bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2021–05–16
fifty-one papers selected by
Catalina Vasilescu, University of Helsinki
  1. Mitochondrial matrix proteases - quality control and beyond.
  2. Phenotypic diversity of brain MRI patterns in mitochondrial aminoacyl-tRNA synthetase mutations.
  3. Inborn disorders of the Malate Aspartate Shuttle.
  4. Nanoscopic quantification of sub-mitochondrial morphology, mitophagy and mitochondrial dynamics in living cells derived from patients with mitochondrial diseases.
  5. Paracoccus denitrificans: a genetically tractable model system for studying respiratory complex I.
  6. Biallelic variants in HPDL cause pure and complicated hereditary spastic paraplegia.
  7. Generation of mitochondrial reactive oxygen species is controlled by ATPase inhibitory factor 1 and regulates cognition.
  8. Physical Exercise: A Novel Tool to Protect Mitochondrial Health.
  9. Oxygen tension modulates the mitochondrial genetic bottleneck and influences the segregation of a heteroplasmic mtDNA variant in vitro.
  10. Cell-specific transcriptional control of mitochondrial metabolism by TIF1γ drives erythropoiesis.
  11. VCP/p97 cofactor UBXN1/SAKS1 regulates mitophagy by modulating MFN2 removal from mitochondria.
  12. TSG101 negatively regulates mitochondrial biogenesis in axons.
  13. Cardiac Energy Metabolism in Heart Failure.
  14. Quantification of Myocardial Mitochondrial Membrane Potential Using PET.
  15. Imaging mass cytometry reveals generalised deficiency in OXPHOS complexes in Parkinson's disease.
  16. An age-downregulated ribosomal RpS28 protein variant regulates the muscle proteome.
  17. Cork-in-bottle mechanism of inhibitor binding to mammalian complex I.
  18. Progresses in both basic research and clinical trials of NAD+ in Parkinson's disease.
  19. Increasing fatty acid oxidation elicits a sex-dependent response in failing mouse hearts.
  20. An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability.
  21. Mitochondrial TNAP controls thermogenesis by hydrolysis of phosphocreatine.
  22. Mild hypothermia facilitates mitochondrial transfer from astrocytes to injured neurons during oxygen-glucose deprivation/reoxygenation.
  23. REVIEW: Practical strategies to maintain anabolism by intravenous nutritional management in children with inborn metabolic diseases.
  24. Long term follow-up of the dietary intake in propionic acidemia.
  25. Mitochondrial fission and mitophagy are independent mechanisms regulating ischemia/reperfusion injury in primary neurons.
  26. Mitofusin-2 stabilizes adherens junctions and suppresses endothelial inflammation via modulation of β-catenin signaling.
  27. FUNDC1-dependent mitochondria-associated endoplasmic reticulum membranes are involved in angiogenesis and neoangiogenesis.
  28. A mitochondrial gatekeeper that helps cells escape death by ferroptosis.
  29. Mitochondrial CHCHD2: Disease-Associated Mutations, Physiological Functions, and Current Animal Models.
  30. Knockdown of insulin-like growth factor 2 gene disrupts mitochondrial functions in the liver.
  31. Identification of a novel MICU1 nonsense variant causes myopathy with extrapyramidal signs in an Iranian consanguineous family.
  32. USP19 promotes hypoxia-induced mitochondrial division via FUNDC1 at ER-mitochondria contact sites.
  33. The role of sigma 1 receptor in organization of endoplasmic reticulum signaling microdomains.
  34. Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data.
  35. No effect of resveratrol in patients with mitochondrial myopathy: A cross-over randomized controlled trial.
  36. Prodromal sensory neuropathy in Pink1-/- SNCAA53T double mutant Parkinson mice.
  37. A novel remitting leukodystrophy associated with a variant in FBP2.
  38. Structure elucidation of the elusive Enzyme I monomer reveals the molecular mechanisms linking oligomerization and enzymatic activity.
  39. The Protective Effect of 1,25(OH)2D3 on Myocardial Function is Mediated via Sirtuin 3-Regulated Fatty Acid Metabolism.
  40. A subcellular map of the human kinome.
  41. Detecting and Rescuing Stalled Ribosomes.
  42. Nicotinamide riboside attenuates age-associated metabolic and functional changes in hematopoietic stem cells.
  43. LBSL: Case Series and DARS2 Variant Analysis in Early Severe Forms With Unexpected Presentations.
  44. A TORC1-histone axis regulates chromatin organisation and non-canonical induction of autophagy to ameliorate ageing.
  45. Polygenic Risk Scores.
  46. Multimodal detection of protein isoforms and nucleic acids from low starting cell numbers.
  47. Extraction of nuclei from archived postmortem tissues for single-nucleus sequencing applications.
  48. Histone H3K9 butyrylation is regulated by dietary fat and stress via an acyl-CoA dehydrogenase short chain-dependent mechanism.
  49. Gene4PD: A Comprehensive Genetic Database of Parkinson's Disease.
  50. DR2S: an integrated algorithm providing reference-grade haplotype sequences from heterozygous samples.
  51. Detecting the epitranscriptome.
  1. FEBS J. 2021 May 10.
    Mitochondrial matrix proteases - quality control and beyond.
    Karolina Szczepanowska, Aleksandra Trifunovic.
      To ensure correct function, mitochondria have developed several mechanisms of protein quality control (QC). Protein homeostasis highly relies on chaperones and proteases to maintain proper folding and remove damaged proteins that might otherwise form cell-toxic aggregates. Besides quality control, mitochondrial proteases modulate and regulate many essential functions, such as trafficking, processing, and activation of mitochondrial proteins, mitochondrial dynamics, mitophagy, and apoptosis. Therefore, the impaired function of mitochondrial proteases is associated with various pathological conditions, including cancer, metabolic syndromes, and neurodegenerative disorders. This review recapitulates and discusses the emerging roles of two major proteases of the mitochondrial matrix, LON and ClpXP. Although commonly acknowledge for their protein quality control role, recent advances have uncovered several highly regulated processes controlled by the LON and ClpXP connected to mitochondrial gene expression and respiratory chain function maintenance. Furthermore, both proteases have been lately recognized as potent targets for anti-cancer therapies, and we summarize those findings.
    Keywords:  ClpXP; LONP1; cancer; degradation; metabolism; mitochondria; mitochondrial matrix; mtDNA; proteases; protein quality control; proteolysis; respiratory complexes
    DOI:  https://doi.org/10.1111/febs.15964
  2. Mol Genet Metab. 2021 Apr 21. pii: S1096-7192(21)00695-8. [Epub ahead of print]
    Phenotypic diversity of brain MRI patterns in mitochondrial aminoacyl-tRNA synthetase mutations.
    Charles-Joris Roux, Giulia Barcia, Manuel Schiff, Marie Sissler, Raphaël Levy, Volodia Dangouloff-Ros, Isabelle Desguerre, Shimon Edvardson, Orli Elpeleg, Agnès Rötig, Arnold Munnich, Nathalie Boddaert.
       BACKGROUND AND PURPOSE: Mitochondrial aminoacyl-tRNA synthetases-encoded by ARS2 genes-are evolutionarily conserved enzymes that catalyse the attachment of amino acids to their cognate tRNAs, ensuring the accuracy of the mitochondrial translation process. ARS2 gene mutations are associated with a wide range of clinical presentations affecting the CNS.
    METHODS: Two senior neuroradiologists analysed brain MRI of 25 patients (age range: 3 d-25 yrs.; 11 males; 14 females) with biallelic pathogenic variants of 11 ARS2 genes in a retrospective study conducted between 2002 and 2019.
    RESULTS: Though several combinations of brain MRI anomalies were highly suggestive of specific aetiologies (DARS2, EARS2, AARS2 and RARS2 mutations), our study detected no MRI pattern common to all patients. Stroke-like lesions were associated with pathogenic SARS2 and FARS2 variants. We also report early onset cerebellar atrophy and calcifications in AARS2 mutations, early white matter involvement in RARS2 mutations, and absent involvement of thalami in EARS2 mutations. Finally, our findings show that normal brain MRI results do not exclude the presence of ARS2 mutations: 5 patients with normal MRI images were carriers of pathogenic IARS2, YARS2, and FARS2 variants.
    CONCLUSION: Our study extends the spectrum of brain MRI anomalies associated with pathogenic ARS2 variants and suggests ARS2 mutations are largely underdiagnosed.
    Keywords:  ARS; Aminoacyl-tRNA synthetases; Brain MRI; Mitochondria; Stroke-like
    DOI:  https://doi.org/10.1016/j.ymgme.2021.04.004
  3. J Inherit Metab Dis. 2021 May 15.
    Inborn disorders of the Malate Aspartate Shuttle.
    Melissa H Broeks, Clara D M van Karnebeek, Ronald J A Wanders, Judith J M Jans, Nanda M Verhoeven-Duif.
      Over the last few years, various inborn disorders have been reported in the malate aspartate shuttle (MAS). The MAS consists of 4 metabolic enzymes and 2 transporters, one of them having two isoforms that are expressed in different tissues. Together they form a biochemical pathway that shuttles electrons from the cytosol into mitochondria, as the inner mitochondrial membrane is impermeable to the electron carrier NADH. By shuttling NADH across the mitochondrial membrane in the form of a reduced metabolite (malate), the MAS plays an important role in mitochondrial respiration. In addition, the MAS maintains the cytosolic NAD+ /NADH redox balance, by using redox reactions for the transfer of electrons. This explains why the MAS is also important in sustaining cytosolic redox-dependent metabolic pathways, such as glycolysis and serine biosynthesis. The current review provides insights into the clinical and biochemical characteristics of MAS deficiencies. To date, 5 out of 7 potential MAS deficiencies have been reported. Most of them present with a clinical phenotype of infantile epileptic encephalopathy. Although not specific, biochemical characteristics include high lactate, high glycerol 3-phosphate, a disturbed redox balance, TCA abnormalities, high ammonia and low serine, which may be helpful in reaching a diagnosis in patients with an infantile epileptic encephalopathy. Current implications for treatment include a ketogenic diet, as well as serine and vitamin B6 supplementation. This article is protected by copyright. All rights reserved.
    Keywords:  AGC1; AGC2; GOT2; Inborn metabolic disorder; MDH1; MDH2; Malate Aspartate Shuttle; NAD(H); Redox
    DOI:  https://doi.org/10.1002/jimd.12402
  4. J Nanobiotechnology. 2021 May 13. 19(1): 136
    Nanoscopic quantification of sub-mitochondrial morphology, mitophagy and mitochondrial dynamics in living cells derived from patients with mitochondrial diseases.
    Weiwei Zou, Qixin Chen, Jesse Slone, Li Yang, Xiaoting Lou, Jiajie Diao, Taosheng Huang.
      SLC25A46 mutations have been found to lead to mitochondrial hyper-fusion and reduced mitochondrial respiratory function, which results in optic atrophy, cerebellar atrophy, and other clinical symptoms of mitochondrial disease. However, it is generally believed that mitochondrial fusion is attributable to increased mitochondrial oxidative phosphorylation (OXPHOS), which is inconsistent with the decreased OXPHOS of highly-fused mitochondria observed in previous studies. In this paper, we have used the live-cell nanoscope to observe and quantify the structure of mitochondrial cristae, and the behavior of mitochondria and lysosomes in patient-derived SLC25A46 mutant fibroblasts. The results show that the cristae have been markedly damaged in the mutant fibroblasts, but there is no corresponding increase in mitophagy. This study suggests that severely damaged mitochondrial cristae might be the predominant cause of reduced OXPHOS in SLC25A46 mutant fibroblasts. This study demonstrates the utility of nanoscope-based imaging for realizing the sub-mitochondrial morphology, mitophagy and mitochondrial dynamics in living cells, which may be particularly valuable for the quick evaluation of pathogenesis of mitochondrial morphological abnormalities.
