bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2022–10–30
fifty-two papers selected by
Catalina Vasilescu, Helmholz Munich
  1. Human mtRF1 terminates COX1 translation and its ablation induces mitochondrial ribosome-associated quality control.
  2. Pathogenic mitochondrial DNA 3243A>G mutation: From genetics to phenotype.
  3. A hypomorphic variant in the translocase of the outer mitochondrial membrane complex subunit TOMM7 causes short stature and developmental delay.
  4. A SARM1/mitochondrial feedback loop drives neuropathogenesis in a Charcot-Marie-Tooth disease type 2A rat model.
  5. Structure and functionality of a multimeric human COQ7:COQ9 complex.
  6. Mitophagy in the aging nervous system.
  7. Cardiolipin Regulates Mitochondrial Ultrastructure and Function in Mammalian Cells.
  8. Mitochondrial Ca2+ Uniporter haploinsufficiency enhances long-term potentiation at hippocampal mossy fibre synapses.
  9. TRPV4 interacts with MFN2 and facilitates endoplasmic reticulum-mitochondrial contact points for Ca2+-buffering.
  10. Early embryonic lethality in complex I associated p.L104P Nubpl mutant mice.
  11. Genotypic and phenotypic spectrum of infantile liver failure due to pathogenic TRMU variants.
  12. Mitochondrial proteotoxicity: implications and ubiquitin-dependent quality control mechanisms.
  13. Metabolic clearance of oxaloacetate and mitochondrial complex II respiration: Divergent control in skeletal muscle and brown adipose tissue.
  14. Mitochondrial dysfunction reactivates α-fetoprotein expression that drives copper-dependent immunosuppression in mitochondrial disease models.
  15. COQ8A-Ataxia as a Manifestation of Primary Coenzyme Q Deficiency.
  16. The absence of Parkin does not promote dopamine or mitochondrial dysfunction in PolgAD257A/D257A mitochondrial mutator mice.
  17. Pooled image-base screening of mitochondria with microraft isolation distinguishes pathogenic mitofusin 2 mutations.
  18. SIAH proteins regulate the degradation and intra-mitochondrial aggregation of PINK1: Implications for mitochondrial pathology in Parkinson's disease.
  19. Mitoguardin-2-mediated lipid transfer preserves mitochondrial morphology and lipid droplet formation.
  20. Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish.
  21. Stimulating Mitochondrial Biogenesis with Deoxyribonucleosides Increases Functional Capacity in ECHS1-Deficient Cells.
  22. OPA1 drives macrophage metabolism and functional commitment via p65 signaling.
  23. Direct evidence of CRISPR-Cas9-mediated mitochondrial genome editing.
  24. Autosomal recessive progeroid syndrome due to homozygosity for a TOMM7 variant.
  25. BCL7A-containing SWI/SNF/BAF complexes modulate mitochondrial bioenergetics during neural progenitor differentiation.
  26. Miro GTPase domains regulate the assembly of the mitochondrial motor-adaptor complex.
  27. Cytoplasmic and mitochondrial aminoacyl-tRNA synthetases differentially regulate lifespan in Caenorhabditis elegans.
  28. Synthetic metabolism without the TCA cycle.
  29. Mitochondrial disease registries worldwide: A scoping review.
  30. Role of mitochondria-associated endoplasmic reticulum membranes in insulin sensitivity, energy metabolism, and contraction of skeletal muscle.
  31. Mitochondrial Dysfunction and Neurodegenerative Disorders: Role of Nutritional Supplementation.
  32. Human platelet mitochondria improve the mitochondrial and cardiac function of donor heart.
  33. Mitochondrial transplantation: opportunities and challenges in the treatment of obesity, diabetes, and nonalcoholic fatty liver disease.
  34. Experimental Investigations on the Structure of Yeast Mitochondrial Pyruvate Carriers.
  35. Application of WGCNA and PloGO2 in the Analysis of Complex Proteomic Data.
  36. Targeting Mitochondrial Function with Chemoptogenetics.
  37. Role of extracellular vesicles in mitochondrial eye diseases.
  38. Establishment of a platform for measuring mitochondrial oxygen consumption rate for cardiac mitochondrial toxicity.
  39. Functional spectrum and specificity of mitochondrial ferredoxins FDX1 and FDX2.
  40. Gene-based burden analysis of damaging private variants in PRKN, PARK7 and PINK1 in Parkinson's disease cohorts of European descent.
  41. Multifaceted mitochondrial quality control in brown adipose tissue.
  42. Metabolomic fingerprinting of renal disease progression in Bardet-Biedl syndrome reveals mitochondrial dysfunction in kidney tubular cells.
  43. A small molecule M1 promotes optic nerve regeneration to restore target-specific neural activity and visual function.
  44. A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies.
  45. The role of mitochondria in the pathogenesis of Kawasaki disease.
  46. Frankenstein Cas9: engineering improved gene editing systems.
  47. Mechanism and modeling of human disease-associated near-exon intronic variants that perturb RNA splicing.
  48. Informing variant assessment using structured evidence from prior classifications (PS1, PM5, and PVS1 sequence variant interpretation criteria).
  49. Quick tips for re-using metabolomics data.
  50. Rapid and comprehensive diagnostic method for repeat expansion diseases using nanopore sequencing.
  51. Annotation of spatially resolved single-cell data with STELLAR.
  52. SPiP: Splicing Prediction Pipeline, a machine learning tool for massive detection of exonic and intronic variant effect on mRNA splicing.
  1. Nat Commun. 2022 Oct 27. 13(1): 6406
    Human mtRF1 terminates COX1 translation and its ablation induces mitochondrial ribosome-associated quality control.
    Franziska Nadler, Elena Lavdovskaia, Angelique Krempler, Luis Daniel Cruz-Zaragoza, Sven Dennerlein, Ricarda Richter-Dennerlein.
      Translation termination requires release factors that read a STOP codon in the decoding center and subsequently facilitate the hydrolysis of the nascent peptide chain from the peptidyl tRNA within the ribosome. In human mitochondria eleven open reading frames terminate in the standard UAA or UAG STOP codon, which can be recognized by mtRF1a, the proposed major mitochondrial release factor. However, two transcripts encoding for COX1 and ND6 terminate in the non-conventional AGA or AGG codon, respectively. How translation termination is achieved in these two cases is not known. We address this long-standing open question by showing that the non-canonical release factor mtRF1 is a specialized release factor that triggers COX1 translation termination, while mtRF1a terminates the majority of other mitochondrial translation events including the non-canonical ND6. Loss of mtRF1 leads to isolated COX deficiency and activates the mitochondrial ribosome-associated quality control accompanied by the degradation of COX1 mRNA to prevent an overload of the ribosome rescue system. Taken together, these results establish the role of mtRF1 in mitochondrial translation, which had been a mystery for decades, and lead to a comprehensive picture of translation termination in human mitochondria.
    DOI:  https://doi.org/10.1038/s41467-022-34088-w
  2. Front Genet. 2022 ;13 951185
    Pathogenic mitochondrial DNA 3243A>G mutation: From genetics to phenotype.
    Danyang Li, Chunmei Liang, Tao Zhang, Jordan Lee Marley, Weiwei Zou, Muqing Lian, Dongmei Ji.
      The mitochondrial DNA (mtDNA) m.3243A>G mutation is one of the most common pathogenic mtDNA variants, showing complex genetics, pathogenic molecular mechanisms, and phenotypes. In recent years, the prevention of mtDNA-related diseases has trended toward precision medicine strategies, such as preimplantation genetic diagnosis (PGD) and mitochondrial replacement therapy (MRT). These techniques are set to allow the birth of healthy children, but clinical implementation relies on thorough insights into mtDNA genetics. The genotype and phenotype of m.3243A>G vary greatly from mother to offspring, which compromises genetic counseling for the disease. This review is the first to systematically elaborate on the characteristics of the m.3243A>G mutation, from genetics to phenotype and the relationship between them, as well as the related influencing factors and potential strategies for preventing disease. These perceptions will provide clarity for clinicians providing genetic counseling to m.3243A>G patients.
    Keywords:  fertility counseling; genetics; heteroplasmy; m.3243A>G; phenotype
    DOI:  https://doi.org/10.3389/fgene.2022.951185
  3. HGG Adv. 2023 Jan 12. 4(1): 100148
    A hypomorphic variant in the translocase of the outer mitochondrial membrane complex subunit TOMM7 causes short stature and developmental delay.
    Cameron Young, Dominyka Batkovskyte, Miyuki Kitamura, Maria Shvedova, Yutaro Mihara, Jun Akiba, Wen Zhou, Anna Hammarsjö, Gen Nishimura, Shuichi Yatsuga, Giedre Grigelioniene, Tatsuya Kobayashi.
      Mitochondrial diseases are a heterogeneous group of genetic disorders caused by pathogenic variants in genes encoding gene products that regulate mitochondrial function. These genes are located either in the mitochondrial or in the nuclear genome. The TOMM7 gene encodes a regulatory subunit of the translocase of outer mitochondrial membrane (TOM) complex that plays an essential role in translocation of nuclear-encoded mitochondrial proteins into mitochondria. We report an individual with a homozygous variant in TOMM7 (c.73T>C, p.Trp25Arg) that presented with a syndromic short stature, skeletal abnormalities, muscle hypotonia, microvesicular liver steatosis, and developmental delay. Analysis of mouse models strongly suggested that the identified variant is hypomorphic because mice homozygous for this variant showed a milder phenotype than those with homozygous Tomm7 deletion. These Tomm7 mutant mice show pathological changes consistent with mitochondrial dysfunction, including growth defects, severe lipoatrophy, and lipid accumulation in the liver. These mice die prematurely following a rapidly progressive weight loss during the last week of their lives. Tomm7 deficiency causes a unique alteration in mitochondrial function; despite the bioenergetic deficiency, mutant cells show increased oxygen consumption with normal responses to electron transport chain (ETC) inhibitors, suggesting that Tomm7 deficiency leads to an uncoupling between oxidation and ATP synthesis without impairing the function of the tricarboxylic cycle metabolism or ETC. This study presents evidence that a hypomorphic variant in one of the genes encoding a subunit of the TOM complex causes mitochondrial disease.
    Keywords:  TOM; TOMM7; developmental delay; fatty liver; growth plate; lipoatrophy; mitochondria; mouse model; skeletal dysplasia; translocase
    DOI:  https://doi.org/10.1016/j.xhgg.2022.100148
  4. J Clin Invest. 2022 Oct 26. pii: e161566. [Epub ahead of print]
    A SARM1/mitochondrial feedback loop drives neuropathogenesis in a Charcot-Marie-Tooth disease type 2A rat model.
    Yurie Yamada, Amy Strickland, Yo Sasaki, A Joseph Bloom, Aaron DiAntonio, Jeffrey Milbrandt.
      Charcot-Marie-Tooth disease (CMT) type 2A is an axonal neuropathy caused by mutations in the mitofusin 2 (MFN2) gene. MFN2 mutations result in profound mitochondrial abnormalities, but the mechanism underlying axonal pathology is unknown. SARM1, the central executioner of axon degeneration, can induce neuropathy and is activated by dysfunctional mitochondria. We tested the role of SARM1 in a rat model carrying a dominant CMT2A mutation (Mfn2H361Y) that exhibits progressive dying-back axonal degeneration, NMJ abnormalities, muscle atrophy, and mitochondrial abnormalities, all hallmarks of the human disease. We generated Sarm1 knockout and Mfn2H361Y, Sarm1 double mutant rats and find that deletion of Sarm1 rescues axonal, synaptic, muscle, and functional phenotypes, demonstrating that SARM1 is responsible for much of the neuropathology in this model. Despite the presence of mutant MFN2 protein in these double mutant rats, loss of SARM1 also dramatically suppressed many mitochondrial defects, including the number, size, and cristae density defects of synaptic mitochondria. This surprising finding indicates that dysfunctional mitochondria activate SARM1, and activated SARM1 feeds back on mitochondria to exacerbate mitochondrial pathology. As such, this work identifies SARM1 inhibition as an exciting therapeutic candidate for the treatment of CMT2A and other neurodegenerative diseases with prominent mitochondrial pathology.
