bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2021–05–30
fifty papers selected by
Catalina Vasilescu, University of Helsinki
  1. Optic neuropathy linked to ACAD9 pathogenic variants: a potentially riboflavin-responsive disorder?
  2. Mitohormesis reprogrammes macrophage metabolism to enforce tolerance.
  3. Mitocytosis, a migrasome-mediated mitochondrial quality-control process.
  4. Improved detection of mitochondrial DNA instability in mitochondrial genome maintenance disorders.
  5. Mitochondrial targeted meganuclease as a platform to eliminate mutant mtDNA in vivo.
  6. A high mutation load of m.14597A>G in MT-ND6 causes Leigh syndrome.
  7. Monitoring PINK1-Parkin Signaling Using Dopaminergic Neurons from iPS Cells.
  8. ECSIT is a critical limiting factor for cardiac function.
  9. Structures of the human LONP1 protease reveal regulatory steps involved in protease activation.
  10. Mechanistic insights into mitochondrial tRNAAla 3'-end metabolism deficiency.
  11. YbeY is required for ribosome small subunit assembly and tRNA processing in human mitochondria.
  12. Cytosolic and Mitochondrial Ca2+ Imaging in Drosophila Dopaminergic Neurons.
  13. Genome-wide CRISPRi screening identifies OCIAD1 as a prohibitin client and regulatory determinant of mitochondrial Complex III assembly in human cells.
  14. Machine learning algorithms reveal the secrets of mitochondrial dynamics.
  15. A De Novo case of autosomal dominant mitochondrial membrane protein-associated neurodegeneration.
  16. Elevated type I interferon responses potentiate metabolic dysfunction, inflammation, and accelerated aging in mtDNA mutator mice.
  17. MPV17-related Hepatocerebral Mitochondrial DNA Depletion Syndrome.
  18. Mitochondrial localization and moderated activity are key to murine erythroid enucleation.
  19. Distal muscle weakness and optic atrophy without central nervous system involvement in a patient with a homozygous missense mutation in the C19ORF12-gene.
  20. Diagnosing newborns with suspected mitochondrial disorders: an economic evaluation comparing early exome sequencing to current typical care.
  21. Mitochondrial Fusion Protein Mfn2 and Its Role in Heart Failure.
  22. CERKL, a retinal dystrophy gene, regulates mitochondrial function and dynamics in the mammalian retina.
  23. The Role of Mitochondrial Dysfunction in Vascular Disease, Tumorigenesis, and Diabetes.
  24. Biparental inheritance of mitochondrial DNA revisited.
  25. Measurement of mitochondrial respiration in the murine retina using a Seahorse extracellular flux analyzer.
  26. Generation of somatic mitochondrial DNA-replaced cells for mitochondrial dysfunction treatment.
  27. Analysis of Dopaminergic Functions in Drosophila.
  28. Loss of C2orf69 defines a fatal autoinflammatory syndrome in humans and zebrafish that evokes a glycogen storage-associated mitochondriopathy.
  29. MicroRNAs and tRNA-Derived Small Fragments: Key Messengers in Nuclear-Mitochondrial Communication.
  30. Identifying genetic modifiers of age-associated penetrance in X-linked dystonia-parkinsonism.
  31. MELAS/LS Overlap Syndrome Associated With Mitochondrial DNA Mutations: Clinical, Genetic, and Radiological Studies.
  32. Mutations in MT-ATP6 are a frequent cause of adult-onset spinocerebellar ataxia.
  33. Samplot: a platform for structural variant visual validation and automated filtering.
  34. Avoiding Extinction: Recent Advances in Understanding Mechanisms of Mitochondrial DNA Purifying Selection in the Germline.
  35. Evaluation of Mitochondrial Function and Morphology in Drosophila.
  36. A Combined Model of Human iPSC-Derived Liver Organoids and Hepatocytes Reveals Ferroptosis in DGUOK Mutant mtDNA Depletion Syndrome.
  37. Astrocyte-Neuron Metabolic Crosstalk in Neurodegeneration: A Mitochondrial Perspective.
  38. The Functions, Methods, and Mobility of Mitochondrial Transfer Between Cells.
  39. Enhancer release and retargeting activates disease-susceptibility genes.
  40. Adaptation to mitochondrial stress requires CHOP-directed tuning of ISR.
  41. Mitochondrial ROS signals prevent excessive immune response.
  42. Cytosolic dsDNA of mitochondrial origin induces cytotoxicity and neurodegeneration in cellular and zebrafish models of Parkinson's disease.
  43. Perm1 promotes cardiomyocyte mitochondrial biogenesis and protects against hypoxia/reoxygenation-induced damage in mice.
  44. Towards population-scale long-read sequencing.
  45. High-Resolution Multicolor Imaging of Mitochondria in Lymphocytes.
  46. NAD+ homeostasis in human health and disease.
  47. Mass-spectrometry-based proteomics reveals mitochondrial supercomplexome plasticity.
  48. Improved methods for RNAseq-based alternative splicing analysis.
  49. Mitochondrial DNA variants in genomic data: diagnostic uplifts and predictive implications.
  50. Metabolic epilepsy in hyperprolinemia type II due to a novel nonsense ALDH4A1 gene variant.
  1. Mitochondrion. 2021 May 20. pii: S1567-7249(21)00073-8. [Epub ahead of print]
    Optic neuropathy linked to ACAD9 pathogenic variants: a potentially riboflavin-responsive disorder?
    Naig Gueguen, Julie Piarroux, Emmanuelle Sarzi, Mehdi Benkirane, Gael Manes, Cécile Delettre, Pascal Amedro, Nicolas Leboucq, Michel Koenig, Pierre Meyer, Isabelle Meunier, Pascal Reynier, Guy Lenaers, Agathe Roubertie.
      Mitochondrial complex I (CI) deficiencies (OMIM 252010) are the commonest inherited mitochondrial disorders in children. Acyl-CoA dehydrogenase 9 (ACAD9) is a flavoenzyme involved chiefly in CI assembly and possibly in fatty acid oxidation. Biallelic pathogenic variants result in CI dysfunction, with a phenotype ranging from early onset and sometimes fatal mitochondrial encephalopathy with lactic acidosis to late-onset exercise intolerance. Cardiomyopathy is often associated. We report a patient with childhood-onset optic and peripheral neuropathies without cardiac involvement, related to CI deficiency. Genetic analysis revealed compound heterozygous pathogenic variants in ACAD9, expanding the clinical spectrum associated to ACAD9 mutations. Importantly, riboflavin treatment (15 mg / kg / day) improved long-distance visual acuity and demonstrated significant rescue of CI activity in vitro.
    Keywords:  ACAD9; Complex I; Optic neuropathy; riboflavin
    DOI:  https://doi.org/10.1016/j.mito.2021.05.002
  2. Nat Metab. 2021 May;3(5): 618-635
    Mitohormesis reprogrammes macrophage metabolism to enforce tolerance.
    Greg A Timblin, Kevin M Tharp, Breanna Ford, Janet M Winchester, Jerome Wang, Stella Zhu, Rida I Khan, Shannon K Louie, Anthony T Iavarone, Johanna Ten Hoeve, Daniel K Nomura, Andreas Stahl, Kaoru Saijo.
      Macrophages generate mitochondrial reactive oxygen species and mitochondrial reactive electrophilic species as antimicrobials during Toll-like receptor (TLR)-dependent inflammatory responses. Whether mitochondrial stress caused by these molecules impacts macrophage function is unknown. Here, we demonstrate that both pharmacologically driven and lipopolysaccharide (LPS)-driven mitochondrial stress in macrophages triggers a stress response called mitohormesis. LPS-driven mitohormetic stress adaptations occur as macrophages transition from an LPS-responsive to LPS-tolerant state wherein stimulus-induced pro-inflammatory gene transcription is impaired, suggesting tolerance is a product of mitohormesis. Indeed, like LPS, hydroxyoestrogen-triggered mitohormesis suppresses mitochondrial oxidative metabolism and acetyl-CoA production needed for histone acetylation and pro-inflammatory gene transcription, and is sufficient to enforce an LPS-tolerant state. Thus, mitochondrial reactive oxygen species and mitochondrial reactive electrophilic species are TLR-dependent signalling molecules that trigger mitohormesis as a negative feedback mechanism to restrain inflammation via tolerance. Moreover, bypassing TLR signalling and pharmacologically triggering mitohormesis represents a new anti-inflammatory strategy that co-opts this stress response to impair epigenetic support of pro-inflammatory gene transcription by mitochondria.
    DOI:  https://doi.org/10.1038/s42255-021-00392-w
  3. Cell. 2021 May 27. pii: S0092-8674(21)00530-4. [Epub ahead of print]184(11): 2896-2910.e13
    Mitocytosis, a migrasome-mediated mitochondrial quality-control process.
    Haifeng Jiao, Dong Jiang, Xiaoyu Hu, Wanqing Du, Liangliang Ji, Yuzhuo Yang, Xiaopeng Li, Takami Sho, Xuan Wang, Ying Li, Yu-Ting Wu, Yau-Huei Wei, Xiaoyu Hu, Li Yu.
      Damaged mitochondria need to be cleared to maintain the quality of the mitochondrial pool. Here, we report mitocytosis, a migrasome-mediated mitochondrial quality-control process. We found that, upon exposure to mild mitochondrial stresses, damaged mitochondria are transported into migrasomes and subsequently disposed of from migrating cells. Mechanistically, mitocytosis requires positioning of damaged mitochondria at the cell periphery, which occurs because damaged mitochondria avoid binding to inward motor proteins. Functionally, mitocytosis plays an important role in maintaining mitochondrial quality. Enhanced mitocytosis protects cells from mitochondrial stressor-induced loss of mitochondrial membrane potential (MMP) and mitochondrial respiration; conversely, blocking mitocytosis causes loss of MMP and mitochondrial respiration under normal conditions. Physiologically, we demonstrate that mitocytosis is required for maintaining MMP and viability in neutrophils in vivo. We propose that mitocytosis is an important mitochondrial quality-control process in migrating cells, which couples mitochondrial homeostasis with cell migration.