    Keywords:  Cristae; Mitochondrial disease; Mitophagy; Nanoscope; SLC25A46
    DOI:  https://doi.org/10.1186/s12951-021-00882-9
  5. Sci Rep. 2021 May 12. 11(1): 10143
    Paracoccus denitrificans: a genetically tractable model system for studying respiratory complex I.
    Owen D Jarman, Olivier Biner, John J Wright, Judy Hirst.
      Mitochondrial complex I (NADH:ubiquinone oxidoreductase) is a crucial metabolic enzyme that couples the free energy released from NADH oxidation and ubiquinone reduction to the translocation of four protons across the inner mitochondrial membrane, creating the proton motive force for ATP synthesis. The mechanism by which the energy is captured, and the mechanism and pathways of proton pumping, remain elusive despite recent advances in structural knowledge. Progress has been limited by a lack of model systems able to combine functional and structural analyses with targeted mutagenic interrogation throughout the entire complex. Here, we develop and present the α-proteobacterium Paracoccus denitrificans as a suitable bacterial model system for mitochondrial complex I. First, we develop a robust purification protocol to isolate highly active complex I by introducing a His6-tag on the Nqo5 subunit. Then, we optimize the reconstitution of the enzyme into liposomes, demonstrating its proton pumping activity. Finally, we develop a strain of P. denitrificans that is amenable to complex I mutagenesis and create a catalytically inactive variant of the enzyme. Our model provides new opportunities to disentangle the mechanism of complex I by combining mutagenesis in every subunit with established interrogative biophysical measurements on both the soluble and membrane bound enzymes.
    DOI:  https://doi.org/10.1038/s41598-021-89575-9
  6. Brain. 2021 May 10. pii: awab041. [Epub ahead of print]
    Biallelic variants in HPDL cause pure and complicated hereditary spastic paraplegia.
    Genomics England Research Consortium, PREPARE network
      Human 4-hydroxyphenylpyruvate dioxygenase-like (HPDL) is a putative iron-containing non-heme oxygenase of unknown specificity and biological significance. We report 25 families containing 34 individuals with neurological disease associated with biallelic HPDL variants. Phenotypes ranged from juvenile-onset pure hereditary spastic paraplegia to infantile-onset spasticity and global developmental delays, sometimes complicated by episodes of neurological and respiratory decompensation. Variants included bona fide pathogenic truncating changes, although most were missense substitutions. Functionality of variants could not be determined directly as the enzymatic specificity of HPDL is unknown; however, when HPDL missense substitutions were introduced into 4-hydroxyphenylpyruvate dioxygenase (HPPD, an HPDL orthologue), they impaired the ability of HPPD to convert 4-hydroxyphenylpyruvate into homogentisate. Moreover, three additional sets of experiments provided evidence for a role of HPDL in the nervous system and further supported its link to neurological disease: (i) HPDL was expressed in the nervous system and expression increased during neural differentiation; (ii) knockdown of zebrafish hpdl led to abnormal motor behaviour, replicating aspects of the human disease; and (iii) HPDL localized to mitochondria, consistent with mitochondrial disease that is often associated with neurological manifestations. Our findings suggest that biallelic HPDL variants cause a syndrome varying from juvenile-onset pure hereditary spastic paraplegia to infantile-onset spastic tetraplegia associated with global developmental delays.
    Keywords:  HPDL; HSP; autosomal recessive; hereditary spastic paraplegia; mitochondrial disorder
    DOI:  https://doi.org/10.1093/brain/awab041
  7. PLoS Biol. 2021 May 13. 19(5): e3001252
    Generation of mitochondrial reactive oxygen species is controlled by ATPase inhibitory factor 1 and regulates cognition.
    Pau B Esparza-Moltó, Inés Romero-Carramiñana, Cristina Núñez de Arenas, Marta P Pereira, Noelia Blanco, Beatriz Pardo, Georgina R Bates, Carla Sánchez-Castillo, Rafael Artuch, Michael P Murphy, José A Esteban, José M Cuezva.
      The mitochondrial ATP synthase emerges as key hub of cellular functions controlling the production of ATP, cellular signaling, and fate. It is regulated by the ATPase inhibitory factor 1 (IF1), which is highly abundant in neurons. Herein, we ablated or overexpressed IF1 in mouse neurons to show that IF1 dose defines the fraction of active/inactive enzyme in vivo, thereby controlling mitochondrial function and the production of mitochondrial reactive oxygen species (mtROS). Transcriptomic, proteomic, and metabolomic analyses indicate that IF1 dose regulates mitochondrial metabolism, synaptic function, and cognition. Ablation of IF1 impairs memory, whereas synaptic transmission and learning are enhanced by IF1 overexpression. Mechanistically, quenching the IF1-mediated increase in mtROS production in mice overexpressing IF1 reduces the increased synaptic transmission and obliterates the learning advantage afforded by the higher IF1 content. Overall, IF1 plays a key role in neuronal function by regulating the fraction of ATP synthase responsible for mitohormetic mtROS signaling.
    DOI:  https://doi.org/10.1371/journal.pbio.3001252
  8. Front Physiol. 2021 ;12 660068
    Physical Exercise: A Novel Tool to Protect Mitochondrial Health.
    Daniela Sorriento, Eugenio Di Vaia, Guido Iaccarino.
      Mitochondrial dysfunction is a crucial contributor to heart diseases. Alterations in energetic metabolism affect crucial homeostatic processes, such asATP production, the generation of reactive oxygen species, and the release of pro-apoptotic factors, associated with metabolic abnormalities. In response to energetic deficiency, the cardiomyocytes activate the Mitochondrial Quality Control (MQC), a critical process in maintaining mitochondrial health. This process is compromised in cardiovascular diseases depending on the pathology's severity and represents, therefore, a potential therapeutic target. Several potential targeting molecules within this process have been identified in the last years, and therapeutic strategies have been proposed to ameliorate mitochondria monitoring and function. In this context, physical exercise is considered a non-pharmacological strategy to protect mitochondrial health. Physical exercise regulates MQC allowing the repair/elimination of damaged mitochondria and synthesizing new ones, thus recovering the metabolic state. In this review, we will deal with the effect of physical exercise on cardiac mitochondrial function tracing its ability to modulate specific steps in MQC both in physiologic and pathologic conditions.
    Keywords:  cardiovascular disease; energetic metabolism; heart; mitochondrial dysfunction; physical activity
    DOI:  https://doi.org/10.3389/fphys.2021.660068
  9. Commun Biol. 2021 May 14. 4(1): 584
    Oxygen tension modulates the mitochondrial genetic bottleneck and influences the segregation of a heteroplasmic mtDNA variant in vitro.
    Mikael G Pezet, Aurora Gomez-Duran, Florian Klimm, Juvid Aryaman, Stephen Burr, Wei Wei, Mitinori Saitou, Julien Prudent, Patrick F Chinnery.
      Most humans carry a mixed population of mitochondrial DNA (mtDNA heteroplasmy) affecting ~1-2% of molecules, but rapid percentage shifts occur over one generation leading to severe mitochondrial diseases. A decrease in the amount of mtDNA within the developing female germ line appears to play a role, but other sub-cellular mechanisms have been implicated. Establishing an in vitro model of early mammalian germ cell development from embryonic stem cells, here we show that the reduction of mtDNA content is modulated by oxygen and reaches a nadir immediately before germ cell specification. The observed genetic bottleneck was accompanied by a decrease in mtDNA replicating foci and the segregation of heteroplasmy, which were both abolished at higher oxygen levels. Thus, differences in oxygen tension occurring during early development likely modulate the amount of mtDNA, facilitating mtDNA segregation and contributing to tissue-specific mutation loads.
    DOI:  https://doi.org/10.1038/s42003-021-02069-2
  10. Science. 2021 May 14. 372(6543): 716-721
    Cell-specific transcriptional control of mitochondrial metabolism by TIF1γ drives erythropoiesis.
    Marlies P Rossmann, Karen Hoi, Victoria Chan, Brian J Abraham, Song Yang, James Mullahoo, Malvina Papanastasiou, Ying Wang, Ilaria Elia, Julie R Perlin, Elliott J Hagedorn, Sara Hetzel, Raha Weigert, Sejal Vyas, Partha P Nag, Lucas B Sullivan, Curtis R Warren, Bilguujin Dorjsuren, Eugenia Custo Greig, Isaac Adatto, Chad A Cowan, Stuart L Schreiber, Richard A Young, Alexander Meissner, Marcia C Haigis, Siegfried Hekimi, Steven A Carr, Leonard I Zon.
      Transcription and metabolism both influence cell function, but dedicated transcriptional control of metabolic pathways that regulate cell fate has rarely been defined. We discovered, using a chemical suppressor screen, that inhibition of the pyrimidine biosynthesis enzyme dihydroorotate dehydrogenase (DHODH) rescues erythroid differentiation in bloodless zebrafish moonshine (mon) mutant embryos defective for transcriptional intermediary factor 1 gamma (tif1γ). This rescue depends on the functional link of DHODH to mitochondrial respiration. The transcription elongation factor TIF1γ directly controls coenzyme Q (CoQ) synthesis gene expression. Upon tif1γ loss, CoQ levels are reduced, and a high succinate/α-ketoglutarate ratio leads to increased histone methylation. A CoQ analog rescues mon's bloodless phenotype. These results demonstrate that mitochondrial metabolism is a key output of a lineage transcription factor that drives cell fate decisions in the early blood lineage.
    DOI:  https://doi.org/10.1126/science.aaz2740
  11. Autophagy. 2021 May 09. 1-20
    VCP/p97 cofactor UBXN1/SAKS1 regulates mitophagy by modulating MFN2 removal from mitochondria.
    Chantal Mengus, Melanie Neutzner, Ana Catarina Pinho Ferreira Bento, Claudia C Bippes, Corina Kohler, Sarah Decembrini, Jessica Häusel, Charles Hemion, Lara Sironi, Stephan Frank, Hendrik P N Scholl, Albert Neutzner.
      Initiation of PINK1- and PRKN-dependent mitophagy is a highly regulated process involving the activity of the AAA-ATPase VCP/p97, a cofactor-guided multifunctional protein central to handling ubiquitinated client proteins. Removal of ubiquitinated substrates such as the mitofusin MFN2 from the outer mitochondrial membrane by VCP is critical for PRKN accumulation on mitochondria, which drives mitophagy. Here we characterize the role of the UBA and UBX-domain containing VCP cofactor UBXN1/SAKS1 during mitophagy. Following mitochondrial depolarization and depending on PRKN, UBXN1 translocated alongside VCP to mitochondria. Prior to mitophagy, loss of UBXN1 led to mitochondrial fragmentation, diminished ATP production, and impaired ER-mitochondrial apposition. When mitophagy was induced in cells lacking UBXN1, mitochondrial translocation of VCP and PRKN was impaired, diminishing mitophagic flux. In addition, UBXN1 physically interacted with PRKN in a UBX-domain depending manner. Interestingly, ectopic expression of the pro-mitophagic VCP cofactor UBXN6/UBXD1 fully reversed impaired PRKN recruitment in UBXN1-/- cells. Mechanistically, UBXN1 acted downstream of PINK1 by facilitating MFN2 removal from mitochondria. In UBXN1-/- cells exposed to mitochondrial stress, MFN2 formed para-mitochondrial blobs likely representing blocked intermediates of the MFN2 removal process partly reversible by expression of UBXN6. Presence of these MFN2 blobs strongly correlated with impaired PRKN translocation to depolarized mitochondria. Our observations connect the VCP cofactor UBXN1 to the initiation and maintenance phase of PRKN-dependent mitophagy, and indicate that, upon mitochondrial stress induction, MFN2 removal from mitochondria occurs through a specialized process.