    Keywords:  Neurodegeneration; Neurological disorders; Neuromuscular disease; Neuroscience
    DOI:  https://doi.org/10.1172/JCI161566
  5. Mol Cell. 2022 Oct 21. pii: S1097-2765(22)00960-1. [Epub ahead of print]
    Structure and functionality of a multimeric human COQ7:COQ9 complex.
    Mateusz Manicki, Halil Aydin, Luciano A Abriata, Katherine A Overmyer, Rachel M Guerra, Joshua J Coon, Matteo Dal Peraro, Adam Frost, David J Pagliarini.
      Coenzyme Q (CoQ) is a redox-active lipid essential for core metabolic pathways and antioxidant defense. CoQ is synthesized upon the mitochondrial inner membrane by an ill-defined "complex Q" metabolon. Here, we present structure-function analyses of a lipid-, substrate-, and NADH-bound complex comprising two complex Q subunits: the hydroxylase COQ7 and the lipid-binding protein COQ9. We reveal that COQ7 adopts a ferritin-like fold with a hydrophobic channel whose substrate-binding capacity is enhanced by COQ9. Using molecular dynamics, we further show that two COQ7:COQ9 heterodimers form a curved tetramer that deforms the membrane, potentially opening a pathway for the CoQ intermediates to translocate from the bilayer to the proteins' lipid-binding sites. Two such tetramers assemble into a soluble octamer with a pseudo-bilayer of lipids captured within. Together, these observations indicate that COQ7 and COQ9 cooperate to access hydrophobic precursors within the membrane and coordinate subsequent synthesis steps toward producing CoQ.
    Keywords:  COQ7; COQ9; coenzyme Q; di-iron proteins; mitochondria; protein-lipid complex; protein-membrane interaction; quinone biosynthesis
    DOI:  https://doi.org/10.1016/j.molcel.2022.10.003
  6. Front Cell Dev Biol. 2022 ;10 978142
    Mitophagy in the aging nervous system.
    Anna Rappe, Thomas G McWilliams.
      Aging is characterised by the progressive accumulation of cellular dysfunction, stress, and inflammation. A large body of evidence implicates mitochondrial dysfunction as a cause or consequence of age-related diseases including metabolic disorders, neuropathies, various forms of cancer and neurodegenerative diseases. Because neurons have high metabolic demands and cannot divide, they are especially vulnerable to mitochondrial dysfunction which promotes cell dysfunction and cytotoxicity. Mitophagy neutralises mitochondrial dysfunction, providing an adaptive quality control strategy that sustains metabolic homeostasis. Mitophagy has been extensively studied as an inducible stress response in cultured cells and short-lived model organisms. In contrast, our understanding of physiological mitophagy in mammalian aging remains extremely limited, particularly in the nervous system. The recent profiling of mitophagy reporter mice has revealed variegated vistas of steady-state mitochondrial destruction across different tissues. The discovery of patients with congenital autophagy deficiency provokes further intrigue into the mechanisms that underpin neural integrity. These dimensions have considerable implications for targeting mitophagy and other degradative pathways in age-related neurological disease.
    Keywords:  aging; autophagy; brain; disease; longevity; mitochondria; mitophagy
    DOI:  https://doi.org/10.3389/fcell.2022.978142
  7. Genes (Basel). 2022 Oct 18. pii: 1889. [Epub ahead of print]13(10):
    Cardiolipin Regulates Mitochondrial Ultrastructure and Function in Mammalian Cells.
    Zhitong Jiang, Tao Shen, Helen Huynh, Xi Fang, Zhen Han, Kunfu Ouyang.
      Cardiolipin (CL) is a unique, tetra-acylated diphosphatidylglycerol lipid that mainly localizes in the inner mitochondria membrane (IMM) in mammalian cells and plays a central role in regulating mitochondrial architecture and functioning. A deficiency of CL biosynthesis and remodeling perturbs mitochondrial functioning and ultrastructure. Clinical and experimental studies on human patients and animal models have also provided compelling evidence that an abnormal CL content, acyl chain composition, localization, and level of oxidation may be directly linked to multiple diseases, including cardiomyopathy, neuronal dysfunction, immune cell defects, and metabolic disorders. The central role of CL in regulating the pathogenesis and progression of these diseases has attracted increasing attention in recent years. In this review, we focus on the advances in our understanding of the physiological roles of CL biosynthesis and remodeling from human patients and mouse models, and we provide an overview of the potential mechanism by which CL regulates the mitochondrial architecture and functioning.
    Keywords:  cardiolipin; mitochondria; mitochondrial function; mouse models
    DOI:  https://doi.org/10.3390/genes13101889
  8. J Cell Sci. 2022 Oct 24. pii: jcs.259823. [Epub ahead of print]
    Mitochondrial Ca2+ Uniporter haploinsufficiency enhances long-term potentiation at hippocampal mossy fibre synapses.
    Michael J Devine, Blanka R Szulc, Jack H Howden, Guillermo López-Doménech, Arnaud Ruiz, Josef T Kittler.
      Long-term changes in synaptic strength form the basis of learning and memory. These changes rely upon energy demanding mechanisms which are regulated by local Ca2+ signaling. Mitochondria are optimised for providing energy and buffering Ca2+. However, our understanding of the role of mitochondria in regulating synaptic plasticity is incomplete. Here we have used optical and electrophysiological techniques in cultured hippocampal neurons and ex vivo hippocampal slices from mice with haploinsufficiency of the mitochondrial Ca2+ uniporter (MCU+/-) to address whether reducing mitochondrial Ca2+ uptake alters synaptic transmission and plasticity. We found that cultured MCU+/- hippocampal neurons have impaired Ca2+ clearance, and consequently enhanced synaptic vesicle fusion at presynapses occupied by mitochondria. Furthermore, long-term potentiation (LTP) at mossy fibre (MF) synapses, a process which is dependent on presynaptic Ca2+ accumulation, is enhanced in MCU+/- slices. Our results reveal a previously unrecognized role for mitochondria in regulating presynaptic plasticity of a major excitatory pathway involved in learning and memory.
    Keywords:  Calcium; Long-term potentiation; MCU; Mitochondria; Mossy fibre synapse
    DOI:  https://doi.org/10.1242/jcs.259823
  9. Life Sci. 2022 Oct 22. pii: S0024-3205(22)00812-8. [Epub ahead of print] 121112
    TRPV4 interacts with MFN2 and facilitates endoplasmic reticulum-mitochondrial contact points for Ca2+-buffering.
    Tusar Kanta Acharya, Ashutosh Kumar, Shamit Kumar, Chandan Goswami.
       AIM: Mitochondrial fission-fusion events, distribution, and Ca2+-buffering abilities are relevant for several diseases, yet are poorly understood events. TRPV4 channels are a group of thermosensitive ion channel which regulate cellular and mitochondrial Ca2+-level. The underlying mechanisms of the change in mitochondrial dynamics upon modulation of TRPV4 channel are ill explored.
    MAIN METHODS: We have used TRPV4 expressing stable cell line CHO-K1-V4 and compared with CHO-K1-MOCK as a control cell. We have also used mouse bone marrow derived mesenchymal stem cells and purified mitochondria from mouse brain for the interaction study.
    KEY FINDINGS: Now we demonstrate that expression and/or pharmacological modulation of TRPV4 regulates mitochondrial morphologies and Ca2+-level. TRPV4 interacts with MFN1/MFN2, the mitochondrial regulatory factors. TRPV4 regulates ER-mito contact points. We used different cellular conditions where cytosolic or ER Ca2+-levels were pharmacologically altered. Analysis of ~55,000 mitochondrial particles, ~125,000 ER-mito contact points from ~900 cells in 10 different cellular conditions suggest that ER-mito contact points are inversely regulated with mitochondrial Ca2+-levels where TRPV4 always elevates mitochondrial Ca2+-levels. These findings link TRPV4 with MFN2-mediated diseases and suggest that different TRPV4-induced channelopathies are likely due to mitochondrial abnormalities.
    Keywords:  CMT disease; Ca(2+)-chelation; Channelopathy; Mitochondria-associated ER membrane; Mitochondrial fission-fusion; Thermosensitive ion channel
    DOI:  https://doi.org/10.1016/j.lfs.2022.121112
  10. Orphanet J Rare Dis. 2022 Oct 24. 17(1): 386
    Early embryonic lethality in complex I associated p.L104P Nubpl mutant mice.
    Cheng Cheng, James Cleak, Lan Weiss, Heather Cater, Michelle Stewart, Sara Wells, Rod Carlo Columbres, Alyaa Shmara, C Alejandra Morato Torres, Faria Zafar, Birgitt Schüle, Jonathan Neumann, Eli Hatchwell, Virginia Kimonis.
       BACKGROUND: Variants in the mitochondrial complex I assembly factor, NUBPL are associated with a rare cause of complex I deficiency mitochondrial disease. Patients affected by complex I deficiency harboring homozygous NUBPL variants typically have neurological problems including seizures, intellectual disability, and ataxia associated with cerebellar hypoplasia. Thus far only 19 cases have been reported worldwide, and no treatment is available for this rare disease.
    METHODS: To investigate the pathogenesis of NUBPL-associated complex I deficiency, and for translational studies, we generated a knock-in mouse harboring a patient-specific variant Nubpl c.311T>C; p. L104P reported in three families.
    RESULTS: Similar to Nubpl global knockout mice, the Nubpl p. L104P homozygous mice are lethal at embryonic day E10.5, suggesting that the Nubpl p. L104P variant is likely a hypomorph allele. Given the recent link between Parkinson's disease and loss-of-function NUBPL variants, we also explored aging-related behaviors and immunocytochemical changes in Nubpl hemizygous mice and did not find significant behavioral and pathological changes for alpha-synuclein and oxidative stress markers .
    CONCLUSION: Our data suggest that homozygotes with Nubpl variants, similar to the null mice, are lethal, and heterozygotes are phenotypically and neuropathologically normal. We propose that a tissue-specific knockout strategy is required to establish a mouse model of Nubpl-associated complex I deficiency disorder for future mechanistic and translational studies.
    Keywords:  Complex I deficiency; Mitochondria; Mouse model; NUBPL; Parkinson’s disease
    DOI:  https://doi.org/10.1186/s13023-022-02446-y
  11. Genet Med. 2022 Oct 28. pii: S1098-3600(22)00953-4. [Epub ahead of print]
    Genotypic and phenotypic spectrum of infantile liver failure due to pathogenic TRMU variants.