    Keywords:  migrasome; mitochondrial quality control; mitochondrion; mitocytosis; mitosome
    DOI:  https://doi.org/10.1016/j.cell.2021.04.027
  4. Genet Med. 2021 May 26.
    Improved detection of mitochondrial DNA instability in mitochondrial genome maintenance disorders.
    Celine Bris, David Goudenège, Valerie Desquiret-Dumas, Naig Gueguen, Sylvie Bannwarth, Pauline Gaignard, Benoit Rucheton, Aurelien Trimouille, Stephane Allouche, Cecile Rouzier, Samira Saadi, Claude Jardel, Abdel Slama, Magalie Barth, Christophe Verny, Marco Spinazzi, Julien Cassereau, Estelle Colin, Magot Armelle, Yann Pereon, Marie Laure Martin-Negrier, Veronique Paquis-Flucklinger, Franck Letournel, Guy Lenaers, Dominique Bonneau, Pascal Reynier, Patrizia Amati-Bonneau, Vincent Procaccio.
       PURPOSE: Diseases caused by defects in mitochondrial DNA (mtDNA) maintenance machinery, leading to mtDNA deletions, form a specific group of disorders. However, mtDNA deletions also appear during aging, interfering with those resulting from mitochondrial disorders.
    METHODS: Here, using next-generation sequencing (NGS) data processed by eKLIPse and data mining, we established criteria distinguishing age-related mtDNA rearrangements from those due to mtDNA maintenance defects. MtDNA deletion profiles from muscle and urine patient samples carrying pathogenic variants in nuclear genes involved in mtDNA maintenance (n = 40) were compared with age-matched controls (n = 90). Seventeen additional patient samples were used to validate the data mining model.
    RESULTS: Overall, deletion number, heteroplasmy level, deletion locations, and the presence of repeats at deletion breakpoints were significantly different between patients and controls, especially in muscle samples. The deletion number was significantly relevant in adults, while breakpoint repeat lengths surrounding deletions were discriminant in young subjects.
    CONCLUSION: Altogether, eKLIPse analysis is a powerful tool for measuring the accumulation of mtDNA deletions between patients of different ages, as well as in prioritizing novel variants in genes involved in mtDNA stability.
    DOI:  https://doi.org/10.1038/s41436-021-01206-w
  5. Nat Commun. 2021 May 28. 12(1): 3210
    Mitochondrial targeted meganuclease as a platform to eliminate mutant mtDNA in vivo.
    Ugne Zekonyte, Sandra R Bacman, Jeff Smith, Wendy Shoop, Claudia V Pereira, Ginger Tomberlin, James Stewart, Derek Jantz, Carlos T Moraes.
      Diseases caused by heteroplasmic mitochondrial DNA mutations have no effective treatment or cure. In recent years, DNA editing enzymes were tested as tools to eliminate mutant mtDNA in heteroplasmic cells and tissues. Mitochondrial-targeted restriction endonucleases, ZFNs, and TALENs have been successful in shifting mtDNA heteroplasmy, but they all have drawbacks as gene therapy reagents, including: large size, heterodimeric nature, inability to distinguish single base changes, or low flexibility and effectiveness. Here we report the adaptation of a gene editing platform based on the I-CreI meganuclease known as ARCUS®. These mitochondrial-targeted meganucleases (mitoARCUS) have a relatively small size, are monomeric, and can recognize sequences differing by as little as one base pair. We show the development of a mitoARCUS specific for the mouse m.5024C>T mutation in the mt-tRNAAla gene and its delivery to mice intravenously using AAV9 as a vector. Liver and skeletal muscle show robust elimination of mutant mtDNA with concomitant restoration of mt-tRNAAla levels. We conclude that mitoARCUS is a potential powerful tool for the elimination of mutant mtDNA.
    DOI:  https://doi.org/10.1038/s41467-021-23561-7
  6. Sci Rep. 2021 May 27. 11(1): 11123
    A high mutation load of m.14597A>G in MT-ND6 causes Leigh syndrome.
    Yoshihito Kishita, Kaori Ishikawa, Kazuto Nakada, Jun-Ichi Hayashi, Takuya Fushimi, Masaru Shimura, Masakazu Kohda, Akira Ohtake, Kei Murayama, Yasushi Okazaki.
      Leigh syndrome (LS) is an early-onset progressive neurodegenerative disorder associated with mitochondrial deficiency. m.14597A>G (p.Ile26Thr) in the MT-ND6 gene was reported to cause Leber's hereditary optic neuropathy (LHON) or dementia/dysarthria. In previous reports, less than 90% heteroplasmy was shown to result in adult-onset disease. Here, by whole mitochondrial sequencing, we identified m.14597A>G mutation of a patient with LS. PCR-RFLP analysis on fibroblasts from the patient revealed a high mutation load (> 90% heteroplasmy). We performed functional assays using cybrid cell models generated by fusing mtDNA-less rho0 HeLa cells with enucleated cells from patient fibroblasts carrying the m.14597A>G variant. Cybrid cell lines bearing the m.14597A>G variant exhibited severe effects on mitochondrial complex I activity. Additionally, impairment of cell proliferation, decreased ATP production and reduced oxygen consumption rate were observed in the cybrid cell lines bearing the m.14597A>G variant when the cells were metabolically stressed in medium containing galactose, indicating mitochondrial respiratory chain defects. These results suggest that a high mutation load of m.14597A>G leads to LS via a mitochondrial complex I defect, rather than LHON or dementia/dysarthria.
    DOI:  https://doi.org/10.1038/s41598-021-90196-5
  7. Methods Mol Biol. 2021 ;2322 81-92
    Monitoring PINK1-Parkin Signaling Using Dopaminergic Neurons from iPS Cells.
    Kahori Shiba-Fukushima, Yuzuru Imai.
      The physiological importance of mitochondrial quality control has been uncovered by the finding that genes for early onset Parkinson's disease (PD), PINK1 and Parkin, regulate mitochondrial autophagy, called mitophagy, and motility. Dopaminergic neurons derived from human-induced pluripotent stem (iPS) cells are a useful tool for analyzing the pathogenesis caused by defects in mitochondrial quality control and for screening candidate drugs for PD. Moreover, dopaminergic neurons could provide new findings not obtained in other cells. In this chapter, we will describe our method for monitoring PINK1-Parkin signaling using iPS cell-derived dopaminergic neurons.
    Keywords:  Autophagy; Dopaminergic neuron; Immunocytochemistry; Mitochondria; PINK1; Parkin; Ubiquitin; Western blot; iPS cells
    DOI:  https://doi.org/10.1007/978-1-0716-1495-2_9
  8. JCI Insight. 2021 May 25. pii: 142801. [Epub ahead of print]
    ECSIT is a critical limiting factor for cardiac function.
    Linan Xu, Fiachra Humphries, Nezira Delagic, Bingwei Wang, Ashling Holland, Kevin S Edgar, Jose R Hombrebueno, Donna Beer Stolz, Ewa Oleszycka, Aoife M Rodgers, Nadezhda Glezeva, Kenneth McDonald, Chris J Watson, Mark T Ledwidge, Rebecca J Ingram, David J Grieve, Paul N Moynagh.
      ECSIT is a protein with roles in early development, activation of the transcription factor NFB and production of mitochondrial reactive oxygen species (mROS) that facilitates clearance of intracellular bacteria like Salmonella. ECSIT is also an important assembly factor for mitochondrial complex I. Unlike the murine form of Ecsit (mEcsit), we demonstrate here that human ECSIT (hECSIT) to be highly labile. In order to explore if the instability of hECSIT affects functions previously ascribed to its murine counterpart, we created a novel transgenic mouse in which the murine Ecsit gene is replaced by the human ECSIT gene. The humanised mouse has low levels of hECSIT protein in keeping with its intrinsic instability. Whereas low level expression of hECSIT was capable of fully compensating for mEcsit in its roles in early development and activation of the NFB pathway, macrophages from humanised mice showed impaired clearance of Salmonella that was associated with reduced production of mROS. Notably, severe cardiac hypertrophy manifested in ageing humanised mice leading to premature death. The cellular and molecular basis to this phenotype is delineated by showing that low levels of human ECSIT protein leads to marked reduction in assembly and activity of mitochondrial complex I with impaired oxidative phosphorylation and reduced production of ATP. Cardiac tissue from humanised hECSIT mice also shows reduced mitochondrial fusion and more fission but impaired clearance of fragmented mitochondria. A cardiomyocyte-intrinsic role for Ecsit in mitochondrial function and cardioprotection is also demonstrated. We also show that cardiac fibrosis and damage in humans correlates with low expression of human ECSIT. In summary, our findings identify a new role for ECSIT in cardioprotection whilst also generating a valuable new experimental model to study mitochondrial dysfunction and cardiac pathophysiology.
    Keywords:  Cardiology; Cardiovascular disease; Metabolism; Mitochondria
    DOI:  https://doi.org/10.1172/jci.insight.142801
  9. Nat Commun. 2021 May 28. 12(1): 3239
    Structures of the human LONP1 protease reveal regulatory steps involved in protease activation.
    Mia Shin, Edmond R Watson, Albert S Song, Jeffrey T Mindrebo, Scott J Novick, Patrick R Griffin, R Luke Wiseman, Gabriel C Lander.
      The human mitochondrial AAA+ protein LONP1 is a critical quality control protease involved in regulating diverse aspects of mitochondrial biology including proteostasis, electron transport chain activity, and mitochondrial transcription. As such, genetic or aging-associated imbalances in LONP1 activity are implicated in pathologic mitochondrial dysfunction associated with numerous human diseases. Despite this importance, the molecular basis for LONP1-dependent proteolytic activity remains poorly defined. Here, we solved cryo-electron microscopy structures of human LONP1 to reveal the underlying molecular mechanisms governing substrate proteolysis. We show that, like bacterial Lon, human LONP1 adopts both an open and closed spiral staircase orientation dictated by the presence of substrate and nucleotide. Unlike bacterial Lon, human LONP1 contains a second spiral staircase within its ATPase domain that engages substrate as it is translocated toward the proteolytic chamber. Intriguingly, and in contrast to its bacterial ortholog, substrate binding within the central ATPase channel of LONP1 alone is insufficient to induce the activated conformation of the protease domains. To successfully induce the active protease conformation in substrate-bound LONP1, substrate binding within the protease active site is necessary, which we demonstrate by adding bortezomib, a peptidomimetic active site inhibitor of LONP1. These results suggest LONP1 can decouple ATPase and protease activities depending on whether AAA+ or both AAA+ and protease domains bind substrate. Importantly, our structures provide a molecular framework to define the critical importance of LONP1 in regulating mitochondrial proteostasis in health and disease.
