bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2023–08–06
fifty-four papers selected by
Catalina Vasilescu, Helmholz Munich
  1. Investigation of hydrated channels and proton pathways in a high-resolution cryo-EM structure of mammalian complex I.
  2. Contact sites between endoplasmic reticulum sheets and mitochondria regulate mitochondrial DNA replication and segregation.
  3. Clinical and molecular characterization of novel FARS2 variants causing neonatal mitochondrial disease.
  4. Phospholipids can regulate complex I assembly independent of their role in maintaining mitochondrial membrane integrity.
  5. Completion of mitochondrial division requires the intermembrane space protein Mdi1/Atg44.
  6. Metabolic switch from fatty acid oxidation to glycolysis in knock-in mouse model of Barth syndrome.
  7. Inter-tissue communication of mitochondrial stress and metabolic health.
  8. FBXO7/ntc and USP30 antagonistically set the ubiquitination threshold for basal mitophagy and provide a target for Pink1 phosphorylation in vivo.
  9. Central role of Tim17 in mitochondrial presequence protein translocation.
  10. Mitochonic acid 5 attenuates age-related neuromuscular dysfunction associated with mitochondrial Ca2+ overload in Caenorhabditis elegans.
  11. Generation of induced pluripotent stem cells, KCi004-A derived from a male with Parkinsońs disease and homozygous for the PINK1 variant c.1366C > T, p.Gln456.
  12. Optimized allotopic expression of mitochondrial ND6 transgene restored complex I and apoptosis deficiencies caused by LHON-linked ND6 14484T > C mutation.
  13. Mitochondrial epigenetics in aging and cardiovascular diseases.
  14. Plausible Role of Mitochondrial DNA Copy Number in Neurodegeneration-a Need for Therapeutic Approach in Parkinson's Disease (PD).
  15. Application of super-resolution microscopy in mitochondria-dynamic diseases.
  16. FAM210A regulates mitochondrial translation and maintains cardiac mitochondrial homeostasis.
  17. Optimized bisulfite sequencing analysis reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA.
  18. Nanoscale details of mitochondrial constriction revealed by cryo-electron tomography.
  19. The Parliamentary Inquiry into Mitochondrial Donation Law Reform (Maeve's Law) Bill 2021 in Australia: A Qualitative Analysis.
  20. MAVS Antagonizes Human Stem Cell Senescence as a Mitochondrial Stabilizer.
  21. Bench to Bedside: Rapid Leber Hereditary Optic Neuropathy Diagnosis.
  22. Neuropathological hallmarks in autopsied cases with mitochondrial diseases caused by the mitochondrial 3243A>G mutation.
  23. Neuromuscular disease genetics in underrepresented populations: increasing data diversity.
  24. The Role of Impaired Mitochondrial Transport in the Development of Neurodegenerative Diseases.
  25. Advancing Understanding of Inequities in Rare Disease Genomics.
  26. Fifty years of research on mitochondrial fatty acid oxidation defects: the remaining challenges.
  27. Genome sequencing and comprehensive rare-variant analysis of 465 families with neurodevelopmental disorders.
  28. Controllable mitochondrial aggregation and fusion by a programmable DNA binder.
  29. Rapid and Sensitive Diagnosis of Leber Hereditary Optic Neuropathy Variants Using CRISPR/Cas12a Detection.
  30. Myonectin protects against skeletal muscle dysfunction in male mice through activation of AMPK/PGC1α pathway.
  31. Genomic testing for rare disease diagnosis-where are we now, and where should we be heading? The reflections of a behavioural scientist.
  32. O-GlcNAcylation of Raptor transduces glucose signals to mTORC1.
  33. The landscape of reported VUS in multi-gene panel and genomic testing: Time for a change.
  34. Beyond genetics: Deciphering the impact of missense variants in CAD deficiency.
  35. Induced pluripotent stem cells for modeling physiological and pathological striated muscle complexity.
  36. Beyond the exome: What's next in diagnostic testing for Mendelian conditions.
  37. Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP.
  38. A diverse ancestrally-matched reference panel increases genotype imputation accuracy in a underrepresented population.
  39. Mitochondria dysregulation contributes to secondary neurodegeneration progression post-contusion injury in human 3D in vitro triculture brain tissue model.
  40. Lipidomic QTL in Diversity Outbred mice identifies a novel function for α/β hydrolase domain 2 (Abhd2) as an enzyme that metabolizes phosphatidylcholine and cardiolipin.
  41. Scientific discovery in the age of artificial intelligence.
  42. High-fat diet causes mitochondrial damage and downregulation of mitofusin-2 and optic atrophy-1 in multiple organs.
  43. Clinical validation of a single NGS targeted panel pipeline using the KAPA HyperChoice system for detection of germline, somatic and mitochondrial sequence and copy number variants.
  44. Mitochondrial protein MPV17 promotes beta-cell apoptosis in diabetogenesis.
  45. Decreased MFN2 activates the cGAS-STING pathway in diabetic myocardial ischaemia-reperfusion by triggering the release of mitochondrial DNA.
  46. Increased cardiac PFK-2 protects against high-fat diet-induced cardiomyopathy and mediates beneficial systemic metabolic effects.
  47. Providing open imaging data at scale: An EMBL-EBI perspective.
  48. Mitochondrial transplantation rescues neuronal cells from ferroptosis.
  49. The expanding organelle lipidomes: current knowledge and challenges.
  50. The non-specific lethal complex regulates genes and pathways genetically linked to Parkinson's disease.
  51. NAD+ metabolism and eye diseases: current status and future directions.
  52. Convergent and divergent mechanisms of peroxisomal and mitochondrial division.
  53. A water-soluble fluorescent organic nano-photosensitizer for the ratiometric detection of mitochondrial G-quadruplexes with photodynamic therapy potential.
  54. An integrative analysis of genotype-phenotype correlation in Charcot Marie Tooth type 2A disease with MFN2 variants: a case and systematic review.
  1. Sci Adv. 2023 Aug 02. 9(31): eadi1359
    Investigation of hydrated channels and proton pathways in a high-resolution cryo-EM structure of mammalian complex I.
    Daniel N Grba, Injae Chung, Hannah R Bridges, Ahmed-Noor A Agip, Judy Hirst.
      Respiratory complex I, a key enzyme in mammalian metabolism, captures the energy released by reduction of ubiquinone by NADH to drive protons across the inner mitochondrial membrane, generating the proton-motive force for ATP synthesis. Despite remarkable advances in structural knowledge of this complicated membrane-bound enzyme, its mechanism of catalysis remains controversial. In particular, how ubiquinone reduction is coupled to proton pumping and the pathways and mechanisms of proton translocation are contested. We present a 2.4-Å resolution cryo-EM structure of complex I from mouse heart mitochondria in the closed, active (ready-to-go) resting state, with 2945 water molecules modeled. By analyzing the networks of charged and polar residues and water molecules present, we evaluate candidate pathways for proton transfer through the enzyme, for the chemical protons for ubiquinone reduction, and for the protons transported across the membrane. Last, we compare our data to the predictions of extant mechanistic models, and identify key questions to answer in future work to test them.
    DOI:  https://doi.org/10.1126/sciadv.adi1359
  2. iScience. 2023 Jul 21. 26(7): 107180
    Contact sites between endoplasmic reticulum sheets and mitochondria regulate mitochondrial DNA replication and segregation.
    Hema Saranya Ilamathi, Sara Benhammouda, Amel Lounas, Khalid Al-Naemi, Justine Desrochers-Goyette, Matthew A Lines, François J Richard, Jackie Vogel, Marc Germain.
      Mitochondria are multifaceted organelles crucial for cellular homeostasis that contain their own genome. Mitochondrial DNA (mtDNA) replication is a spatially regulated process essential for the maintenance of mitochondrial function, its defect causing mitochondrial diseases. mtDNA replication occurs at endoplasmic reticulum (ER)-mitochondria contact sites and is affected by mitochondrial dynamics: The absence of mitochondrial fusion is associated with mtDNA depletion whereas loss of mitochondrial fission causes the aggregation of mtDNA within abnormal structures termed mitobulbs. Here, we show that contact sites between mitochondria and ER sheets, the ER structure associated with protein synthesis, regulate mtDNA replication and distribution within mitochondrial networks. DRP1 loss or mutation leads to modified ER sheets and alters the interaction between ER sheets and mitochondria, disrupting RRBP1-SYNJ2BP interaction. Importantly, mtDNA distribution and replication were rescued by promoting ER sheets-mitochondria contact sites. Our work identifies the role of ER sheet-mitochondria contact sites in regulating mtDNA replication and distribution.
    Keywords:  Biochemistry; Biological sciences; Cell biology
    DOI:  https://doi.org/10.1016/j.isci.2023.107180
  3. Mol Genet Metab. 2023 Jul 24. pii: S1096-7192(23)00287-1. [Epub ahead of print]140(3): 107657
    Clinical and molecular characterization of novel FARS2 variants causing neonatal mitochondrial disease.
    Wenqian Chen, Preeya Rehsi, Kyle Thompson, Mildrid Yeo, Karen Stals, Langping He, Paul Schimmel, Zofia M A Chrzanowska-Lightowlers, Emma Wakeling, Robert W Taylor, Bernhard Kuhle.
      FARS2 encodes the mitochondrial phenylalanyl-tRNA synthetase (mtPheRS), which is essential for charging mitochondrial (mt-) tRNAPhe with phenylalanine for use in intramitochondrial translation. Many biallelic, pathogenic FARS2 variants have been described previously, which are mostly associated with two distinct clinical phenotypes; an early onset epileptic mitochondrial encephalomyopathy or a later onset spastic paraplegia. In this study, we report on a patient who presented at 3 weeks of age with tachypnoea and poor feeding, which progressed to severe metabolic decompensation with lactic acidosis and seizure activity followed by death at 9 weeks of age. Rapid trio whole exome sequencing identified compound heterozygous FARS2 variants including a pathogenic exon 2 deletion on one allele and a rare missense variant (c.593G > T, p.(Arg198Leu)) on the other allele, necessitating further work to aid variant classification. Assessment of patient fibroblasts demonstrated severely decreased steady-state levels of mtPheRS, but no obvious defect in any components of the oxidative phosphorylation system. To investigate the potential pathogenicity of the missense variant, we determined its high-resolution crystal structure, demonstrating a local structural destabilization in the catalytic domain. Moreover, the R198L mutation reduced the thermal stability and impaired the enzymatic activity of mtPheRS due to a lower binding affinity for tRNAPhe and a slower turnover rate. Together these data confirm the pathogenicity of this FARS2 variant in causing early-onset mitochondrial epilepsy.
