing Mitochondrial Leukodystrophies.
    S D Roosendaal, T van de Brug, C A P F Alves, S Blaser, A Vanderver, N I Wolf, M S van der Knaap.
       BACKGROUND AND PURPOSE: Achieving a specific diagnosis in leukodystrophies is often difficult due to clinical and genetic heterogeneity. Mitochondrial defects cause 5%-10% of leukodystrophies. Our objective was to define MR imaging features commonly shared by mitochondrial leukodystrophies and to distinguish MR imaging patterns related to specific genetic defects.
    MATERIALS AND METHODS: One hundred thirty-two patients with a mitochondrial leukodystrophy with known genetic defects were identified in the data base of the Amsterdam Leukodystrophy Center. Numerous anatomic structures were systematically assessed on brain MR imaging. Additionally, lesion characteristics were scored. Statistical group analysis was performed for 57 MR imaging features by hierarchic testing on clustered genetic subgroups.
    RESULTS: MR imaging features indicative of mitochondrial disease that were frequently found included white matter rarefaction (n = 50 patients), well-delineated cysts (n = 20 patients), T2 hyperintensity of the middle blade of the corpus callosum (n = 85 patients), and symmetric abnormalities in deep gray matter structures (n = 42 patients). Several disorders or clusters of disorders had characteristic features. The combination of T2 hyperintensity in the brain stem, middle cerebellar peduncles, and thalami was associated with complex 2 deficiency. Predominantly periventricular localization of T2 hyperintensities and cystic lesions with a distinct border was associated with defects in complexes 3 and 4. T2-hyperintense signal of the cerebellar cortex was specifically associated with variants in the gene NUBPL. T2 hyperintensities predominantly affecting the directly subcortical cerebral white matter, globus pallidus, and substantia nigra were associated with Kearns-Sayre syndrome.
    CONCLUSIONS: In a large group of patients with a mitochondrial leukodystrophy, general MR imaging features suggestive of mitochondrial disease were found. Additionally, we identified several MR imaging patterns correlating with specific genotypes. Recognition of these patterns facilitates the diagnosis in future patients.
    DOI:  https://doi.org/10.3174/ajnr.A7097
  57. Neurol Sci. 2021 Jul 15.
    A new phenotype of MT-ND6 gene mutation for Leber's hereditary optic neuropathy.
    Chaeyeon Lee, Ja-Hyun Jang, Kyung-Ah Park, Ga-In Lee, Sei Yeul Oh.
      
    DOI:  https://doi.org/10.1007/s10072-021-05405-w
  58. Cureus. 2021 Jun;13(6): e15487
    Stroke-Like Lesion in an m.3243A>G Carrier Presenting as Hyperperfusion and Hypometabolism.
    Josef Finsterer, Martina Kudlacek, Siroos Mirzaei.
      Carriers of the m.3243A>G variant typically manifest with stroke-like episodes (SLEs), of which the morphological correlate on imaging is the stroke-like lesion (SLL). The pathophysiology of SLLs is poorly understood but acute and chronic stages are delineated. Here we present the case of an m.3243A>G carrier who presented with hypometabolism during his second SLL. The patient was a 56-year-old male who was diagnosed with MELAS (mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes) at the age of 50 upon a third SLE, muscle biopsy, and the detection of the m.3243A>G variant in the muscle. A fluorodeoxyglucose-positron emission tomography (FDG-PET) during the second SLE revealed hypometabolism in the occipital lobes bilaterally. The patient was misdiagnosed for years and was repeatedly exposed to mitochondrion-toxic drugs (metformin, steroids, valproic acid, oxcarbazepine, zolpidem). The previous data and the present findings indicate that the hypometabolism on FDG-PET together with reduced oxygen-extraction fraction (OEF) on OEF-MRI and hyperperfusion on perfusion-weighted imaging (PWI) characterise best the acute stage of an SLL. In conclusion, an acute SLE in m.3243A>G carriers typically manifests with a mismatch between hyperperfusion on PWI or single-photon emission computed tomography (SPECT) and hypometabolism on FDG-PET and hypointensity on OEF-MRI. Since SLEs are not vascular events, they should be managed by a multispecialist approach and not by general or stroke neurologists.
    Keywords:  m.3243a>g; melas; mtdna; multisystem; stroke-like epsuode
    DOI:  https://doi.org/10.7759/cureus.15487
  59. Adv Exp Med Biol. 2021 ;1332 129-149
    Interorgan Metabolism of Amino Acids in Human Health and Disease.
    Patrick J Ryan, Steven E Riechman, James D Fluckey, Guoyao Wu.