    DOI:  https://doi.org/10.1038/s41467-021-23495-0
  10. J Biol Chem. 2021 May 20. pii: S0021-9258(21)00612-8. [Epub ahead of print] 100816
    Mechanistic insights into mitochondrial tRNAAla 3'-end metabolism deficiency.
    Yanchun Ji, Zhipeng Nie, Feilong Meng, Cuifang Hu, Hui Chen, Lihao Jin, Mengquan Chen, Minglian Zhang, Juanjuan Zhang, Min Liang, Meng Wang, Min-Xin Guan.
      Mitochondrial tRNA 3'-end metabolism is critical for the formation of functional tRNAs. Deficient mitochondrial tRNA 3'-end metabolism is linked to an array of human diseases, including optic neuropathy, but their pathophysiology remains poorly understood. In this report, we investigated the molecular mechanism underlying the Leber's hereditary optic neuropathy (LHON)-associated tRNAAla 5587A>G mutation, which changes a highly conserved adenosine at position 73 (A73) to guanine (G73) on the 3'-end of the tRNA acceptor stem. The m.5587A>G mutation was identified in three Han Chinese families with suggested maternal inheritance of LHON. We hypothesized that the m.5877A>G mutation altered tRNAAla 3'-end metabolism and mitochondrial function. In vitro processing experiments showed that the m.5587A>G mutation impaired the 3'-end processing of tRNAAla precursors by RNase Z, and inhibited the addition of CCA by tRNA nucleotidyltransferase (TRNT1). Northern blot analysis revealed that the m.5587A>G mutation perturbed tRNAAla aminoacylation, as evidenced by decreased efficiency of aminoacylation and faster electrophoretic mobility of mutated tRNAAla in these cells. The impact of m.5587A>G mutation on tRNAAla function was further supported by increased melting temperature, conformational changes, and reduced levels of this tRNA. Failures in tRNAAla metabolism impaired mitochondrial translation, perturbed assembly and activity of oxidative phosphorylation complexes, diminished ATP production and membrane potential, and increased production of reactive oxygen species. These pleiotropic defects elevated apoptotic cell death and promoted mitophagy in cells carrying the m.5587A>G mutation, thereby contributing to visual impairment. Our findings may provide new insights into the pathophysiology of LHON arising from mitochondrial tRNA 3'-end metabolism deficiency.
    Keywords:  Leber’s hereditary optic neuropathy; Mitochondrial tRNA 3’-end metabolisms; apoptosis; autophagy; oxidative phosphorylation
    DOI:  https://doi.org/10.1016/j.jbc.2021.100816
  11. Nucleic Acids Res. 2021 May 25. pii: gkab404. [Epub ahead of print]
    YbeY is required for ribosome small subunit assembly and tRNA processing in human mitochondria.
    Aaron R D'Souza, Lindsey Van Haute, Christopher A Powell, Christian D Mutti, Petra Páleníková, Pedro Rebelo-Guiomar, Joanna Rorbach, Michal Minczuk.
      Mitochondria contain their own translation apparatus which enables them to produce the polypeptides encoded in their genome. The mitochondrially-encoded RNA components of the mitochondrial ribosome require various post-transcriptional processing steps. Additional protein factors are required to facilitate the biogenesis of the functional mitoribosome. We have characterized a mitochondrially-localized protein, YbeY, which interacts with the assembling mitoribosome through the small subunit. Loss of YbeY leads to a severe reduction in mitochondrial translation and a loss of cell viability, associated with less accurate mitochondrial tRNASer(AGY) processing from the primary transcript and a defect in the maturation of the mitoribosomal small subunit. Our results suggest that YbeY performs a dual, likely independent, function in mitochondria being involved in precursor RNA processing and mitoribosome biogenesis. Issue Section: Nucleic Acid Enzymes.
    DOI:  https://doi.org/10.1093/nar/gkab404
  12. Methods Mol Biol. 2021 ;2322 207-214
    Cytosolic and Mitochondrial Ca2+ Imaging in Drosophila Dopaminergic Neurons.
    Tsuyoshi Inoshita, Yuzuru Imai.
      The ATP-producing organelle mitochondrion controls cellular or synaptic Ca2+ concentrations through temporal uptake of Ca2+ outside of the mitochondria. Although intracellular Ca2+ influx occurs during neuronal activity, a persistently higher concentration of intracellular Ca2+ is neurotoxic. Healthy mitochondria ensure rapid Ca2+ uptake, which is necessary for proper neuronal activity. Mitochondrial Ca2+ buffering activity decreases in aged or sick neurons. In this chapter, we will introduce our protocol for evaluating Ca2+ buffering activity through the mitochondria during neuronal activity of dopaminergic neurons.
    Keywords:  Ca2+ buffering; Dopaminergic neuron; Drosophila; GCaMP; Live imaging; Mitochondria; Synaptic activity
    DOI:  https://doi.org/10.1007/978-1-0716-1495-2_20
  13. Elife. 2021 May 26. pii: e67624. [Epub ahead of print]10
    Genome-wide CRISPRi screening identifies OCIAD1 as a prohibitin client and regulatory determinant of mitochondrial Complex III assembly in human cells.
    Maxence Le Vasseur, Jonathan Friedman, Marco Jost, Jiawei Xu, Justin Yamada, Martin Kampmann, Max A Horlbeck, Michelle R Salemi, Brett S Phinney, Jonathan S Weissman, Jodi Nunnari.
      Dysfunction of the mitochondrial electron transport chain (mETC) is a major cause of human mitochondrial diseases. To identify determinants of mETC function, we screened a genome-wide human CRISPRi library under oxidative metabolic conditions with selective inhibition of mitochondrial Complex III and identified ovarian carcinoma immunoreactive antigen (OCIA) domain-containing protein 1 (OCIAD1) as a Complex III assembly factor. We find that OCIAD1 is an inner mitochondrial membrane protein that forms a complex with supramolecular prohibitin assemblies. Our data indicate that OCIAD1 is required for maintenance of normal steady-state levels of Complex III and the proteolytic processing of the catalytic subunit cytochrome c1 (CYC1). In OCIAD1 depleted mitochondria, unprocessed CYC1 is hemylated and incorporated into Complex III. We propose that OCIAD1 acts as an adaptor within prohibitin assemblies to stabilize and/or chaperone CYC1 and to facilitate its proteolytic processing by the IMMP2L protease.
    Keywords:  Complex III; cell biology; cytochrome c1; electron transport chain; human; mitochondria; prohibitin; protease
    DOI:  https://doi.org/10.7554/eLife.67624
  14. EMBO Mol Med. 2021 May 27. e14316
    Machine learning algorithms reveal the secrets of mitochondrial dynamics.
    Jack J Collier, Robert W Taylor.
      Mitochondria exist as dynamic networks whose morphology is driven by the complex interplay between fission and fusion events. Failure to modulate these processes can be detrimental to human health as evidenced by dominantly inherited, pathogenic variants in OPA1, an effector enzyme of mitochondrial fusion, that lead to network fragmentation, cristae dysmorphology and impaired oxidative respiration, manifesting typically as isolated optic atrophy. However, a significant number of patients develop more severe, systemic phenotypes, although no genetic modifiers of OPA1-related disease have been identified to date. In this issue of EMBO Molecular Medicine, supervised machine learning algorithms underlie a novel tool that enables automated, high throughput and unbiased screening of changes in mitochondrial morphology measured using confocal microscopy. By coupling this approach with a bespoke siRNA library targeting the entire mitochondrial proteome, the work described by Cretin and colleagues yielded significant insight into mitochondrial biology, discovering 91 candidate genes whose endogenous depletion can remedy impaired mitochondrial dynamics caused by OPA1 deficiency.
    DOI:  https://doi.org/10.15252/emmm.202114316
  15. Mol Genet Genomic Med. 2021 May 27. e1706
    A De Novo case of autosomal dominant mitochondrial membrane protein-associated neurodegeneration.
    Stuart Fraser, Mary Koenig, Laura Farach, Pedro Mancias, Kate Mowrey.
       BACKGROUND: Mitochondrial membrane protein-associated neurodegeneration (MPAN) is a genetic neurodegenerative condition previously thought to be inherited only in an autosomal recessive pattern through biallelic pathogenic variants in C19orf12. Recent evidence has proposed that MPAN can also follow autosomal dominant forms of inheritance. We present a case of a de novo pathogenic variant in C19orf12 identified in a female with clinical features consistent with a diagnosis of MPAN, adding further evidence that the disease can be inherited in an autosomal dominant fashion.
    METHODS: A 17-year-old Hispanic female was born to non-consanguineous healthy parents. She developed progressive muscle weakness and dystonia beginning when she was 12 years old. Trio, whole-exome sequencing with mitochondrial genome sequencing, and deletion/duplication analysis of both nuclear and mitochondrial genomes was performed in December 2019.
    RESULTS: Whole-exome sequencing analysis revealed a single de novo variant in C19orf12. The specific variant is c.256C>T (p.Q86X) located in exon 3.
    CONCLUSION: Our clinical report provides further clinical evidence that MPAN can be inherited in an autosomal dominant or recessive fashion. The patient's age of onset and clinical symptoms are very similar to the previous patient published with this specific variant as well as others with heterozygous pathogenic variants in C19orf12 in Gregory et al. 2019. Our case report highlights the importance of considering both autosomal dominant and autosomal recessive version of MPAN with all patients demonstrating clinical features suggestive of MPAN.