    Keywords:  FARS2; Functional assays; Mitochondrial disease; Mitochondrial phenylalanyl-tRNA synthetase; Variant classification
    DOI:  https://doi.org/10.1016/j.ymgme.2023.107657
  4. Cell Rep. 2023 Jul 29. pii: S2211-1247(23)00857-4. [Epub ahead of print]42(8): 112846
    Phospholipids can regulate complex I assembly independent of their role in maintaining mitochondrial membrane integrity.
    Anjaneyulu Murari, Shauna-Kay Rhooms, Divya Vimal, Kaniz Fatima Binte Hossain, Sanjay Saini, Maximino Villanueva, Michael Schlame, Edward Owusu-Ansah.
      Several phospholipid (PL) molecules are intertwined with some mitochondrial complex I (CI) subunits in the membrane domain of CI, but their function is unclear. We report that when the Drosophila melanogaster ortholog of the intramitochondrial PL transporter, STARD7, is severely disrupted, assembly of the oxidative phosphorylation (OXPHOS) system is impaired, and the biogenesis of several CI subcomplexes is hampered. However, intriguingly, a restrained knockdown of STARD7 impairs the incorporation of NDUFS5 and NDUFA1 into the proximal part of the CI membrane domain without directly affecting the incorporation of subunits in the distal part of the membrane domain, OXPHOS complexes already assembled, or mitochondrial cristae integrity. Importantly, the restrained knockdown of STARD7 appears to induce a modest amount of cardiolipin remodeling, indicating that there could be some alteration in the composition of the mitochondrial phospholipidome. We conclude that PLs can regulate CI biogenesis independent of their role in maintaining mitochondrial membrane integrity.
    Keywords:  CP: Molecular biology; Drosophila; NDUFA1; NDUFS5; OXPHOS; STARD7; complex I; mitochondria; phospholipid
    DOI:  https://doi.org/10.1016/j.celrep.2023.112846
  5. J Cell Biol. 2023 Oct 02. pii: e202303147. [Epub ahead of print]222(10):
    Completion of mitochondrial division requires the intermembrane space protein Mdi1/Atg44.
    Olivia M Connor, Srujan K Matta, Jonathan R Friedman.
      Mitochondria are highly dynamic double membrane-bound organelles that maintain their shape in part through fission and fusion. Mitochondrial fission is performed by a dynamin-related protein, Dnm1 (Drp1 in humans), that constricts and divides the mitochondria in a GTP hydrolysis-dependent manner. However, it is unclear whether factors inside mitochondria help coordinate the process and if Dnm1/Drp1 activity is sufficient to complete the fission of both mitochondrial membranes. Here, we identify an intermembrane space protein required for mitochondrial fission in yeast, which we propose to name Mdi1 (also named Atg44). Loss of Mdi1 causes mitochondrial hyperfusion due to defects in fission, but not the lack of Dnm1 recruitment to mitochondria. Mdi1 is conserved in fungal species, and its homologs contain an amphipathic α-helix, mutations of which disrupt mitochondrial morphology. One model is that Mdi1 distorts mitochondrial membranes to enable Dnm1 to robustly complete fission. Our work reveals that Dnm1 cannot efficiently divide mitochondria without the coordinated function of Mdi1 inside mitochondria.
    DOI:  https://doi.org/10.1083/jcb.202303147
  6. EMBO Mol Med. 2023 Aug 03. e17399
    Metabolic switch from fatty acid oxidation to glycolysis in knock-in mouse model of Barth syndrome.
    Arpita Chowdhury, Angela Boshnakovska, Abhishek Aich, Aditi Methi, Ana Maria Vergel Leon, Ivan Silbern, Christian Lüchtenborg, Lukas Cyganek, Jan Prochazka, Radislav Sedlacek, Jiri Lindovsky, Dominic Wachs, Zuzana Nichtova, Dagmar Zudova, Gizela Koubkova, André Fischer, Henning Urlaub, Britta Brügger, Dörthe M Katschinski, Jan Dudek, Peter Rehling.
      Mitochondria are central for cellular metabolism and energy supply. Barth syndrome (BTHS) is a severe disorder, due to dysfunction of the mitochondrial cardiolipin acyl transferase tafazzin. Altered cardiolipin remodeling affects mitochondrial inner membrane organization and function of membrane proteins such as transporters and the oxidative phosphorylation (OXPHOS) system. Here, we describe a mouse model that carries a G197V exchange in tafazzin, corresponding to BTHS patients. TAZG197V mice recapitulate disease-specific pathology including cardiac dysfunction and reduced oxidative phosphorylation. We show that mutant mitochondria display defective fatty acid-driven oxidative phosphorylation due to reduced levels of carnitine palmitoyl transferases. A metabolic switch in ATP production from OXPHOS to glycolysis is apparent in mouse heart and patient iPSC cell-derived cardiomyocytes. An increase in glycolytic ATP production inactivates AMPK causing altered metabolic signaling in TAZG197V . Treatment of mutant cells with AMPK activator reestablishes fatty acid-driven OXPHOS and protects mice against cardiac dysfunction.
    Keywords:  Barth syndrome; cardiolipin; cardiomyopathy; mitochondria; tafazzin
    DOI:  https://doi.org/10.15252/emmm.202317399
  7. Life Metab. 2023 Feb;pii: load001. [Epub ahead of print]2(1):
    Inter-tissue communication of mitochondrial stress and metabolic health.
    Hanlin Zhang, Xinyu Li, Wudi Fan, Sentibel Pandovski, Ye Tian, Andrew Dillin.
      Mitochondria function as a hub of the cellular metabolic network. Mitochondrial stress is closely associated with aging and a variety of diseases, including neurodegeneration and cancer. Cells autonomously elicit specific stress responses to cope with mitochondrial stress to maintain mitochondrial homeostasis. Interestingly, mitochondrial stress responses may also be induced in a non-autonomous manner in cells or tissues that are not directly experiencing such stress. Such non-autonomous mitochondrial stress responses are mediated by secreted molecules called mitokines. Due to their significant translational potential in improving human metabolic health, there has been a surge in mitokine-focused research. In this review, we summarize the findings regarding inter-tissue communication of mitochondrial stress in animal models. In addition, we discuss the possibility of mitokine-mediated intercellular mitochondrial communication originating from bacterial quorum sensing.
    Keywords:  inter-tissue communication; metabolic health; mitochondria; mitokine; quorum sensing
    DOI:  https://doi.org/10.1093/lifemeta/load001
  8. PLoS Biol. 2023 Aug 03. 21(8): e3002244
    FBXO7/ntc and USP30 antagonistically set the ubiquitination threshold for basal mitophagy and provide a target for Pink1 phosphorylation in vivo.
    Alvaro Sanchez-Martinez, Aitor Martinez, Alexander J Whitworth.
      Functional analyses of genes linked to heritable forms of Parkinson's disease (PD) have revealed fundamental insights into the biological processes underpinning pathogenic mechanisms. Mutations in PARK15/FBXO7 cause autosomal recessive PD and FBXO7 has been shown to regulate mitochondrial homeostasis. We investigated the extent to which FBXO7 and its Drosophila orthologue, ntc, share functional homology and explored its role in mitophagy in vivo. We show that ntc mutants partially phenocopy Pink1 and parkin mutants and ntc overexpression supresses parkin phenotypes. Furthermore, ntc can modulate basal mitophagy in a Pink1- and parkin-independent manner by promoting the ubiquitination of mitochondrial proteins, a mechanism that is opposed by the deubiquitinase USP30. This basal ubiquitination serves as the substrate for Pink1-mediated phosphorylation that triggers stress-induced mitophagy. We propose that FBXO7/ntc works in equilibrium with USP30 to provide a checkpoint for mitochondrial quality control in basal conditions in vivo and presents a new avenue for therapeutic approaches.
    DOI:  https://doi.org/10.1371/journal.pbio.3002244
  9. Nature. 2023 Aug 01.
    Central role of Tim17 in mitochondrial presequence protein translocation.
    Laura F Fielden, Jakob D Busch, Sandra G Merkt, Iniyan Ganesan, Conny Steiert, Hanna B Hasselblatt, Jon V Busto, Christophe Wirth, Nicole Zufall, Sibylle Jungbluth, Katja Noll, Julia M Dung, Ludmila Butenko, Karina von der Malsburg, Hans-Georg Koch, Carola Hunte, Martin van der Laan, Nils Wiedemann.
      The presequence translocase of the mitochondrial inner membrane (TIM23) represents the major route for the import of nuclear-encoded proteins into mitochondria1,2. About 60% of more than 1,000 different mitochondrial proteins are synthesised with amino-terminal targeting signals, termed presequences, which form positively charged amphiphilic α-helices3,4. TIM23 sorts the presequence proteins into the inner membrane or matrix. Various views including regulatory and coupling functions have been reported on the essential TIM23 subunit Tim175-7. We mapped the interaction of Tim17 with matrix-targeted and inner membrane-sorted preproteins during translocation in the native membrane environment. We show that Tim17 contains conserved negative charges close to the intermembrane space side of the bilayer, which are essential to initiate presequence protein translocation along a distinct transmembrane cavity of Tim17 for both classes of preproteins. The amphiphilic character of mitochondrial presequences directly matches this Tim17-dependent translocation mechanism. This mechanism permits direct lateral release of transmembrane segments of inner membrane-sorted precursors into the inner membrane.
    DOI:  https://doi.org/10.1038/s41586-023-06477-8
  10. NPJ Aging. 2023 Aug 01. 9(1): 20
    Mitochonic acid 5 attenuates age-related neuromuscular dysfunction associated with mitochondrial Ca2+ overload in Caenorhabditis elegans.
    XinTong Wu, Miku Seida, Takaaki Abe, Atsushi Higashitani.
      Mitochonic acid-5 ameliorates the pathophysiology of human mitochondrial-disease fibroblasts and Caenorhabditis elegans Duchenne muscular dystrophy and Parkinson's disease models. Here, we found that 10 μM MA-5 attenuates the age-related decline in motor performance, loss of muscle mitochondria, and degeneration of dopaminergic neurons associated with mitochondrial Ca2+ overload in C. elegans. These findings suggest that MA-5 may act as an anti-aging agent against a wide range of neuromuscular dysfunctions in metazoans.
    DOI:  https://doi.org/10.1038/s41514-023-00116-2
  11. Stem Cell Res. 2023 Jul 26. pii: S1873-5061(23)00161-7. [Epub ahead of print]71 103175
    Generation of induced pluripotent stem cells, KCi004-A derived from a male with Parkinsońs disease and homozygous for the PINK1 variant c.1366C > T, p.Gln456.
    Lasse Jonsgaard Larsen, Lisbeth Birk Møller.