    Keywords:  MFN2; PRKN; UBXN1; UBXN6; VCP; mitophagy
    DOI:  https://doi.org/10.1080/15548627.2021.1922982
  12. Proc Natl Acad Sci U S A. 2021 May 18. pii: e2018770118. [Epub ahead of print]118(20):
    TSG101 negatively regulates mitochondrial biogenesis in axons.
    Tzu-Huai Lin, Dana M Bis-Brewer, Amy E Sheehan, Louise N Townsend, Daniel C Maddison, Stephan Züchner, Gaynor A Smith, Marc R Freeman.
      There is a tight association between mitochondrial dysfunction and neurodegenerative diseases and axons that are particularly vulnerable to degeneration, but how mitochondria are maintained in axons to support their physiology remains poorly defined. In an in vivo forward genetic screen for mutants altering axonal mitochondria, we identified tsg101 Neurons mutant for tsg101 exhibited an increase in mitochondrial number and decrease in mitochondrial size. TSG101 is best known as a component of the endosomal sorting complexes required for transport (ESCRT) complexes; however, loss of most other ESCRT components did not affect mitochondrial numbers or size, suggesting TSG101 regulates mitochondrial biology in a noncanonical, ESCRT-independent manner. The TSG101-mutant phenotype was not caused by lack of mitophagy, and we found that autophagy blockade was detrimental only to the mitochondria in the cell bodies, arguing mitophagy and autophagy are dispensable for the regulation of mitochondria number in axons. Interestingly, TSG101 mitochondrial phenotypes were instead caused by activation of PGC-1ɑ/Nrf2-dependent mitochondrial biogenesis, which was mTOR independent and TFEB dependent and required the mitochondrial fission-fusion machinery. Our work identifies a role for TSG101 in inhibiting mitochondrial biogenesis, which is essential for the maintenance of mitochondrial numbers and sizes, in the axonal compartment.
    Keywords:  ESCRT; TSG101; mitochondria; mitochondrial biogenesis; neurodegeneration
    DOI:  https://doi.org/10.1073/pnas.2018770118
  13. Circ Res. 2021 May 14. 128(10): 1487-1513
    Cardiac Energy Metabolism in Heart Failure.
    Gary D Lopaschuk, Qutuba G Karwi, Rong Tian, Adam R Wende, E Dale Abel.
      Alterations in cardiac energy metabolism contribute to the severity of heart failure. However, the energy metabolic changes that occur in heart failure are complex and are dependent not only on the severity and type of heart failure present but also on the co-existence of common comorbidities such as obesity and type 2 diabetes. The failing heart faces an energy deficit, primarily because of a decrease in mitochondrial oxidative capacity. This is partly compensated for by an increase in ATP production from glycolysis. The relative contribution of the different fuels for mitochondrial ATP production also changes, including a decrease in glucose and amino acid oxidation, and an increase in ketone oxidation. The oxidation of fatty acids by the heart increases or decreases, depending on the type of heart failure. For instance, in heart failure associated with diabetes and obesity, myocardial fatty acid oxidation increases, while in heart failure associated with hypertension or ischemia, myocardial fatty acid oxidation decreases. Combined, these energy metabolic changes result in the failing heart becoming less efficient (ie, a decrease in cardiac work/O2 consumed). The alterations in both glycolysis and mitochondrial oxidative metabolism in the failing heart are due to both transcriptional changes in key enzymes involved in these metabolic pathways, as well as alterations in NAD redox state (NAD+ and nicotinamide adenine dinucleotide levels) and metabolite signaling that contribute to posttranslational epigenetic changes in the control of expression of genes encoding energy metabolic enzymes. Alterations in the fate of glucose, beyond flux through glycolysis or glucose oxidation, also contribute to the pathology of heart failure. Of importance, pharmacological targeting of the energy metabolic pathways has emerged as a novel therapeutic approach to improving cardiac efficiency, decreasing the energy deficit and improving cardiac function in the failing heart.
    Keywords:  acetylation; diabetic cardiomyopathies; insulin resistance; ketones; mitochondria
    DOI:  https://doi.org/10.1161/CIRCRESAHA.121.318241
  14. Curr Cardiol Rep. 2021 May 10. 23(6): 70
    Quantification of Myocardial Mitochondrial Membrane Potential Using PET.
    Matthieu Pelletier-Galarneau, Felicitas J Detmer, Yoann Petibon, Marc Normandin, Chao Ma, Nathaniel M Alpert, Georges El Fakhri.
       PURPOSE OF REVIEW: To present a method enabling in vivo quantification of tissue membrane potential (ΔΨT), a proxy of mitochondrial membrane potential (ΔΨm), to review the origin and role of ΔΨm, and to highlight potential applications of myocardial ΔΨT imaging.
    RECENT FINDINGS: Radiolabelled lipophilic cations have been used for decades to measure ΔΨm in vitro. Using similar compounds labeled with positron emitters and appropriate compartment modeling, this technique now allows in vivo quantification of ΔΨT with positron emission tomography. Studies have confirmed the feasibility of measuring myocardial ΔΨT in both animals and humans. In addition, ΔΨT showed very low variability among healthy subjects, suggesting that this method could allow detection of relatively small pathological changes. In vivo assessment of myocardial ΔΨT provides a new tool to study the pathophysiology of cardiovascular diseases and has the potential to serve as a new biomarker to assess disease stage, prognosis, and response to therapy.
    Keywords:  Heart failure; Mitochondria; Mitochondrial membrane potential; Positron emission tomography; Tissue membrane potential; Triphenylphosphonium
    DOI:  https://doi.org/10.1007/s11886-021-01500-8
  15. NPJ Parkinsons Dis. 2021 May 12. 7(1): 39
    Imaging mass cytometry reveals generalised deficiency in OXPHOS complexes in Parkinson's disease.
    Chun Chen, David McDonald, Alasdair Blain, Ashwin Sachdeva, Laura Bone, Anna L M Smith, Charlotte Warren, Sarah J Pickett, Gavin Hudson, Andrew Filby, Amy E Vincent, Doug M Turnbull, Amy K Reeve.
      Here we report the application of a mass spectrometry-based technology, imaging mass cytometry, to perform in-depth proteomic profiling of mitochondrial complexes in single neurons, using metal-conjugated antibodies to label post-mortem human midbrain sections. Mitochondrial dysfunction, particularly deficiency in complex I has previously been associated with the degeneration of dopaminergic neurons in Parkinson's disease. To further our understanding of the nature of this dysfunction, and to identify Parkinson's disease specific changes, we validated a panel of antibodies targeting subunits of all five mitochondrial oxidative phosphorylation complexes in dopaminergic neurons from Parkinson's disease, mitochondrial disease, and control cases. Detailed analysis of the expression profile of these proteins, highlighted heterogeneity between individuals. There is a widespread decrease in expression of all complexes in Parkinson's neurons, although more severe in mitochondrial disease neurons, however, the combination of affected complexes varies between the two groups. We also provide evidence of a potential neuronal response to mitochondrial dysfunction through a compensatory increase in mitochondrial mass. This study highlights the use of imaging mass cytometry in the assessment and analysis of expression of oxidative phosphorylation proteins, revealing the complexity of deficiencies of these proteins within individual neurons which may contribute to and drive neurodegeneration in Parkinson's disease.
    DOI:  https://doi.org/10.1038/s41531-021-00182-x
  16. G3 (Bethesda). 2021 May 11. pii: jkab165. [Epub ahead of print]
    An age-downregulated ribosomal RpS28 protein variant regulates the muscle proteome.
    Jianqin Jiao, Kanisha Kavdia, Vishwajeeth Pagala, Lance Palmer, David Finkelstein, Yiping Fan, Junmin Peng, Fabio Demontis.
      Recent evidence indicates that the composition of the ribosome is heterogeneous and that multiple types of specialized ribosomes regulate the synthesis of specific protein subsets. In Drosophila, we find that expression of the ribosomal RpS28 protein variants RpS28a and RpS28-like preferentially occurs in the germline, a tissue resistant to aging, and that it significantly declines in skeletal muscle during aging. Muscle-specific overexpression of RpS28a at levels similar to those seen in the germline decreases early mortality and promotes the synthesis of a subset of proteins with known anti-aging roles, some of which have preferential expression in the germline. These findings indicate a contribution of specialized ribosomal proteins to the regulation of the muscle proteome during aging.
    Keywords:  Drosophila; aging; germline; protein translation; ribosome; skeletal muscle
    DOI:  https://doi.org/10.1093/g3journal/jkab165
  17. Sci Adv. 2021 May;pii: eabg4000. [Epub ahead of print]7(20):
    Cork-in-bottle mechanism of inhibitor binding to mammalian complex I.
    Injae Chung, Riccardo Serreli, Jason B Cross, M Emilia Di Francesco, Joseph R Marszalek, Judy Hirst.
      Mitochondrial complex I (NADH:ubiquinone oxidoreductase), a major contributor of free energy for oxidative phosphorylation, is increasingly recognized as a promising drug target for ischemia-reperfusion injury, metabolic disorders, and various cancers. Several pharmacologically relevant but structurally unrelated small molecules have been identified as specific complex I inhibitors, but their modes of action remain unclear. Here, we present a 3.0-Å resolution cryo-electron microscopy structure of mammalian complex I inhibited by a derivative of IACS-010759, which is currently in clinical development against cancers reliant on oxidative phosphorylation, revealing its unique cork-in-bottle mechanism of inhibition. We combine structural and kinetic analyses to deconvolute cross-species differences in inhibition and identify the structural motif of a "chain" of aromatic rings as a characteristic that promotes inhibition. Our findings provide insights into the importance of π-stacking residues for inhibitor binding in the long substrate-binding channel in complex I and a guide for future biorational drug design.
    DOI:  https://doi.org/10.1126/sciadv.abg4000
  18. Mech Ageing Dev. 2021 May 11. pii: S0047-6374(21)00071-3. [Epub ahead of print] 111499
    Progresses in both basic research and clinical trials of NAD+ in Parkinson's disease.
    María José Pérez, Pascale Baden, Michela Deleidi.
      The decline of nicotinamide adenine dinucleotide (NAD+) levels is a hallmark of aging in multiple organisms and tissues, including the human brain. Hence, agents that increase intracellular NAD + could have beneficial effects in aging and age-related neurodegenerative diseases. Disturbances in NAD + metabolism have also been observed in Parkinson's disease (PD), supporting a link between neuronal bioenergetics failure and disease pathogenesis. Here, we review emerging findings revealing key roles for NAD + and related metabolites in experimental models of dopaminergic neurodegeneration and in PD patients. We discuss how increased NAD + levels might ameliorate disease phenotypes by restoring neuronal mitochondrial energy metabolism, promoting cellular proteostasis, and modulating the immune system. Finally, we describe ongoing clinical trials targeting NAD + in PD and highlight the need for further investigations to better delineate the association between NAD+, brain aging and disease, and optimal strategies for efficiently and safely raising NAD + levels. A more comprehensive understanding of the basic mechanisms linking NAD+, energy metabolism, and PD, and of the impact of life-long NAD + targeting strategies, are critical to inform future clinical applications.