    Keywords:  brain-iron accumulation; clinical genetics; movement disorders; neurodegeneration
    DOI:  https://doi.org/10.1002/mgg3.1706
  16. Sci Adv. 2021 May;pii: eabe7548. [Epub ahead of print]7(22):
    Elevated type I interferon responses potentiate metabolic dysfunction, inflammation, and accelerated aging in mtDNA mutator mice.
    Yuanjiu Lei, Camila Guerra Martinez, Sylvia Torres-Odio, Samantha L Bell, Christine E Birdwell, Joshua D Bryant, Carl W Tong, Robert O Watson, Laura Ciaccia West, A Phillip West.
      Mitochondrial dysfunction is a key driver of inflammatory responses in human disease. However, it remains unclear whether alterations in mitochondria-innate immune cross-talk contribute to the pathobiology of mitochondrial disorders and aging. Using the polymerase gamma (POLG) mutator model of mitochondrial DNA instability, we report that aberrant activation of the type I interferon (IFN-I) innate immune axis potentiates immunometabolic dysfunction, reduces health span, and accelerates aging in mutator mice. Mechanistically, elevated IFN-I signaling suppresses activation of nuclear factor erythroid 2-related factor 2 (NRF2), which increases oxidative stress, enhances proinflammatory cytokine responses, and accelerates metabolic dysfunction. Ablation of IFN-I signaling attenuates hyperinflammatory phenotypes by restoring NRF2 activity and reducing aerobic glycolysis, which combine to lessen cardiovascular and myeloid dysfunction in aged mutator mice. These findings further advance our knowledge of how mitochondrial dysfunction shapes innate immune responses and provide a framework for understanding mitochondria-driven immunopathology in POLG-related disorders and aging.
    DOI:  https://doi.org/10.1126/sciadv.abe7548
  17. Korean J Gastroenterol. 2021 May 25. 77(5): 248-252
    MPV17-related Hepatocerebral Mitochondrial DNA Depletion Syndrome.
    Ki Teak Hong, Byung Chan Lim, Jin Soo Moon, Jae Sung Ko.
      Mitochondrial DNA (mtDNA) depletion syndrome comprises diseases resulting from a deficiency of proteins involved in mtDNA synthesis. MPV17 is a mitochondrial membrane protein whose mutation causes mitochondrial deoxynucleotide insufficiency. MPV17-related hepatocerebral mtDNA depletion syndrome is a rare autosomal recessive disease. This case report describes the clinical manifestations of MPV17-related hepatocerebral mtDNA depletion syndrome analyzed by performing whole-exome sequencing (WES). A 17-month-old girl presented with developmental delay, jaundice, and failure to thrive. The laboratory findings revealed cholestatic hepatitis, increased lactate-to-pyruvate ratio, and prolongation of the prothrombin time. She developed a hypoglycemic seizure. Brain magnetic resonance imaging revealed extensive demyelination of the white matter. WES detected the p.Leu151fs and p.Pro98Leu variants in MPV17. Her parents and sibling were found to be MPV17 heterozygous carriers. She was administered supportive treatment, such as replacement of fat-soluble vitamins and cornstarch to prevent further hypoglycemic events. The patient is currently being considered for liver transplantation. Overall, WES can help diagnose hepatocerebral mtDNA depletion syndrome in patients with hepatopathy, developmental delay, lactic acidosis, and hypomyelination based on brain magnetic resonance imaging.
    Keywords:  MPV17 protein; Mitochondrial DNA depletion syndrome, hepatocerebral form; Whole exome sequencing
    DOI:  https://doi.org/10.4166/kjg.2020.170
  18. Blood Adv. 2021 05 25. 5(10): 2490-2504
    Mitochondrial localization and moderated activity are key to murine erythroid enucleation.
    Raymond Liang, Vijay Menon, Jiajing Qiu, Tasleem Arif, Santosh Renuse, Miao Lin, Roberta Nowak, Boris Hartmann, Nikos Tzavaras, Deanna L Benson, Jerry E Chipuk, Miguel Fribourg, Akhilesh Pandey, Velia Fowler, Saghi Ghaffari.
      Mammalian red blood cells (RBCs), which primarily contain hemoglobin, exemplify an elaborate maturation process, with the terminal steps of RBC generation involving extensive cellular remodeling. This encompasses alterations of cellular content through distinct stages of erythroblast maturation that result in the expulsion of the nucleus (enucleation) followed by the loss of mitochondria and all other organelles and a transition to anaerobic glycolysis. Whether there is any link between erythroid removal of the nucleus and the function of any other organelle, including mitochondria, remains unknown. Here we demonstrate that mitochondria are key to nuclear clearance. Using live and confocal microscopy and high-throughput single-cell imaging, we show that before nuclear polarization, mitochondria progressively move toward one side of maturing erythroblasts and aggregate near the nucleus as it extrudes from the cell, a prerequisite for enucleation to proceed. Although we found active mitochondrial respiration is required for nuclear expulsion, levels of mitochondrial activity identify distinct functional subpopulations, because terminally maturing erythroblasts with low relative to high mitochondrial membrane potential are at a later stage of maturation, contain greatly condensed nuclei with reduced open chromatin-associated acetylation histone marks, and exhibit higher enucleation rates. Lastly, to our surprise, we found that late-stage erythroblasts sustain mitochondrial metabolism and subsequent enucleation, primarily through pyruvate but independent of in situ glycolysis. These findings demonstrate the critical but unanticipated functions of mitochondria during the erythroblast enucleation process. They are also relevant to the in vitro production of RBCs as well as to disorders of the erythroid lineage.
    DOI:  https://doi.org/10.1182/bloodadvances.2021004259
  19. Clin Neurol Neurosurg. 2021 Apr 20. pii: S0303-8467(21)00164-5. [Epub ahead of print]206 106637
    Distal muscle weakness and optic atrophy without central nervous system involvement in a patient with a homozygous missense mutation in the C19ORF12-gene.
    R J de Vries, B Jaeger, D M E I Hellebrekers, L Reneman, C Verhamme, H J M Smeets, M C van Maarle, M de Visser, F E Bleeker.
      Variants of the C19ORF12-gene have been described in patients with spastic paraplegia type 43 and in patients with mitochondrial membrane protein-associated neurodegeneration (MPAN), a subtype of neurodegeneration associated with brain iron accumulation (NBIA). In both subtypes optic atrophy and neuropathy have been frequently described. This case report describes a patient with bilateral optic atrophy and severe distal muscle weakness based on motor neuropathy without involvement of the central nervous system. Exome sequencing revealed a homozygous pathogenic missense variant (c.187G>C;p.Ala63Pro) of the C19ORF12-gene while iron deposits were absent on repeat MR-imaging of the brain, thus showing that peripheral neuropathy and optic neuropathy can be the sole manifestations of the C19ORF12-related disease spectrum whereby iron accumulation in the brain may be absent.
    Keywords:  C19ORF12; Mitochondrial membrane protein-associated neurodegeneration (MPAN); Motor neuropathy; Neurodegeneration with Brain Iron Accumulation (NBIA)
    DOI:  https://doi.org/10.1016/j.clineuro.2021.106637
  20. Genet Med. 2021 May 26.
    Diagnosing newborns with suspected mitochondrial disorders: an economic evaluation comparing early exome sequencing to current typical care.
    Samuel A Crawford, Cynthia L Gong, Leah Yieh, Linda M Randolph, Joel W Hay.
       PURPOSE: To determine the value of early exome sequencing (eES) relative to the current typical care (TC) in the diagnosis of newborns with suspected severe mitochondrial disorders (MitD).
    METHODS: We used a decision tree-Markov hybrid to model neonatal intensive care unit (NICU)-related outcomes and costs, lifetime costs and quality-adjusted life-years among patients with MitD. Probabilities, costs, and utilities were populated using published literature, expert opinion, and the Pediatric Health Information System database. Incremental cost-effectiveness ratios (ICER) and net monetary benefits (NMB) were calculated from lifetime costs and quality-adjusted life-years for singleton and trio eES, and TC. Robustness was assessed using univariate and probabilistic sensitivity analyses (PSA). Scenario analyses were also conducted.
    RESULTS: Findings indicate trio eES is a cost-minimizing and cost-effective alternative to current TC. Diagnostic probabilities and NICU length-of-stay were the most sensitive model parameters. Base case analysis demonstrates trio eES has the highest incremental NMB, and PSA demonstrates trio eES had the highest likelihood of being cost-effective at a willingness-to-pay (WTP) of $200,000 relative to TC, singleton eES, and no ES.
    CONCLUSION: Trio and singleton eES are cost-effective and cost-minimizing alternatives to current TC in diagnosing newborns suspected of having a severe MitD.
    DOI:  https://doi.org/10.1038/s41436-021-01210-0
  21. Front Mol Biosci. 2021 ;8 681237
    Mitochondrial Fusion Protein Mfn2 and Its Role in Heart Failure.
    Lei Chen, Bilin Liu, Yuan Qin, Anqi Li, Meng Gao, Hanyu Liu, Guohua Gong.
      Mitofusin 2 (Mfn2) is a transmembrane GTPase located on the mitochondrial outer membrane that contributes to mitochondrial network regulation. It is an essential multifunctional protein that participates in various biological processes under physical and pathological conditions, including mitochondrial fusion, reticulum-mitochondria contacts, mitochondrial quality control, and apoptosis. Mfn2 dysfunctions have been found to contribute to cardiovascular diseases, such as ischemia-reperfusion injury, heart failure, and dilated cardiomyopathy. Here, this review mainly focuses on what is known about the structure and function of Mfn2 and its crucial role in heart failure.
    Keywords:  Mfn2; endoplasmic reticulum–mitochondria contacts; heart failure; mitochondria fusion; mitophagy
    DOI:  https://doi.org/10.3389/fmolb.2021.681237
  22. Neurobiol Dis. 2021 May 25. pii: S0969-9961(21)00154-6. [Epub ahead of print] 105405
    CERKL, a retinal dystrophy gene, regulates mitochondrial function and dynamics in the mammalian retina.
    Serena Mirra, Rocío García Arroyo, Elena B Domènech, Aleix Gavaldà-Navarro, Carlos Herrera-Úbeda, Clara Oliva, Jordi Garcia-Fernàndez, Rafael Artuch, Francesc Villarroya, Gemma Marfany.