      Disease causing variants in PINK1 lead to Parkinsońs disease (PD) with early age of onset and slow disease progression. Loss of mitochondrial function is a signal of bioenergetic stress, PINK1 accumulates on the outer mitochondrial membrane and initiates ubiquitination and degradation of damaged mitochondria by mitophagy. Here we describe the successful generation of an induced pluripotent stem cell line (iPSC) KCi004-A from a PD patient homozygous for the disease- causing variant c.1366C > T, p.Gln456* in PINK1. For the generation we transfect a fibroblast culture from the patient with a non-integrative self-replicating RNA vector.
    DOI:  https://doi.org/10.1016/j.scr.2023.103175
  12. J Biomed Sci. 2023 Aug 03. 30(1): 63
    Optimized allotopic expression of mitochondrial ND6 transgene restored complex I and apoptosis deficiencies caused by LHON-linked ND6 14484T > C mutation.
    Jing Wang, Yanchun Ji, Cheng Ai, Jia-Rong Chen, Dingyi Gan, Juanjuan Zhang, Jun Q Mo, Min-Xin Guan.
       BACKGROUND: Leber's hereditary optic neuropathy (LHON) is a maternally inherited eye disease due to mutations in mitochondrial DNA. However, there is no effective treatment for this disease. LHON-linked ND6 14484T > C (p.M64V) mutation caused complex I deficiency, diminished ATP production, increased production of reactive oxygen species (ROS), elevated apoptosis, and impaired mitophagy. Here, we investigated if the allotopic expression of human mitochondrial ND6 transgene corrected the mitochondrial dysfunctions due to LHON-associated m.14484T > C mutation.
    METHODS: Nucleus-versions of ND6 was generated by changing 6 non-universal codons with universal codons and added to mitochondrial targeting sequence of COX8. Stable transfectants were generated by transferring human ND6 cDNA expressed in a pCDH-puro vector into mutant cybrids carrying the m.14484T > C mutation and control cybrids. The effect of allotopic expression of ND6 on oxidative phosphorylation (OXPHOS) was evaluated using Blue Native gel electrophoresis and extracellular flux analyzer. Assessment of ROS production in cell lines was performed by flow cytometry with MitoSOX Red reagent. Analyses for apoptosis and mitophagy were undertaken via flow cytometry, TUNEL and immunofluorescence assays.
    RESULTS: The transfer of human ND6 into the cybrids carrying the m.14484T > C mutation raised the levels of ND6, ND1 and ND4L but did not change the levels of other mitochondrial proteins. The overexpression of ND6 led to 20~23% increases in the assembly and activity of complex I, and ~ 53% and ~ 33% increases in the levels of mitochondrial ATP and ΔΨm in the mutant cybrids bearing m.14484T > C mutation. Furthermore, mutant cybrids with overexpression of ND6 exhibited marked reductions in the levels of mitochondrial ROS. Strikingly, ND6 overexpression markedly inhibited the apoptosis process and restored impaired mitophagy in the cells carrying m.14484T > C mutation. However, overexpression of ND6 did not affect the ND6 level and mitochondrial functions in the wild-type cybrids, indicating that this ND6 level appeared to be the maximum threshold level to maintain the normal cell function.
    CONCLUSION: We demonstrated that allotopic expression of nucleus-versions of ND6 restored complex I, apoptosis and mitophagy deficiencies caused by the m.14484T > C mutation. The restoration of m.14484T > C mutation-induced mitochondrial dysfunctions by overexpression of ND6 is a step toward therapeutic interventions for LHON and mitochondrial diseases.
    Keywords:  Allotopic expression; Apoptosis; Complex I; Leber’s hereditary optic neuropathy; Mitochondrial DNA mutation; Mitophagy
    DOI:  https://doi.org/10.1186/s12929-023-00951-1
  13. Front Cardiovasc Med. 2023 ;10 1204483
    Mitochondrial epigenetics in aging and cardiovascular diseases.
    Alessia Mongelli, Alessandro Mengozzi, Martin Geiger, Era Gorica, Shafeeq Ahmed Mohammed, Francesco Paneni, Frank Ruschitzka, Sarah Costantino.
      Mitochondria are cellular organelles which generate adenosine triphosphate (ATP) molecules for the maintenance of cellular energy through the oxidative phosphorylation. They also regulate a variety of cellular processes including apoptosis and metabolism. Of interest, the inner part of mitochondria-the mitochondrial matrix-contains a circular molecule of DNA (mtDNA) characterised by its own transcriptional machinery. As with genomic DNA, mtDNA may also undergo nucleotide mutations that have been shown to be responsible for mitochondrial dysfunction. During physiological aging, the mitochondrial membrane potential declines and associates with enhanced mitophagy to avoid the accumulation of damaged organelles. Moreover, if the dysfunctional mitochondria are not properly cleared, this could lead to cellular dysfunction and subsequent development of several comorbidities such as cardiovascular diseases (CVDs), diabetes, respiratory and cardiovascular diseases as well as inflammatory disorders and psychiatric diseases. As reported for genomic DNA, mtDNA is also amenable to chemical modifications, namely DNA methylation. Changes in mtDNA methylation have shown to be associated with altered transcriptional programs and mitochondrial dysfunction during aging. In addition, other epigenetic signals have been observed in mitochondria, in particular the interaction between mtDNA methylation and non-coding RNAs. Mitoepigenetic modifications are also involved in the pathogenesis of CVDs where oxygen chain disruption, mitochondrial fission, and ROS formation alter cardiac energy metabolism leading to hypertrophy, hypertension, heart failure and ischemia/reperfusion injury. In the present review, we summarize current evidence on the growing importance of epigenetic changes as modulator of mitochondrial function in aging. A better understanding of the mitochondrial epigenetic landscape may pave the way for personalized therapies to prevent age-related diseases.
    Keywords:  aging; cardiovascular diseases; methylation; mitochondria; mitoepigenetics; mtDNA; ncRNAs
    DOI:  https://doi.org/10.3389/fcvm.2023.1204483
  14. Mol Neurobiol. 2023 Jul 31.
    Plausible Role of Mitochondrial DNA Copy Number in Neurodegeneration-a Need for Therapeutic Approach in Parkinson's Disease (PD).
    Dhivya Venkatesan, Mahalaxmi Iyer, Arul Narayanasamy, Abilash Valsala Gopalakrishnan, Balachandar Vellingiri.
      Parkinson's disease (PD) is an advancing age-associated progressive brain disorder which has various diverse factors, among them mitochondrial dysfunction involves in dopaminergic (DA) degeneration. Aging causes a rise in mitochondrial abnormalities which leads to structural and functional modifications in neuronal activity and cell death in PD. This ends in deterioration of mitochondrial function, mitochondrial alterations, mitochondrial DNA copy number (mtDNA CN) and oxidative phosphorylation (OXPHOS) capacity. mtDNA levels or mtDNA CN in PD have reported that mtDNA depletion would be a predisposing factor in PD pathogenesis. To maintain the mtDNA levels, therapeutic approaches have been focused on mitochondrial biogenesis in PD. The depletion of mtDNA levels in PD can be influenced by autophagic dysregulation, apoptosis, neuroinflammation, oxidative stress, sirtuins, and calcium homeostasis. The current review describes the regulation of mtDNA levels and discusses the plausible molecular pathways in mtDNA CN depletion in PD pathogenesis. We conclude by suggesting further research on mtDNA depletion which might show a promising effect in predicting and diagnosing PD.
    Keywords:  Copy number; Mitochondrial DNA; Molecular pathways; Parkinson’s disease; TFAM; Therapeutic strategies
    DOI:  https://doi.org/10.1007/s12035-023-03500-x
  15. Adv Drug Deliv Rev. 2023 Aug 01. pii: S0169-409X(23)00358-7. [Epub ahead of print] 115043
    Application of super-resolution microscopy in mitochondria-dynamic diseases.
    Weiwei Zou, Li Yang, Hedong Lu, Min Li, Dongmei Ji, Jesse Slone, Taosheng Huang.
      Limited by spatial and temporal resolution, traditional optical microscopy cannot image the delicate ultra-structure organelles and sub-organelles. The emergence of super-resolution microscopy makes it possible. In this review, we focus on mitochondria. We summarize the process of mitochondrial dynamics, the primary proteins that regulate mitochondrial morphology, the diseases related to mitochondrial dynamics.-, The purpose is to apply super-resolution microscopy developed during recent years to the mitochondrial research. By providing the right research tools, we will help to promote the application of this technique to the in-depth elucidation of the pathogenesis of diseases related to mitochondrial dynamics, assistdiagnosis and develop the therapeutic treatment .
    Keywords:  Disease; Dynamics; Mitochondria; Sub-organelle structures; Super-resolution microscopy
    DOI:  https://doi.org/10.1016/j.addr.2023.115043
  16. Cardiovasc Res. 2023 Jul 31. pii: cvad124. [Epub ahead of print]
    FAM210A regulates mitochondrial translation and maintains cardiac mitochondrial homeostasis.
    Jiangbin Wu, Kadiam C Venkata Subbaiah, Omar Hedaya, Si Chen, Joshua Munger, Wai Hong Wilson Tang, Chen Yan, Peng Yao.
       AIMS: Mitochondria play a vital role in cellular metabolism and energetics and support normal cardiac function. Disrupted mitochondrial function and homeostasis cause a variety of heart diseases. Fam210a (family with sequence similarity 210 member A), a novel mitochondrial gene, is identified as a hub gene in mouse cardiac remodeling by multi-omics studies. Human FAM210A mutations are associated with sarcopenia. However, the physiological role and molecular function of FAM210A remain elusive in the heart. We aim to determine the biological role and molecular mechanism of FAM210A in regulating mitochondrial function and cardiac health in vivo.
    METHODS AND RESULTS: Tamoxifen-induced αMHCMCM-driven conditional knockout of Fam210a in the mouse cardiomyocytes induced progressive dilated cardiomyopathy and heart failure, ultimately causing mortality. Fam210a deficient cardiomyocytes exhibit severe mitochondrial morphological disruption and functional decline accompanied by myofilament disarray at the late stage of cardiomyopathy. Furthermore, we observed increased mitochondrial reactive oxygen species production, disturbed mitochondrial membrane potential, and reduced respiratory activity in cardiomyocytes at the early stage before contractile dysfunction and heart failure. Multi-omics analyses indicate that FAM210A deficiency persistently activates integrated stress response (ISR), resulting in transcriptomic, translatomic, proteomic, and metabolomic reprogramming, ultimately leading to pathogenic progression of heart failure. Mechanistically, mitochondrial polysome profiling analysis shows that FAM210A loss of function compromises mitochondrial mRNA translation and leads to reduced mitochondrial encoded proteins, followed by disrupted proteostasis. We observed decreased FAM210A protein expression in human ischemic heart failure and mouse myocardial infarction tissue samples. To further corroborate FAM210A function in the heart, AAV9-mediated overexpression of FAM210A promotes mitochondrial-encoded protein expression, improves cardiac mitochondrial function, and partially rescues murine hearts from cardiac remodeling and damage in ischemia-induced heart failure.