    Keywords:  NAD+; Parkinson's disease; aging; energy metabolism; mitochondria
    DOI:  https://doi.org/10.1016/j.mad.2021.111499
  19. J Mol Cell Cardiol. 2021 May 11. pii: S0022-2828(21)00098-5. [Epub ahead of print]
    Increasing fatty acid oxidation elicits a sex-dependent response in failing mouse hearts.
    Julia Ritterhoff, Timothy S McMillen, Outi Villet, Sara Young, Stephen C Kolwicz, Taurence Senn, Arianne Caudal, Rong Tian.
       BACKGROUND: Reduced fatty acid oxidation (FAO) is a hallmark of metabolic remodeling in heart failure. Enhancing mitochondrial long-chain fatty acid uptake by Acetyl-CoA carboxylase 2 (ACC2) deletion increases FAO and prevents cardiac dysfunction during chronic stresses, but therapeutic efficacy of this approach has not been determined.
    METHODS: Male and female ACC2f/f-MCM (ACC2KO) and their respective littermate controls were subjected to chronic pressure overload by TAC surgery. Tamoxifen injection 3 weeks after TAC induced ACC2 deletion and increased FAO in ACC2KO mice with pathological hypertrophy.
    RESULTS: ACC2 deletion in mice with pre-existing cardiac pathology promoted FAO in female and male hearts, but improved cardiac function only in female mice. In males, pressure overload caused a downregulation in the mitochondrial oxidative function. Stimulating FAO by ACC2 deletion caused unproductive acyl-carnitine accumulation, which failed to improve cardiac energetics. In contrast, mitochondrial oxidative capacity was sustained in female pressure overloaded hearts and ACC2 deletion improved myocardial energetics. Mechanistically, we revealed a sex-dependent regulation of PPARα signaling pathway in heart failure, which accounted for the differential response to ACC2 deletion.
    CONCLUSION: Metabolic remodeling in the failing heart is sex-dependent which could determine the response to metabolic intervention. The findings suggest that both mitochondrial oxidative capacity and substrate preference should be considered for metabolic therapy of heart failure.
    Keywords:  Energy metabolism; Fatty acid oxidation; Heart failure
    DOI:  https://doi.org/10.1016/j.yjmcc.2021.05.004
  20. Nat Genet. 2021 May 13.
    An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability.
    Lei Li, Kai-Lieh Huang, Yipeng Gao, Ya Cui, Gao Wang, Nathan D Elrod, Yumei Li, Yiling Elaine Chen, Ping Ji, Fanglue Peng, William K Russell, Eric J Wagner, Wei Li.
      Genome-wide association studies have identified thousands of noncoding variants associated with human traits and diseases. However, the functional interpretation of these variants is a major challenge. Here, we constructed a multi-tissue atlas of human 3'UTR alternative polyadenylation (APA) quantitative trait loci (3'aQTLs), containing approximately 0.4 million common genetic variants associated with the APA of target genes, identified in 46 tissues isolated from 467 individuals (Genotype-Tissue Expression Project). Mechanistically, 3'aQTLs can alter poly(A) motifs, RNA secondary structure and RNA-binding protein-binding sites, leading to thousands of APA changes. Our CRISPR-based experiments indicate that such 3'aQTLs can alter APA regulation. Furthermore, we demonstrate that mapping 3'aQTLs can identify APA regulators, such as La-related protein 4. Finally, 3'aQTLs are colocalized with approximately 16.1% of trait-associated variants and are largely distinct from other QTLs, such as expression QTLs. Together, our findings show that 3'aQTLs contribute substantially to the molecular mechanisms underlying human complex traits and diseases.
    DOI:  https://doi.org/10.1038/s41588-021-00864-5
  21. Nature. 2021 May 12.
    Mitochondrial TNAP controls thermogenesis by hydrolysis of phosphocreatine.
    Yizhi Sun, Janane F Rahbani, Mark P Jedrychowski, Christopher L Riley, Sara Vidoni, Dina Bogoslavski, Bo Hu, Phillip A Dumesic, Xing Zeng, Alex B Wang, Nelson H Knudsen, Caroline R Kim, Anthony Marasciullo, José L Millán, Edward T Chouchani, Lawrence Kazak, Bruce M Spiegelman.
      Adaptive thermogenesis has attracted much attention because of its ability to increase systemic energy expenditure and to counter obesity and diabetes1-3. Recent data have indicated that thermogenic fat cells use creatine to stimulate futile substrate cycling, dissipating chemical energy as heat4,5. This model was based on the super-stoichiometric relationship between the amount of creatine added to mitochondria and the quantity of oxygen consumed. Here we provide direct evidence for the molecular basis of this futile creatine cycling activity in mice. Thermogenic fat cells have robust phosphocreatine phosphatase activity, which is attributed to tissue-nonspecific alkaline phosphatase (TNAP). TNAP hydrolyses phosphocreatine to initiate a futile cycle of creatine dephosphorylation and phosphorylation. Unlike in other cells, TNAP in thermogenic fat cells is localized to the mitochondria, where futile creatine cycling occurs. TNAP expression is powerfully induced when mice are exposed to cold conditions, and its inhibition in isolated mitochondria leads to a loss of futile creatine cycling. In addition, genetic ablation of TNAP in adipocytes reduces whole-body energy expenditure and leads to rapid-onset obesity in mice, with no change in movement or feeding behaviour. These data illustrate the critical role of TNAP as a phosphocreatine phosphatase in the futile creatine cycle.
    DOI:  https://doi.org/10.1038/s41586-021-03533-z
  22. Neurosci Lett. 2021 May 07. pii: S0304-3940(21)00318-9. [Epub ahead of print] 135940
    Mild hypothermia facilitates mitochondrial transfer from astrocytes to injured neurons during oxygen-glucose deprivation/reoxygenation.
    Xiaowei Li, Yanli Li, Zhiqiang Zhang, Qinghu Bian, Zan Gao, Shan Zhang.
      Mitochondrial dysfunction is now considered an important sign of neuronal death during cerebral ischemia/reperfusion (I/R) injury. Studies have shown that the transfer of mitochondria from astrocytes to injured neurons contributes to endogenous neuroprotection after stroke. Basic and clinical studies have shown that mild hypothermia exerts a clear protective effect on neurons after cerebral ischemic injury, but the role of mild hypothermia in this endogenous neuroprotective mechanism remains unclear. Here, we established a neuronal cell oxygen-glucose deprivation (OGD)/reoxygenation (OGD/R)-induced injury model and explored the effect of mild hypothermia on the transfer of mitochondria from astrocytes to injured neurons. Astrocytes in the hypothermia group (33 °C) released more functional mitochondria into the extracellular medium than those in the normal temperature group (37 °C). Compared with cells in the normal temperature group, OGD-injured neuronal cells in the mild hypothermia group exhibited an increased intracellular ATP content, mitochondrial membrane potential (MMP) and cellular viability and a decreased death rate after the addition of astrocyte-derived conditioned medium. Based on the results of this study, mild hypothermia promotes endogenous neuroprotective effects through a mechanism related to functional mitochondria released from astrocytes into the extracellular space and transferred into injured neurons.
    Keywords:  Mild hypothermia; Mitochondrial transfer; Oxygen-glucose deprivation/reoxygenation
    DOI:  https://doi.org/10.1016/j.neulet.2021.135940
  23. Mol Genet Metab. 2021 May 07. pii: S1096-7192(21)00700-9. [Epub ahead of print]
    REVIEW: Practical strategies to maintain anabolism by intravenous nutritional management in children with inborn metabolic diseases.
    Kimberly A Kripps, Peter R Baker, Janet A Thomas, Heather E Skillman, Laurie Bernstein, Sommer Gaughan, Casey Burns, Curtis R Coughlin, Shawn E McCandless, Austin A Larson, Aaina Kochar, Chelsey F Stillman, Erica M Wymore, Ellie G Hendricks, Michael Woontner, Johan L K Van Hove.
      One of the most vital elements of management for patients with inborn errors of intermediary metabolism is the promotion of anabolism, the state in which the body builds new components, and avoidance of catabolism, the state in which the body breaks down its own stores for energy. Anabolism is maintained through the provision of a sufficient supply of substrates for energy, as well as critical building blocks of essential amino acids, essential fatty acids, and vitamins for synthetic function and growth. Patients with metabolic diseases are at risk for decompensation during prolonged fasting, which often occurs during illnesses in which enteral intake is compromised. During these times, intravenous nutrition must be supplied to fully meet the specific nutritional needs of the patient. We detail our approach to intravenous management for metabolic patients and its underlying rationale. This generally entails a combination of intravenous glucose and lipid as well as early introduction of protein and essential vitamins. We exemplify the utility of our approach in case studies, as well as scenarios and specific disorders which require a more careful administration of nutritional substrates or a modification of macronutrient ratios.
    Keywords:  Anabolism; Caloric requirements; Catabolism; Essential amino acid deficiency; Inborn errors of metabolism; Intravenous; Ketogenic diet; Protein restriction; Treatment approach
    DOI:  https://doi.org/10.1016/j.ymgme.2021.04.007
  24. Mol Genet Metab Rep. 2021 Jun;27 100757
    Long term follow-up of the dietary intake in propionic acidemia.
    A Mobarak, S Stockler, R Salvarinova, C Van Karnebeek, G Horvath.
      Long-term dietary management of Propionic acidemia (PA) includes natural protein restriction, and supplementation with medical formula enriched with leucine (Leu) and free of valine (Val), isoleucine (Ileu), methionine (Met), and threonine (Thr). As PA medical formulas have high leucine content, concerns started to arise regarding potential long-term health risks of unbalanced leucine intake. PA patients have chronically low plasma levels of Ile and Val, which led to the paradoxical need to supplement with propiogenic single amino acids (AAs). Our report takes a retrospective look at the long-term dietary management of four patients and its reflection on their plasma amino acids. The patients' total protein intake was above the recommended dietary allowance (RDA) and had a high Leu/Val and Leu/Ile intake ratios in diet. Despite adequate total protein intake, patients had chronically low plasma Ile and Val and a high plasma Leu/Val and Leu/Ile ratios, which could be attributed to high Leu intake. We conclude that the best approach to PA dietary management is to only use medical formula with patients not meeting their RDA through natural protein, and to monitor plasma amino acids levels closely.
    Keywords:  Dietary management; Leucine intake; Propionic acidemia
    DOI:  https://doi.org/10.1016/j.ymgmr.2021.100757
  25. Cell Death Dis. 2021 May 12. 12(5): 475
    Mitochondrial fission and mitophagy are independent mechanisms regulating ischemia/reperfusion injury in primary neurons.
    Anthony R Anzell, Garrett M Fogo, Zoya Gurm, Sarita Raghunayakula, Joseph M Wider, Kathleen J Maheras, Katlynn J Emaus, Timothy D Bryson, Madison Wang, Robert W Neumar, Karin Przyklenk, Thomas H Sanderson.