      The retina is a highly active metabolic organ that displays a particular vulnerability to genetic and environmental factors causing stress and homeostatic imbalance. Mitochondria constitute a bioenergetic hub that coordinates stress response and cellular homeostasis, therefore structural and functional regulation of the mitochondrial dynamic network is essential for the mammalian retina. CERKL (ceramide kinase like) is a retinal degeneration gene whose mutations cause Retinitis Pigmentosa in humans, a visual disorder characterized by photoreceptors neurodegeneration and progressive vision loss. CERKL produces multiple isoforms with a dynamic subcellular localization. Here we show that a pool of CERKL isoforms localizes at mitochondria in mouse retinal ganglion cells. The depletion of CERKL levels in CerklKD/KO(knockdown/knockout) mouse retinas cause increase of autophagy, mitochondrial fragmentation, alteration of mitochondrial distribution, and dysfunction of mitochondrial-dependent bioenergetics and metabolism. Our results support CERKL as a regulator of autophagy and mitochondrial biology in the mammalian retina.
    Keywords:  CERKL; Mitochondrial dysfunction; Retinal dystrophies; Retinitis pigmentosa
    DOI:  https://doi.org/10.1016/j.nbd.2021.105405
  23. Front Mol Biosci. 2021 ;8 671908
    The Role of Mitochondrial Dysfunction in Vascular Disease, Tumorigenesis, and Diabetes.
    Olga A Zhunina, Nikita G Yabbarov, Andrey V Grechko, Antonina V Starodubova, Ekaterina Ivanova, Nikita G Nikiforov, Alexander N Orekhov.
      Mitochondrial dysfunction is known to be associated with a wide range of human pathologies, such as cancer, metabolic, and cardiovascular diseases. One of the possible ways of mitochondrial involvement in the cellular damage is excessive production of reactive oxygen and nitrogen species (ROS and RNS) that cannot be effectively neutralized by existing antioxidant systems. In mitochondria, ROS and RNS can contribute to protein and mitochondrial DNA (mtDNA) damage causing failure of enzymatic chains and mutations that can impair mitochondrial function. These processes further lead to abnormal cell signaling, premature cell senescence, initiation of inflammation, and apoptosis. Recent studies have identified numerous mtDNA mutations associated with different human pathologies. Some of them result in imbalanced oxidative phosphorylation, while others affect mitochondrial protein synthesis. In this review, we discuss the role of mtDNA mutations in cancer, diabetes, cardiovascular diseases, and atherosclerosis. We provide a list of currently described mtDNA mutations associated with each pathology and discuss the possible future perspective of the research.
    Keywords:  DNA damage; atherosclerosis; cancer; diabetes; mitochondria; reactive nitrogen species; reactive oxygen species
    DOI:  https://doi.org/10.3389/fmolb.2021.671908
  24. Nat Rev Genet. 2021 May 24.
    Biparental inheritance of mitochondrial DNA revisited.
    Alistair T Pagnamenta, Wei Wei, Shamima Rahman, Patrick F Chinnery.
      
    DOI:  https://doi.org/10.1038/s41576-021-00380-6
  25. STAR Protoc. 2021 Jun 18. 2(2): 100533
    Measurement of mitochondrial respiration in the murine retina using a Seahorse extracellular flux analyzer.
    Trupti Shetty, Bomina Park, Timothy W Corson.
      Mitochondrial metabolism is a critical mechanism that is deregulated in numerous retinal diseases. Here, we elaborate a protocol to quantify oxygen consumption rate as a measure of mitochondrial respiration directly from mouse retinal tissue pieces. Our procedure combines the use of Seahorse extracellular flux technology and ex vivo retinal tissue isolation and is robustly reproducible under different treatment conditions. This protocol allows direct assessment of mitochondrial function in response to drug treatments or genetic manipulation in mouse models. For complete details on the use and execution of this protocol, please refer to Shetty et al. (2020), Sardar Pasha et al. (2021), Kooragayala et al. (2015), and Joyal et al. (2016).
    Keywords:  Metabolism; Model Organisms; Neuroscience
    DOI:  https://doi.org/10.1016/j.xpro.2021.100533
  26. Sci Rep. 2021 May 25. 11(1): 10897
    Generation of somatic mitochondrial DNA-replaced cells for mitochondrial dysfunction treatment.
    Hideki Maeda, Daisuke Kami, Ryotaro Maeda, Akira Shikuma, Satoshi Gojo.
      Mitochondrial diseases currently have no cure regardless of whether the cause is a nuclear or mitochondrial genome mutation. Mitochondrial dysfunction notably affects a wide range of disorders in aged individuals, including neurodegenerative diseases, cancers, and even senescence. Here, we present a procedure to generate mitochondrial DNA-replaced somatic cells with a combination of a temporal reduction in endogenous mitochondrial DNA and coincubation with exogeneous isolated mitochondria. Heteroplasmy in mitochondrial disease patient-derived fibroblasts in which the mutant genotype was dominant over the wild-type genotype was reversed. Mitochondrial disease patient-derived fibroblasts regained respiratory function and showed lifespan extension. Mitochondrial membranous components were utilized as a vehicle to deliver the genetic materials into endogenous mitochondria-like horizontal genetic transfer in prokaryotes. Mitochondrial DNA-replaced cells could be a resource for transplantation to treat maternal inherited mitochondrial diseases.
    DOI:  https://doi.org/10.1038/s41598-021-90316-1
  27. Methods Mol Biol. 2021 ;2322 185-193
    Analysis of Dopaminergic Functions in Drosophila.
    Tsuyoshi Inoshita, Daisaku Takemoto, Yuzuru Imai.
      Dopaminergic (DA) neurons regulate various physiological functions, including motor function, emotion, learning, sleep, and arousal. Degeneration of DA neurons in the substantia nigra of the midbrain causes motor disturbance in Parkinson's disease (PD). Studies on familial PD have revealed that a subset of PD genes encode proteins that regulate mitochondrial function and synaptic dynamics. Drosophila is a powerful model of PD, whereby genetic interactions of PD genes with well-conserved cellular signaling can be evaluated. Morphological changes in mitochondria, along with dysfunction and degeneration of DA neurons, have been reported in many studies using Drosophila PD models. In this chapter, we will describe imaging methods to visualize mitochondria in DA neurons and to evaluate spontaneous neural activity of DA neurons in the Drosophila brain.
    Keywords:  Dopaminergic neuron; Drosophila; Immunohistochemistry; Live imaging; Mitochondria; Synaptic vesicle release; pHluorin
    DOI:  https://doi.org/10.1007/978-1-0716-1495-2_18
  28. Am J Hum Genet. 2021 May 21. pii: S0002-9297(21)00187-7. [Epub ahead of print]
    Loss of C2orf69 defines a fatal autoinflammatory syndrome in humans and zebrafish that evokes a glycogen storage-associated mitochondriopathy.
    Hui Hui Wong, Sze Hwee Seet, Michael Maier, Ayse Gurel, Ricardo Moreno Traspas, Cheryl Lee, Shan Zhang, Beril Talim, Abigail Y T Loh, Crystal Y Chia, Tze Shin Teoh, Danielle Sng, Jarred Rensvold, Sule Unal, Evgenia Shishkova, Ece Cepni, Fatima M Nathan, Fernanda L Sirota, Chao Liang, Nese Yarali, Pelin O Simsek-Kiper, Tadahiro Mitani, Serdar Ceylaner, Ozlem Arman-Bilir, Hamdi Mbarek, Fatma Gumruk, Stephanie Efthymiou, Deniz Uğurlu Çi Men, Danai Georgiadou, Kortessa Sotiropoulou, Henry Houlden, Franziska Paul, Davut Pehlivan, Candice Lainé, Guoliang Chai, Nur Ain Ali, Siew Chin Choo, Soh Sok Keng, Bertrand Boisson, Elanur Yılmaz, Shifeng Xue, Joshua J Coon, Thanh Thao Nguyen Ly, Naser Gilani, Dana Hasbini, Hulya Kayserili, Maha Zaki, Robert J Isfort, Natalia Ordonez, Kornelia Tripolszki, Peter Bauer, Nima Rezaei, Simin Seyedpour, Ghamar Taj Khotaei, Charles C Bascom, Reza Maroofian, Myriam Chaabouni, Afaf Alsubhi, Wafaa Eyaid, Sedat Işıkay, Joseph G Gleeson, James R Lupski, Jean-Laurent Casanova, David J Pagliarini, Nurten A Akarsu, Sebastian Maurer-Stroh, Arda Cetinkaya, Aida Bertoli-Avella, Ajay S Mathuru, Lena Ho, Frederic A Bard, Bruno Reversade.
      Human C2orf69 is an evolutionarily conserved gene whose function is unknown. Here, we report eight unrelated families from which 20 children presented with a fatal syndrome consisting of severe autoinflammation and progredient leukoencephalopathy with recurrent seizures; 12 of these subjects, whose DNA was available, segregated homozygous loss-of-function C2orf69 variants. C2ORF69 bears homology to esterase enzymes, and orthologs can be found in most eukaryotic genomes, including that of unicellular phytoplankton. We found that endogenous C2ORF69 (1) is loosely bound to mitochondria, (2) affects mitochondrial membrane potential and oxidative respiration in cultured neurons, and (3) controls the levels of the glycogen branching enzyme 1 (GBE1) consistent with a glycogen storage-associated mitochondriopathy. We show that CRISPR-Cas9-mediated inactivation of zebrafish C2orf69 results in lethality by 8 months of age due to spontaneous epileptic seizures, which is preceded by persistent brain inflammation. Collectively, our results delineate an autoinflammatory Mendelian disorder of C2orf69 deficiency that disrupts the development/homeostasis of the immune and central nervous systems.
    Keywords:  C2ORF69, mitochondriopathy, inflammation, GBE1, encephalopathy, zebrafish, Elbracht-Işikay syndrome, lipase, glycogen, Mendelian genetics
    DOI:  https://doi.org/10.1016/j.ajhg.2021.05.003
  29. Front Mol Biosci. 2021 ;8 643575
    MicroRNAs and tRNA-Derived Small Fragments: Key Messengers in Nuclear-Mitochondrial Communication.