    Georg F Vogel, Yael Mozer-Glassberg, Yuval E Landau, Lea D Schlieben, Holger Prokisch, René G Feichtinger, Johannes A Mayr, Heiko Brennenstuhl, Julian Schröter, Agnes Pechlaner, Fowzan S Alkuraya, Joshua J Baker, Giulia Barcia, Ivo Baric, Nancy Braverman, Birute Burnyte, John Christodoulou, Elzbieta Ciara, David Coman, Anibh M Das, Niklas Darin, Adela Della Marina, Felix Distelmaier, Erik A Eklund, Melike Ersoy, Weiyan Fang, Pauline Gaignard, Rebecca D Ganetzky, Emmanuel Gonzales, Caoimhe Howard, Joanne Hughes, Vassiliki Konstantopoulou, Melis Kose, Marina Kerr, Aneal Khan, Dominic Lenz, Robert McFarland, Merav Gil Margolis, Kevin Morrison, Thomas Müller, Kei Murayama, Emanuele Nicastro, Alessandra Pennisi, Heidi Peters, Dorota Piekutowska-Abramczuk, Agnès Rötig, René Santer, Fernando Scaglia, Manuel Schiff, Mohmmad Shagrani, Mark Sharrard, Claudia Soler-Alfonso, Christian Staufner, Imogen Storey, Michael Stormon, Robert W Taylor, David R Thorburn, Elisa Leao Teles, Jian-She Wang, Daniel Weghuber, Saskia Wortmann.
       PURPOSE: The study aimed to define the genotypic and phenotypic spectrum of reversible acute liver failure (ALF) of infancy resulting from biallelic pathogenic TRMU variants and to determine the role of cysteine supplementation in its treatment.
    METHODS: Individuals with biallelic (likely) pathogenic variants in TRMU were studied through an international retrospective collection of de-identified patient data.
    RESULTS: In 62 individuals, including 30 previously unreported cases, we described 48 (likely) pathogenic TRMU variants, of which, 18 were novel. Of these 62 individuals, 42 were alive at a median age of 6.8 (0.6-22) years after a median follow up of 3.6 (0.1-22) years. The most frequent finding, occurring in all but 2 individuals, was liver involvement. ALF occurred only in the first year of life and was reported in 43 of 62 individuals, 11 of whom received liver transplantation. Loss-of-function TRMU variants were associated with poor survival. Supplementation with at least 1 cysteine source, typically N-acetylcysteine, improved survival significantly. Neurodevelopmental delay was observed in 11 individuals and persisted in 4 of the survivors, but we were unable to determine whether this was a primary or a secondary consequence of TRMU deficiency.
    CONCLUSION: In most patients, TRMU-associated ALF is a transient, reversible disease and cysteine supplementation improved survival.
    Keywords:  Acute liver failure; Cysteine; Liver transplantation; Mitochondrial disease; Treatment
    DOI:  https://doi.org/10.1016/j.gim.2022.09.015
  12. Cell Mol Life Sci. 2022 Oct 29. 79(11): 574
    Mitochondrial proteotoxicity: implications and ubiquitin-dependent quality control mechanisms.
    Mariusz Karbowski, Yumiko Oshima, Nicolas Verhoeven.
      Through their role in energy generation and regulation of several vital pathways, including apoptosis and inflammation, mitochondria are critical for the life of eukaryotic organisms. Mitochondrial dysfunction is a major problem implicated in the etiology of many pathologies, including neurodegenerative diseases, such as Parkinson's disease (PD), Alzheimer's disease (AD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS), diabetes, cardiovascular diseases, and many others. Proteotoxic stress, here defined as a reduction in bioenergetic activity induced by the accumulation of aberrant proteins in the mitochondria, is likely to be implicated in disease-linked mitochondrial and cellular decline. Various quality control pathways, such as mitochondrial unfolded protein response (mtUPR), the ubiquitin (Ub)-dependent degradation of aberrant mitochondrial proteins, and mitochondria-specific autophagy (mitophagy), respond to proteotoxic stress and eliminate defective proteins or dysfunctional mitochondria. This work provides a concise review of mechanisms by which disease-linked aberrant proteins affect mitochondrial function and an overview of mitochondrial quality control pathways that counteract mitochondrial proteotoxicity. We focus on mitochondrial quality control mechanisms relying on the Ub-mediated protein degradation, such as mitochondria-specific autophagy and the mitochondrial arm of the Ub proteasome system (UPS). We highlight the importance of a widening perspective of how these pathways protect mitochondria from proteotoxic stress to better understand mitochondrial proteotoxicity in overlapping pathophysiological pathways. Implications of these mechanisms in disease development are also briefly summarized.
    Keywords:  Mitochondria; Mitophagy; Proteotoxicity; Quality control; Ubiquitin
    DOI:  https://doi.org/10.1007/s00018-022-04604-8
  13. Biochim Biophys Acta Bioenerg. 2022 Oct 19. pii: S0005-2728(22)00400-5. [Epub ahead of print]1864(1): 148930
    Metabolic clearance of oxaloacetate and mitochondrial complex II respiration: Divergent control in skeletal muscle and brown adipose tissue.
    Liping Yu, Brian D Fink, Ritu Som, Adam J Rauckhorst, Eric B Taylor, William I Sivitz.
      At low inner mitochondrial membrane potential (ΔΨ) oxaloacetate (OAA) accumulates in the organelles concurrently with decreased complex II-energized respiration. This is consistent with ΔΨ-dependent OAA inhibition of succinate dehydrogenase. To assess the metabolic importance of this process, we tested the hypothesis that perturbing metabolic clearance of OAA in complex II-energized mitochondria would alter O2 flux and, further, that this would occur in both ΔΨ and tissue-dependent fashion. We carried out respiratory and metabolite studies in skeletal muscle and interscapular brown adipose tissue (IBAT) directed at the effect of OAA transamination to aspartate (catalyzed by the mitochondrial form of glutamic-oxaloacetic transaminase, Got2) on complex II-energized respiration. Addition of low amounts of glutamate to succinate-energized mitochondria at low ΔΨ increased complex II (succinate)-energized respiration in muscle but had little effect in IBAT mitochondria. The transaminase inhibitor, aminooxyacetic acid, increased OAA concentrations and impaired succinate-energized respiration in muscle but not IBAT mitochondria at low but not high ΔΨ. Immunoblotting revealed that Got2 expression was far greater in muscle than IBAT mitochondria. Because we incidentally observed metabolism of OAA to pyruvate in IBAT mitochondria, more so than in muscle mitochondria, we also examined the expression of mitochondrial oxaloacetate decarboxylase (ODX). ODX was detected only in IBAT mitochondria. In summary, at low but not high ΔΨ, mitochondrial transamination clears OAA preventing loss of complex II respiration: a process far more active in muscle than IBAT mitochondria. We also provide evidence that OAA decarboxylation clears OAA to pyruvate in IBAT mitochondria.
    Keywords:  Brown adipose tissue; Mitochondria; Mitochondrial complex II; Muscle; Oxaloacetate; Succinate dehydrogenase
    DOI:  https://doi.org/10.1016/j.bbabio.2022.148930
  14. J Clin Invest. 2022 Oct 27. pii: e154684. [Epub ahead of print]
    Mitochondrial dysfunction reactivates α-fetoprotein expression that drives copper-dependent immunosuppression in mitochondrial disease models.
    Kimberly A Jett, Zakery N Baker, Amzad Hossain, Aren Boulet, Paul A Cobine, Sagnika Ghosh, Philip Ng, Orhan Yilmaz, Kris Barreto, John DeCoteau, Karen Mochoruk, George N Ioannou, Christopher Savard, Sai Yuan, Osama Hmh Abdalla, Christopher Lowden, Byung-Eun Kim, Hai-Ying Mary Cheng, Brendan J Battersby, Vishal M Gohil, Scot C Leary.
      Signaling circuits crucial to systemic physiology are widespread, yet uncovering their molecular underpinnings remains a barrier to understanding the etiology of many metabolic disorders. Here, we identify a copper-linked signaling circuit activated by disruption of mitochondrial function in the murine liver or heart that results in atrophy of the spleen and thymus and causes a peripheral white blood cell deficiency. We demonstrate that the leukopenia is caused by α-fetoprotein, which requires copper and the cell surface receptor CCR5 to promote white blood cell death. We further show that α-fetoprotein expression is upregulated in several cell types upon inhibition of oxidative phosphorylation, including a muscle cell model of Barth syndrome. Collectively, our data argue that α-fetoprotein secreted by bioenergetically stressed tissue suppresses the immune system, an effect which may explain the recurrent infections that are observed in a subset of mitochondrial diseases or in other disorders with mitochondrial involvement.
    Keywords:  Metabolism; Mitochondria
    DOI:  https://doi.org/10.1172/JCI154684
  15. Metabolites. 2022 Oct 08. pii: 955. [Epub ahead of print]12(10):
    COQ8A-Ataxia as a Manifestation of Primary Coenzyme Q Deficiency.
    Justyna Paprocka, Magdalena Nowak, Piotr Chuchra, Robert Śmigiel.
      COQ8A-ataxia is a mitochondrial disease in which a defect in coenzyme Q10 synthesis leads to dysfunction of the respiratory chain. The disease is usually present as childhood-onset progressive ataxia with developmental regression and cerebellar atrophy. However, due to variable phenotype, it may be hard to distinguish from other mitochondrial diseases and a wide spectrum of childhood-onset cerebellar ataxia. COQ8A-ataxia is a potentially treatable condition with the supplementation of coenzyme Q10 as a main therapy; however, even 50% may not respond to the treatment. In this study we review the clinical manifestation and management of COQ8A-ataxia, focusing on current knowledge of coenzyme Q10 supplementation and approach to further therapies. Moreover, the case of a 22-month-old girl with cerebellar ataxia and developmental regression will be presented.
    Keywords:  COQ8A; COQ8A-ataxia; cerebellar ataxia; coenzyme Q10; primary coenzyme Q10 deficiency; primary coenzyme Q10 deficiency-4
    DOI:  https://doi.org/10.3390/metabo12100955
  16. J Neurosci. 2022 Oct 24. pii: JN-RM-0545-22. [Epub ahead of print]
    The absence of Parkin does not promote dopamine or mitochondrial dysfunction in PolgAD257A/D257A mitochondrial mutator mice.
    Laura Scott, Senthilkumar S Karuppagounder, Stewart Neifert, Bong Gu Kang, Hu Wang, Valina L Dawson, Ted M Dawson.
      Parkinson's disease (PD) is characterized by the progressive loss of dopaminergic neurons in the substantia nigra pars compacta. In this study, we generated a transgenic model by crossing germline Parkin-/- mice with PolgAD257A mice, an established model of premature aging and mitochondrial stress. We hypothesized that loss of Parkin-/- in PolgAD257A/D257A mice would exacerbate mitochondrial dysfunction, leading to loss of dopamine neurons and nigral-striatal specific neurobehavioral motor dysfunction. We found that aged Parkin-/-/PolgAD257A/D257A male and female mice exhibited severe behavioral deficits, nonspecific to the nigral-striatal pathway, with neither dopaminergic neurodegeneration nor reductions in striatal dopamine. We saw no difference in expression levels of nuclear-encoded subunits of mitochondrial markers and mitochondrial complex I and IV activities, though we did observe substantial reductions in mitochondrial-encoded COX41I, indicating mitochondrial dysfunction as a result of PolgAD257A/D257A mtDNA mutations. Expression levels of mitophagy markers LC3I/LC3II remained unchanged between cohorts, suggesting no overt mitophagy defects. Expression levels of the parkin substrates, VDAC, NLRP3, and AIMP2 remained unchanged, suggesting no parkin dysfunction. In summary, we were unable to observe dopaminergic neurodegeneration with corresponding nigral-striatal neurobehavioral deficits, nor Parkin or mitochondrial dysfunction in Parkin-/-/PolgAD257A/D257A mice. These findings support a lack of synergism of Parkin loss on mitochondrial dysfunction in mouse models of mitochondrial deficits.SIGNIFICANCE STATEMENT:Producing a mouse model of PD that is etiologically relevant, recapitulates clinical hallmarks, and exhibits reproducible results is crucial to understanding the underlying pathology and in developing disease-modifying therapies. Here, we show that Parkin-/-/PolgAD257A/D257A mice, a previously reported PD mouse model, fails to reproduce a Parkinsonian phenotype. We show that these mice do not display dopaminergic neurodegeneration nor nigral-striatal-dependent motor deficits. Furthermore, we report that Parkin loss does not synergize with mitochondrial dysfunction. Our results demonstrate that Parkin-/-/PolgAD257A/D257A mice are not a reliable model for PD and adds to a growing body of work demonstrating that Parkin loss does not synergize with mitochondrial dysfunction in mouse models of mitochondrial deficits.