    CONCLUSION: These results suggest that FAM210A is a mitochondrial translation regulator to maintain mitochondrial homeostasis and normal cardiomyocyte contractile function. This study also offers a new therapeutic target for treating ischemic heart disease.
    Keywords:  FAM210A; cardiomyopathy; heart failure; integrated stress response; mRNA translation; metabolism; mitochondria; myocardial infarction
    DOI:  https://doi.org/10.1093/cvr/cvad124
  17. BMC Genomics. 2023 Aug 04. 24(1): 439
    Optimized bisulfite sequencing analysis reveals the lack of 5-methylcytosine in mammalian mitochondrial DNA.
    Zhenyu Shao, Yang Han, Dan Zhou.
       BACKGROUND: DNA methylation is one of the best characterized epigenetic modifications in the mammalian nuclear genome and is known to play a significant role in various biological processes. Nonetheless, the presence of 5-methylcytosine (5mC) in mitochondrial DNA remains controversial, as data ranging from the lack of 5mC to very extensive 5mC have been reported.
    RESULTS: By conducting comprehensive bioinformatic analyses of both published and our own data, we reveal that previous observations of extensive and strand-biased mtDNA-5mC are likely artifacts due to a combination of factors including inefficient bisulfite conversion, extremely low sequencing reads in the L strand, and interference from nuclear mitochondrial DNA sequences (NUMTs). To reduce false positive mtDNA-5mC signals, we establish an optimized procedure for library preparation and data analysis of bisulfite sequencing. Leveraging our modified workflow, we demonstrate an even distribution of 5mC signals across the mtDNA and an average methylation level ranging from 0.19% to 0.67% in both cell lines and primary cells, which is indistinguishable from the background noise.
    CONCLUSIONS: We have developed a framework for analyzing mtDNA-5mC through bisulfite sequencing, which enables us to present multiple lines of evidence for the lack of extensive 5mC in mammalian mtDNA. We assert that the data available to date do not support the reported presence of mtDNA-5mC.
    Keywords:  Bisulfite sequencing; DNA methylation; Mitochondria; NUMTs
    DOI:  https://doi.org/10.1186/s12864-023-09541-9
  18. Biophys J. 2023 Aug 01. pii: S0006-3495(23)00481-2. [Epub ahead of print]
    Nanoscale details of mitochondrial constriction revealed by cryo-electron tomography.
    Shrawan Kumar Mageswaran, Danielle Ann Grotjahn, Xiangrui Zeng, Benjamin Asher Barad, Michaela Medina, My Hanh Hoang, Megan J Dobro, Yi-Wei Chang, Min Xu, Wei Yuan Yang, Grant J Jensen.
      Mitochondria adapt to changing cellular environments, stress stimuli, and metabolic demands through dramatic morphological remodeling of their shape, and thus function. Such mitochondrial dynamics is often dependent on cytoskeletal filament interactions. However, the precise organization of these filamentous assemblies remains speculative. Here, we apply cryogenic electron tomography to directly image the nanoscale architecture of the cytoskeletal-membrane interactions involved in mitochondrial dynamics in response to damage. We induced mitochondrial damage via membrane depolarization, a cellular stress associated with mitochondrial fragmentation and mitophagy. We find that, in response to acute membrane depolarization, mammalian mitochondria predominantly organize into tubular morphology that abundantly displays constrictions. We observe long bundles of both unbranched actin and septin filaments enriched at these constrictions. We also observed septin-microtubule interactions at these sites and elsewhere suggesting that these two filaments guide each other in the cytosolic space. Together, our results provide empirical parameters for the architecture of mitochondrial constriction factors to validate/refine existing models and inform the development of new ones.
    DOI:  https://doi.org/10.1016/j.bpj.2023.07.030
  19. J Bioeth Inq. 2023 Aug 02.
    The Parliamentary Inquiry into Mitochondrial Donation Law Reform (Maeve's Law) Bill 2021 in Australia: A Qualitative Analysis.
    Jemima W Allen, Christopher Gyngell, Julian J Koplin, Danya F Vears.
      Recently, Australia became the second jurisdiction worldwide to legalize the use of mitochondrial donation technology. The Mitochondrial Donation Law Reform (Maeve's Law) Bill 2021 allows individuals with a family history of mitochondrial disease to access assisted reproductive techniques that prevent the inheritance of mitochondrial disease. Using inductive content analysis, we assessed submissions sent to the Senate Committee as part of a programme of scientific inquiry and public consultation that informed drafting of the Bill. These submissions discussed a range of bioethical and legal considerations of central importance to the political debate. Significantly, submissions from those with a first-hand experience of mitochondrial disease, including clinicians and those with a family history of mitochondrial disease, were in strong support of this legislation. Those in support of the Bill commended the two-staged approach and rigorous licencing requirements as part of the Bill's implementation strategy. Submissions which outlined arguments against the legislation either opposed the use of these techniques in general or opposed aspects of the implementation strategy in Australia. These findings offer a window into the ethical arguments and perspectives that matter most to those Australians who took part in the Senate inquiry into mitochondrial donation. The insights garnered from these submissions may be used to help refine policy and guidelines as the field progresses.
    Keywords:  Bioethics; Gene technology; Gene technology regulation; Medical technology legislation; Mitochondrial donation; Technological and regulatory advances
    DOI:  https://doi.org/10.1007/s11673-023-10257-4
  20. Research (Wash D C). 2023 ;6 0192
    MAVS Antagonizes Human Stem Cell Senescence as a Mitochondrial Stabilizer.
    Cui Wang, Kuan Yang, Xiaoqian Liu, Si Wang, Moshi Song, Juan Carlos Izpisua Belmonte, Jing Qu, Guang-Hui Liu, Weiqi Zhang.
      Mitochondrial dysfunction is a hallmark feature of cellular senescence and organ aging. Here, we asked whether the mitochondrial antiviral signaling protein (MAVS), which is essential for driving antiviral response, also regulates human stem cell senescence. To answer this question, we used CRISPR/Cas9-mediated gene editing and directed differentiation techniques to generate various MAVS-knockout human stem cell models. We found that human mesenchymal stem cells (hMSCs) were sensitive to MAVS deficiency, as manifested by accelerated senescence phenotypes. We uncovered that the role of MAVS in maintaining mitochondrial structural integrity and functional homeostasis depends on its interaction with the guanosine triphosphatase optic atrophy type 1 (OPA1). Depletion of MAVS or OPA1 led to the dysfunction of mitochondria and cellular senescence, whereas replenishment of MAVS or OPA1 in MAVS-knockout hMSCs alleviated mitochondrial defects and premature senescence phenotypes. Taken together, our data underscore an uncanonical role of MAVS in safeguarding mitochondrial homeostasis and antagonizing human stem cell senescence.
    DOI:  https://doi.org/10.34133/research.0192
  21. J Mol Diagn. 2023 08;pii: S1525-1578(23)00125-3. [Epub ahead of print]25(8): 536-539
    Bench to Bedside: Rapid Leber Hereditary Optic Neuropathy Diagnosis.
    Benjamin Hilton.
      
    DOI:  https://doi.org/10.1016/j.jmoldx.2023.06.001
  22. Brain Pathol. 2023 Aug 03. e13199
    Neuropathological hallmarks in autopsied cases with mitochondrial diseases caused by the mitochondrial 3243A>G mutation.
    Hiroaki Miyahara, Chisato Tamai, Masanori Inoue, Kazuhito Sekiguchi, Daisuke Tahara, Nao Tahara, Kazuhiro Takeda, Shusei Arafuka, Hideyuki Moriyoshi, Ryuichi Koizumi, Akio Akagi, Yuichi Riku, Jun Sone, Mari Yoshida, Kenji Ihara, Yasushi Iwasaki.
      The mitochondrial (m.) 3243A>G mutation is known to be associated with various mitochondrial diseases including mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS). Their clinical symptoms have been estimated to occur with an increased mitochondrial DNA (mtDNA) heteroplasmy and reduced activity of oxidative phosphorylation (OXPHOS) complexes, but their trends in the central nervous system remain unknown. Six autopsied mutant cases and three disease control cases without the mutation were enrolled in this study. The mutant cases had a disease duration of 1-27 years. Five of six mutant cases were compatible with MELAS. In the mutant cases, cortical lesions including a laminar necrosis were frequently observed in the parietal, lateral temporal, and occipital lobes; less frequently in the frontal lobe including precentral gyrus; and not at all in the medial temporal lobe. The mtDNA heteroplasmy in brain tissue samples of the mutant cases was strikingly high, ranging from 53.8% to 85.2%. The medial temporal lobe was preserved despite an inhospitable environment having high levels of mtDNA heteroplasmy and lactic acid. OXPHOS complex I was widely decreased in the mutant cases. The swelling of smooth muscle cells in the vessels on the leptomeninges, with immunoreactivity (IR) against mitochondria antibody, and a decreased nuclear/cytoplasmic ratio of choroidal epithelial cells were observed in all mutant cases but in none without the mutation. Common neuropathological findings such as cortical laminar necrosis and basal ganglia calcification were not always observed in the mutant cases. A high level of mtDNA heteroplasmy was observed throughout the brain in spite of heterogeneous cortical lesions. A lack of medial temporal lesion, mitochondrial vasculopathy in vessels on the leptomeninges, and an increased cytoplasmic size of epithelial cells in the choroid plexus could be neuropathological hallmarks helpful in the diagnosis of mitochondrial diseases.
    Keywords:  MELAS; choroidal epithelial cell swelling; mitochondrial 3243A>G mutation; mitochondrial vasculopathy; mtDNA heteroplasmy; stroke-like episodes
    DOI:  https://doi.org/10.1111/bpa.13199
  23. Brain. 2023 Jul 30. pii: awad254. [Epub ahead of print]
    Neuromuscular disease genetics in underrepresented populations: increasing data diversity.