    Salvador Meseguer.
      Mitochondria are not only important as energy suppliers in cells but also participate in other biological processes essential for cell growth and survival. They arose from α-proteobacterial predecessors through endosymbiosis and evolved transferring a large part of their genome to the host cell nucleus. Such a symbiotic relationship has been reinforced over time through increasingly complex signaling mechanisms between the host cell and mitochondria. So far, we do not have a complete view of the mechanisms that allow the mitochondria to communicate their functional status to the nucleus and trigger adaptive and compensatory responses. Recent findings place two classes of small non-coding RNAs (sncRNAs), microRNAs (miRNAs), and tRNA-derived small fragments, in such a scenario, acting as key pieces in the mitochondria-nucleus cross-talk. This review highlights the emerging roles and the interrelation of these sncRNAs in different signaling pathways between mitochondria and the host cell. Moreover, we describe in what way alterations of these complex regulatory mechanisms involving sncRNAs lead to diseases associated with mitochondrial dysfunction. In turn, these discoveries provide novel prognostic biomarker candidates and/or potential therapeutic targets.
    Keywords:  microRNA; mitochondrial dysfunction; mitochondrial tRNA; mitochondrial tRNA modification; mt tRF; retrograde signaling; sncRNA; tRNA fragment
    DOI:  https://doi.org/10.3389/fmolb.2021.643575
  30. Nat Commun. 2021 May 28. 12(1): 3216
    Identifying genetic modifiers of age-associated penetrance in X-linked dystonia-parkinsonism.
    Björn-Hergen Laabs, Christine Klein, Jelena Pozojevic, Aloysius Domingo, Norbert Brüggemann, Karen Grütz, Raymond L Rosales, Roland Dominic Jamora, Gerard Saranza, Cid Czarina E Diesta, Michael Wittig, Susen Schaake, Marija Dulovic-Mahlow, Jana Quismundo, Pia Otto, Patrick Acuna, Criscely Go, Nutan Sharma, Trisha Multhaupt-Buell, Ulrich Müller, Henrike Hanssen, Fabian Kilpert, Andre Franke, Arndt Rolfs, Peter Bauer, Valerija Dobričić, Katja Lohmann, Laurie J Ozelius, Frank J Kaiser, Inke R König, Ana Westenberger.
      X-linked dystonia-parkinsonism is a neurodegenerative disorder caused by a founder retrotransposon insertion, in which a polymorphic hexanucleotide repeat accounts for ~50% of age at onset variability. Employing a genome-wide association study to identify additional factors modifying age at onset, we establish that three independent loci are significantly associated with age at onset (p < 5 × 10-8). The lead single nucleotide polymorphisms collectively account for 25.6% of the remaining variance not explained by the hexanucleotide repeat and 13.0% of the overall variance in age at onset in X-linked dystonia-parkinsonism with the protective alleles delaying disease onset by seven years. These regions harbor or lie adjacent to MSH3 and PMS2, the genes that were recently implicated in modifying age at onset in Huntington's disease, likely through a common pathway influencing repeat instability. Our work indicates the existence of three modifiers of age at onset in X-linked dystonia-parkinsonism that likely affect the DNA mismatch repair pathway.
    DOI:  https://doi.org/10.1038/s41467-021-23491-4
  31. Front Neurol. 2021 ;12 648740
    MELAS/LS Overlap Syndrome Associated With Mitochondrial DNA Mutations: Clinical, Genetic, and Radiological Studies.
    Yanping Wei, Yan Huang, Yingmai Yang, Min Qian.
      Introduction: Mitochondrial diseases are characterized by considerable clinical and genetic heterogeneity. Mitochondrial encephalomyopathy with lactate acidosis and stroke-like episodes (MELAS) and Leigh syndrome (LS) are both established mitochondrial syndromes; sometimes they can overlap. Methods: A retrospective observational cohort study was done to analyze the clinical manifestations, biochemical findings, neuroimaging and genetic data, and disease outcomes of 14 patients with identified MELAS/LS overlap syndrome. Results: A total of 14 patients, 9 males and 5 females, were enrolled. The median age at onset was 14 years, while the average age was 12.6 years. As for clinical features in concordance with MELAS, the top three most common symptoms were seizures, cognitive impairment, and stroke-like episodes (SLE). Brain atrophy was present in seven patients. As for the clinical hallmarks of LS, the top three most common symptoms were ataxia, spastic paraplegia, and bulbar palsy. Patients presented with individual syndrome or overlap syndromes with similar frequency, and the prognosis did not seem to be related to the initial presentation. Thirteen patients were identified with MTND mutations, among which m.13513G>A mutation in the MT-ND5 gene was the most common. Only one patient with m.8344A>G mutation of MTTK gene was found. Discussion: Our study demonstrated that MTND genes are important mutation hot spots in MELAS/LS overlap syndrome. The follow-up is very important for the final diagnosis of overlap syndrome.
    Keywords:  Leigh syndrome; MTND; mitochondrial DNA; mitochondrial encephalomyopathy with lactate acidosis and stroke-like episodes; overlap syndrome
    DOI:  https://doi.org/10.3389/fneur.2021.648740
  32. J Neurol. 2021 May 26.
    Mutations in MT-ATP6 are a frequent cause of adult-onset spinocerebellar ataxia.
    Dagmar Nolte, Jun-Suk Kang, Amrei Hofmann, Eva Schwaab, Heidrun H Krämer, Ulrich Müller.
      Adult-onset ataxias are a genetically and clinically heterogeneous group of movement disorders. In addition to nuclear gene mutations, sequence changes have also been described in the mitochondrial genome. Here, we present findings of mutation analysis of the mitochondrial gene MT-ATP6. We analyzed 94 patients with adult-onset spinocerebellar ataxia (SCA), including 34 sporadic cases. In all patients, common sequence changes found in SCAs such as repeat expansions and point mutations had been excluded previously. We found pathogenic MT-ATP variants in five of these patients (5.32%), two of whom were sporadic. Four of the five mutations have not previously been described in ataxias. All but one of these mutations affect transmembrane helices of subunit-α of ATP synthase. Two mutations (p.G16S, and p.P18S) disrupt transmembrane helix 1 (TMH1), one mutation (p.G167D) affects TMH5, and another one (p.L217P) TMH6. The fifth mutation (p.T96A) describes an amino acid change in close proximity to transmembrane helix 3 (TMH3). The level of heteroplasmy was either complete or very high ranging from 87 to 99%. The high prevalence of pathogenic MT-ATP6 variants suggests that analysis of this gene should be included in the routine workup of both hereditary and sporadic ataxias.
    Keywords:  ATP synthase; Adult-onset ataxia; Complex V defect; MT-ATP6
    DOI:  https://doi.org/10.1007/s00415-021-10607-5
  33. Genome Biol. 2021 May 25. 22(1): 161
    Samplot: a platform for structural variant visual validation and automated filtering.
    Jonathan R Belyeu, Murad Chowdhury, Joseph Brown, Brent S Pedersen, Michael J Cormier, Aaron R Quinlan, Ryan M Layer.
      Visual validation is an important step to minimize false-positive predictions from structural variant (SV) detection. We present Samplot, a tool for creating images that display the read depth and sequence alignments necessary to adjudicate purported SVs across samples and sequencing technologies. These images can be rapidly reviewed to curate large SV call sets. Samplot is applicable to many biological problems such as SV prioritization in disease studies, analysis of inherited variation, or de novo SV review. Samplot includes a machine learning package that dramatically decreases the number of false positives without human review. Samplot is available at https://github.com/ryanlayer/samplot .
    DOI:  https://doi.org/10.1186/s13059-021-02380-5
  34. Annu Rev Genomics Hum Genet. 2021 May 26.
    Avoiding Extinction: Recent Advances in Understanding Mechanisms of Mitochondrial DNA Purifying Selection in the Germline.
    Swathi P Jeedigunta, Anastasia V Minenkova, Jonathan M Palozzi, Thomas R Hurd.
      Mitochondria are unusual organelles in that they contain their own genomes, which are kept apart from the rest of the DNA in the cell. While mitochondrial DNA (mtDNA) is essential for respiration and most multicellular life, maintaining a genome outside the nucleus brings with it a number of challenges. Chief among these is preserving mtDNA genomic integrity from one generation to the next. In this review, we discuss what is known about negative (purifying) selection mechanisms that prevent deleterious mutations from accumulating in mtDNA in the germline. Throughout, we focus on the female germline, as it is the tissue through which mtDNA is inherited in most organisms and, therefore, the tissue that most profoundly shapes the genome. We discuss recent progress in uncovering the mechanisms of germline mtDNA selection, from humans to invertebrates. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
    DOI:  https://doi.org/10.1146/annurev-genom-121420-081805
  35. Methods Mol Biol. 2021 ;2322 195-206
    Evaluation of Mitochondrial Function and Morphology in Drosophila.
    Yinglu Tang, Foozhan Tahmasebinia, Zhihao Wu.
      Drosophila melanogaster (Drosophila, fruit fly, or fly) is an important model organism in the studies of molecular genetic analysis and mechanism of Parkinson's disease (PD), benefiting from its powerful genetic tools and massive available genetic mutants. People have generated different fly models to mimic the inherited PDs and most of them have obvious mitochondrial abnormalities. Here, we describe some common approaches to analyze mitochondrial functions and morphological changes in Drosophila PD models.
    Keywords:  ATP; Drosophila; Mitochondrial aggregation; Mitochondrial function; Mitochondrial morphology; Movement; Parkinson’s disease (PD); Reactive oxygen species (ROS); Respiration; Wing posture
    DOI:  https://doi.org/10.1007/978-1-0716-1495-2_19
  36. Adv Sci (Weinh). 2021 May;8(10): 2004680
    A Combined Model of Human iPSC-Derived Liver Organoids and Hepatocytes Reveals Ferroptosis in DGUOK Mutant mtDNA Depletion Syndrome.
    Jingyi Guo, Lifan Duan, Xueying He, Shengbiao Li, Yi Wu, Ge Xiang, Feixiang Bao, Liang Yang, Hongyan Shi, Mi Gao, Lingjun Zheng, Huili Hu, Xingguo Liu.