    DOI:  https://doi.org/10.1523/JNEUROSCI.0545-22.2022
  17. Commun Biol. 2022 Oct 25. 5(1): 1128
    Pooled image-base screening of mitochondria with microraft isolation distinguishes pathogenic mitofusin 2 mutations.
    Alex L Yenkin, John C Bramley, Colin L Kremitzki, Jason E Waligorski, Mariel J Liebeskind, Xinyuan E Xu, Vinay D Chandrasekaran, Maria A Vakaki, Graham W Bachman, Robi D Mitra, Jeffrey D Milbrandt, William J Buchser.
      Most human genetic variation is classified as variants of uncertain significance. While advances in genome editing have allowed innovation in pooled screening platforms, many screens deal with relatively simple readouts (viability, fluorescence) and cannot identify the complex cellular phenotypes that underlie most human diseases. In this paper, we present a generalizable functional genomics platform that combines high-content imaging, machine learning, and microraft isolation in a method termed "Raft-Seq". We highlight the efficacy of our platform by showing its ability to distinguish pathogenic point mutations of the mitochondrial regulator Mitofusin 2, even when the cellular phenotype is subtle. We also show that our platform achieves its efficacy using multiple cellular features, which can be configured on-the-fly. Raft-Seq enables a way to perform pooled screening on sets of mutations in biologically relevant cells, with the ability to physically capture any cell with a perturbed phenotype and expand it clonally, directly from the primary screen.
    DOI:  https://doi.org/10.1038/s42003-022-04089-y
  18. Aging Cell. 2022 Oct 28. e13731
    SIAH proteins regulate the degradation and intra-mitochondrial aggregation of PINK1: Implications for mitochondrial pathology in Parkinson's disease.
    Fatimah Abd Elghani, Hazem Safory, Haya Hamza, Mor Savyon, Malik Farhoud, Michal Toren-Hershoviz, Zagorka Vitic, Kirsten Ebanks, Vered Shani, Sleman Bisharat, Lihi Shaulov, Claude Brodski, Zhiyin Song, Rina Bandopadhyay, Simone Engelender.
      Parkinson's disease (PD) is characterized by degeneration of neurons, particularly dopaminergic neurons in the substantia nigra. PD brains show accumulation of α-synuclein in Lewy bodies and accumulation of dysfunctional mitochondria. However, the mechanisms leading to mitochondrial pathology in sporadic PD are poorly understood. PINK1 is a key for mitophagy activation and recycling of unfit mitochondria. The activation of mitophagy depends on the accumulation of uncleaved PINK1 at the outer mitochondrial membrane and activation of a cascade of protein ubiquitination at the surface of the organelle. We have now found that SIAH3, a member of the SIAH proteins but lacking ubiquitin-ligase activity, is increased in PD brains and cerebrospinal fluid and in neurons treated with α-synuclein preformed fibrils (α-SynPFF). We also observed that SIAH3 is aggregated together with PINK1 in the mitochondria of PD brains. SIAH3 directly interacts with PINK1, leading to their intra-mitochondrial aggregation in cells and neurons and triggering a cascade of toxicity with PINK1 inactivation along with mitochondrial depolarization and neuronal death. We also found that SIAH1 interacts with PINK1 and promotes ubiquitination and proteasomal degradation of PINK1. Similar to the dimerization of SIAH1/SIAH2, SIAH3 interacts with SIAH1, promoting its translocation to mitochondria and preventing its ubiquitin-ligase activity toward PINK1. Our results support the notion that the increase in SIAH3 and intra-mitochondrial aggregation of SIAH3-PINK1 may mediate α-synuclein pathology by promoting proteotoxicity and preventing the elimination of dysfunctional mitochondria. We consider it possible that PINK1 activity is decreased in sporadic PD, which impedes proper mitochondrial renewal in the disease.
    Keywords:  PINK1; Parkinson's disease; SIAH1; SIAH3; intra-mitochondrial protein aggregation; mitochondrial dysfunction; mitophagy; ubiquitin
    DOI:  https://doi.org/10.1111/acel.13731
  19. J Cell Biol. 2022 Dec 05. pii: e202207022. [Epub ahead of print]221(12):
    Mitoguardin-2-mediated lipid transfer preserves mitochondrial morphology and lipid droplet formation.
    Zhouping Hong, Jyoti Adlakha, Neng Wan, Emily Guinn, Fabian Giska, Kallol Gupta, Thomas J Melia, Karin M Reinisch.
      Lipid transport proteins at membrane contacts, where organelles are closely apposed, are critical in redistributing lipids from the endoplasmic reticulum (ER), where they are made, to other cellular membranes. Such protein-mediated transfer is especially important for maintaining organelles disconnected from secretory pathways, like mitochondria. We identify mitoguardin-2, a mitochondrial protein at contacts with the ER and/or lipid droplets (LDs), as a lipid transporter. An x-ray structure shows that the C-terminal domain of mitoguardin-2 has a hydrophobic cavity that binds lipids. Mass spectrometry analysis reveals that both glycerophospholipids and free-fatty acids co-purify with mitoguardin-2 from cells, and that each mitoguardin-2 can accommodate up to two lipids. Mitoguardin-2 transfers glycerophospholipids between membranes in vitro, and this transport ability is required for roles both in mitochondrial and LD biology. While it is not established that protein-mediated transfer at contacts plays a role in LD metabolism, our findings raise the possibility that mitoguardin-2 functions in transporting fatty acids and glycerophospholipids at mitochondria-LD contacts.
    DOI:  https://doi.org/10.1083/jcb.202207022
  20. Life Sci Alliance. 2023 Jan;pii: e202201514. [Epub ahead of print]6(1):
    Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish.
    Barbara Uszczynska-Ratajczak, Sreedevi Sugunan, Monika Kwiatkowska, Maciej Migdal, Silvia Carbonell-Sala, Anna Sokol, Cecilia L Winata, Agnieszka Chacinska.
      Most mitochondrial proteins are encoded by nuclear genes, synthetized in the cytosol and targeted into the organelle. To characterize the spatial organization of mitochondrial gene products in zebrafish (Danio rerio), we sequenced RNA from different cellular fractions. Our results confirmed the presence of nuclear-encoded mRNAs in the mitochondrial fraction, which in unperturbed conditions, are mainly transcripts encoding large proteins with specific properties, like transmembrane domains. To further explore the principles of mitochondrial protein compartmentalization in zebrafish, we quantified the transcriptomic changes for each subcellular fraction triggered by the chchd4a -/- mutation, causing the disorders in the mitochondrial protein import. Our results indicate that the proteostatic stress further restricts the population of transcripts on the mitochondrial surface, allowing only the largest and the most evolutionary conserved proteins to be synthetized there. We also show that many nuclear-encoded mitochondrial transcripts translated by the cytosolic ribosomes stay resistant to the global translation shutdown. Thus, vertebrates, in contrast to yeast, are not likely to use localized translation to facilitate synthesis of mitochondrial proteins under proteostatic stress conditions.
    DOI:  https://doi.org/10.26508/lsa.202201514
  21. Int J Mol Sci. 2022 Oct 20. pii: 12610. [Epub ahead of print]23(20):
    Stimulating Mitochondrial Biogenesis with Deoxyribonucleosides Increases Functional Capacity in ECHS1-Deficient Cells.
    Harrison James Burgin, Jordan James Crameri, Diana Stojanovski, M Isabel G Lopez Sanchez, Mark Ziemann, Matthew McKenzie.
      The lack of effective treatments for mitochondrial disease has seen the development of new approaches, including those that stimulate mitochondrial biogenesis to boost ATP production. Here, we examined the effects of deoxyribonucleosides (dNs) on mitochondrial biogenesis and function in Short chain enoyl-CoA hydratase 1 (ECHS1) 'knockout' (KO) cells, which exhibit combined defects in both oxidative phosphorylation (OXPHOS) and mitochondrial fatty acid β-oxidation (FAO). DNs treatment increased mitochondrial DNA (mtDNA) copy number and the expression of mtDNA-encoded transcripts in both CONTROL (CON) and ECHS1 KO cells. DNs treatment also altered global nuclear gene expression, with key gene sets including 'respiratory electron transport' and 'formation of ATP by chemiosmotic coupling' increased in both CON and ECHS1 KO cells. Genes involved in OXPHOS complex I biogenesis were also upregulated in both CON and ECHS1 KO cells following dNs treatment, with a corresponding increase in the steady-state levels of holocomplex I in ECHS1 KO cells. Steady-state levels of OXPHOS complex V, and the CIII2/CIV and CI/CIII2/CIV supercomplexes, were also increased by dNs treatment in ECHS1 KO cells. Importantly, treatment with dNs increased both basal and maximal mitochondrial oxygen consumption in ECHS1 KO cells when metabolizing either glucose or the fatty acid palmitoyl-L-carnitine. These findings highlight the ability of dNs to improve overall mitochondrial respiratory function, via the stimulation mitochondrial biogenesis, in the face of combined defects in OXPHOS and FAO due to ECHS1 deficiency.
    Keywords:  ECHS1 deficiency; deoxyribonucleosides; mitochondria; mitochondrial biogenesis; mitochondrial disease
    DOI:  https://doi.org/10.3390/ijms232012610
  22. Cell Death Differ. 2022 Oct 28.
    OPA1 drives macrophage metabolism and functional commitment via p65 signaling.
    Ricardo Sánchez-Rodríguez, Caterina Tezze, Andrielly H R Agnellini, Roberta Angioni, Francisca C Venegas, Chiara Cioccarelli, Fabio Munari, Nicole Bertoldi, Marcella Canton, Maria Andrea Desbats, Leonardo Salviati, Rosanna Gissi, Alessandra Castegna, Maria Eugenia Soriano, Marco Sandri, Luca Scorrano, Antonella Viola, Barbara Molon.
      Macrophages are essential players for the host response against pathogens, regulation of inflammation and tissue regeneration. The wide range of macrophage functions rely on their heterogeneity and plasticity that enable a dynamic adaptation of their responses according to the surrounding environmental cues. Recent studies suggest that metabolism provides synergistic support for macrophage activation and elicitation of desirable immune responses; however, the metabolic pathways orchestrating macrophage activation are still under scrutiny. Optic atrophy 1 (OPA1) is a mitochondria-shaping protein controlling mitochondrial fusion, cristae biogenesis and respiration; clear evidence shows that the lack or dysfunctional activity of this protein triggers the accumulation of metabolic intermediates of the TCA cycle. In this study, we show that OPA1 has a crucial role in macrophage activation. Selective Opa1 deletion in myeloid cells impairs M1-macrophage commitment. Mechanistically, Opa1 deletion leads to TCA cycle metabolite accumulation and defective NF-κB signaling activation. In an in vivo model of muscle regeneration upon injury, Opa1 knockout macrophages persist within the damaged tissue, leading to excess collagen deposition and impairment in muscle regeneration. Collectively, our data indicate that OPA1 is a key metabolic driver of macrophage functions.