      Amino acids are integral for human health, influencing an array of physiological processes from gene expression to vasodilation to the immune response. In accordance with this expansive range of unique functions, the tissues of the body engage in a complex interplay of amino acid exchange and metabolism to respond to the organism's dynamic needs for a range of nitrogenous products. Interorgan amino acid metabolism is required for numerous metabolic pathways, including the synthesis of functional amino acids like arginine, glutamate, glutamine, and glycine. This physiological process requires the cooperative handling of amino acids by organs (e.g., the small intestine, skeletal muscle, kidneys, and liver), as well as the complete catabolism of nutritionally essential amino acids such as the BCAAs, with their α-ketoacids shuttled from muscle to liver. These exchanges are made possible by several mechanisms, including organ location, as well as the functional zonation of enzymes and the cell-specific expression of amino acid transporters. The cooperative handling of amino acids between the various organs does not appear to be under the control of any centralized regulation, but is instead influenced by factors such as fluctuations in nutrient availability, hormones, changes associated with development, and altered environmental factors. While the normal function of these pathways is associated with health and homeostasis, affected by physical activity, diet and body composition, dysregulation is observed in numerous disease states, including cardiovascular disease and cancer cachexia, presenting potential avenues for the manipulation of amino acid consumption as part of the therapeutic approach to these conditions in individuals.
    Keywords:  Amino acids; Diets; Diseases; Exercise; Health; Humans; Supplementation
    DOI:  https://doi.org/10.1007/978-3-030-74180-8_8
  60. Sci Rep. 2021 Jul 12. 11(1): 14291
    Mitofusion is required for MOTS-c induced GLUT4 translocation.
    Khushwant S Bhullar, Nan Shang, Evan Kerek, Kaiyu Wu, Jianping Wu.
      MOTS-c (mitochondrial ORF of the twelve S-c) is a 16-amino-acid mitochondrial peptide that has been shown to counter insulin resistance and alleviate obesity in vivo. However, the mechanisms involved in the pharmacological action of MOTS-c remain elusive. Based on the ability of MOTS-c to improve insulin resistance and promote cold adaptation, we hypothesized that MOTS-c might play a role in boosting the number of mitochondria in a cell. We found that treatment of mammalian cells with MOTS-c increased protein levels of TFAM, COX4, and NRF1, which are markers for mitochondrial biogenesis. However, flow cytometry analysis using MitoTracker Green revealed a sharp reduction in the mitochondrial count after MOTS-c treatment. We then anticipated possible synchronized activation of mitofusion/mitochondrial fusion by MOTS-c following the onset of mitochondrial biogenesis. This was confirmed after a significant increase in protein levels two GTPases, OPA1, and MFN2, both vital for the fusion of mammalian mitochondria. Finally, we found that inhibition of the two GTPases by TNFα abrogated the ability of MOTS-c to prompt GLUT4 translocation and glucose uptake. Similar results were obtained by siRNA KD of MFN2 as well. Our results reveal for the first time a pathway that links mitofusion to MOTS-c-induced GLUT4 translocation.
    DOI:  https://doi.org/10.1038/s41598-021-93735-2
  61. Chem Sci. 2021 Jul 01. 12(25): 8648-8659
    Predicting enzymatic reactions with a molecular transformer.
    David Kreutter, Philippe Schwaller, Jean-Louis Reymond.
      The use of enzymes for organic synthesis allows for simplified, more economical and selective synthetic routes not accessible to conventional reagents. However, predicting whether a particular molecule might undergo a specific enzyme transformation is very difficult. Here we used multi-task transfer learning to train the molecular transformer, a sequence-to-sequence machine learning model, with one million reactions from the US Patent Office (USPTO) database combined with 32 181 enzymatic transformations annotated with a text description of the enzyme. The resulting enzymatic transformer model predicts the structure and stereochemistry of enzyme-catalyzed reaction products with remarkable accuracy. One of the key novelties is that we combined the reaction SMILES language of only 405 atomic tokens with thousands of human language tokens describing the enzymes, such that our enzymatic transformer not only learned to interpret SMILES, but also the natural language as used by human experts to describe enzymes and their mutations.
    DOI:  https://doi.org/10.1039/d1sc02362d
  62. J Phys Chem B. 2021 Jul 09.
    Allosteric Mechanism of Human Mitochondrial Phenylalanyl-tRNA Synthetase: An Atomistic MD Simulation and a Mutual Information-Based Network Study.
    Qi Shao, Zhongjie Han, Jingmin Cheng, Qiankun Wang, Weikang Gong, Chunhua Li.