      Mitochondrial DNA depletion syndrome (MDS) is a group of severe inherited disorders caused by mutations in genes, such as deoxyribonucleoside kinase (DGUOK). A great majority of DGUOK mutant MDS patients develop iron overload progressing to severe liver failure. However, the pathological mechanisms connecting iron overload and hepatic damage remains uncovered. Here, two patients' skin fibroblasts are reprogrammed to induced pluripotent stem cells (iPSCs) and then corrected by CRISPR/Cas9. Patient-specific iPSCs and corrected iPSCs-derived high purity hepatocyte organoids (iHep-Orgs) and hepatocyte-like cells (iHep) are generated as cellular models for studying hepatic pathology. DGUOK mutant iHep and iHep-Orgs, but not control and corrected one, are more sensitive to iron overload-induced ferroptosis, which can be rescued by N-Acetylcysteine (NAC). Mechanically, this ferroptosis is a process mediated by nuclear receptor co-activator 4 (NCOA4)-dependent degradation of ferritin in lysosome and cellular labile iron release. This study reveals the underlying pathological mechanisms and the viable therapeutic strategies of this syndrome, and is the first pure iHep-Orgs model in hereditary liver diseases.
    Keywords:  N‐acetylcysteine; ferroptosis; induced pluripotent stem cells; mitochondria; mitochondrial DNA
    DOI:  https://doi.org/10.1002/advs.202004680
  37. Front Endocrinol (Lausanne). 2021 ;12 668517
    Astrocyte-Neuron Metabolic Crosstalk in Neurodegeneration: A Mitochondrial Perspective.
    Patrycja Mulica, Anne Grünewald, Sandro L Pereira.
      Converging evidence made clear that declining brain energetics contribute to aging and are implicated in the initiation and progression of neurodegenerative disorders such as Alzheimer's and Parkinson's disease. Indeed, both pathologies involve instances of hypometabolism of glucose and oxygen in the brain causing mitochondrial dysfunction, energetic failure and oxidative stress. Importantly, recent evidence suggests that astrocytes, which play a key role in supporting neuronal function and metabolism, might contribute to the development of neurodegenerative diseases. Therefore, exploring how the neuro-supportive role of astrocytes may be impaired in the context of these disorders has great therapeutic potential. In the following, we will discuss some of the so far identified features underlining the astrocyte-neuron metabolic crosstalk. Thereby, special focus will be given to the role of mitochondria. Furthermore, we will report on recent advancements concerning iPSC-derived models used to unravel the metabolic contribution of astrocytes to neuronal demise. Finally, we discuss how mitochondrial dysfunction in astrocytes could contribute to inflammatory signaling in neurodegenerative diseases.
    Keywords:  Alzheimer’s disease; Parkinson’s disease; astrocytes; metabolism; neurodegeneration; neurons
    DOI:  https://doi.org/10.3389/fendo.2021.668517
  38. Front Oncol. 2021 ;11 672781
    The Functions, Methods, and Mobility of Mitochondrial Transfer Between Cells.
    Yiming Qin, Xin Jiang, Qi Yang, Jiaqi Zhao, Qiong Zhou, Yanhong Zhou.
      Mitochondria are vital organelles in cells, regulating energy metabolism and apoptosis. Mitochondrial transcellular transfer plays a crucial role during physiological and pathological conditions, such as rescuing recipient cells from bioenergetic deficit and tumorigenesis. Studies have shown several structures that conduct transcellular transfer of mitochondria, including tunneling nanotubes (TNTs), extracellular vesicles (EVs), and Cx43 gap junctions (GJs). The intra- and intercellular transfer of mitochondria is driven by a transport complex. Mitochondrial Rho small GTPase (MIRO) may be the adaptor that connects the transport complex with mitochondria, and myosin XIX is the motor protein of the transport complex, which participates in the transcellular transport of mitochondria through TNTs. In this review, the roles of TNTs, EVs, GJs, and related transport complexes in mitochondrial transcellular transfer are discussed in detail, as well as the formation mechanisms of TNTs and EVs. This review provides the basis for the development of potential clinical therapies targeting the structures of mitochondrial transcellular transfer.
    Keywords:  Cx43 gap junction; Miro; extracellular vesicles; mitochondria; myosin XIX; transcellular transport; tunneling nanotubes
    DOI:  https://doi.org/10.3389/fonc.2021.672781
  39. Nature. 2021 May 26.
    Enhancer release and retargeting activates disease-susceptibility genes.
    Soohwan Oh, Jiaofang Shao, Joydeep Mitra, Feng Xiong, Matteo D'Antonio, Ruoyu Wang, Ivan Garcia-Bassets, Qi Ma, Xiaoyu Zhu, Joo-Hyung Lee, Sreejith J Nair, Feng Yang, Kenneth Ohgi, Kelly A Frazer, Zhengdong D Zhang, Wenbo Li, Michael G Rosenfeld.
      The functional engagement between an enhancer and its target promoter ensures precise gene transcription1. Understanding the basis of promoter choice by enhancers has important implications for health and disease. Here we report that functional loss of a preferred promoter can release its partner enhancer to loop to and activate an alternative promoter (or alternative promoters) in the neighbourhood. We refer to this target-switching process as 'enhancer release and retargeting'. Genetic deletion, motif perturbation or mutation, and dCas9-mediated CTCF tethering reveal that promoter choice by an enhancer can be determined by the binding of CTCF at promoters, in a cohesin-dependent manner-consistent with a model of 'enhancer scanning' inside the contact domain. Promoter-associated CTCF shows a lower affinity than that at chromatin domain boundaries and often lacks a preferred motif orientation or a partnering CTCF at the cognate enhancer, suggesting properties distinct from boundary CTCF. Analyses of cancer mutations, data from the GTEx project and risk loci from genome-wide association studies, together with a focused CRISPR interference screen, reveal that enhancer release and retargeting represents an overlooked mechanism that underlies the activation of disease-susceptibility genes, as exemplified by a risk locus for Parkinson's disease (NUCKS1-RAB7L1) and three loci associated with cancer (CLPTM1L-TERT, ZCCHC7-PAX5 and PVT1-MYC).
    DOI:  https://doi.org/10.1038/s41586-021-03577-1
  40. Sci Adv. 2021 May;pii: eabf0971. [Epub ahead of print]7(22):
    Adaptation to mitochondrial stress requires CHOP-directed tuning of ISR.
    Sophie Kaspar, Christian Oertlin, Karolina Szczepanowska, Alexandra Kukat, Katharina Senft, Christina Lucas, Susanne Brodesser, Maria Hatzoglou, Ola Larsson, Ivan Topisirovic, Aleksandra Trifunovic.
      In response to disturbed mitochondrial gene expression and protein synthesis, an adaptive transcriptional response sharing a signature of the integrated stress response (ISR) is activated. We report an intricate interplay between three transcription factors regulating the mitochondrial stress response: CHOP, C/EBPβ, and ATF4. We show that CHOP acts as a rheostat that attenuates prolonged ISR, prevents unfavorable metabolic alterations, and postpones the onset of mitochondrial cardiomyopathy. Upon mitochondrial dysfunction, CHOP interaction with C/EBPβ is needed to adjust ATF4 levels, thus preventing overactivation of the ATF4-regulated transcriptional program. Failure of this interaction switches ISR from an acute to a chronic state, leading to early respiratory chain deficiency, energy crisis, and premature death. Therefore, contrary to its previously proposed role as a transcriptional activator of mitochondrial unfolded protein response, our results highlight a role of CHOP in the fine-tuning of mitochondrial ISR in mammals.
    DOI:  https://doi.org/10.1126/sciadv.abf0971
  41. Nat Metab. 2021 May;3(5): 588-589
    Mitochondrial ROS signals prevent excessive immune response.
    Kim Zarse, Michael Ristow.
      
    DOI:  https://doi.org/10.1038/s42255-021-00387-7
  42. Nat Commun. 2021 May 25. 12(1): 3101
    Cytosolic dsDNA of mitochondrial origin induces cytotoxicity and neurodegeneration in cellular and zebrafish models of Parkinson's disease.
    Hideaki Matsui, Junko Ito, Noriko Matsui, Tamayo Uechi, Osamu Onodera, Akiyoshi Kakita.
      Mitochondrial dysfunction and lysosomal dysfunction have been implicated in Parkinson's disease (PD), but the links between these dysfunctions in PD pathogenesis are still largely unknown. Here we report that cytosolic dsDNA of mitochondrial origin escaping from lysosomal degradation was shown to induce cytotoxicity in cultured cells and PD phenotypes in vivo. The depletion of PINK1, GBA and/or ATP13A2 causes increases in cytosolic dsDNA of mitochondrial origin and induces type I interferon (IFN) responses and cell death in cultured cell lines. These phenotypes are rescued by the overexpression of DNase II, a lysosomal DNase that degrades discarded mitochondrial DNA, or the depletion of IFI16, which acts as a sensor for cytosolic dsDNA of mitochondrial origin. Reducing the abundance of cytosolic dsDNA by overexpressing human DNase II ameliorates movement disorders and dopaminergic cell loss in gba mutant PD model zebrafish. Furthermore, IFI16 and cytosolic dsDNA puncta of mitochondrial origin accumulate in the brain of patients with PD. These results support a common causative role for the cytosolic leakage of mitochondrial DNA in PD pathogenesis.
    DOI:  https://doi.org/10.1038/s41467-021-23452-x
  43. J Biol Chem. 2021 May 21. pii: S0021-9258(21)00623-2. [Epub ahead of print] 100825
    Perm1 promotes cardiomyocyte mitochondrial biogenesis and protects against hypoxia/reoxygenation-induced damage in mice.
    Yoshitake Cho, Shizuko Tachibana, Kayla Lam, Yoh Arita, Shamim Khosrowjerdi, Oliver Zhang, Alex Liang, Ruixia Li, Aleksander Andreyev, Anne N Murphy, Robert S Ross.