    DOI:  https://doi.org/10.1038/s41418-022-01076-y
  23. Innovation (Camb). 2022 Nov 08. 3(6): 100329
    Direct evidence of CRISPR-Cas9-mediated mitochondrial genome editing.
    Rui Bi, Yu Li, Min Xu, Quanzhen Zheng, Deng-Feng Zhang, Xiao Li, Guolan Ma, Bolin Xiang, Xiaojia Zhu, Hui Zhao, Xingxu Huang, Ping Zheng, Yong-Gang Yao.
      Pathogenic mitochondrial DNA (mtDNA) mutations can cause a variety of human diseases. The recent development of genome-editing technologies to manipulate mtDNA, such as mitochondria-targeted DNA nucleases and base editors, offer a promising way for curing mitochondrial diseases caused by mtDNA mutations. The CRISPR-Cas9 system is a widely used tool for genome editing; however, its application in mtDNA editing is still under debate. In this study, we developed a mito-Cas9 system by adding the mitochondria-targeted sequences and 3' untranslated region of nuclear-encoded mitochondrial genes upstream and downstream of the Cas9 gene, respectively. We confirmed that the mito-Cas9 system was transported into mitochondria and enabled knockin of exogenous single-stranded DNA oligonucleotides (ssODNs) into mtDNA based on proteinase and DNase protection assays. Successful knockin of exogenous ssODNs into mtDNA was further validated using polymerase chain reaction-free third-generation sequencing technology. We also demonstrated that RS-1, an agonist of RAD51, significantly increased knockin efficiency of the mito-Cas9 system. Collectively, we provide direct evidence that mtDNA can be edited using the CRISPR-Cas9 system. The mito-Cas9 system could be optimized as a promising approach for the treatment of mitochondrial diseases caused by pathogenic mtDNA mutations, especially those with homoplasmic mtDNA mutations.
    Keywords:  mitochondrial disease; mtDNA editing, mito-Cas9; third-generation sequencing
    DOI:  https://doi.org/10.1016/j.xinn.2022.100329
  24. J Clin Invest. 2022 Oct 25. pii: e156864. [Epub ahead of print]
    Autosomal recessive progeroid syndrome due to homozygosity for a TOMM7 variant.
    Abhimanyu Garg, Wee-Teik Keng, Zhenkang Chen, Adwait Amod Sathe, Chao Xing, Pavithira Devi Kailasam, Yanqiu Shao, Nicholas P Lesner, Claire B Llamas, Anil K Agarwal, Prashant Mishra.
      Multiple genetic loci have been reported for progeroid syndromes. However, the molecular defects in some extremely rare forms of progeria have yet to be elucidated. Here we report a 21-year-old man of Chinese origin who had a novel autosomal recessive form of progeria, characterized by severe dwarfism, mandibular hypoplasia, hyperopia and partial lipodystrophy. Analyses of exome sequencing data of the entire family revealed only one rare homozygous missense variant, (c.86C>T; p.Pro29Leu), in TOMM7 in the proband, while the parents and two unaffected siblings were heterozygous for the variant. TOMM7, a nuclear gene, encodes a translocase in the outer mitochondrial membrane. The TOMM complex constitutes the outer membrane pore for import of several preproteins into mitochondria. Proteomics analyses of mitochondria from cultured fibroblasts of the proband, as compared to control fibroblasts, revealed increases in several proteins involved in oxidative phosphorylation, but reduced abundance of proteins involved in the phospholipid metabolism. We also observed elevated basal and maximal oxygen consumption rates in the fibroblasts from the proband as compared to control fibroblasts. We conclude that altered mitochondrial protein import due to loss of function bi-allelic variant in TOMM7 can cause severe growth retardation and progeroid features.
    Keywords:  Endocrinology; Genetic diseases; Genetics; Mitochondria
    DOI:  https://doi.org/10.1172/JCI156864
  25. EMBO J. 2022 Oct 28. e110595
    BCL7A-containing SWI/SNF/BAF complexes modulate mitochondrial bioenergetics during neural progenitor differentiation.
    Lena Wischhof, Hang-Mao Lee, Janine Tutas, Clemens Overkott, Eileen Tedt, Miriam Stork, Michael Peitz, Oliver Brüstle, Thomas Ulas, Kristian Händler, Joachim L Schultze, Dan Ehninger, Pierluigi Nicotera, Paolo Salomoni, Daniele Bano.
      Mammalian SWI/SNF/BAF chromatin remodeling complexes influence cell lineage determination. While the contribution of these complexes to neural progenitor cell (NPC) proliferation and differentiation has been reported, little is known about the transcriptional profiles that determine neurogenesis or gliogenesis. Here, we report that BCL7A is a modulator of the SWI/SNF/BAF complex that stimulates the genome-wide occupancy of the ATPase subunit BRG1. We demonstrate that BCL7A is dispensable for SWI/SNF/BAF complex integrity, whereas it is essential to regulate Notch/Wnt pathway signaling and mitochondrial bioenergetics in differentiating NPCs. Pharmacological stimulation of Wnt signaling restores mitochondrial respiration and attenuates the defective neurogenic patterns observed in NPCs lacking BCL7A. Consistently, treatment with an enhancer of mitochondrial biogenesis, pioglitazone, partially restores mitochondrial respiration and stimulates neuronal differentiation of BCL7A-deficient NPCs. Using conditional BCL7A knockout mice, we reveal that BCL7A expression in NPCs and postmitotic neurons is required for neuronal plasticity and supports behavioral and cognitive performance. Together, our findings define the specific contribution of BCL7A-containing SWI/SNF/BAF complexes to mitochondria-driven NPC commitment, thereby providing a better understanding of the cell-intrinsic transcriptional processes that connect metabolism, neuronal morphogenesis, and cognitive flexibility.
    Keywords:  BCL7A; SWI/SNF/BAF complex; cognitive function; mitochondrial OXPHOS; neural progenitor cells (NPCs)
    DOI:  https://doi.org/10.15252/embj.2022110595
  26. Life Sci Alliance. 2023 Jan;pii: e202201406. [Epub ahead of print]6(1):
    Miro GTPase domains regulate the assembly of the mitochondrial motor-adaptor complex.
    Kayla Davis, Himanish Basu, Ismael Izquierdo-Villalba, Ethan Shurberg, Thomas L Schwarz.
      Mitochondrial transport relies on a motor-adaptor complex containing Miro1, a mitochondrial outer membrane protein with two GTPase domains, and TRAK1/2, kinesin-1, and dynein. Using a peroxisome-directed Miro1, we quantified the ability of GTPase mutations to influence the peroxisomal recruitment of complex components. Miro1 whose N-GTPase is locked in the GDP state does not recruit TRAK1/2, kinesin, or P135 to peroxisomes, whereas the GTP state does. Similarly, the expression of the MiroGAP VopE dislodges TRAK1 from mitochondria. Miro1 C-GTPase mutations have little influence on complex recruitment. Although Miro2 is thought to support mitochondrial motility, peroxisome-directed Miro2 did not recruit the other complex components regardless of the state of its GTPase domains. Neurons expressing peroxisomal Miro1 with the GTP-state form of the N-GTPase had markedly increased peroxisomal transport to growth cones, whereas the GDP-state caused their retention in the soma. Thus, the N-GTPase domain of Miro1 is critical for regulating Miro1's interaction with the other components of the motor-adaptor complex and thereby for regulating mitochondrial motility.
    DOI:  https://doi.org/10.26508/lsa.202201406
  27. iScience. 2022 Nov 18. 25(11): 105266
    Cytoplasmic and mitochondrial aminoacyl-tRNA synthetases differentially regulate lifespan in Caenorhabditis elegans.
    Tianlin Zheng, Qiang Luo, Chengxuan Han, Jiejun Zhou, Jianke Gong, Lei Chun, X Z Shawn Xu, Jianfeng Liu.
      Reducing the rate of translation promotes longevity in multiple organisms, representing a conserved mechanism for lifespan extension. Aminoacyl-tRNA synthetases (ARSs) catalyze the loading of amino acids to their cognate tRNAs, thereby playing an essential role in translation. Mutations in ARS genes are associated with various human diseases. However, little is known about the role of ARSs in aging, particularly whether and how these genes regulate lifespan. Here, using Caenorhabditis elegans as a model, we systematically characterized the role of all three types of ARS genes in lifespan regulation, including mitochondrial, cytoplasmic, and cyto-mito bifunctional ARS genes. We found that, as expected, RNAi knockdown of mitochondrial ARS genes extended lifespan. Surprisingly, knocking down cytoplasmic or cyto-mito bifunctional ARS genes shortened lifespan, though such treatment reduced the rate of translation. These results reveal opposing roles of mitochondrial and cytoplasmic ARSs in lifespan regulation, demonstrating that inhibiting translation may not always extend lifespan.
    Keywords:  Cell biology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2022.105266
  28. Nat Metab. 2022 Oct 27.
    Synthetic metabolism without the TCA cycle.
    Steffen N Lindner, Markus Ralser.
      
    DOI:  https://doi.org/10.1038/s42255-022-00668-9
  29. PLoS One. 2022 ;17(10): e0276883
    Mitochondrial disease registries worldwide: A scoping review.
    Ammanie Abdul-Fatah, Leila Esmaeilisaraji, Crisel Mae Juan, Martin Holcik.
       BACKGROUND: Mitochondrial diseases are a large group of genetically heterogeneous and clinically diverse disorders. Diagnosis often takes many years for which treatment may not exist. Registries are often used to conduct research, establish natural disease progression, engage the patient community, and develop best disease management practices. In Canada, there are limited centralized registries for mitochondrial disease patients, presenting a challenge for patients and professionals.
    OBJECTIVE: To support the creation of such a registry, a systematic scoping review was conducted to map the landscape of mitochondrial disease patient registries worldwide, with a focus on registry design and challenges. Furthermore, it addresses a knowledge gap by providing a narrative synthesis of published literature that describes these registries.
    METHODS: Arksey and O'Malley's methodological framework was followed to systematically search English-language literature in PubMed and CINAHL describing the designs of mitochondrial disease patient registries, supplemented by a grey literature search. Data were extracted in Microsoft Excel. Stakeholder consultations were also performed with patient caregivers, advocates, and researchers to provide perspectives beyond those found in the literature. These data were thematically analyzed and were reported in accordance with the PRISMA-ScR reporting guidelines.
    RESULTS: A total of 17 articles were identified describing 13 unique registries located in North America, Europe, Australia, and West Asia. These papers described the registries' designs, their strengths, and weaknesses, as well as their tangible outcomes such as facilitating recruitment for research and supporting epidemiological studies.
    CONCLUSION: Based on our findings in this review, recommendations were formulated. These include establishing registry objectives, respecting patients and their roles in the registry, adopting international data standards, data evaluations, and considerations to privacy legislation, among others. These recommendations could be used to support designing a future Canadian mitochondrial disease patient registry, and to further research directly engaging these registries worldwide.
    DOI:  https://doi.org/10.1371/journal.pone.0276883
  30. Front Mol Biosci. 2022 ;9 959844
    Role of mitochondria-associated endoplasmic reticulum membranes in insulin sensitivity, energy metabolism, and contraction of skeletal muscle.
    Bianca Nieblas, Perla Pérez-Treviño, Noemí García.