    Lindsay A Wilson, William L Macken, Luke D Perry, Christopher J Record, Katherine R Schon, Rodrigo S S Frezatti, Sharika Raga, Kireshnee Naidu, Özlem Yayıcı Köken, Ipek Polat, Musambo M Kapapa, Natalia Dominik, Stephanie Efthymiou, Heba Morsy, Melissa Nel, Mahmoud R Fassad, Fei Gao, Krutik Patel, Maryke Schoonen, Michelle Bisschoff, Armand Vorster, Hallgeir Jonvik, Ronel Human, Elsa Lubbe, Malebo Nonyane, Seena Vengalil, Saraswati Nashi, Kosha Srivastava, Richard J L F Lemmers, Alisha Reyaz, Rinkle Mishra, Ana Töpf, Christina I Trainor, Elizabeth C Steyn, Amokelani C Mahungu, Patrick J van der Vliet, Ahmet Cevdet Ceylan, A Semra Hiz, Büşranur Çavdarlı, C Nur Semerci Gündüz, Gülay Güleç Ceylan, Madhu Nagappa, Karthik B Tallapaka, Periyasamy Govindaraj, Silvère M van der Maarel, Gayathri Narayanappa, Bevinahalli N Nandeesh, Somwe Wa Somwe, David R Bearden, Michelle P Kvalsund, Gita M Ramdharry, Yavuz Oktay, Uluç Yiş, Haluk Topaloğlu, Anna Sarkozy, Enrico Bugiardini, Franclo Henning, Jo M Wilmshurst, Jeannine M Heckmann, Robert McFarland, Robert W Taylor, Izelle Smuts, Francois H van der Westhuizen, Claudia Ferreira da Rosa Sobreira, Pedro J Tomaselli, Wilson Marques, Rohit Bhatia, Ashwin Dalal, M V Padma Srivastava, Sireesha Yareeda, Atchayaram Nalini, Venugopalan Y Vishnu, Kumarasamy Thangaraj, Volker Straub, Rita Horvath, Patrick F Chinnery, Robert D S Pitceathly, Francesco Muntoni, Henry Houlden, Jana Vandrovcova, Mary M Reilly, Michael G Hanna.
      Neuromuscular diseases (NMDs) affect ∼15 million people globally. In high income settings DNA-based diagnosis has transformed care pathways and led to gene-specific therapies. However, most affected families are in low-middle income countries (LMICs) with limited access to DNA-based diagnosis. Most (86%) published genetic data is derived from European ancestry. This marked genetic data inequality hampers understanding of genetic diversity and hinders accurate genetic diagnosis in all income settings. We developed a cloud-based transcontinental partnership to build diverse, deeply-phenotyped and genetically characterised cohorts to improve genetic architecture knowledge, and potentially advance diagnosis and clinical management. We connected 18 centres in Brazil, India, South Africa, Turkey, Zambia, Netherlands and the UK. We co-developed a cloud-based data solution and trained 17 international neurology fellows in clinical genomic data interpretation. Single gene and whole exome data was analysed via a bespoke bioinformatics pipeline and reviewed alongside clinical and phenotypic data in global webinars to inform genetic outcome decisions. We recruited 6001 participants in the first 43 months. Initial genetic analyses "solved" or "possibly solved" ∼56% probands overall. In-depth genetic data review of the four commonest clinical categories (limb girdle muscular dystrophy, inherited peripheral neuropathies, congenital myopathy/muscular dystrophies and Duchenne/Becker muscular dystrophy) delivered a ∼59% "solved and ∼13% "possibly solved" outcome. Almost 29% of disease causing variants were novel, increasing diverse pathogenic variant knowledge. Unsolved participants represent a new discovery cohort. The dataset provides a large resource from underrepresented populations for genetic and translational research. In conclusion, we established a remote transcontinental partnership to assess genetic architecture of NMDs across diverse populations. It supported DNA-based diagnosis potentially enabling genetic counselling, care pathways and eligibility for gene-specific trials. Similar virtual partnerships could be adopted by other areas of global genomic neurological practice, to reduce genetic data inequality and benefit patients globally.
    Keywords:  capacity building; equality and diversity; genomic medicine; inherited neuromuscular disease; low-to-middle income country
    DOI:  https://doi.org/10.1093/brain/awad254
  24. J Integr Neurosci. 2023 Jul 03. 22(4): 86
    The Role of Impaired Mitochondrial Transport in the Development of Neurodegenerative Diseases.
    Alexander Blagov, Evgeny Borisov, Andrey Grechko, Mikhail Popov, Vasily Sukhorukov, Alexander Orekhov.
      The fight against neurodegenerative diseases is one of the key direction of modern medicine. Unfortunately, the difficulties in understanding the factors underlying the development of neurodegeneration hinder the development of breakthrough therapeutics that can stop or at least greatly slow down the progression of these diseases. In this review, it is considered the disruption of mitochondrial transport as one of the pathogenesis factors contributing to neurodegeneration using the examples of Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and Huntington's disease. Here, the mechanism of mitochondrial transport under normal conditions and the mechanisms of disturbances for the indicated diseases will be considered.
    Keywords:  Alzheimer's disease; Parkinson's disease; mitochondria; mitochondrial transport; neurodegenerative diseases
    DOI:  https://doi.org/10.31083/j.jin2204086
  25. Clin Ther. 2023 Jul 28. pii: S0149-2918(23)00204-7. [Epub ahead of print]
    Advancing Understanding of Inequities in Rare Disease Genomics.
    Jillian G Serrano, Melanie O'Leary, Grace E VanNoy, Brian E Mangilog, Ingrid A Holm, Yarden S Fraiman, Heidi L Rehm, Anne O'Donnell-Luria, Monica H Wojcik.
       PURPOSE: Advances in genomic research have facilitated rare disease diagnosis for thousands of individuals. Unfortunately, the benefits of advanced genetic diagnostic technology are not distributed equitably among the population, as has been seen in many other health care contexts. Quantifying and describing inequities in genetic diagnostic yield is inherently challenging due to barriers to both clinical and research genetic testing. We therefore present an implementation protocol developed to expand access to our rare disease genomic research study and to further understand existing inequities.
    METHODS AND FINDINGS: The Rare Genomes Project (RGP) at the Broad Institute of MIT and Harvard offers research genome sequencing to individuals with rare disease who remain genetically undiagnosed through direct interaction with the individual or family. This presents an opportunity for diagnosis beyond the clinical context, thus eliminating many barriers to access. An initial goal of RGP was to equalize access to genomic sequencing by decoupling testing access from proximity to a major medical center and physician referral. However, study participants over the initial 3 years of this project were predominantly white and well resourced. To further understand and address the lack of diversity within RGP, we developed a novel protocol embedded within the larger RGP study, in an approach informed by an implementation science framework. The aims of this protocol were: (1) to diversify recruitment and enrollment within RGP; (2) understand the process and context of implementing genomic medicine for rare disease diagnosis; and (3) investigate the value of a diagnosis for underserved populations.
    IMPLICATIONS: Improved understanding of existing inequities and potential strategies to address them are needed to advance equity in rare disease genetic diagnosis and research. In addition to the moral imperative of equity in genomic medicine, this approach is critical in order to fully understand the genomic underpinnings of rare disease.
    Keywords:  Disparities; Genetics; Genomics; Implementation; Inequities; Rare disease
    DOI:  https://doi.org/10.1016/j.clinthera.2023.06.010
  26. J Inherit Metab Dis. 2023 Aug 02.
    Fifty years of research on mitochondrial fatty acid oxidation defects: the remaining challenges.
    Christine Vianey-Saban, Nathalie Guffon, Alain Fouilhoux, Cécile Acquaviva.
      Since the identification of the first disorder of mitochondrial fatty acid oxidation (FAOD) in 1973, more than twenty defects have been identified. Although there are some differences, most FAOD have similar clinical signs, which are mainly due to energy depletion and toxicity of accumulated metabolites. However, some of them have an unusual clinical phenotype or specific clinical signs. This manuscript focuses on what we have learnt so far on the pathophysiology of these disorders which present with clinical signs that are not typical of categorical FAOD. It also highlights that some disorders have not yet been identified and tries to make assumptions to explain why. It also deals with new treatments under consideration in FAOD, including triheptanoin and similar anaplerotic substrates, ketone body treatments, RNA and gene therapy approaches. Finally, it suggests challenges for the diagnosis of FAOD in the coming years, both for symptomatic patients and for those diagnosed through newborn screening. The ultimate goal would be to identify all the patients born with FAOD and ensure for them the best possible quality of life. TAKE HOME MESSAGE: Tentative hypotheses to improve the diagnosis and the treatment of fatty acid oxidation defects. This article is protected by copyright. All rights reserved.
    Keywords:  inborn errors of riboflavin metabolism; mitochondrial fatty acid oxidation disorders
    DOI:  https://doi.org/10.1002/jimd.12664
  27. Am J Hum Genet. 2023 Aug 03. pii: S0002-9297(23)00247-1. [Epub ahead of print]110(8): 1343-1355
    Genome sequencing and comprehensive rare-variant analysis of 465 families with neurodevelopmental disorders.
    NIHR BioResource
      Despite significant progress in unraveling the genetic causes of neurodevelopmental disorders (NDDs), a substantial proportion of individuals with NDDs remain without a genetic diagnosis after microarray and/or exome sequencing. Here, we aimed to assess the power of short-read genome sequencing (GS), complemented with long-read GS, to identify causal variants in participants with NDD from the National Institute for Health and Care Research (NIHR) BioResource project. Short-read GS was conducted on 692 individuals (489 affected and 203 unaffected relatives) from 465 families. Additionally, long-read GS was performed on five affected individuals who had structural variants (SVs) in technically challenging regions, had complex SVs, or required distal variant phasing. Causal variants were identified in 36% of affected individuals (177/489), and a further 23% (112/489) had a variant of uncertain significance after multiple rounds of re-analysis. Among all reported variants, 88% (333/380) were coding nuclear SNVs or insertions and deletions (indels), and the remainder were SVs, non-coding variants, and mitochondrial variants. Furthermore, long-read GS facilitated the resolution of challenging SVs and invalidated variants of difficult interpretation from short-read GS. This study demonstrates the value of short-read GS, complemented with long-read GS, in investigating the genetic causes of NDDs. GS provides a comprehensive and unbiased method of identifying all types of variants throughout the nuclear and mitochondrial genomes in individuals with NDD.
    Keywords:  long-read sequencing; neurodevelopmental disorders; structural variants; whole-genome sequencing
    DOI:  https://doi.org/10.1016/j.ajhg.2023.07.007
  28. Chem Sci. 2023 Aug 02. 14(30): 8084-8094
    Controllable mitochondrial aggregation and fusion by a programmable DNA binder.
    Longyi Zhu, Yiting Shen, Shengyuan Deng, Ying Wan, Jun Luo, Yan Su, Mingxu You, Chunhai Fan, Kewei Ren.
      DNA nanodevices have been feasibly applied for various chemo-biological applications, but their functions as precise regulators of intracellular organelles are still limited. Here, we report a synthetic DNA binder that can artificially induce mitochondrial aggregation and fusion in living cells. The rationally designed DNA binder consists of a long DNA chain, which is grafted with multiple mitochondria-targeting modules. Our results indicated that the DNA binder-induced in situ self-assembly of mitochondria can be used to successfully repair ROS-stressed neuron cells. Meanwhile, this DNA binder design is highly programmable. Customized molecular switches can be easily implanted to further achieve stimuli-triggered mitochondrial aggregation and fusion inside living cells. We believe this new type of DNA regulator system will become a powerful chemo-biological tool for subcellular manipulation and precision therapy.