      Mitochondrial dynamics and mitophagy are constitutive and complex systems that ensure a healthy mitochondrial network through the segregation and subsequent degradation of damaged mitochondria. Disruption of these systems can lead to mitochondrial dysfunction and has been established as a central mechanism of ischemia/reperfusion (I/R) injury. Emerging evidence suggests that mitochondrial dynamics and mitophagy are integrated systems; however, the role of this relationship in the context of I/R injury remains unclear. To investigate this concept, we utilized primary cortical neurons isolated from the novel dual-reporter mitochondrial quality control knockin mice (C57BL/6-Gt(ROSA)26Sortm1(CAG-mCherry/GFP)Ganl/J) with conditional knockout (KO) of Drp1 to investigate changes in mitochondrial dynamics and mitophagic flux during in vitro I/R injury. Mitochondrial dynamics was quantitatively measured in an unbiased manner using a machine learning mitochondrial morphology classification system, which consisted of four different classifications: network, unbranched, swollen, and punctate. Evaluation of mitochondrial morphology and mitophagic flux in primary neurons exposed to oxygen-glucose deprivation (OGD) and reoxygenation (OGD/R) revealed extensive mitochondrial fragmentation and swelling, together with a significant upregulation in mitophagic flux. Furthermore, the primary morphology of mitochondria undergoing mitophagy was classified as punctate. Colocalization using immunofluorescence as well as western blot analysis revealed that the PINK1/Parkin pathway of mitophagy was activated following OGD/R. Conditional KO of Drp1 prevented mitochondrial fragmentation and swelling following OGD/R but did not alter mitophagic flux. These data provide novel evidence that Drp1 plays a causal role in the progression of I/R injury, but mitophagy does not require Drp1-mediated mitochondrial fission.
    DOI:  https://doi.org/10.1038/s41419-021-03752-2
  26. Nat Commun. 2021 May 12. 12(1): 2736
    Mitofusin-2 stabilizes adherens junctions and suppresses endothelial inflammation via modulation of β-catenin signaling.
    Young-Mee Kim, Sarah Krantz, Ankit Jambusaria, Peter T Toth, Hyung-Geun Moon, Isuru Gunarathna, Gye Young Park, Jalees Rehman.
      Endothelial barrier integrity is ensured by the stability of the adherens junction (AJ) complexes comprised of vascular endothelial (VE)-cadherin as well as accessory proteins such as β-catenin and p120-catenin. Disruption of the endothelial barrier due to disassembly of AJs results in tissue edema and the influx of inflammatory cells. Using three-dimensional structured illumination microscopy, we observe that the mitochondrial protein Mitofusin-2 (Mfn2) co-localizes at the plasma membrane with VE-cadherin and β-catenin in endothelial cells during homeostasis. Upon inflammatory stimulation, Mfn2 is sulfenylated, the Mfn2/β-catenin complex disassociates from the AJs and Mfn2 accumulates in the nucleus where Mfn2 negatively regulates the transcriptional activity of β-catenin. Endothelial-specific deletion of Mfn2 results in inflammatory activation, indicating an anti-inflammatory role of Mfn2 in vivo. Our results suggest that Mfn2 acts in a non-canonical manner to suppress the inflammatory response by stabilizing cell-cell adherens junctions and by binding to the transcriptional activator β-catenin.
    DOI:  https://doi.org/10.1038/s41467-021-23047-6
  27. Nat Commun. 2021 May 10. 12(1): 2616
    FUNDC1-dependent mitochondria-associated endoplasmic reticulum membranes are involved in angiogenesis and neoangiogenesis.
    Cheng Wang, Xiaoyan Dai, Shengnan Wu, Wenjing Xu, Ping Song, Kai Huang.
      FUN14 domain-containing protein 1 (FUNDC1) is an integral mitochondrial outer-membrane protein, and mediates the formation of mitochondria-associated endoplasmic reticulum membranes (MAMs). This study aims to determine the contributions of FUNDC1-mediated MAMs to angiogenesis in vitro and in vivo. In cultured endothelial cells, VEGF significantly increases the formation of MAMs and MAM-related proteins, including FUNDC1. Endothelial cell-specific deletion of FUNDC1, which disrupts MAM formation in endothelial cells, lowers VEGFR2 expression and reduces tube formation, spheroid-sprouting, and functional blood vessel formation in vitro and in vivo. Conversely, increased MAM formation using MAM linkers mimics the effects of VEGF and promotes endothelial angiogenesis. Mechanistically, increased MAMs formation led to increased levels of Ca2+ in cytosol, promoted the phosphorylation of serum response factor (SRF) and enhanced the binding of SRF to VEGFR2 promoter, resulting in increased VEGFR2 production, with consequent angiogenesis. Moreover, blocking FUNDC1-related MAM formation with a cell-penetrating inhibitory peptide significantly suppresses the expressions of downstream angiogenic genes and inhibits tumor angiogenesis. We conclude that decreased MAMs formation by silencing FUNDC1 can inhibit angiogenesis by decreasing VEGFR2 expression, and targeting FUNDC1-dependent MAMs might be a promising approach for treating human disorders characterized by defective angiogenesis.
    DOI:  https://doi.org/10.1038/s41467-021-22771-3
  28. Nature. 2021 May 12.
    A mitochondrial gatekeeper that helps cells escape death by ferroptosis.
    Javier Garcia-Bermudez, Kıvanç Birsoy.
      
    Keywords:  Cancer; Cell biology
    DOI:  https://doi.org/10.1038/d41586-021-01203-8
  29. Front Aging Neurosci. 2021 ;13 660843
    Mitochondrial CHCHD2: Disease-Associated Mutations, Physiological Functions, and Current Animal Models.
    Teresa R Kee, Pamela Espinoza Gonzalez, Jessica L Wehinger, Mohammed Zaheen Bukhari, Aizara Ermekbaeva, Apoorva Sista, Peter Kotsiviras, Tian Liu, David E Kang, Jung-A A Woo.
      Rare mutations in the mitochondrial protein coiled-coil-helix-coiled-coil-helix domain containing 2 (CHCHD2) are associated with Parkinson's disease (PD) and other Lewy body disorders. CHCHD2 is a bi-organellar mediator of oxidative phosphorylation, playing crucial roles in regulating electron flow in the mitochondrial electron transport chain and acting as a nuclear transcription factor for a cytochrome c oxidase subunit (COX4I2) and itself in response to hypoxic stress. CHCHD2 also regulates cell migration and differentiation, mitochondrial cristae structure, and apoptosis. In this review, we summarize the known disease-associated mutations of CHCHD2 in Asian and Caucasian populations, the physiological functions of CHCHD2, how CHCHD2 mutations contribute to α-synuclein pathology, and current animal models of CHCHD2. Further, we discuss the necessity of continued investigation into the divergent functions of CHCHD2 and CHCHD10 to determine how mutations in these similar mitochondrial proteins contribute to different neurodegenerative diseases.
    Keywords:  CHCHD10; CHCHD2; Lewy body disorders; Parkinson’s disease; mitochondria
    DOI:  https://doi.org/10.3389/fnagi.2021.660843
  30. J Mol Cell Biol. 2021 May 14. pii: mjab030. [Epub ahead of print]
    Knockdown of insulin-like growth factor 2 gene disrupts mitochondrial functions in the liver.
    Weiwei Gui, Yiyi Zhu, Shuiya Sun, WeiFen Zhu, Bowen Tan, Hanxin Zhao, Chengxin Shang, Fenping Zheng, Xihua Lin, Hong Li.
      Even though insulin-like growth factor 2 (IGF2) has been reported to be overexpressed in nonalcoholic fatty liver disease (NAFLD), its role in the progression of NAFLD and the potential mechanism remain largely unclear. Using in vitro models, we found that IGF2 was the key overexpressed gene in steatosis, suggesting a possible association between IGF2 and NAFLD. Interestingly, loss-of-function experiments revealed that inhibition of IGF2 protein impaired mitochondrial biogenesis and respiration. It additionally disrupted the expression changes of mitochondrial fusion and fission-related proteins necessary in maintaining mitochondrial homeostasis. Consistently, IGF2 knockdown reduced the mitochondrial membrane potential and increased the production of reactive oxygen species. Mechanistically, IGF2 regulates mitochondrial functions by modulating the expression of SIRT1 and its downstream gene PGC1α. This research opens a new frontier on the role of IGF2 in energy metabolism, which potentially participates in the development of NAFLD. As such, IGF2 is a potential therapeutic target against NAFLD.
    Keywords:  Insulin-like growth factor 2; mitochondrial function; nonalcoholic fatty liver
    DOI:  https://doi.org/10.1093/jmcb/mjab030
  31. Mol Cell Pediatr. 2021 May 09. 8(1): 6
    Identification of a novel MICU1 nonsense variant causes myopathy with extrapyramidal signs in an Iranian consanguineous family.
    Fatemeh Bitarafan, Mehrnoosh Khodaeian, Elham Amjadi Sardehaei, Fatemeh Zahra Darvishi, Navid Almadani, Yalda Nilipour, Masoud Garshasbi.
       BACKGROUND: Ca2+ as a universal second messenger regulates basic biological functions including cell cycle, cell proliferation, cell differentiation, and cell death. Lack of the protein mitochondrial calcium uptake1 (MICU1), which has been regarded as a gatekeeper of Ca ions, leads to the abnormal mitochondrial Ca2+ handling, excessive production of reactive oxygen species (ROS), and increased cell death. Mutations in MICU1 gene causes a very rare neuromuscular disease, myopathy with extrapyramidal signs (MPXPS), due to primary alterations in mitochondrial calcium signaling which demonstrates the key role of mitochondrial Ca2+ uptake. To date, 13 variants have been reported in MICU1 gene in 44 patients presented with the vast spectrum of symptoms.
    CASE PRESENTATION: Here, we report a 44-year-old Iranian patient presented with learning disability, muscle weakness, easy fatigability, reduced tendon reflexes, ataxia, gait disturbance, elevated hepatic transaminases, elevated serum creatine kinase (CK), and elevated lactate dehydrogenase (LDH). We identified a novel nonsense variant c.385C>T; p.(R129*) in MICU1 gene by whole exome sequencing (WES) and segregation analysis.
    CONCLUSIONS: Our finding along with previous studies provides more evidence on the clinical presentation of the disease caused by pathogenic mutations in MICU1. Finding more variants and expanding the spectrum of the disease increases the diagnostic rate of molecular testing in screening of this kind of diseases and in turn improves the quality of counseling for at risk couples and helps them to minimize the risks of having affected children.
    Keywords:  Ca2+; Mitochondrial calcium uptake 1 (MICU1); Myopathy with extrapyramidal signs (MPXPS); Whole exome sequencing (WES)
    DOI:  https://doi.org/10.1186/s40348-021-00116-w
  32. J Cell Biol. 2021 Jul 05. pii: e202010006. [Epub ahead of print]220(7):
    USP19 promotes hypoxia-induced mitochondrial division via FUNDC1 at ER-mitochondria contact sites.
    Peiyuan Chai, Yiru Cheng, Chuyi Hou, Lei Yin, Donghui Zhang, Yingchun Hu, Qingzhou Chen, Pengli Zheng, Junlin Teng, Jianguo Chen.