      Skeletal muscle has a critical role in the regulation of the energy balance of the organism, particularly as the principal tissue responsible for insulin-stimulated glucose disposal and as the major site of peripheral insulin resistance (IR), which has been related to accumulation of lipid intermediates, reduced oxidative capacity of mitochondria and endoplasmic reticulum (ER) stress. These organelles form contact sites, known as mitochondria-associated ER membranes (MAMs). This interconnection seems to be involved in various cellular processes, including Ca2+ transport and energy metabolism; therefore, MAMs could play an important role in maintaining cellular homeostasis. Evidence suggests that alterations in MAMs may contribute to IR. However, the evidence does not refer to a specific subcellular location, which is of interest due to the fact that skeletal muscle is constituted by oxidative and glycolytic fibers as well as different mitochondrial populations that appear to respond differently to stimuli and pathological conditions. In this review, we show the available evidence of possible differential responses in the formation of MAMs in skeletal muscle as well as its role in insulin signaling and the beneficial effect it could have in the regulation of energetic metabolism and muscular contraction.
    Keywords:  insulin resistance; mitochondria-associated ER membranes (MAMs); mitochondrial dysfunction; mitochondrial skeletal muscle; mitochondrial subpopulations; obesity
    DOI:  https://doi.org/10.3389/fmolb.2022.959844
  31. Int J Mol Sci. 2022 Oct 20. pii: 12603. [Epub ahead of print]23(20):
    Mitochondrial Dysfunction and Neurodegenerative Disorders: Role of Nutritional Supplementation.
    David Mantle, Iain Parry Hargreaves.
      Mitochondrial dysfunction has been implicated in the pathogenesis of a number of neurodegenerative disorders, including Parkinson's disease, Alzheimer's disease, amyotrophic lateral sclerosis, multisystem atrophy, and progressive supranuclear palsy. This article is concerned specifically with mitochondrial dysfunction as defined by reduced capacity for ATP production, the role of depleted levels of key nutritionally related metabolites, and the potential benefit of supplementation with specific nutrients of relevance to normal mitochondrial function in the above neurodegenerative disorders. The article provides a rationale for a combination of CoQ10, B-vitamins/NADH, L-carnitine, vitamin D, and alpha-lipoic acid for the treatment of the above neurodegenerative disorders.
    Keywords:  B-vitamins; alpha-lipoic acid; coenzyme Q10; l-carnitine; mitochondrial dysfunction; neurodegenerative disorders; selenium; vitamin D
    DOI:  https://doi.org/10.3390/ijms232012603
  32. Pflugers Arch. 2022 Oct 24.
    Human platelet mitochondria improve the mitochondrial and cardiac function of donor heart.
    Zhi Jun Lin, Soomin Kim, Hui Xing Cui, Kyuboem Han, Hong Kyu Lee, Chun-Hyung Kim, Young Cheol Kang, Yin Hua Zhang.
      Mitochondria transplantation emerges as an effective therapeutic strategy for ischemic-related diseases but the roles in the donor hearts for transplant remain unidentified. Here, we investigated whether the preservation of the donor heart with human platelet-derived mitochondria (pl-MT) could improve mitochondrial and cardiac function. Incubation with pl-MT resulted in the internalization of pl-MT and the enhancement of ATP production in primary cardiomyocytes. In addition, incubation of rat hearts with pl-MT ex vivo for 9 h clearly demonstrated pl-MT transfusion into the myocardium. Mitochondria isolated from the hearts incubated with pl-MT showed increased mitochondrial membrane potential and greater ATP synthase activity and citrate synthase activity. Importantly, the production of reactive oxygen species from cardiac mitochondria was not different with and without pl-MT incubation. Functionally, the heartbeat and the volume of coronary circulation perfusate were significantly increased in the Langendorff perfusion system and the viability of cardiomyocytes was increased from pl-MT hearts.Taken together, these results suggest that incubation with Pl-MT improves mitochondrial activity and maintains the cardiac function of rat hearts with prolonged preservation time. The study provides the proof of principle for pl-MT application as an enhancer of the donor heart.
    Keywords:  Cardiac function; Donor heart; Mitochondrial function; Pl-MT transplantation; Preservation time
    DOI:  https://doi.org/10.1007/s00424-022-02763-y
  33. J Transl Med. 2022 Oct 22. 20(1): 483
    Mitochondrial transplantation: opportunities and challenges in the treatment of obesity, diabetes, and nonalcoholic fatty liver disease.
    Yifei Chen, Fuji Yang, Ying Chu, Zhihua Yun, Yongmin Yan, Jianhua Jin.
      Metabolic diseases, including obesity, diabetes, and nonalcoholic fatty liver disease (NAFLD), are rising in both incidence and prevalence and remain a major global health and socioeconomic burden in the twenty-first century. Despite an increasing understanding of these diseases, the lack of effective treatments remains an ongoing challenge. Mitochondria are key players in intracellular energy production, calcium homeostasis, signaling, and apoptosis. Emerging evidence shows that mitochondrial dysfunction participates in the pathogeneses of metabolic diseases. Exogenous supplementation with healthy mitochondria is emerging as a promising therapeutic approach to treating these diseases. This article reviews recent advances in the use of mitochondrial transplantation therapy (MRT) in such treatment.
    Keywords:  Diabetes; Extracellular vesicles; Mitochondrial transfer; Nonalcoholic fatty liver disease; Obesity
    DOI:  https://doi.org/10.1186/s12967-022-03693-0
  34. Membranes (Basel). 2022 Sep 22. pii: 916. [Epub ahead of print]12(10):
    Experimental Investigations on the Structure of Yeast Mitochondrial Pyruvate Carriers.
    Ling Li, Maorong Wen, Changqing Run, Bin Wu, Bo OuYang.
      Mitochondrial pyruvate carrier (MPC) transports pyruvate from the cytoplasm into the mitochondrial matrix to participate in the tricarboxylic acid (TCA) cycle, which further generates the energy for the physiological activities of cells. Two interacting subunits, MPC1 and MPC2 or MPC3, form a heterodimer to conduct transport function. However, the structural basis of how the MPC complex transports pyruvate is still lacking. Here, we described the detailed expression and purification procedures to obtain large amounts of yeast MPC1 and MPC2 for structural characterization. The purified yeast MPC1 and MPC2 were reconstituted in dodecylphosphocholine (DPC) micelles and examined using nuclear magnetic resonance (NMR) spectroscopy, showing that both subunits contain three α-helical transmembrane regions with substantial differences from what was predicted by AlphaFold2. Furthermore, the new protocol producing the recombinant MPC2 using modified maltose-binding protein (MBP) with cyanogen bromide (CNBr) cleavage introduced general way to obtain small membrane proteins. These findings provide a preliminary understanding for the structure of the MPC complex and useful guidance for further studies.
    Keywords:  AlphaFold2; NMR spectroscopy; mitochondrial pyruvate carrier (MPC); protein expression and purification; pyruvate
    DOI:  https://doi.org/10.3390/membranes12100916
  35. Methods Mol Biol. 2023 ;2426 375-390
    Application of WGCNA and PloGO2 in the Analysis of Complex Proteomic Data.
    Jemma X Wu, Dana Pascovici, Yunqi Wu, Adam K Walker, Mehdi Mirzaei.
      In this protocol we describe our workflow for analyzing complex, multi-condition quantitative proteomic experiments, with the aim to extract biological insights. The tool we use is an R package, PloGO2, contributed to Bioconductor, which we can optionally precede by running correlation network analysis with WGCNA. We describe the data required and the steps we take, including detailed code examples and outputs explanation. The package was designed to generate gene ontology or pathway summaries for many data subsets at the same time, visualize protein abundance summaries for each biological category examined, help determine enriched protein subsets by comparing them all to a reference set, and suggest key highly correlated hub proteins, if the optional network analysis is employed.
    Keywords:  Functional enrichment analysis; Gene ontology; Pathway; Proteomics; Statistical R package; WGCNA
    DOI:  https://doi.org/10.1007/978-1-0716-1967-4_17
  36. Biomedicines. 2022 Oct 01. pii: 2459. [Epub ahead of print]10(10):
    Targeting Mitochondrial Function with Chemoptogenetics.
    Amy Romesberg, Bennett Van Houten.
      Mitochondria are ATP-generating organelles in eukaryotic cells that produce reactive oxygen species (ROS) during oxidative phosphorylation (OXPHOS). Mitochondrial DNA (mtDNA) is packaged within nucleoids and, due to its close proximity to ROS production, endures oxidative base damage. This damage can be repaired by base excision repair (BER) within the mitochondria, or it can be degraded via exonucleases or mitophagy. Persistent mtDNA damage may drive the production of dysfunctional OXPHOS components that generate increased ROS, or OXPHOS components may be directly damaged by ROS, which then can cause more mtDNA damage and create a vicious cycle of ROS production and mitochondrial dysfunction. If mtDNA damage is left unrepaired, mtDNA mutations including deletions can result. The accumulation of mtDNA mutations has been associated with conditions ranging from the aging process to cancer and neurodegenerative conditions, but the sequence of events leading to mtDNA mutations and deletions is yet unknown. Researchers have utilized many systems and agents for generating ROS in mitochondria to observe the downstream effects on mtDNA, ROS, and mitochondrial function; yet, there are various drawbacks to these methodologies that limit their precision. Here, we describe a novel chemoptogenetic approach to target oxidative damage to mitochondria and mtDNA with a high spatial and temporal resolution so that the downstream effects of ROS-induced damage can be measured with a high precision in order to better understand the mechanism of mitochondrial dysfunction in aging, cancer, and neurodegenerative diseases.
    Keywords:  base excision repair; chemoptogenetics; mitochondria; mitochondrial DNA; mitochondrial dysfunction; reactive oxygen species
    DOI:  https://doi.org/10.3390/biomedicines10102459
  37. IUBMB Life. 2022 Oct 29.
    Role of extracellular vesicles in mitochondrial eye diseases.
    Sushma Anand, Ian A Trounce, Lahiru Gangoda.
      Extracellular vesicles (EVs) are small packages that are released by almost all types of cells. While the role of EVs in pathogenesis of certain diseases such as cancer is well established, EVs role in ocular health and disease is still at early stages of investigation. Given the significant role of EVs in pathological development and progression of diseases such as cancer, EVs present a similar opportunity for investigation in ocular pathophysiology. Studies have shown the presence of EVs in fluids from the ocular environment have close links with ocular health and disease. Hence the cargo carried in EVs from ocular fluids can be used for monitoring disease phenotypes or therapeutic outcomes in eye related disorders. Furthermore, in recent times EVs have increasingly gained attention as therapeutics and drug delivery vehicles for treatment of eye diseases. There is a close relationship between EVs and mitochondria functioning with mitochondria dysfunction leading to a significant number of ophthalmic disorders. This review discusses the current knowledge of EVs in visual systems with a special focus on eye diseases resulting from dysfunctional mitochondria. This article is protected by copyright. All rights reserved.
    Keywords:  disease biomarkers; extracellular vesicles; mesenchymal stem cells; mitochondria | reactive oxygen species; mitochondrial disorders; ophthalmology; retina
    DOI:  https://doi.org/10.1002/iub.2687
  38. Toxicol Res. 2022 Oct;38(4): 511-522
    Establishment of a platform for measuring mitochondrial oxygen consumption rate for cardiac mitochondrial toxicity.
    Cho-Won Kim, Hee-Jin Lee, Dohee Ahn, Ryeo-Eun Go, Kyung-Chul Choi.