      Aminoacyl-tRNA synthetases (aaRSs), a family of ubiquitous and essential enzymes, can bind target tRNAs and catalyze the aminoacylation reaction in genetic code translation. In this work, we explore the dynamic properties and allosteric communication of human mitochondrial phenylalanyl-tRNA synthetase (hmPheRS) in free and bound states to understand the mechanisms of its tRNAPhe recognition and allostery using molecular dynamics simulations combined with the torsional mutual information-based network model. Our results reveal that hmPheRS's residue mobility and inter-residue motional coupling are significantly enhanced by tRNAPhe binding, and there occurs a strong allosteric communication which is critical for the aminoacylation reaction, suggesting the vital role of tRNAPhe binding in the enzyme's function. The identified signaling pathways mainly make the connections between the anticodon binding domain (ABD) and catalytic domain (CAD), as well as within the CAD composed of many functional fragments and active sites, revealing the co-regulation role of them to act coordinately and achieve hmPheRS's aminoacylation function. Besides, several key residues along the communication pathways are identified to be involved in mediating the coordinated coupling between anticodon recognition at the ABD and activation process at the CAD, showing their pivotal role in the allosteric network, which are well consistent with the experimental observation. This study sheds light on the allosteric communication mechanism in hmPheRS and can provide important information for the structure-based drug design targeting aaRSs.
    DOI:  https://doi.org/10.1021/acs.jpcb.1c03228
  63. FEBS J. 2021 Jul 14.
    Reducing embryonic mtDNA copy number alters epigenetic profile of key hepatic lipolytic genes and causes abnormal lipid accumulation in adult mice.
    Yakun Wang, Xuan Wang, Qiaoming Long, Yuanwu Liu, Tao Yin, Inna Sirota, Fazheng Ren, Zhenglong Gu, Junjie Luo.
      Adverse fetal environment, in particular a shortage or excess of nutrients, is associated with increased risks of metabolic diseases later in life. However, the molecular mechanisms underlying this developmental origin of adult diseases remain unclear. Here, we directly tested the role of mitochondrial stress in mediating fetal programming in mice by enzymatically depleting mitochondrial DNA (mtDNA) in zygotes. mtDNA-targeted plasmid microinjection is used to reduce embryonic mtDNA copy number directly, followed by embryo transfer. Mice with reduced zygote mtDNA copy number were born morphologically normal and showed no accelerated body weight gain. However, at five-month of age these mice showed markedly increased hepatic lipidosis and became glucose intolerant. Hepatic mRNA and protein expression of peroxisome proliferator-activated receptor α (Pparα), a key transcriptional regulator of lipid metabolism, were significantly decreased as a result of increased DNA methylation in its proximal regulatory region. These results indicate that perturbation of mitochondrial function around the periconceptional period causes hypermethylation and thus suppressed expression of PPARα in fetal liver, leading to impaired hepatic lipid metabolism. Our findings provide the first direct evidence that mitochondrial stress mediates epigenetic changes associated with fetal programming of adult diseases in a mammalian system.
    Keywords:  DNA methylation; Lipid metabolism; PPARα signaling; Preimplantation embryo; mtDNA copy number
    DOI:  https://doi.org/10.1111/febs.16121
  64. Methods Mol Biol. 2021 ;2358 221-228
    The Application of an R Language-Based Platform cRacker for Phosphoproteomics Data Analysis.
    Mingjie He, Zhi Li.
      Phosphoproteomics has drawn great attention of biologist since phosphorylation is proven to play an important role in regulation of proteins. Mass spectrometry technology has helped with the development of phosphoproteomics due to its ability in generating large amount of detailed information after analyzing the phosphoproteome samples. However, interpreting the phosphoproteome data deprived from mass spectrometry can be time-consuming. Here, we introduced a free R language-based platform which can be used in accelerating phosphoproteome data analysis. This platform has integrated different functions and methods which are popularly used in phosphoproteome data analysis, so users can customize their analysis according to their demands.
    Keywords:  Mass spectrometry; Phosphoproteomics data analysis; R language; cRacker
    DOI:  https://doi.org/10.1007/978-1-0716-1625-3_16
  65. Nat Rev Mol Cell Biol. 2021 Jul 13.
    Molecular and cellular basis of genetically inherited skeletal muscle disorders.
    James J Dowling, Conrad C Weihl, Melissa J Spencer.