      The ER tethers tightly to mitochondria and the mitochondrial protein FUNDC1 recruits Drp1 to ER-mitochondria contact sites, subsequently facilitating mitochondrial fission and preventing mitochondria from undergoing hypoxic stress. However, the mechanisms by which the ER modulates hypoxia-induced mitochondrial fission are poorly understood. Here, we show that USP19, an ER-resident deubiquitinase, accumulates at ER-mitochondria contact sites under hypoxia and promotes hypoxia-induced mitochondrial division. In response to hypoxia, USP19 binds to and deubiquitinates FUNDC1 at ER-mitochondria contact sites, which facilitates Drp1 oligomerization and Drp1 GTP-binding and hydrolysis activities, thereby promoting mitochondrial division. Our findings reveal a unique hypoxia response pathway mediated by an ER protein that regulates mitochondrial dynamics.
    DOI:  https://doi.org/10.1083/jcb.202010006
  33. Elife. 2021 May 11. pii: e65192. [Epub ahead of print]10
    The role of sigma 1 receptor in organization of endoplasmic reticulum signaling microdomains.
    Vladimir Zhemkov, Jonathon A Ditlev, Wan-Ru Lee, Mikaela Wilson, Jen Liou, Michael K Rosen, Ilya Bezprozvanny.
      Sigma 1 receptor (S1R) is a 223-amino-acid-long transmembrane endoplasmic reticulum (ER) protein. S1R modulates activity of multiple effector proteins and is a well-established drug target. However, signaling functions of S1R in cells are poorly understood. Here, we test the hypothesis that biological activity of S1R in cells can be explained by its ability to interact with cholesterol and to form cholesterol-enriched microdomains in the ER membrane. By performing experiments in reduced reconstitution systems, we demonstrate direct effects of cholesterol on S1R clustering. We identify a novel cholesterol-binding motif in the transmembrane region of human S1R. Mutations of this motif impair association of recombinant S1R with cholesterol beads, affect S1R clustering in vitro and disrupt S1R subcellular localization. We demonstrate that S1R-induced membrane microdomains have increased local membrane thickness and that increased local cholesterol concentration and/or membrane thickness in these microdomains can modulate signaling of inositol-requiring enzyme 1α in the ER. Further, S1R agonists cause disruption of S1R clusters, suggesting that biological activity of S1R agonists is linked to remodeling of ER membrane microdomains. Our results provide novel insights into S1R-mediated signaling mechanisms in cells.
    Keywords:  cell biology; cholesterol; endoplasmic reticulum; human; lipid microdomains; mitochondria-associated membranes; neurodegeneration; neuroscience; sigma-1 receptor
    DOI:  https://doi.org/10.7554/eLife.65192
  34. Nat Commun. 2021 May 10. 12(1): 2580
    Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data.
    Greta Pintacuda, Frederik H Lassen, Yu-Han H Hsu, April Kim, Jacqueline M Martín, Edyta Malolepsza, Justin K Lim, Nadine Fornelos, Kevin C Eggan, Kasper Lage.
      Combining genetic and cell-type-specific proteomic datasets can generate biological insights and therapeutic hypotheses, but a technical and statistical framework for such analyses is lacking. Here, we present an open-source computational tool called Genoppi (lagelab.org/genoppi) that enables robust, standardized, and intuitive integration of quantitative proteomic results with genetic data. We use Genoppi to analyze 16 cell-type-specific protein interaction datasets of four proteins (BCL2, TDP-43, MDM2, PTEN) involved in cancer and neurological disease. Through systematic quality control of the data and integration with published protein interactions, we show a general pattern of both cell-type-independent and cell-type-specific interactions across three cancer cell types and one human iPSC-derived neuronal cell type. Furthermore, through the integration of proteomic and genetic datasets in Genoppi, our results suggest that the neuron-specific interactions of these proteins are mediating their genetic involvement in neurodegenerative diseases. Importantly, our analyses suggest that human iPSC-derived neurons are a relevant model system for studying the involvement of BCL2 and TDP-43 in amyotrophic lateral sclerosis.
    DOI:  https://doi.org/10.1038/s41467-021-22648-5
  35. J Inherit Metab Dis. 2021 May 02.
    No effect of resveratrol in patients with mitochondrial myopathy: A cross-over randomized controlled trial.
    Nicoline Løkken, Tahmina Khawajazada, Jesper Helbo Storgaard, Daniel Raaschou-Pedersen, Maja Elling Christensen, Tessa Munkeboe Hornsyld, Thomas Krag, Mette C Ørngreen, John Vissing.
      Mitochondrial myopathies (MM) are caused by mutations that typically affect genes involved in oxidative phosphorylation. Main symptoms are exercise intolerance and fatigue. Currently, there is no specific treatment for MM. Resveratrol (RSV) is a nutritional supplement that in preclinical studies has been shown to stimulate mitochondrial function. We hypothesized that RSV could improve exercise capacity in patients with MM. The study design was randomized, double-blind, cross-over and placebo-controlled. Eleven patients with genetically verified MM were randomized to receive either 1000 mg/day RSV or placebo (P) for 8 weeks followed by a 4-week washout and then the opposite treatment. Primary outcomes were changes in heart rate (HR) during submaximal cycling exercise and peak oxygen utilization (VO2 max) during maximal exercise. Secondary outcomes included reduction in perceived exertion, changes in lactate concentrations, self-rated function (SF-36) and fatigue scores (FSS), activities of electron transport chain complexes I and IV in mononuclear cells and mitochondrial biomarkers in muscle tissue among others. There were no significant differences in primary and secondary outcomes between treatments. Mean HR changes were -0.3 ± 4.3 (RSV) vs 1.8 ± 5.0 bpm (P), P = .241. Mean VO2 max changes were 0.7 ± 1.4 (RSV) vs -0.2 ± 2.3 mL/min/kg (P), P = .203. The study provides evidence that 1000 mg RSV daily is ineffective in improving exercise capacity in adults with MM. These findings indicate that previous in vitro studies suggesting a therapeutic potential for RSV in MM, do not translate into clinically meaningful effects in vivo.
    Keywords:  RCT; exercise capacity; mitochondrial metabolism; mitochondrial myopathy; resveratrol
    DOI:  https://doi.org/10.1002/jimd.12393
  36. Neuropathol Appl Neurobiol. 2021 May 11.
    Prodromal sensory neuropathy in Pink1-/- SNCAA53T double mutant Parkinson mice.
    Lucie Valek, Bao Tran, Annett Wilken-Schmitz, Sandra Trautmann, Juliana Heidler, Tobias Schmid, Bernhard Brüne, Dominique Thomas, Thomas Deller, Gerd Geisslinger, Georg Auburger, Irmgard Tegeder.
       AIMS: Parkinson's Disease (PD) is frequently associated with a prodromal sensory neuropathy manifesting with sensory loss and chronic pain. We have recently shown that PD-associated sensory neuropathy in patients is associated with high levels of glucosylceramides. Here, we assessed the underlying pathology and mechanisms in Pink1-/- SNCAA53T double mutant mice.
    METHODS: We studied nociceptive and olfactory behaviour and the neuropathology of dorsal root ganglia (DRGs), including ultrastructure, mitochondrial respiration, transcriptomes, outgrowth and calcium currents of primary neurons, and tissue ceramides and sphingolipids before the onset of a PD-like disease that spontaneously develops in Pink1-/- SNCAA53T double mutant mice after 15 months of age.
    RESULTS: Similar to PD patients, Pink1-/- SNCAA53T mice developed a progressive prodromal sensory neuropathy with a loss of thermal sensitivity starting as early as four months of age. In analogy to human plasma, lipid analyses revealed an accumulation of glucosylceramides (GlcCer) in the DRGs and sciatic nerves, which was associated with pathologic mitochondria, impairment of mitochondrial respiration, and deregulation of transient receptor potential and TRPV and TRPA channels at mRNA, protein and functional levels in DRGs. Direct exposure of DRG neurons to GlcCer caused transient hyperexcitability, followed by a premature decline of the viability of sensory neurons cultures upon repeated GlcCer application.
    CONCLUSIONS: The results suggest that pathological GlcCer contribute to prodromal sensory disease in PD mice via mitochondrial damage and calcium channel hyperexcitability. GlcCer-associated sensory neuron pathology might be amenable to GlcCer lowering therapeutic strategies.
    Keywords:  PTEN inducible kinase 1; Parkinson's Disease; alpha-synuclein; glucosylceramides; innate immunity; mitochondrial respiration; pain; sensory loss
    DOI:  https://doi.org/10.1111/nan.12734
  37. Brain Commun. 2021 ;3(2): fcab036
    A novel remitting leukodystrophy associated with a variant in FBP2.
    Agnieszka Gizak, Susann Diegmann, Steffi Dreha-Kulaczewski, Janusz Wiśniewski, Przemysław Duda, Andreas Ohlenbusch, Brenda Huppke, Marco Henneke, Wolfgang Höhne, Janine Altmüller, Holger Thiele, Peter Nürnberg, Dariusz Rakus, Jutta Gärtner, Peter Huppke.
      Leukodystrophies are genetic disorders of cerebral white matter that almost exclusively have a progressive disease course. We became aware of three members of a family with a disorder characterized by a sudden loss of all previously acquired abilities around 1 year of age followed by almost complete recovery within 2 years. Cerebral MRI and myelin sensitive imaging showed a pronounced demyelination that progressed for several months despite signs of clinical improvement and was followed by remyelination. Exome sequencing did not-identify any mutations in known leukodystrophy genes but revealed a heterozygous variant in the FBP2 gene, c.343G>A, p. Val115Met, shared by the affected family members. Cerebral MRI of other family members demonstrated similar white matter abnormalities in all carriers of the variant in FBP2. The FBP2 gene codes for muscle fructose 1,6-bisphosphatase, an enzyme involved in gluconeogenesis that is highly expressed in brain tissue. Biochemical analysis showed that the variant has a dominant negative effect on enzymatic activity, substrate affinity, cooperativity and thermal stability. Moreover, it also affects the non-canonical functions of muscle fructose 1,6-bisphosphatase involved in mitochondrial protection and regulation of several nuclear processes. In patients' fibroblasts, muscle fructose 1,6-bisphosphatase shows no colocalization with mitochondria and nuclei leading to increased reactive oxygen species production and a disturbed mitochondrial network. In conclusion, the results of this study indicate that the variant in FBP2 disturbs cerebral energy metabolism and is associated with a novel remitting leukodystrophy.
    Keywords:  leukodystrophy; muscle fructose 1,6-bisphosphatase; remitting
    DOI:  https://doi.org/10.1093/braincomms/fcab036
  38. Proc Natl Acad Sci U S A. 2021 May 18. pii: e2100298118. [Epub ahead of print]118(20):
    Structure elucidation of the elusive Enzyme I monomer reveals the molecular mechanisms linking oligomerization and enzymatic activity.
    Trang T Nguyen, Rodolfo Ghirlando, Julien Roche, Vincenzo Venditti.