      The heart has an abundance of mitochondria since cardiac muscles require copious amounts of energy for providing continuous blood through the circulatory system, thereby implying that myocardial function is largely reliant on mitochondrial energy. Thus, cardiomyocytes are susceptible to mitochondrial dysfunction and are likely targets of mitochondrial toxic drugs. Various methods have been developed to evaluate mitochondrial toxicity by evaluating toxicological mechanisms, but an optimized and standardized assay for cardiomyocytes remains unmet. We have therefore attempted to standardize the evaluation system for determining cardiac mitochondrial toxicity, using AC16 human and H9C2 rat cardiomyocytes. Three clinically administered drugs (acetaminophen, amiodarone, and valproic acid) and two anticancer drugs (doxorubicin and tamoxifen) which are reported to have mitochondrial effects, were applied in this study. The oxygen consumption rate (OCR), which directly reflects mitochondrial function, and changes in mRNA levels of mitochondrial respiratory complex I to complex V, were analyzed. Our results reveal that exposure to all five drugs results in a concentration-dependent decrease in the basal and maximal levels of OCR in AC16 cells and H9C2 cells. In particular, marked reduction in the OCR was observed after treatment with doxorubicin. The reduction in OCR after exposure to mitochondrial toxic drugs was found to be associated with reduced mRNA expression in the mitochondrial respiratory complexes, suggesting that the cardiac mitochondrial toxicity of drugs is majorly due to dysfunction of mitochondrial respiration. Based on the results of this study, we established and standardized a protocol to measure OCR in cardiomyocytes. We expect that this standardized evaluation system for mitochondrial toxicity can be applied as basic data for establishing a screening platform to evaluate cardiac mitochondrial toxicity of drugs, during the developmental stage of new drug discovery.
    Keywords:  Cardiomyocytes; Mitochondrial dysfunction; Mitochondrial toxicity; Oxygen consumption rate
    DOI:  https://doi.org/10.1007/s43188-022-00136-2
  39. Nat Chem Biol. 2022 Oct 24.
    Functional spectrum and specificity of mitochondrial ferredoxins FDX1 and FDX2.
    Vinzent Schulz, Somsuvro Basu, Sven-A Freibert, Holger Webert, Linda Boss, Ulrich Mühlenhoff, Fabien Pierrel, Lars-O Essen, Douglas M Warui, Squire J Booker, Oliver Stehling, Roland Lill.
      Ferredoxins comprise a large family of iron-sulfur (Fe-S) proteins that shuttle electrons in diverse biological processes. Human mitochondria contain two isoforms of [2Fe-2S] ferredoxins, FDX1 (aka adrenodoxin) and FDX2, with known functions in cytochrome P450-dependent steroid transformations and Fe-S protein biogenesis. Here, we show that only FDX2, but not FDX1, is involved in Fe-S protein maturation. Vice versa, FDX1 is specific not only for steroidogenesis, but also for heme a and lipoyl cofactor biosyntheses. In the latter pathway, FDX1 provides electrons to kickstart the radical chain reaction catalyzed by lipoyl synthase. We also identified lipoylation as a target of the toxic antitumor copper ionophore elesclomol. Finally, the striking target specificity of each ferredoxin was assigned to small conserved sequence motifs. Swapping these motifs changed the target specificity of these electron donors. Together, our findings identify new biochemical tasks of mitochondrial ferredoxins and provide structural insights into their functional specificity.
    DOI:  https://doi.org/10.1038/s41589-022-01159-4
  40. Neurobiol Aging. 2022 Nov;pii: S0197-4580(22)00165-8. [Epub ahead of print]119 136-138
    Gene-based burden analysis of damaging private variants in PRKN, PARK7 and PINK1 in Parkinson's disease cohorts of European descent.
    International Parkinson's Disease Genomics Consortium (IPDGC)
      Recessive mutations in PRKN, PARK7, and PINK1 are established causes of early-onset Parkinson's disease (EOPD). Previous studies have interrogated the role of heterozygous variants in these genes but mainly focused on rare (minor allele frequency [MAF] <1%) damaging variants or established mutations. Here, we assessed heterozygous private PRKN, PARK7 and PINK1 variants in PD risk in four large-scale PD case-control datasets by performing gene-wise burden analyses using sequencing data totaling 5,829 PD cases and 7,221 controls, and summary allele counts from 9,501 PD cases and 48,207 controls. Results showed no significant burden in all three genes after meta-analyses. Burden in EOPD (age at onset <50 years) and late-onset PD (≥50 years) remained nonsignificant. In summary, we found no evidence to support the association of the excess burden of heterozygous private variants in PRKN, PARK7, and PINK1 with PD risk in the European population. Larger, more diverse cohorts are needed to accurately determine their role in PD.
    Keywords:  Genetics; PARK7; PINK1; PRKN; Parkinson's disease; Private variants
    DOI:  https://doi.org/10.1016/j.neurobiolaging.2022.07.012
  41. Trends Cell Biol. 2022 Oct 19. pii: S0962-8924(22)00230-6. [Epub ahead of print]
    Multifaceted mitochondrial quality control in brown adipose tissue.
    Katia Aquilano, Beiyan Zhou, Jonathan R Brestoff, Daniele Lettieri-Barbato.
      Brown adipose tissue (BAT) controls mammalian core body temperature by non-shivering thermogenesis. BAT is extraordinarily rich in mitochondria, which have the peculiarity of generating heat by uncoupled respiration. Since the mitochondrial activity of BAT is subject to cycles of activation and deactivation in response to environmental temperature changes, an integrated mitochondrial quality control (MQC) system is of fundamental importance to ensure BAT physiology. Here, we provide an overview of the conventional and alternative mechanisms through which thermogenic adipocytes selectively remove damaged parts of mitochondria and how macrophages participate in the MQC system by removing extracellular mitochondrial waste to maintain the thermogenic function of BAT.
    Keywords:  adipocytes; extracellular vesicles; immune cells; metabolism; mitochondrial transfer; thermogenesis
    DOI:  https://doi.org/10.1016/j.tcb.2022.09.008
  42. iScience. 2022 Nov 18. 25(11): 105230
    Metabolomic fingerprinting of renal disease progression in Bardet-Biedl syndrome reveals mitochondrial dysfunction in kidney tubular cells.
    Emanuela Marchese, Marianna Caterino, Davide Viggiano, Armando Cevenini, Salvatore Tolone, Ludovico Docimo, Valentina Di Iorio, Francesca Del Vecchio Blanco, Roberta Fedele, Francesca Simonelli, Alessandra Perna, Vincenzo Nigro, Giovambattista Capasso, Margherita Ruoppolo, Miriam Zacchia.
      Chronic kidney disease (CKD) is a major clinical sign of patients with Bardet-Biedl syndrome (BBS), especially in those carrying BBS10 mutations. Twenty-nine patients with BBS and 30 controls underwent a serum-targeted metabolomic analysis. In vitro studies were conducted in two kidney-derived epithelial cell lines, where Bbs10 was stably deleted (IMCD3-Bbs10-/-cells) and over-expressed. The CKD status affected plasmatic metabolite fingerprinting in both patients with BBS and controls. Specific phosphatidylcholine and acylcarnitines discriminated eGFR decline only in patients with BBS. IMCD3-Bbs10-/ cells displayed intracellular lipidaccumulation, reduced mitochondrial potential membrane and citrate synthase staining. Mass-Spectrometry-based analysis revealed that human BBS10 interacted with six mitochondrial proteins, in vitro. In conclusion, renal dysfunction correlated with abnormal phosphatidylcholine and acylcarnitines plasma levels in patients with BBS; in vitro, Bbs10 depletion caused mitochondrial defects while human BBS10 interacted with several mitochondria-related proteins, suggesting an unexplored role of this protein.
    Keywords:  Pathophysiology; metabolomics
    DOI:  https://doi.org/10.1016/j.isci.2022.105230
  43. Proc Natl Acad Sci U S A. 2022 Nov;119(44): e2121273119
    A small molecule M1 promotes optic nerve regeneration to restore target-specific neural activity and visual function.
    Ngan Pan Bennett Au, Raza Chand, Gajendra Kumar, Pallavi Asthana, Wing Yip Tam, Kin Man Tang, Chi-Chiu Ko, Chi Him Eddie Ma.
      Axon regeneration is an energy-demanding process that requires active mitochondrial transport. In contrast to the central nervous system (CNS), axonal mitochondrial transport in regenerating axons of the peripheral nervous system (PNS) increases within hours and sustains for weeks after injury. Yet, little is known about targeting mitochondria in nervous system repair. Here, we report the induction of sustained axon regeneration, neural activities in the superior colliculus (SC), and visual function recovery after optic nerve crush (ONC) by M1, a small molecule that promotes mitochondrial fusion and transport. We demonstrated that M1 enhanced mitochondrial dynamics in cultured neurons and accelerated in vivo axon regeneration in the PNS. Ex vivo time-lapse imaging and kymograph analysis showed that M1 greatly increased mitochondrial length, axonal mitochondrial motility, and transport velocity in peripheral axons of the sciatic nerves. Following ONC, M1 increased the number of axons regenerating through the optic chiasm into multiple subcortical areas and promoted the recovery of local field potentials in the SC after optogenetic stimulation of retinal ganglion cells, resulting in complete recovery of the pupillary light reflex, and restoration of the response to looming visual stimuli was detected. M1 increased the gene expression of mitochondrial fusion proteins and major axonal transport machinery in both the PNS and CNS neurons without inducing inflammatory responses. The knockdown of two key mitochondrial genes, Opa1 or Mfn2, abolished the growth-promoting effects of M1 after ONC, suggesting that maintaining a highly dynamic mitochondrial population in axons is required for successful CNS axon regeneration.
    Keywords:  axon regeneration; mitochondrial dynamics; optic nerve crush; peripheral nerve injury; visual function recovery
    DOI:  https://doi.org/10.1073/pnas.2121273119
  44. Nat Methods. 2022 Oct 27.
    A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies.
    NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium
      Large-scale whole-genome sequencing studies have enabled analysis of noncoding rare-variant (RV) associations with complex human diseases and traits. Variant-set analysis is a powerful approach to study RV association. However, existing methods have limited ability in analyzing the noncoding genome. We propose a computationally efficient and robust noncoding RV association detection framework, STAARpipeline, to automatically annotate a whole-genome sequencing study and perform flexible noncoding RV association analysis, including gene-centric analysis and fixed window-based and dynamic window-based non-gene-centric analysis by incorporating variant functional annotations. In gene-centric analysis, STAARpipeline uses STAAR to group noncoding variants based on functional categories of genes and incorporate multiple functional annotations. In non-gene-centric analysis, STAARpipeline uses SCANG-STAAR to incorporate dynamic window sizes and multiple functional annotations. We apply STAARpipeline to identify noncoding RV sets associated with four lipid traits in 21,015 discovery samples from the Trans-Omics for Precision Medicine (TOPMed) program and replicate several of them in an additional 9,123 TOPMed samples. We also analyze five non-lipid TOPMed traits.
    DOI:  https://doi.org/10.1038/s41592-022-01640-x
  45. Front Immunol. 2022 ;13 1017401
    The role of mitochondria in the pathogenesis of Kawasaki disease.
    Mikayla A Beckley, Sadeep Shrestha, Keshav K Singh, Michael A Portman.