      Neuromuscular disorders comprise a diverse group of human inborn diseases that arise from defects in the structure and/or function of the muscle tissue - encompassing the muscle cells (myofibres) themselves and their extracellular matrix - or muscle fibre innervation. Since the identification in 1987 of the first genetic lesion associated with a neuromuscular disorder - mutations in dystrophin as an underlying cause of Duchenne muscular dystrophy - the field has made tremendous progress in understanding the genetic basis of these diseases, with pathogenic variants in more than 500 genes now identified as underlying causes of neuromuscular disorders. The subset of neuromuscular disorders that affect skeletal muscle are referred to as myopathies or muscular dystrophies, and are due to variants in genes encoding muscle proteins. Many of these proteins provide structural stability to the myofibres or function in regulating sarcolemmal integrity, whereas others are involved in protein turnover, intracellular trafficking, calcium handling and electrical excitability - processes that ensure myofibre resistance to stress and their primary activity in muscle contraction. In this Review, we discuss how defects in muscle proteins give rise to muscle dysfunction, and ultimately to disease, with a focus on pathologies that are most common, best understood and that provide the most insight into muscle biology.
    DOI:  https://doi.org/10.1038/s41580-021-00389-z
  66. Nat Metab. 2021 Jul 09.
    Quick-start infrastructure for untargeted metabolomics analysis in GNPS.
    Tiago F Leao, Chase M Clark, Anelize Bauermeister, Emmanuel O Elijah, Emily C Gentry, Makhai Husband, Michelli F Oliveira, Nuno Bandeira, Mingxun Wang, Pieter C Dorrestein.
      
    DOI:  https://doi.org/10.1038/s42255-021-00429-0
  67. Ther Adv Reprod Health. 2021 Jan-Dec;15:15 26334941211023544
    Mitochondrial enrichment in infertile patients: a review of different mitochondrial replacement therapies.
    Cristina Rodríguez-Varela, Sonia Herraiz, Elena Labarta.
      Poor ovarian responders exhibit a quantitative reduction in their follicular pool, and most cases are also associated with poor oocyte quality due to patient's age, which leads to impaired in vitro fertilisation outcomes. In particular, poor oocyte quality has been related to mitochondrial dysfunction and/or low mitochondrial count as these organelles are crucial in many essential oocyte processes. Therefore, mitochondrial enrichment has been proposed as a potential therapy option in infertile patients to improve oocyte quality and subsequent in vitro fertilisation outcomes. Nowadays, different options are available for mitochondrial enrichment treatments that are encompassed in two main approaches: heterologous and autologous. In the heterologous approach, mitochondria come from an external source, which is an oocyte donor. These techniques include transferring either a portion of the donor's oocyte cytoplasm to the recipient oocyte or nuclear material from the patient to the donor's oocyte. In any case, this approach entails many ethical and safety concerns that mainly arise from the uncertain degree of mitochondrial heteroplasmy deriving from it. Thus the autologous approach is considered a suitable potential tool to improve oocyte quality by overcoming the heteroplasmy issue. Autologous mitochondrial transfer, however, has not yielded as many beneficial outcomes as initially expected. Proposed mitochondrial autologous sources include immature oocytes, granulosa cells, germline stem cells, and adipose-derived stem cells. Presently, it would seem that these autologous techniques do not improve clinical outcomes in human infertile patients. However, further trials still need to be performed to confirm these results. Besides these two main categories, new strategies have arisen for oocyte rejuvenation by improving patient's own mitochondrial function and avoiding the unknown consequences of third-party genetic material. This is the case of antioxidants, which may enhance mitochondrial activity by counteracting and/or preventing oxidative stress damage. Among others, coenzyme-Q10 and melatonin have shown promising results in low-prognosis infertile patients, although further randomised clinical trials are still necessary.
    Keywords:  mitochondria; mitochondrial enrichment; oocyte rejuvenation; poor oocyte quality
    DOI:  https://doi.org/10.1177/26334941211023544
  68. Orphanet J Rare Dis. 2021 Jul 13. 16(1): 310
    The long and winding road: perspectives of people and parents of children with mitochondrial conditions negotiating management after diagnosis.
    Janet C Long, Stephanie Best, Sarah Hatem, Tahlia Theodorou, Toni Catton, Sean Murray, Jeffrey Braithwaite, John Christodoulou.
       BACKGROUND: The diagnostic odyssey for people with a rare disease is well known, but difficulties do not stop at diagnosis. Here we investigate the experience of people, or parents of children with a diagnosed mitochondrial respiratory chain disorder (MRCD) in the management of their disease. The work complements ongoing projects around implementation of consensus recommendations for management of people with MRCD. People with or caring for a child with a formally diagnosed MRCD were invited to take part in an hour-long focus group held via videoconference. Questions elicited experiences of receiving management advice or information specific to their MRCD in four areas drawn from the consensus recommendations: diet and supplements, exercise, access to social services, and mental health. Sessions were audio-recorded, transcribed and analysed using a combination of inductive and deductive coding.