      Enzyme I (EI) is a phosphotransferase enzyme responsible for converting phosphoenolpyruvate (PEP) into pyruvate. This reaction initiates a five-step phosphorylation cascade in the bacterial phosphotransferase (PTS) transduction pathway. Under physiological conditions, EI exists in an equilibrium between a functional dimer and an inactive monomer. The monomer-dimer equilibrium is a crucial factor regulating EI activity and the phosphorylation state of the overall PTS. Experimental studies of EI's monomeric state have yet been hampered by the dimer's high thermodynamic stability, which prevents its characterization by standard structural techniques. In this study, we modified the dimerization domain of EI (EIC) by mutating three amino acids involved in the formation of intersubunit salt bridges. The engineered variant forms an active dimer in solution that can bind and hydrolyze PEP. Using hydrostatic pressure as an additional perturbation, we were then able to study the complete dissociation of the variant from 1 bar to 2.5 kbar in the absence and the presence of EI natural ligands. Backbone residual dipolar couplings collected under high-pressure conditions allowed us to determine the conformational ensemble of the isolated EIC monomeric state in solution. Our calculations reveal that three catalytic loops near the dimerization interface become unstructured upon monomerization, preventing the monomeric enzyme from binding its natural substrate. This study provides an atomic-level characterization of EI's monomeric state and highlights the role of the catalytic loops as allosteric connectors controlling both the activity and oligomerization of the enzyme.
    Keywords:  carbon metabolism; enzyme regulation; high pressure; phosphotransferase system; solution NMR
    DOI:  https://doi.org/10.1073/pnas.2100298118
  39. Front Cell Dev Biol. 2021 ;9 627135
    The Protective Effect of 1,25(OH)2D3 on Myocardial Function is Mediated via Sirtuin 3-Regulated Fatty Acid Metabolism.
    Jingxin Yang, Yalin Zhang, Yiming Pan, Can Sun, Zuwang Liu, Ning Liu, Yu Fu, Xiaofeng Li, Ye Li, Juan Kong.
      Energy substrate imbalance is a major cause of cardiac dysfunction. Vitamin D/vitamin D receptor (VD/VDR) deficiency is involved in the pathogenesis of various cardiac diseases; however, the exact underlying mechanism remains unclear. The aim of this study was to investigate whether vitamin D modulates mitochondrial fatty acid oxidase via sirtuin 3 signaling to protect the myocardium. 1-Alpha-hydroxylase-defficient mice exhibited a high metabolic rate and lower myocardial contractility than wild-type mice. Sirtuin 3 upregulation was detected in high-fat diet-fed mice receiving vitamin D3 compared with that in high-fat diet-fed mice. Both sirtuin 3 blockade and knockout inhibited the VD/VDR-induced downregulation of fatty acid oxidase in myocardial mitochondria. VD/VDR suppressed fatty acid metabolism by upregulating sirtuin 3 and lowering mitochondrial fat uptake, thereby improving myocardial function and balancing energy substrates, rather than by altering fat endocytosis and exocytosis.
    Keywords:  Sirtuin 3; Vitamin D; cardiac function; fatty acid metabolism; mitochondria
    DOI:  https://doi.org/10.3389/fcell.2021.627135
  40. Elife. 2021 May 14. pii: e64943. [Epub ahead of print]10
    A subcellular map of the human kinome.
    Haitao Zhang, Xiaolei Cao, Mei Tang, Guoxuan Zhong, Yuan Si, Haidong Li, Feifeng Zhu, Qinghua Liao, Liuju Li, Jianhui Zhao, Jia Feng, Shuaifeng Li, Chenliang Wang, Manuel Kaulich, Fangwei Wang, Liangyi Chen, Li Li, Zongping Xia, Tingbo Liang, Huasong Lu, Xin-Hua Feng, Bin Zhao.
      The human kinome comprises 538 kinases playing essential functions by catalyzing protein phosphorylation. Annotation of subcellular distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 cellular compartments. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a similar condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other structures. Furthermore, KA demonstrated the role of liquid-liquid phase separation in formation of kinase condensates. Identification of MOK as a mitochondrial kinase revealed its function in cristae dynamics, respiration, and oxidative stress response. Although limited by possible mislocalization due to overexpression or epitope tagging, this subcellular map of the kinome can be used to refine regulatory mechanisms involving protein phosphorylation.
    Keywords:  biochemistry; cell biology; chemical biology; human
    DOI:  https://doi.org/10.7554/eLife.64943
  41. Trends Biochem Sci. 2021 May 06. pii: S0968-0004(21)00066-9. [Epub ahead of print]
    Detecting and Rescuing Stalled Ribosomes.
    Matthew C J Yip, Sichen Shao.
      Ribosomes that stall inappropriately during protein synthesis harbor proteotoxic components linked to cellular stress and neurodegenerative diseases. Molecular mechanisms that rescue stalled ribosomes must selectively detect rare aberrant translational complexes and process the heterogeneous components. Ribosome-associated quality control pathways eliminate problematic messenger RNAs and nascent proteins on stalled translational complexes. In addition, recent studies have uncovered general principles of stall recognition upstream of quality control pathways and fail-safe mechanisms that ensure nascent proteome integrity. Here, we discuss developments in our mechanistic understanding of the detection and rescue of stalled ribosomal complexes in eukaryotes.
    Keywords:  ribosome collisions; ribosome stalling; ribosome-associated quality control (RQC)
    DOI:  https://doi.org/10.1016/j.tibs.2021.03.008
  42. Nat Commun. 2021 May 11. 12(1): 2665
    Nicotinamide riboside attenuates age-associated metabolic and functional changes in hematopoietic stem cells.
    Xuan Sun, Benjamin Cao, Marina Naval-Sanchez, Tony Pham, Yu Bo Yang Sun, Brenda Williams, Shen Y Heazlewood, Nikita Deshpande, Jinhua Li, Felix Kraus, James Rae, Quan Nguyen, Hamed Yari, Jan Schröder, Chad K Heazlewood, Madeline Fulton, Jessica Hatwell-Humble, Kaustav Das Gupta, Ronan Kapetanovic, Xiaoli Chen, Matthew J Sweet, Robert G Parton, Michael T Ryan, Jose M Polo, Christian M Nefzger, Susan K Nilsson.
      With age, hematopoietic stem cells (HSC) undergo changes in function, including reduced regenerative potential and loss of quiescence, which is accompanied by a significant expansion of the stem cell pool that can lead to haematological disorders. Elevated metabolic activity has been implicated in driving the HSC ageing phenotype. Here we show that nicotinamide riboside (NR), a form of vitamin B3, restores youthful metabolic capacity by modifying mitochondrial function in multiple ways including reduced expression of nuclear encoded metabolic pathway genes, damping of mitochondrial stress and a decrease in mitochondrial mass and network-size. Metabolic restoration is dependent on continuous NR supplementation and accompanied by a shift of the aged transcriptome towards the young HSC state, more youthful bone marrow cellular composition and an improved regenerative capacity in a transplant setting. Consequently, NR administration could support healthy ageing by re-establishing a more youthful hematopoietic system.
    DOI:  https://doi.org/10.1038/s41467-021-22863-0
  43. Neurol Genet. 2021 Apr;7(2): e559
    LBSL: Case Series and DARS2 Variant Analysis in Early Severe Forms With Unexpected Presentations.
    Menno D Stellingwerff, Sonia Figuccia, Emanuele Bellacchio, Karin Alvarez, Claudia Castiglioni, Pinar Topaloglu, Chloe A Stutterd, Corrie E Erasmus, Amarilis Sanchez-Valle, Sebastien Lebon, Sarah Hughes, Thomas Schmitt-Mechelke, Gessica Vasco, Gabriel Chow, Elisa Rahikkala, Cristina Dallabona, Cecilia Okuma, Chiara Aiello, Paola Goffrini, Truus E M Abbink, Enrico S Bertini, Marjo S Van der Knaap.
       Objective: Leukoencephalopathy with brainstem and spinal cord involvement and lactate elevation (LBSL) is regarded a relatively mild leukodystrophy, diagnosed by characteristic long tract abnormalities on MRI and biallelic variants in DARS2, encoding mitochondrial aspartyl-tRNA synthetase (mtAspRS). DARS2 variants in LBSL are almost invariably compound heterozygous; in 95% of cases, 1 is a leaky splice site variant in intron 2. A few severely affected patients, still fulfilling the MRI criteria, have been described. We noticed highly unusual MRI presentations in 15 cases diagnosed by WES. We examined these cases to determine whether they represent consistent novel LBSL phenotypes.
    Methods: We reviewed clinical features, MRI abnormalities, and gene variants and investigated the variants' impact on mtAspRS structure and mitochondrial function.
    Results: We found 2 MRI phenotypes: early severe cerebral hypoplasia/atrophy (9 patients, group 1) and white matter abnormalities without long tract involvement (6 patients, group 2). With antenatal onset, microcephaly, and arrested development, group 1 patients were most severely affected. DARS2 variants were severer than for classic LBSL and severer for group 1 than group 2. All missense variants hit mtAspRS regions involved in tRNAAsp binding, aspartyl-adenosine-5'-monophosphate binding, and/or homodimerization. Missense variants expressed in the yeast DARS2 ortholog showed severely affected mitochondrial function.
    Conclusions: DARS2 variants are associated with highly heterogeneous phenotypes. New MRI presentations are profound cerebral hypoplasia/atrophy and white matter abnormalities without long tract involvement. Our findings have implications for diagnosis and understanding disease mechanisms, pointing at dominant neuronal/axonal involvement in severe cases. In line with this conclusion, activation of biallelic DARS2 null alleles in conditional transgenic mice leads to massive neuronal apoptosis.
    DOI:  https://doi.org/10.1212/NXG.0000000000000559
  44. Elife. 2021 May 14. pii: e62233. [Epub ahead of print]10
    A TORC1-histone axis regulates chromatin organisation and non-canonical induction of autophagy to ameliorate ageing.
    Yu-Xuan Lu, Jennifer C Regan, Jacqueline Eßer, Lisa F Drews, Thomas Weinseis, Julia Stinn, Oliver Hahn, Richard A Miller, Sebastian Grönke, Linda Partridge.
      Age-related changes to histone levels are seen in many species. However, it is unclear whether changes to histone expression could be exploited to ameliorate the effects of ageing in multicellular organisms. Here we show that inhibition of mTORC1 by the lifespan-extending drug rapamycin increases expression of histones H3 and H4 post-transcriptionally, through eIF3-mediated translation. Elevated expression of H3/H4 in intestinal enterocytes in Drosophila alters chromatin organization, induces intestinal autophagy through transcriptional regulation, prevents age-related decline in the intestine. Importantly, it also mediates rapamycin-induced longevity and intestinal health. Histones H3/H4 regulate expression of an autophagy cargo adaptor Bchs (WDFY3 in mammals), increased expression of which in enterocytes mediates increased H3/H4-dependent healthy longevity. In mice, rapamycin treatment increases expression of histone proteins and Wdfy3 transcription, and alters chromatin organisation in the small intestine, suggesting the mTORC1-histone axis is at least partially conserved in mammals and may offer new targets for anti-ageing interventions.
    Keywords:  D. melanogaster; cell biology; chromosomes; gene expression; mouse
    DOI:  https://doi.org/10.7554/eLife.62233
  45. Curr Protoc. 2021 May;1(5): e126
    Polygenic Risk Scores.
    Michael D Osterman, Tyler G Kinzy, Jessica N Cooke Bailey.