    DOI:  https://doi.org/10.1039/d2sc07095b
  29. J Mol Diagn. 2023 08;pii: S1525-1578(23)00104-6. [Epub ahead of print]25(8): 540-554
    Rapid and Sensitive Diagnosis of Leber Hereditary Optic Neuropathy Variants Using CRISPR/Cas12a Detection.
    Xiaoling Wan, Jieqiong Chen, Yidong Wu, Zhixuan Chen, Yin Liu, Tong Li, Junran Sun, Ting Zhang, Fuling Zhou, Xingxu Huang, Yang Li, Xinjie Wang, Xiaodong Sun.
      Leber hereditary optic neuropathy (LHON) is the most common maternally inherited mitochondrial disease, with >90% of cases harboring one of three point variants (m.3460G>A, m.11778G>A, and m.14484T>C). Rapid and sensitive diagnosis of LHON variants is urgently needed for early diagnosis and timely treatment after onset, which is currently limited. Herein, we adapted the Cas12a-based DNA detection platform for LHON mitochondrial variant diagnosis. Single-strand guide CRISPR RNAs and enzymatic recombinase amplification primers were first screened, the CRISPR/Cas12a system was then optimized with restriction enzymes, and finally compared with Sanger sequencing and next-generation sequencing (NGS) in multicenter clinical samples. This approach can be completed within 30 minutes using only one drop of blood and could reach a sensitivity of 1% of heteroplasmy. Among the 182 multicenter clinical samples, the CRISPR/Cas12a detection system showed high consistency with Sanger sequencing and NGS in both specificity and sensitivity. Notably, a sample harboring a de novo 3.78% m.11778G>A variant detected by NGS, but not by Sanger sequencing, was successfully confirmed using the CRISPR/Cas12a assay, which proved the effectiveness of our method. Overall, our CRISPR/Cas12a detection system provides an alternative for rapid, convenient, and sensitive detection of LHON variants, exhibiting great potential for clinical practice.
    DOI:  https://doi.org/10.1016/j.jmoldx.2023.04.006
  30. Nat Commun. 2023 Aug 04. 14(1): 4675
    Myonectin protects against skeletal muscle dysfunction in male mice through activation of AMPK/PGC1α pathway.
    Yuta Ozaki, Koji Ohashi, Naoya Otaka, Hiroshi Kawanishi, Tomonobu Takikawa, Lixin Fang, Kunihiko Takahara, Minako Tatsumi, Sohta Ishihama, Mikito Takefuji, Katsuhiro Kato, Yuuki Shimizu, Yasuko K Bando, Aiko Inoue, Masafumi Kuzuya, Shinji Miura, Toyoaki Murohara, Noriyuki Ouchi.
      To maintain and restore skeletal muscle mass and function is essential for healthy aging. We have found that myonectin acts as a cardioprotective myokine. Here, we investigate the effect of myonectin on skeletal muscle atrophy in various male mouse models of muscle dysfunction. Disruption of myonectin exacerbates skeletal muscle atrophy in age-associated, sciatic denervation-induced or dexamethasone (DEX)-induced muscle atrophy models. Myonectin deficiency also contributes to exacerbated mitochondrial dysfunction and reduces expression of mitochondrial biogenesis-associated genes including PGC1α in denervated muscle. Myonectin supplementation attenuates denervation-induced muscle atrophy via activation of AMPK. Myonectin also reverses DEX-induced atrophy of cultured myotubes through the AMPK/PGC1α signaling. Furthermore, myonectin treatment suppresses muscle atrophy in senescence-accelerated mouse prone (SAMP) 8 mouse model of accelerated aging or mdx mouse model of Duchenne muscular dystrophy. These data indicate that myonectin can ameliorate skeletal muscle dysfunction through AMPK/PGC1α-dependent mechanisms, suggesting that myonectin could represent a therapeutic target of muscle atrophy.
    DOI:  https://doi.org/10.1038/s41467-023-40435-2
  31. Eur J Hum Genet. 2023 Aug 01.
    Genomic testing for rare disease diagnosis-where are we now, and where should we be heading? The reflections of a behavioural scientist.
    Celine Lewis.
      
    DOI:  https://doi.org/10.1038/s41431-023-01439-0
  32. Mol Cell. 2023 Jul 28. pii: S1097-2765(23)00526-9. [Epub ahead of print]
    O-GlcNAcylation of Raptor transduces glucose signals to mTORC1.
    Chenchen Xu, Xiaoqing Pan, Dong Wang, Yuanyuan Guan, Wenyu Yang, Xing Chen, Ying Liu.
      The mechanistic target of rapamycin complex 1 (mTORC1) regulates metabolism and cell growth in response to nutrient levels. Dysregulation of mTORC1 results in a broad spectrum of diseases. Glucose is the primary energy supply of cells, and therefore, glucose levels must be accurately conveyed to mTORC1 through highly responsive signaling mechanisms to control mTORC1 activity. Here, we report that glucose-induced mTORC1 activation is regulated by O-GlcNAcylation of Raptor, a core component of mTORC1, in HEK293T cells. Mechanistically, O-GlcNAcylation of Raptor at threonine 700 facilitates the interactions between Raptor and Rag GTPases and promotes the translocation of mTOR to the lysosomal surface, consequently activating mTORC1. In addition, we show that AMPK-mediated phosphorylation of Raptor suppresses Raptor O-GlcNAcylation and inhibits Raptor-Rags interactions. Our findings reveal an exquisitely controlled mechanism, which suggests how glucose coordinately regulates cellular anabolism and catabolism.
    Keywords:  O-GlcNAcylation; Raptor; glucose sensing; mTOR
    DOI:  https://doi.org/10.1016/j.molcel.2023.07.011
  33. Genet Med. 2023 Jul 30. pii: S1098-3600(23)00960-7. [Epub ahead of print] 100947
    The landscape of reported VUS in multi-gene panel and genomic testing: Time for a change.
    Medical Genome Initiative
       PURPOSE: Variants of uncertain significance (VUS) are a common result of diagnostic genetic testing and can be difficult to manage with potential misinterpretation and downstream costs, including time investment by clinicians. We investigated the rate of VUS reported on diagnostic testing via multi-gene panels (MGPs) and exome and genome sequencing (ES/GS) to measure the magnitude of uncertain results and explore ways to reduce their potentially detrimental impact.
    METHODS: Rates of inconclusive results due to VUS were collected from over 1.5 million sequencing test results from 19 clinical laboratories in North America from 2020 - 2021.
    RESULTS: We found a lower rate of inconclusive test results due to VUSs from ES/GS (22.5%) compared to MGPs (32.6%; p<0.0001). For MGPs, the rate of inconclusive results correlated with panel size. The use of trios reduced inconclusive rates (18.9% vs 27.6%; p<0.001) whereas the use of GS compared to ES had no impact (22.2% vs 22.6%; p=ns).
    CONCLUSION: The high rate of VUS observed in diagnostic MGP testing warrants examining current variant reporting practices. We propose several approaches to reduce reported VUS rates, while directing clinician resources towards important VUS follow-up.
    Keywords:  laboratory reporting methods; multi-gene panels; variants of uncertain significance
    DOI:  https://doi.org/10.1016/j.gim.2023.100947
  34. J Inherit Metab Dis. 2023 Aug 04.
    Beyond genetics: Deciphering the impact of missense variants in CAD deficiency.
    Francisco Del Caño-Ochoa, Bobby G Ng, Antonio Rubio-Del-Campo, Sonal Mahajan, Matthew P Wilson, Marçal Vilar, Daisy Rymen, Paula Sánchez-Pintos, Janna Kenny, Myriam Ley Martos, Teresa Campos, Saskia B Wortmann, Hudson H Freeze, Santiago Ramón-Maiques.
      CAD is a large, 2,225 amino acid multi-enzymatic protein required for de novo pyrimidine biosynthesis. Pathological CAD variants cause a developmental and epileptic encephalopathy which is highly responsive to uridine supplements. CAD deficiency is difficult to diagnose because symptoms are non-specific, there is no biomarker, and the protein has over 1,000 known variants. To improve diagnosis, we assessed the pathogenicity of 20 unreported missense CAD variants using a growth complementation assay that identified 11 pathogenic variants in 7 affected individuals; they would benefit from uridine treatment. We also tested 9 variants previously reported as pathogenic and confirmed the damaging effect of 7. However, we reclassified two variants as likely benign based on our assay, which is consistent with their long-term follow-up with uridine. We found that several computational methods are unreliable predictors of pathogenic CAD variants, so we extended the functional assay results by studying the impact of pathogenic variants at the protein level. We focused on CAD's dihydroorotase (DHO) domain because it accumulates the largest density of damaging missense changes. The atomic-resolution structures of 8 DHO pathogenic variants, combined with functional and molecular dynamics analyses, provided a comprehensive structural and functional understanding of the activity, stability, and oligomerization of CAD's DHO domain. Combining our functional and protein structural analysis can help refine clinical diagnostic workflow for CAD variants in the genomics era. This article is protected by copyright. All rights reserved.
    Keywords:  Developmental and epileptic encephalopathy; X-ray crystallography; dihydroorotase; epilepsy; functional validation assay; inborn metabolic disease; molecular dynamics; protein structure-function; pyrimidine metabolism; treatment; uridine; variant of uncertain significance
    DOI:  https://doi.org/10.1002/jimd.12667
  35. J Neuromuscul Dis. 2023 Jul 28.
    Induced pluripotent stem cells for modeling physiological and pathological striated muscle complexity.
    Leslie Caron, Stefano Testa, Frédérique Magdinier.
      Neuromuscular disorders (NMDs) are a large group of diseases associated with either alterations of skeletal muscle fibers, motor neurons or neuromuscular junctions. Most of these diseases is characterized with muscle weakness or wasting and greatly alter the life of patients. Animal models do not always recapitulate the phenotype of patients. The development of innovative and representative human preclinical models is thus strongly needed for modeling the wide diversity of NMDs, characterization of disease-associated variants, investigation of novel genes function, or the development of therapies. Over the last decade, the use of patient's derived induced pluripotent stem cells (hiPSC) has resulted in tremendous progress in biomedical research, including for NMDs. Skeletal muscle is a complex tissue with multinucleated muscle fibers supported by a dense extracellular matrix and multiple cell types including motor neurons required for the contractile activity. Major challenges need now to be tackled by the scientific community to increase maturation of muscle fibers in vitro, in particular for modeling adult-onset diseases affecting this tissue (neuromuscular disorders, cachexia, sarcopenia) and the evaluation of therapeutic strategies. In the near future, rapidly evolving bioengineering approaches applied to hiPSC will undoubtedly become highly instrumental for investigating muscle pathophysiology and the development of therapeutic strategies.