    RESULTS: Focus groups were conducted with 20 participants from five Australian states in June-September 2020. Fourteen adults with a MRCD (three of whom also had a child with a MRCD), and six who cared for a child with a MRCD took part. The overarching finding was that of the need for ongoing negotiation to access the advice and service required to manage their condition. The nature of these negotiations varied across contexts but mostly related to joint decision-making, and more commonly, the need to advocate for their care with non-specialist services (e.g., dieticians, schools). The effort required for this self-advocacy was a prominent theme. While most participants reported receiving adequate advice around supplements, and to a lesser extent diet and exercise, the majority reported no formal advice around mental health or practical assistance accessing social services.
    CONCLUSION: These focus groups have revealed several gaps in the system for people with a MRCD, interacting with care providers after diagnosis. Focus group participants had to negotiate with a range of different stakeholders in order to secure appropriate advice or services. Notable was the gap in appropriate generalist services (e.g., dieticians) with sufficient knowledge of MRCD to support people with their day-to-day challenges.
    Keywords:  Consumer experience; Management; Mitochondrial; Qualitative research; Rare disease
    DOI:  https://doi.org/10.1186/s13023-021-01939-6
  69. J Neurosci Methods. 2021 Jul 06. pii: S0165-0270(21)00220-X. [Epub ahead of print] 109285
    Protein-retention expansion microscopy for visualizing subcellular organelles in fixed brain tissue.
    Logan A Campbell, Katy E Pannoni, Niesha A Savory, Dinesh Lal, Shannon Farris.
       BACKGROUND: Protein expansion microscopy (proExM) is a powerful technique that crosslinks proteins to a swellable hydrogel to physically expand and optically clear biological samples. The resulting increased resolution (~70nm) and physical separation of labeled proteins make it an attractive tool for studying the localization of subcellular organelles in densely packed tissues, such as the brain. However, the digestion and expansion process greatly reduce fluorescence signals making it necessary to optimize ExM conditions per sample for specific end goals.
    NEW METHOD: Here we compare the staining and digestion conditions of existing proExM workflows to identify the optimal protocol for visualizing subcellular organelles (mitochondria and the Golgi apparatus) within reporter-labeled neurons in fixed mouse brain tissue.
    RESULTS: We found that immunostaining before proExM and using a proteinase K based digestion for 8hours consistently resulted in robust fluorescence retention for immunolabeled subcellular organelles and genetically-encoded reporters.
    COMPARISON WITH EXISTING METHODS: With these methods, we more accurately quantified mitochondria size and number and better visualized Golgi ultrastructure in individual CA2 neurons in the mouse hippocampus.
    CONCLUSIONS: This organelle optimized proExM protocol will be broadly useful for investigators interested in visualizing the spatial distribution of immunolabeled subcellular organelles in various reporter mouse lines, reducing effort, time and resources on the optimization process.
    Keywords:  Expansion microscopy; Golgi apparatus; hippocampus; mitochondria; spines; subcellular localization
    DOI:  https://doi.org/10.1016/j.jneumeth.2021.109285
  70. Genet Med. 2021 Jun 10.
    A framework for automated gene selection in genomic applications.
    L Lazo de la Vega, W Yu, K Machini, C A Austin-Tse, L Hao, C L Blout Zawatsky, H Mason-Suares, R C Green, H L Rehm, M S Lebo.
       PURPOSE: An efficient framework to identify disease-associated genes is needed to evaluate genomic data for both individuals with an unknown disease etiology and those undergoing genomic screening. Here, we propose a framework for gene selection used in genomic analyses, including applications limited to genes with strong or established evidence levels and applications including genes with less or emerging evidence of disease association.
    METHODS: We extracted genes with evidence for gene-disease association from the Human Gene Mutation Database, OMIM, and ClinVar to build a comprehensive gene list of 6,145 genes. Next, we applied stringent filters in conjunction with computationally curated evidence (DisGeNET) to create a restrictive list limited to 3,929 genes with stronger disease associations.
    RESULTS: When compared to manual gene curation efforts, including the Clinical Genome Resource, genes with strong or definitive disease associations are included in both gene lists at high percentages, while genes with limited evidence are largely removed. We further confirmed the utility of this approach in identifying pathogenic and likely pathogenic variants in 45 genomes.
    CONCLUSION: Our approach efficiently creates highly sensitive gene lists for genomic applications, while remaining dynamic and updatable, enabling time savings in genomic applications.
    DOI:  https://doi.org/10.1038/s41436-021-01213-x
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