      Kawasaki disease is a systemic vasculitis, especially of the coronary arteries, affecting children. Despite extensive research, much is still unknown about the principal driver behind the amplified inflammatory response. We propose mitochondria may play a critical role. Mitochondria serve as a central hub, influencing energy generation, cell proliferation, and bioenergetics. Regulation of these biological processes, however, comes at a price. Release of mitochondrial DNA into the cytoplasm acts as damage-associated molecular patterns, initiating the development of inflammation. As a source of reactive oxygen species, they facilitate activation of the NLRP3 inflammasome. Kawasaki disease involves many of these inflammatory pathways. Progressive mitochondrial dysfunction alters the activity of immune cells and may play a role in the pathogenesis of Kawasaki disease. Because they contain their own genome, mitochondria are susceptible to mutation which can propagate their dysfunction and immunostimulatory potential. Population-specific variants in mitochondrial DNA have also been linked to racial disparities in disease risk and treatment response. Our objective is to critically examine the current literature of mitochondria's role in coordinating proinflammatory signaling pathways, focusing on potential mitochondrial dysfunction in Kawasaki disease. No association between impaired mitochondrial function and Kawasaki disease exists, but we suggest a relationship between the two. We hypothesize a framework of mitochondrial determinants that may contribute to ethnic/racial disparities in the progression of Kawasaki disease.
    Keywords:  Kawasaki disease; inflammasome; inflammation; mitochondria; mitochondrial DNA; mitophagy; reactive oxygen species
    DOI:  https://doi.org/10.3389/fimmu.2022.1017401
  46. Biochem Soc Trans. 2022 Oct 28. pii: BST20220873. [Epub ahead of print]
    Frankenstein Cas9: engineering improved gene editing systems.
    Pascal D Vos, Aleksandra Filipovska, Oliver Rackham.
      The discovery of CRISPR-Cas9 and its widespread use has revolutionised and propelled research in biological sciences. Although the ability to target Cas9's nuclease activity to specific sites via an easily designed guide RNA (gRNA) has made it an adaptable gene editing system, it has many characteristics that could be improved for use in biotechnology. Cas9 exhibits significant off-target activity and low on-target nuclease activity in certain contexts. Scientists have undertaken ambitious protein engineering campaigns to bypass these limitations, producing several promising variants of Cas9. Cas9 variants with improved and alternative activities provide exciting new tools to expand the scope and fidelity of future CRISPR applications.
    Keywords:  CRISPR; designer Cas9; enzyme design; gene editing; protein engineering; synthetic biology
    DOI:  https://doi.org/10.1042/BST20220873
  47. Nat Struct Mol Biol. 2022 Oct 27.
    Mechanism and modeling of human disease-associated near-exon intronic variants that perturb RNA splicing.
    Hung-Lun Chiang, Yi-Ting Chen, Jia-Ying Su, Hsin-Nan Lin, Chen-Hsin Albert Yu, Yu-Jen Hung, Yun-Lin Wang, Yen-Tsung Huang, Chien-Ling Lin.
      It is estimated that 10%-30% of disease-associated genetic variants affect splicing. Splicing variants may generate deleteriously altered gene product and are potential therapeutic targets. However, systematic diagnosis or prediction of splicing variants is yet to be established, especially for the near-exon intronic splice region. The major challenge lies in the redundant and ill-defined branch sites and other splicing motifs therein. Here, we carried out unbiased massively parallel splicing assays on 5,307 disease-associated variants that overlapped with branch sites and collected 5,884 variants across the 5' splice region. We found that strong splice sites and exonic features preserve splicing from intronic sequence variation. Whereas the splice-altering mechanism of the 3' intronic variants is complex, that of the 5' is mainly splice-site destruction. Statistical learning combined with these molecular features allows precise prediction of altered splicing from an intronic variant. This statistical model provides the identity and ranking of biological features that determine splicing, which serves as transferable knowledge and out-performs the benchmarking predictive tool. Moreover, we demonstrated that intronic splicing variants may associate with disease risks in the human population. Our study elucidates the mechanism of splicing response of intronic variants, which classify disease-associated splicing variants for the promise of precision medicine.
    DOI:  https://doi.org/10.1038/s41594-022-00844-1
  48. Genet Med. 2022 Oct 28. pii: S1098-3600(22)00947-9. [Epub ahead of print]
    Informing variant assessment using structured evidence from prior classifications (PS1, PM5, and PVS1 sequence variant interpretation criteria).
    Vineel Bhat, Ivan A Adzhubei, James D Fife, Matthew Lebo, Christopher A Cassa.
       PURPOSE: This study aimed to explore whether evidence of pathogenicity from prior variant classifications in ClinVar could be used to inform variant interpretation using the American College of Medical Genetics and Genomics/Association for Molecular Pathology clinical guidelines.
    METHODS: We identified distinct single-nucleotide variants (SNVs) that are either similar in location or in functional consequence to pathogenic variants in ClinVar and analyzed evidence in support of pathogenicity using 3 interpretation criteria.
    RESULTS: Thousands of variants, including many in clinically actionable disease genes (American College of Medical Genetics and Genomics secondary findings v3.0), have evidence of pathogenicity from existing variant classifications, accounting for 2.5% of nonsynonymous SNVs within ClinVar. Notably, there are many variants with uncertain or conflicting classifications that cause the same amino acid substitution as other pathogenic variants (PS1, N = 323), variants that are predicted to cause different amino acid substitutions in the same codon as pathogenic variants (PM5, N = 7692), and loss-of-function variants that are present in genes in which many loss-of-function variants are classified as pathogenic (PVS1, N = 3635). Most of these variants have similar computational predictions of pathogenicity and splicing effect as their associated pathogenic variants.
    CONCLUSION: Broadly, for >1.4 million SNVs exome wide, information from previously classified variants could be used to provide evidence of pathogenicity. We have developed a pipeline to identify variants meeting these criteria that may inform interpretation efforts.
    Keywords:  ACMG/AMP; ClinVar; PS1/PM5/PVS1 evidence; Sequence variant interpretation guidelines; Variants of uncertain significance
    DOI:  https://doi.org/10.1016/j.gim.2022.09.009
  49. Nat Cell Biol. 2022 Oct 24.
    Quick tips for re-using metabolomics data.
    Ethan Stancliffe, Gary J Patti.
      
    DOI:  https://doi.org/10.1038/s41556-022-01019-2
  50. NPJ Genom Med. 2022 Oct 26. 7(1): 62
    Rapid and comprehensive diagnostic method for repeat expansion diseases using nanopore sequencing.
    Satoko Miyatake, Eriko Koshimizu, Atsushi Fujita, Hiroshi Doi, Masaki Okubo, Taishi Wada, Kohei Hamanaka, Naohisa Ueda, Hitaru Kishida, Gaku Minase, Atsuhiro Matsuno, Minori Kodaira, Katsuhisa Ogata, Rumiko Kato, Atsuhiko Sugiyama, Ayako Sasaki, Takabumi Miyama, Mai Satoh, Yuri Uchiyama, Naomi Tsuchida, Haruka Hamanoue, Kazuharu Misawa, Kiyoshi Hayasaka, Yoshiki Sekijima, Hiroaki Adachi, Kunihiro Yoshida, Fumiaki Tanaka, Takeshi Mizuguchi, Naomichi Matsumoto.
      We developed a diagnostic method for repeat expansion diseases using a long-read sequencer to improve currently available, low throughput diagnostic methods. We employed the real-time target enrichment system of the nanopore GridION sequencer using the adaptive sampling option, in which software-based target assignment is available without prior sample enrichment, and built an analysis pipeline that prioritized the disease-causing loci. Twenty-two patients with various neurological and neuromuscular diseases, including 12 with genetically diagnosed repeat expansion diseases and 10 manifesting cerebellar ataxia, but without genetic diagnosis, were analyzed. We first sequenced the 12 molecularly diagnosed patients and accurately confirmed expanded repeats in all with uniform depth of coverage across the loci. Next, we applied our method and a conventional method to 10 molecularly undiagnosed patients. Our method corrected inaccurate diagnoses of two patients by the conventional method. Our method is superior to conventional diagnostic methods in terms of speed, accuracy, and comprehensiveness.
    DOI:  https://doi.org/10.1038/s41525-022-00331-y
  51. Nat Methods. 2022 Oct 24.
    Annotation of spatially resolved single-cell data with STELLAR.
    Maria Brbić, Kaidi Cao, John W Hickey, Yuqi Tan, Michael P Snyder, Garry P Nolan, Jure Leskovec.
      Accurate cell-type annotation from spatially resolved single cells is crucial to understand functional spatial biology that is the basis of tissue organization. However, current computational methods for annotating spatially resolved single-cell data are typically based on techniques established for dissociated single-cell technologies and thus do not take spatial organization into account. Here we present STELLAR, a geometric deep learning method for cell-type discovery and identification in spatially resolved single-cell datasets. STELLAR automatically assigns cells to cell types present in the annotated reference dataset and discovers novel cell types and cell states. STELLAR transfers annotations across different dissection regions, different tissues and different donors, and learns cell representations that capture higher-order tissue structures. We successfully applied STELLAR to CODEX multiplexed fluorescent microscopy data and multiplexed RNA imaging datasets. Within the Human BioMolecular Atlas Program, STELLAR has annotated 2.6 million spatially resolved single cells with dramatic time savings.
    DOI:  https://doi.org/10.1038/s41592-022-01651-8
  52. Hum Mutat. 2022 Oct 23.
    SPiP: Splicing Prediction Pipeline, a machine learning tool for massive detection of exonic and intronic variant effect on mRNA splicing.
    Raphaël Leman, Béatrice Parfait, Dominique Vidaud, Emmanuelle Girodon, Laurence Pacot, Gérald Le Gac, Chandran Ka, Claude Ferec, Yann Fichou, Céline Quesnelle, Camille Aucouturier, Etienne Muller, Dominique Vaur, Laurent Castera, Flavie Boulouard, Agathe Ricou, Hélène Tubeuf, Omar Soukarieh, Pascaline Gaildrat, Florence Riant, Marine Guillaud-Bataille, Sandrine M Caputo, Virginie Caux-Moncoutier, Nadia Boutry-Kryza, Françoise Bonnet-Dorion, Ines Schultz, Maria Rossing, Olivier Quenez, Louis Goldenberg, Valentin Harter, Michael T Parsons, Amanda B Spurdle, Thierry Frébourg, Alexandra Martins, Claude Houdayer, Sophie Krieger.
      Modeling splicing is essential for tackling the challenge of variant interpretation as each nucleotide variation can be pathogenic by affecting pre-mRNA splicing via disruption/creation of splicing motifs such as 5'/3' splice sites, branch sites or splicing regulatory elements. Unfortunately, most in silico tools focus on a specific type of splicing motif, which is why we developed the Splicing Prediction Pipeline (SPiP) to perform, in one single bioinformatic analysis based on machine learning approach, comprehensive assessment of variant effect on different splicing motifs. We gathered a curated set of 4,616 variants scattered all along the sequence of 227 genes, with their corresponding splicing studies. Bayesian analysis provided us the number of control variants, i.e. variants without impact on splicing, to mimic the deluge of variants from high throughput sequencing data. Results show that SPiP can deal with the diversity of splicing alterations, with 83.13% sensitivity and 99% specificity to detect spliceogenic variants. Overall performance as measured by area under the receiving operator curve was 0.986, better than SpliceAI and SQUIRLS (0.965 and 0.766) for the same dataset. SPiP lends itself to a unique suite for comprehensive prediction of spliceogenicity in the genomic medicine era. SPiP is available at: https://sourceforge.net/projects/splicing-prediction-pipeline/ This article is protected by copyright. All rights reserved.
    Keywords:  RNA; SPiP; machine learning; sequence variants; splicing predictions
    DOI:  https://doi.org/10.1002/humu.24491
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