    Keywords:  3D culture; Induced pluripotent stem cells; motor neurons; myoblasts; myotubes; neuromuscular disorders; neuromuscular junctions; satellite cells; therapy
    DOI:  https://doi.org/10.3233/JND-230076
  36. Am J Hum Genet. 2023 Aug 03. pii: S0002-9297(23)00210-0. [Epub ahead of print]110(8): 1229-1248
    Beyond the exome: What's next in diagnostic testing for Mendelian conditions.
    Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium
      Despite advances in clinical genetic testing, including the introduction of exome sequencing (ES), more than 50% of individuals with a suspected Mendelian condition lack a precise molecular diagnosis. Clinical evaluation is increasingly undertaken by specialists outside of clinical genetics, often occurring in a tiered fashion and typically ending after ES. The current diagnostic rate reflects multiple factors, including technical limitations, incomplete understanding of variant pathogenicity, missing genotype-phenotype associations, complex gene-environment interactions, and reporting differences between clinical labs. Maintaining a clear understanding of the rapidly evolving landscape of diagnostic tests beyond ES, and their limitations, presents a challenge for non-genetics professionals. Newer tests, such as short-read genome or RNA sequencing, can be challenging to order, and emerging technologies, such as optical genome mapping and long-read DNA sequencing, are not available clinically. Furthermore, there is no clear guidance on the next best steps after inconclusive evaluation. Here, we review why a clinical genetic evaluation may be negative, discuss questions to be asked in this setting, and provide a framework for further investigation, including the advantages and disadvantages of new approaches that are nascent in the clinical sphere. We present a guide for the next best steps after inconclusive molecular testing based upon phenotype and prior evaluation, including when to consider referral to research consortia focused on elucidating the underlying cause of rare unsolved genetic disorders.
    Keywords:  PacBio sequencing; RNA sequencing; exome reanalysis; long-read sequencing; meatabolomics; nanopore sequencing; non-diagnostic exome; optical genome mapping
    DOI:  https://doi.org/10.1016/j.ajhg.2023.06.009
  37. BMC Bioinformatics. 2023 Aug 03. 24(1): 308
    Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP.
    Huijing Yu, Zhenxian Zheng, Junhao Su, Tak-Wah Lam, Ruibang Luo.
       BACKGROUND: With the continuous advances in third-generation sequencing technology and the increasing affordability of next-generation sequencing technology, sequencing data from different sequencing technology platforms is becoming more common. While numerous benchmarking studies have been conducted to compare variant-calling performance across different platforms and approaches, little attention has been paid to the potential of leveraging the strengths of different platforms to optimize overall performance, especially integrating Oxford Nanopore and Illumina sequencing data.
    RESULTS: We investigated the impact of multi-platform data on the performance of variant calling through carefully designed experiments with a deep learning-based variant caller named Clair3-MP (Multi-Platform). Through our research, we not only demonstrated the capability of ONT-Illumina data for improved variant calling, but also identified the optimal scenarios for utilizing ONT-Illumina data. In addition, we revealed that the improvement in variant calling using ONT-Illumina data comes from an improvement in difficult genomic regions, such as the large low-complexity regions and segmental and collapse duplication regions. Moreover, Clair3-MP can incorporate reference genome stratification information to achieve a small but measurable improvement in variant calling. Clair3-MP is accessible as an open-source project at: https://github.com/HKU-BAL/Clair3-MP .
    CONCLUSIONS: These insights have important implications for researchers and practitioners alike, providing valuable guidance for improving the reliability and efficiency of genomic analysis in diverse applications.
    Keywords:  Deep learning; Multi-platform sequencing data; Variant calling
    DOI:  https://doi.org/10.1186/s12859-023-05434-6
  38. Sci Rep. 2023 07 31. 13(1): 12360
    A diverse ancestrally-matched reference panel increases genotype imputation accuracy in a underrepresented population.
    John Mauleekoonphairoj, Sissades Tongsima, Apichai Khongphatthanayothin, Sean J Jurgens, Dominic S Zimmerman, Boosamas Sutjaporn, Pharawee Wandee, Connie R Bezzina, Koonlawee Nademanee, Yong Poovorawan.
      Variant imputation, a common practice in genome-wide association studies, relies on reference panels to infer unobserved genotypes. Multiple public reference panels are currently available with variations in size, sequencing depth, and represented populations. Currently, limited data exist regarding the performance of public reference panels when used in an imputation of populations underrepresented in the reference panel. Here, we compare the performance of various public reference panels: 1000 Genomes Project, Haplotype Reference Consortium, GenomeAsia 100 K, and the recent Trans-Omics for Precision Medicine (TOPMed) program, when used in an imputation of samples from the Thai population. Genotype yields were assessed, and imputation accuracies were examined by comparison with high-depth whole genome sequencing data of the same sample. We found that imputation using the TOPMed panel yielded the largest number of variants (~ 271 million). Despite being the smallest in size, GenomeAsia 100 K achieved the best imputation accuracy with a median genotype concordance rate of 0.97. For rare variants, GenomeAsia 100 K also offered the best accuracy, although rare variants were less accurately imputable than common variants (30.3% reduction in concordance rates). The high accuracy observed when using GenomeAsia 100 K is likely attributable to the diverse representation of populations genetically similar to the study cohort emphasizing the benefits of sequencing populations classically underrepresented in human genomics.
    DOI:  https://doi.org/10.1038/s41598-023-39429-3
  39. Cell Death Dis. 2023 Aug 03. 14(8): 496
    Mitochondria dysregulation contributes to secondary neurodegeneration progression post-contusion injury in human 3D in vitro triculture brain tissue model.
    Volha Liaudanskaya, Nicholas J Fiore, Yang Zhang, Yuka Milton, Marilyn F Kelly, Marly Coe, Ariana Barreiro, Victoria K Rose, Matthew R Shapiro, Adam S Mullis, Anna Shevzov-Zebrun, Mathew Blurton-Jones, Michael J Whalen, Aviva J Symes, Irene Georgakoudi, Thomas J F Nieland, David L Kaplan.
      Traumatic Brain injury-induced disturbances in mitochondrial fission-and-fusion dynamics have been linked to the onset and propagation of neuroinflammation and neurodegeneration. However, cell-type-specific contributions and crosstalk between neurons, microglia, and astrocytes in mitochondria-driven neurodegeneration after brain injury remain undefined. We developed a human three-dimensional in vitro triculture tissue model of a contusion injury composed of neurons, microglia, and astrocytes and examined the contributions of mitochondrial dysregulation to neuroinflammation and progression of injury-induced neurodegeneration. Pharmacological studies presented here suggest that fragmented mitochondria released by microglia are a key contributor to secondary neuronal damage progression after contusion injury, a pathway that requires astrocyte-microglia crosstalk. Controlling mitochondrial dysfunction thus offers an exciting option for developing therapies for TBI patients.
    DOI:  https://doi.org/10.1038/s41419-023-05980-0
  40. PLoS Genet. 2023 Jul 31. 19(7): e1010713
    Lipidomic QTL in Diversity Outbred mice identifies a novel function for α/β hydrolase domain 2 (Abhd2) as an enzyme that metabolizes phosphatidylcholine and cardiolipin.
    Tara R Price, Donnie S Stapleton, Kathryn L Schueler, Marie K Norris, Brian W Parks, Brian S Yandell, Gary A Churchill, William L Holland, Mark P Keller, Alan D Attie.
      We and others have previously shown that genetic association can be used to make causal connections between gene loci and small molecules measured by mass spectrometry in the bloodstream and in tissues. We identified a locus on mouse chromosome 7 where several phospholipids in liver showed strong genetic association to distinct gene loci. In this study, we integrated gene expression data with genetic association data to identify a single gene at the chromosome 7 locus as the driver of the phospholipid phenotypes. The gene encodes α/β-hydrolase domain 2 (Abhd2), one of 23 members of the ABHD gene family. We validated this observation by measuring lipids in a mouse with a whole-body deletion of Abhd2. The Abhd2KO mice had a significant increase in liver levels of phosphatidylcholine and phosphatidylethanolamine. Unexpectedly, we also found a decrease in two key mitochondrial lipids, cardiolipin and phosphatidylglycerol, in male Abhd2KO mice. These data suggest that Abhd2 plays a role in the synthesis, turnover, or remodeling of liver phospholipids.
    DOI:  https://doi.org/10.1371/journal.pgen.1010713
  41. Nature. 2023 Aug;620(7972): 47-60
    Scientific discovery in the age of artificial intelligence.
    Hanchen Wang, Tianfan Fu, Yuanqi Du, Wenhao Gao, Kexin Huang, Ziming Liu, Payal Chandak, Shengchao Liu, Peter Van Katwyk, Andreea Deac, Anima Anandkumar, Karianne Bergen, Carla P Gomes, Shirley Ho, Pushmeet Kohli, Joan Lasenby, Jure Leskovec, Tie-Yan Liu, Arjun Manrai, Debora Marks, Bharath Ramsundar, Le Song, Jimeng Sun, Jian Tang, Petar Veličković, Max Welling, Linfeng Zhang, Connor W Coley, Yoshua Bengio, Marinka Zitnik.
      Artificial intelligence (AI) is being increasingly integrated into scientific discovery to augment and accelerate research, helping scientists to generate hypotheses, design experiments, collect and interpret large datasets, and gain insights that might not have been possible using traditional scientific methods alone. Here we examine breakthroughs over the past decade that include self-supervised learning, which allows models to be trained on vast amounts of unlabelled data, and geometric deep learning, which leverages knowledge about the structure of scientific data to enhance model accuracy and efficiency. Generative AI methods can create designs, such as small-molecule drugs and proteins, by analysing diverse data modalities, including images and sequences. We discuss how these methods can help scientists throughout the scientific process and the central issues that remain despite such advances. Both developers and users of AI toolsneed a better understanding of when such approaches need improvement, and challenges posed by poor data quality and stewardship remain. These issues cut across scientific disciplines and require developing foundational algorithmic approaches that can contribute to scientific understanding or acquire it autonomously, making them critical areas of focus for AI innovation.
    DOI:  https://doi.org/10.1038/s41586-023-06221-2
  42. J Clin Biochem Nutr. 2023 Jul;73(1): 61-76
    High-fat diet causes mitochondrial damage and downregulation of mitofusin-2 and optic atrophy-1 in multiple organs.
    Peng Zheng, Wenjing Ma, Yilu Gu, Hengfang Wu, Zhiping Bian, Nannan Liu, Di Yang, Xiangjian Chen.