      As genome-wide association studies have continued to identify loci associated with complex traits, the implications of and necessity for proper use of these findings, including prediction of disease risk, have become apparent. Many complex diseases have numerous associated loci with detectable effects implicating risk for or protection from disease. A common contemporary approach to using this information for disease prediction is through the application of genetic risk scores. These scores estimate an individual's liability for a specific outcome by aggregating the effects of associated loci into a single measure as described in the previous version of this article. Although genetic risk scores have traditionally included variants that meet criteria for genome-wide significance, an extension known as the polygenic risk score has been developed to include the effects of more variants across the entire genome. Here, we describe common methods and software packages for calculating and interpreting polygenic risk scores. In this revised version of the article, we detail information that is needed to perform a polygenic risk score analysis, considerations for planning the analysis and interpreting results, as well as discussion of the limitations based on the choices made. We also provide simulated sample data and a walkthrough for four different polygenic risk score software. © 2021 Wiley Periodicals LLC.
    Keywords:  area under the curve; complex traits and diseases; disease prediction; genetic risk score; polygenic risk score
    DOI:  https://doi.org/10.1002/cpz1.126
  46. Lab Chip. 2021 May 11.
    Multimodal detection of protein isoforms and nucleic acids from low starting cell numbers.
    Elisabet Rosàs-Canyelles, Andrew J Modzelewski, Ana E Gomez Martinez, Alisha Geldert, Anjali Gopal, Lin He, Amy E Herr.
      Protein isoforms play a key role in disease progression and arise from mechanisms involving multiple molecular subtypes, including DNA, mRNA and protein. Recently introduced multimodal assays successfully link genomes and transcriptomes to protein expression landscapes. However, the specificity of the protein measurement relies on antibodies alone, leading to major challenges when measuring different isoforms of the same protein. Here we utilize microfluidic design to perform same-cell profiling of DNA, mRNA and protein isoforms (triBlot) on low starting cell numbers (1-100 s of cells). After fractionation lysis, cytoplasmic proteins are resolved by molecular mass during polyacrylamide gel electrophoresis (PAGE), adding a degree of specificity to the protein measurement, while nuclei are excised from the device in sections termed "gel pallets" for subsequent off-chip nucleic acid analysis. By assaying TurboGFP-transduced glioblastoma cells, we observe a strong correlation between protein expression prior to lysis and immunoprobed protein. We measure both mRNA and DNA from retrieved nuclei, and find that mRNA levels correlate with protein abundance in TurboGFP-expressing cells. Furthermore, we detect the presence of TurboGFP isoforms differing by an estimated <1 kDa in molecular mass, demonstrating the ability to discern different proteoforms with the same antibody probe. By directly relating nucleic acid modifications to protein isoform expression in 1-100 s of cells, the triBlot assay holds potential as a screening tool for novel biomarkers in diseases driven by protein isoform expression.
    DOI:  https://doi.org/10.1039/d1lc00073j
  47. Nat Protoc. 2021 May 10.
    Extraction of nuclei from archived postmortem tissues for single-nucleus sequencing applications.
    Malosree Maitra, Corina Nagy, Anjali Chawla, Yu Chang Wang, Camila Nascimento, Matthew Suderman, Jean-François Théroux, Naguib Mechawar, Jiannis Ragoussis, Gustavo Turecki.
      Single-cell and single-nucleus sequencing techniques are a burgeoning field with various biological, biomedical and clinical applications. Numerous high- and low-throughput methods have been developed for sequencing the RNA and DNA content of single cells. However, for all these methods, the key requirement is high-quality input of a single-cell or single-nucleus suspension. Preparing such a suspension is the limiting step when working with fragile, archived tissues of variable quality. This hurdle can prevent such tissues from being extensively investigated with single-cell technologies. We describe a protocol for preparing single-nucleus suspensions within the span of a few hours that reliably works for multiple postmortem and archived tissue types using standard laboratory equipment. The stages of the protocol include tissue preparation and dissociation, nuclei extraction, and nuclei concentration assessment and capture. The protocol is comparable to other published protocols but does not require fluorescence-assisted nuclei sorting (FANS) or ultracentrifugation. The protocol can be carried out by a competent graduate student familiar with basic laboratory techniques and equipment. Moreover, these preparations are compatible with single-nucleus (sn)RNA-seq and assay for transposase-accessible chromatin (ATAC)-seq using the 10X Genomics Chromium system. The protocol reliably results in efficient capture of single nuclei for high-quality snRNA-seq libraries.
    DOI:  https://doi.org/10.1038/s41596-021-00514-4
  48. Mol Metab. 2021 May 11. pii: S2212-8778(21)00094-6. [Epub ahead of print] 101249
    Histone H3K9 butyrylation is regulated by dietary fat and stress via an acyl-CoA dehydrogenase short chain-dependent mechanism.
    Zhi Yang, Minzhen He, Julianne Austin, Jessica Pfleger, Maha Abdellatif.
       OBJECTIVE: We previously reported that β-oxidation enzymes are present in the nucleus in close proximity to transcriptionally active promoters. Thus, we hypothesized that the fatty acid intermediate, butyryl-CoA, is the substrate for histone butyrylation and its abundance is regulated by acyl-CoA dehydrogenase short chain (ACADS). The objective of this study was to determine the genomic distribution of H3K9-butyryl (H3K9Bu) and its regulation by dietary fat, stress, and ACADS, and its correlation with gene expression under these conditions.
    METHODS AND RESULTS: Using genome-wide chromatin immunoprecipitation-sequencing (ChIP-Seq), we show that H3K9Bu is abundant at all transcriptionally active promoters, where, paradoxically, it is most enriched in mice fed a fat-free versus a high-fat diet. Deletion of fatty acid synthetase (FASN) abolished H3K9Bu in cells maintained in a glucose-rich, but not fatty acid-rich, medium, signifying that fatty acid synthesis from carbohydrates substitutes for dietary fat as a source butyryl-CoA. Meanwhile, a high-fat diet induced an increase in ACADS expression that accompanied the decrease in H3K9Bu. Conversely, deletion of ACADS increased H3K9Bu in human cells and mouse hearts, and reversed high-fat- and stress-induced reduction in promoter-H3K9Bu, whose abundance coincided with diminished stress-regulated gene expression, as revealed by RNA-sequencing. In contrast, H3K9-acetyl (H3K9Ac) abundance was minimally impacted by diet.
    CONCLUSION: Promoter H3K9 butyrylation is a major histone modification, which is negatively regulated by high-fat and stress in an ACADS-dependent fashion, and moderates stress-regulated gene expression.
    DOI:  https://doi.org/10.1016/j.molmet.2021.101249
  49. Front Neurosci. 2021 ;15 679568
    Gene4PD: A Comprehensive Genetic Database of Parkinson's Disease.
    Bin Li, Guihu Zhao, Qiao Zhou, Yali Xie, Zheng Wang, Zhenghuan Fang, Bin Lu, Lixia Qin, Yuwen Zhao, Rui Zhang, Li Jiang, Hongxu Pan, Yan He, Xiaomeng Wang, Tengfei Luo, Yi Zhang, Yijing Wang, Qian Chen, Zhenhua Liu, Jifeng Guo, Beisha Tang, Jinchen Li.
      Parkinson's disease (PD) is a complex neurodegenerative disorder with a strong genetic component. A growing number of variants and genes have been reported to be associated with PD; however, there is no database that integrate different type of genetic data, and support analyzing of PD-associated genes (PAGs). By systematic review and curation of multiple lines of public studies, we integrate multiple layers of genetic data (rare variants and copy-number variants identified from patients with PD, associated variants identified from genome-wide association studies, differentially expressed genes, and differential DNA methylation genes) and age at onset in PD. We integrated five layers of genetic data (8302 terms) with different levels of evidences from more than 3,000 studies and prioritized 124 PAGs with strong or suggestive evidences. These PAGs were identified to be significantly interacted with each other and formed an interconnected functional network enriched in several functional pathways involved in PD, suggesting these genes may contribute to the pathogenesis of PD. Furthermore, we identified 10 genes were associated with a juvenile-onset (age ≤ 30 years), 11 genes were associated with an early-onset (age of 30-50 years), whereas another 10 genes were associated with a late-onset (age > 50 years). Notably, the AAOs of patients with loss of function variants in five genes were significantly lower than that of patients with deleterious missense variants, while patients with VPS13C (P = 0.01) was opposite. Finally, we developed an online database named Gene4PD (http://genemed.tech/gene4pd) which integrated published genetic data in PD, the PAGs, and 63 popular genomic data sources, as well as an online pipeline for prioritize risk variants in PD. In conclusion, Gene4PD provides researchers and clinicians comprehensive genetic knowledge and analytic platform for PD, and would also improve the understanding of pathogenesis in PD.
    Keywords:  Gene4PD database; PD-associated genes; Parkinson’s disease; age at onset; genetic variant
    DOI:  https://doi.org/10.3389/fnins.2021.679568
  50. BMC Bioinformatics. 2021 May 10. 22(1): 236
    DR2S: an integrated algorithm providing reference-grade haplotype sequences from heterozygous samples.
    Steffen Klasberg, Alexander H Schmidt, Vinzenz Lange, Gerhard Schöfl.
       BACKGROUND: High resolution HLA genotyping of donors and recipients is a crucially important prerequisite for haematopoetic stem-cell transplantation and relies heavily on the quality and completeness of immunogenetic reference sequence databases of allelic variation.
    RESULTS: Here, we report on DR2S, an R package that leverages the strengths of two sequencing technologies-the accuracy of next-generation sequencing with the read length of third-generation sequencing technologies like PacBio's SMRT sequencing or ONT's nanopore sequencing-to reconstruct fully-phased high-quality full-length haplotype sequences. Although optimised for HLA and KIR genes, DR2S is applicable to all loci with known reference sequences provided that full-length sequencing data is available for analysis. In addition, DR2S integrates supporting tools for easy visualisation and quality control of the reconstructed haplotype to ensure suitability for submission to public allele databases.
    CONCLUSIONS: DR2S is a largely automated workflow designed to create high-quality fully-phased reference allele sequences for highly polymorphic gene regions such as HLA or KIR. It has been used by biologists to successfully characterise and submit more than 500 HLA alleles and more than 500 KIR alleles to the IPD-IMGT/HLA and IPD-KIR databases.
    Keywords:  HLA; KIR; Phasing; Reference sequencing; Sequence analysis; Third-generation sequencing
    DOI:  https://doi.org/10.1186/s12859-021-04153-0
  51. Wiley Interdiscip Rev RNA. 2021 May 13. e1663
    Detecting the epitranscriptome.
    Anwesha Sarkar, William Gasperi, Ulrike Begley, Steven Nevins, Sabrina M Huber, Peter C Dedon, Thomas J Begley.
      RNA modifications and their corresponding epitranscriptomic writer and eraser enzymes regulate gene expression. Altered RNA modification levels, dysregulated writers, and sequence changes that disrupt epitranscriptomic marks have been linked to mitochondrial and neurological diseases, cancer, and multifactorial disorders. The detection of epitranscriptomics marks is challenging, but different next generation sequencing (NGS)-based and mass spectrometry-based approaches have been used to identify and quantitate the levels of individual and groups of RNA modifications. NGS and mass spectrometry-based approaches have been coupled with chemical, antibody or enzymatic methodologies to identify modifications in most RNA species, mapped sequence contexts and demonstrated the dynamics of specific RNA modifications, as well as the collective epitranscriptome. While epitranscriptomic analysis is currently limited to basic research applications, specific approaches for the detection of individual RNA modifications and the epitranscriptome have potential biomarker applications in detecting human conditions and diseases. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Processing > tRNA Processing RNA in Disease and Development > RNA in Disease.
    Keywords:  RNA modification detection; epitranscriptomics; human disease
    DOI:  https://doi.org/10.1002/wrna.1663
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