      Normal contractile function of the heart depends on a constant and reliable production of ATP by cardiomyocytes. Dysregulation of cardiac energy metabolism can result in immature heart development and disrupt the ability of the adult myocardium to adapt to stress, potentially leading to heart failure. Further, restoration of abnormal mitochondrial function can have beneficial effects on cardiac dysfunction. Previously, we identified a novel protein termed Perm1 (PGC-1 and ERR induced regulator, muscle 1) that is enriched in skeletal and cardiac-muscle mitochondria and transcriptionally regulated by PGC-1 (Peroxisome proliferator-activated receptor gamma coactivator 1) and ERR (Estrogen-related receptor). The role of Perm1 in the heart is poorly understood and was studied here. We utilized cell culture, mouse models and human tissue, to study its expression and transcriptional control, as well as its role in transcription of other factors. Critically, we tested Perm1's role in cardiomyocyte mitochondrial function and its ability to protect myocytes from stress-induced damage. Our studies show Perm1 expression increases throughout mouse cardiogenesis, demonstrate that Perm1 interacts with PGC-1α and enhances activation of PGC-1 and ERR, increases mitochondrial DNA copy number, and augments oxidative capacity in cultured neonatal mouse cardiomyocytes. Moreover, we found that Perm1 reduced cellular damage produced as a result of hypoxia and reoxygenation-induced stress and mitigated cell death of cardiomyocytes. Taken together, our results show that Perm1 promotes mitochondrial biogenesis in mouse cardiomyocytes. Future studies can assess the potential of Perm1 to be used as a novel therapeutic to restore cardiac dysfunction induced by ischemic injury.
    Keywords:  Perm1; cardiomyocytes; mitochondrial biogenesis; oxidative metabolism
    DOI:  https://doi.org/10.1016/j.jbc.2021.100825
  44. Nat Rev Genet. 2021 May 28.
    Towards population-scale long-read sequencing.
    Wouter De Coster, Matthias H Weissensteiner, Fritz J Sedlazeck.
      Long-read sequencing technologies have now reached a level of accuracy and yield that allows their application to variant detection at a scale of tens to thousands of samples. Concomitant with the development of new computational tools, the first population-scale studies involving long-read sequencing have emerged over the past 2 years and, given the continuous advancement of the field, many more are likely to follow. In this Review, we survey recent developments in population-scale long-read sequencing, highlight potential challenges of a scaled-up approach and provide guidance regarding experimental design. We provide an overview of current long-read sequencing platforms, variant calling methodologies and approaches for de novo assemblies and reference-based mapping approaches. Furthermore, we summarize strategies for variant validation, genotyping and predicting functional impact and emphasize challenges remaining in achieving long-read sequencing at a population scale.
    DOI:  https://doi.org/10.1038/s41576-021-00367-3
  45. Methods Mol Biol. 2021 ;2304 131-145
    High-Resolution Multicolor Imaging of Mitochondria in Lymphocytes.
    Munir Akkaya, Pietro Miozzo, Margery G Smelkinson.
      The identification of cellular changes that accompany immune activation has been a long-standing interest for immunologists. Among these, alterations in the metabolic states of these cells have gained particular attention in the last decade due to the emergence of the field of immunometabolism. A thorough investigation of these metabolic changes can only be achieved with an in-depth visualization of mitochondrial organization; however, current strategies for mitochondrial imaging have been optimized in model cells with a high cytoplasm-to-nucleus ratio and thus are not readily adaptable for many immune cells. Here, we devised a multicolor high-resolution microscopy strategy to image mitochondrial morphology in lymphocytes at both their resting and activated states. Our method allowed us to stain both the mitochondrial surface (by targeting TOM-20) and the mitochondrial matrix (through the use of Mitotracker dyes) while efficiently excluding nonviable cells. Our novel imaging strategy offers a powerful tool to study changes in mitochondrial morphology and complements any research focusing on lymphocyte metabolism.
    Keywords:  Deconvolution; High-resolution; Lymphocyte; Mitochondria; STED
    DOI:  https://doi.org/10.1007/978-1-0716-1402-0_6
  46. EMBO Mol Med. 2021 May 27. e13943
    NAD+ homeostasis in human health and disease.
    Rubén Zapata-Pérez, Ronald J A Wanders, Clara D M van Karnebeek, Riekelt H Houtkooper.
      Depletion of nicotinamide adenine dinucleotide (NAD+ ), a central redox cofactor and the substrate of key metabolic enzymes, is the causative factor of a number of inherited and acquired diseases in humans. Primary deficiencies of NAD+ homeostasis are the result of impaired biosynthesis, while secondary deficiencies can arise due to other factors affecting NAD+ homeostasis, such as increased NAD+ consumption or dietary deficiency of its vitamin B3 precursors. NAD+ depletion can manifest in a wide variety of pathological phenotypes, ranging from rare inherited defects, characterized by congenital malformations, retinal degeneration, and/or encephalopathy, to more common multifactorial, often age-related, diseases. Here, we discuss NAD+ biochemistry and metabolism and provide an overview of the etiology and pathological consequences of alterations of the NAD+ metabolism in humans. Finally, we discuss the state of the art of the potential therapeutic implications of NAD+ repletion for boosting health as well as treating rare and common diseases, and the possibilities to achieve this by means of the different NAD+ -enhancing agents.
    Keywords:  NAD+; NAD+ homeostasis; disease; metabolism; therapy
    DOI:  https://doi.org/10.15252/emmm.202113943
  47. Cell Rep. 2021 May 25. pii: S2211-1247(21)00525-8. [Epub ahead of print]35(8): 109180
    Mass-spectrometry-based proteomics reveals mitochondrial supercomplexome plasticity.
    Alba Gonzalez-Franquesa, Ben Stocks, Sabina Chubanava, Helle B Hattel, Roger Moreno-Justicia, Lone Peijs, Jonas T Treebak, Juleen R Zierath, Atul S Deshmukh.
      Mitochondrial respiratory complex subunits assemble in supercomplexes. Studies of supercomplexes have typically relied upon antibody-based quantification, often limited to a single subunit per respiratory complex. To provide a deeper insight into mitochondrial and supercomplex plasticity, we combine native electrophoresis and mass spectrometry to determine the supercomplexome of skeletal muscle from sedentary and exercise-trained mice. We quantify 422 mitochondrial proteins within 10 supercomplex bands in which we show the debated presence of complexes II and V. Exercise-induced mitochondrial biogenesis results in non-stoichiometric changes in subunits and incorporation into supercomplexes. We uncover the dynamics of supercomplex-related assembly proteins and mtDNA-encoded subunits after exercise. Furthermore, exercise affects the complexing of Lactb, an obesity-associated mitochondrial protein, and ubiquinone biosynthesis proteins. Knockdown of ubiquinone biosynthesis proteins leads to alterations in mitochondrial respiration. Our approach can be applied to broad biological systems. In this instance, comprehensively analyzing respiratory supercomplexes illuminates previously undetectable complexity in mitochondrial plasticity.
    Keywords:  complexome; exercise; mitochondrial respiratory complexes; mitochondrial supercomplexes; oxidative phosphorylation; protein complexes
    DOI:  https://doi.org/10.1016/j.celrep.2021.109180
  48. Sci Rep. 2021 May 24. 11(1): 10740
    Improved methods for RNAseq-based alternative splicing analysis.
    C4RCD Research Group
      The robust detection of disease-associated splice events from RNAseq data is challenging due to the potential confounding effect of gene expression levels and the often limited number of patients with relevant RNAseq data. Here we present a novel statistical approach to splicing outlier detection and differential splicing analysis. Our approach tests for differences in the percentages of sequence reads representing local splice events. We describe a software package called Bisbee which can predict the protein-level effect of splice alterations, a key feature lacking in many other splicing analysis resources. We leverage Bisbee's prediction of protein level effects as a benchmark of its capabilities using matched sets of RNAseq and mass spectrometry data from normal tissues. Bisbee exhibits improved sensitivity and specificity over existing approaches and can be used to identify tissue-specific splice variants whose protein-level expression can be confirmed by mass spectrometry. We also applied Bisbee to assess evidence for a pathogenic splicing variant contributing to a rare disease and to identify tumor-specific splice isoforms associated with an oncogenic mutation. Bisbee was able to rediscover previously validated results in both of these cases and also identify common tumor-associated splice isoforms replicated in two independent melanoma datasets.
    DOI:  https://doi.org/10.1038/s41598-021-89938-2
  49. Nat Rev Genet. 2021 May 28.
    Mitochondrial DNA variants in genomic data: diagnostic uplifts and predictive implications.
    William L Macken, Anneke M Lucassen, Michael G Hanna, Robert D S Pitceathly.
      
    DOI:  https://doi.org/10.1038/s41576-021-00381-5
  50. Metab Brain Dis. 2021 May 26.
    Metabolic epilepsy in hyperprolinemia type II due to a novel nonsense ALDH4A1 gene variant.
    Rajdeep Kaur, Pradip Paria, Arushi Gahlot Saini, Renu Suthar, Vikas Bhatia, Savita Verma Attri.
      Hyperprolinemia type II (HPII) is a rare autosomal recessive disorder of proline degradation pathway due to deficiency of delta-1-pyrroline-5-carboxylate dehydrogenase. Pathogenic variants in the ALDH4A1 gene are responsible for this disorder. We here describe an 11-month-old infant with recurrent seizures refractory to multiple antiepileptic drugs. She was hospitalized in view of acute-onset encephalopathy, exacerbation of generalized seizures following an upper respiratory infection. Laboratory investigation revealed significantly elevated proline levels in dried blood spots. DNA sample of the child was subjected to a targeted next-generation sequencing gene panel for hyperprolinemias. We detected a novel nonsense homozygous variant in the ALDH4A1 gene in the child and the heterozygous variant of the same in both the parents. Based on the location of the variant i.e. in the last exon, truncated protein is expected to be expressed by skipping nonsense-mediated decay and such point-nonsense variants could be an ideal target for readthrough drugs to correct genetic defects.
    Keywords:  ALDH4A1; Hyperprolinemia; Inborn error of metabolism; Metabolic epilepsy; Proline; Refractory seizures
    DOI:  https://doi.org/10.1007/s11011-021-00757-w
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