      High-fat consumption promotes the development of obesity, which is associated with various chronic illnesses. Mitochondria are the energy factories of eukaryotic cells, maintaining self-stability through a fine-tuned quality-control network. In the present study, we evaluated high-fat diet (HFD)-induced changes in mitochondrial ultrastructure and dynamics protein expression in multiple organs. C57BL/6J male mice were fed HFD or normal diet (ND) for 24 weeks. Compared with ND-fed mice, HFD-fed mice exhibited increased body weight, cardiomyocyte enlargement, pulmonary fibrosis, hepatic steatosis, renal and splenic structural abnormalities. The cellular apoptosis of the heart, liver, and kidney increased. Cellular lipid droplet deposition and mitochondrial deformations were observed. The proteins related to mitochondrial biogenesis (TFAM), fission (DRP1), autophagy (LC3 and LC3-II: LC3-I ratio), and mitophagy (PINK1) presented different changes in different organs. The mitochondrial fusion regulators mitofusin-2 (MFN2) and optic atrophy-1 (OPA1) were consistently downregulated in multiple organs, even the spleen. TOMM20 and ATP5A protein were enhanced in the heart, skeletal muscle, and spleen, and attenuated in the kidney. These results indicated that high-fat feeding caused pathological changes in multiple organs, accompanied by mitochondrial ultrastructural damage, and MFN2 and OPA1 downregulation. The mitochondrial fusion proteins may become promising targets and/or markers for treating metabolic disease.
    Keywords:  high-fat diet; hyperlipidemia; mitochondria; mitofusin-2; optic atrophy-1
    DOI:  https://doi.org/10.3164/jcbn.22-73
  43. Expert Rev Mol Diagn. 2023 Aug 05.
    Clinical validation of a single NGS targeted panel pipeline using the KAPA HyperChoice system for detection of germline, somatic and mitochondrial sequence and copy number variants.
    Jennifer Kerkhof, Cassandra Rastin, Laila Schenkel, Hanxin Lin, Bekim Sadikovic.
       BACKGROUND: Comprehensive molecular diagnostics are highly dependent on the technical performance of next-generation sequencing (NGS) pipelines, which are assessed by data quality, cost, turnaround time, and accuracy of detecting a range of sequence and copy number variants.
    METHODS: A dataset of 285 clinically validated cases (205 retrospective and 80 prospective), carrying complex sequence and copy number variants and thousands of genetic polymorphisms underwent a clinical validation of the KAPA HyperChoice target enrichment system with parallel sample fidelity assessment across a number of NGS panels. The analysis included assessment of peripheral blood, urine, muscle and FFPE tissues.
    RESULTS: High-quality and exceptionally uniform data with 100% coverage of all targeted panels were obtained, resulting in complete sensitivity and specificity for all variant types across nearly all panels and tissue types. Overall reduction in cost and turnaround times was obtained with the implementation of a parallel genotyping sample fidelity system.
    CONCLUSION: Results of the laboratory quality improvement study focused on a single NGS pipeline that includes both nuclear and mitochondrial genomes demonstrated utility in the clinical setting to assess a range of referral reasons, necessary due to the complex molecular etiology of human genetic disorders, while reducing costs and turnaround times.
    Keywords:  Clinical Diagnostics; Germline and mitochondrial NGS; Germline and somatic NGS; Sample fidelity; Sequence and copy number variant
    DOI:  https://doi.org/10.1080/14737159.2023.2245747
  44. Clin Sci (Lond). 2023 Jul 31. pii: CS20230164. [Epub ahead of print]
    Mitochondrial protein MPV17 promotes beta-cell apoptosis in diabetogenesis.
    Qiaoli Tang, Wanting Shi, Ming Liu, Li-Qin Tang, Wei Ren, Shaolin Shi.
      MPV17 is a mitochondrial inner membrane protein, and its deficiency can cause mitochondrial DNA (mtDNA) depletion, increase reactive oxygen species (ROS), and promote apoptosis in several cell types, suggesting that MPV17 plays a protective role in cells although the underlying mechanism remains unknown. To test whether MPV17 is also protective in diabetic kidney disease, we treated MPV17-deficient mice with streptozotocin (STZ) and surprisingly found that they were resistant to diabetes. MPV17 deficiency was also found to confer resistance to the diabetes induced by an insulin mutation (Ins2Akita), which represents a mouse model of monogenic diabetes characterized by proinsulin misfolding and beta-cell failure. In both STZ and Ins2Akita models, Mpv17 mutants had significantly less severe beta-cell loss and apoptosis compared with the wild-type mice. We next showed that Mpv17 is expressed in beta-cells of mice normally, suggesting that MPV17 acts beta-cells autonomously to facilitate apoptosis. Consistently, Mpv17 knockdown improved the viability and ameliorated the apoptosis of cultured MIN6 cells treated with STZ and palmitic acid (PA), respectively, accompanied by prevention of caspase 3 activation. The proapoptotic effect of MPV17 in beta-cells is in contrast with its known anti-apoptotic effect in other cell types. Thus, we have identified a novel regulator of beta-cell death in diabetes development.
    Keywords:  MPV17; apoptosis; beta-cell; diabetes
    DOI:  https://doi.org/10.1042/CS20230164
  45. Cell Commun Signal. 2023 Aug 03. 21(1): 192
    Decreased MFN2 activates the cGAS-STING pathway in diabetic myocardial ischaemia-reperfusion by triggering the release of mitochondrial DNA.
    Yonghong Xiong, Yan Leng, Hao Tian, Xinqi Deng, Wenyuan Li, Wei Li, Zhongyuan Xia.
       BACKGROUND: The cause of aggravation of diabetic myocardial damage is yet to be elucidated; damage to mitochondrial function has been a longstanding focus of research. During diabetic myocardial ischaemia-reperfusion (MI/R), it remains unclear whether reduced mitochondrial fusion exacerbates myocardial injury by generating free damaged mitochondrial DNA (mitoDNA) and activating the cGAS-STING pathway.
    METHODS: In this study, a mouse model of diabetes was established (by feeding mice a high-fat diet (HFD) plus a low dose of streptozotocin (STZ)), a MI/R model was established by cardiac ischaemia for 2 h and reperfusion for 30 min, and a cellular model of glycolipid toxicity induced by high glucose (HG) and palmitic acid (PA) was established in H9C2 cells.
    RESULTS: We observed that altered mitochondrial dynamics during diabetic MI/R led to increased mitoDNA in the cytosol, activation of the cGAS-STING pathway, and phosphorylation of the downstream targets TBK1 and IRF3. In the cellular model we found that cytosolic mitoDNA was the result of reduced mitochondrial fusion induced by HG and PA, which also resulted in cGAS-STING signalling and activation of downstream targets. Moreover, inhibition of STING by H-151 significantly ameliorated myocardial injury induced by MFN2 knockdown in both the cell and mouse models. The use of a fat-soluble antioxidant CoQ10 improved cardiac function in the mouse models.
    CONCLUSIONS: Our study elucidated the critical role of cGAS-STING activation, triggered by increased cytosolic mitoDNA due to decreased mitochondrial fusion, in the pathogenesis of diabetic MI/R injury. This provides preclinical insights for the treatment of diabetic MI/R injury. Video Abstract.
    Keywords:  Diabetes; Mitochondrial DNA; Myocardial ischaemia–reperfusion; cGAS-STING
    DOI:  https://doi.org/10.1186/s12964-023-01216-y
  46. iScience. 2023 Jul 21. 26(7): 107131
    Increased cardiac PFK-2 protects against high-fat diet-induced cardiomyopathy and mediates beneficial systemic metabolic effects.
    Maria F Mendez Garcia, Satoshi Matsuzaki, Albert Batushansky, Ryan Newhardt, Caroline Kinter, Yan Jin, Shivani N Mann, Michael B Stout, Haiwei Gu, Ying Ann Chiao, Michael Kinter, Kenneth M Humphries.
      A healthy heart adapts to changes in nutrient availability and energy demands. In metabolic diseases like type 2 diabetes (T2D), increased reliance on fatty acids for energy production contributes to mitochondrial dysfunction and cardiomyopathy. A principal regulator of cardiac metabolism is 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFK-2), which is a central driver of glycolysis. We hypothesized that increasing PFK-2 activity could mitigate cardiac dysfunction induced by high-fat diet (HFD). Wild type (WT) and cardiac-specific transgenic mice expressing PFK-2 (GlycoHi) were fed a low fat or HFD for 16 weeks to induce metabolic dysfunction. Metabolic phenotypes were determined by measuring mitochondrial bioenergetics and performing targeted quantitative proteomic and metabolomic analysis. Increasing cardiac PFK-2 had beneficial effects on cardiac and mitochondrial function. Unexpectedly, GlycoHi mice also exhibited sex-dependent systemic protection from HFD, including increased glucose homeostasis. These findings support improving glycolysis via PFK-2 activity can mitigate mitochondrial and functional changes that occur with metabolic syndrome.
    Keywords:  Metabolomics; Molecular biology; Physiology; Proteomics
    DOI:  https://doi.org/10.1016/j.isci.2023.107131
  47. Histochem Cell Biol. 2023 Aug 03.
    Providing open imaging data at scale: An EMBL-EBI perspective.
    Matthew Hartley, Andrii Iudin, Ardan Padwardhan, Ugis Sarkans, Aybüke Küpcü Yoldaş, Gerard J Kleywegt.
      Biological imaging is one of the primary tools by which we understand living systems across scales from atoms to organisms. Rapid advances in imaging technology have increased both the spatial and temporal resolutions at which we examine those systems, as well as enabling visualisation of larger tissue volumes. These advances have huge potential but also generate ever increasing amounts of imaging data that must be stored and analysed. Public image repositories provide a critical scientific service through open data provision, supporting reproducibility of scientific results, access to reference imaging datasets and reuse of data for new scientific discovery and acceleration of image analysis methods development. The scale and scope of imaging data provides both challenges and opportunities for open sharing of image data. In this article, we provide a perspective influenced by decades of provision of open data resources for biological information, suggesting areas to focus on and a path towards global interoperability.
    Keywords:  Bioimaging; Data integration; Data management; Metadata
    DOI:  https://doi.org/10.1007/s00418-023-02216-2
  48. Free Radic Biol Med. 2023 Aug 01. pii: S0891-5849(23)00571-3. [Epub ahead of print]
    Mitochondrial transplantation rescues neuronal cells from ferroptosis.
    Tingting Chen, Nad'a Majerníková, Alejandro Marmolejo-Garza, Marina Trombetta-Lima, Angélica María Sabogal-Guáqueta, Yuequ Zhang, Ruth Ten Kate, Minte Zuidema, Patty P M F A Mulder, Wilfred den Dunnen, Reinoud Gosens, Elisabeth Verpoorte, Carsten Culmsee, Ulrich L M Eisel, Amalia M Dolga.
      Ferroptosis is a type of oxidative cell death that can occur in neurodegenerative diseases and involves damage to mitochondria. Previous studies demonstrated that preventing mitochondrial dysfunction can rescue cells from ferroptotic cell death. However, the complexity of mitochondrial dysfunction and the timing of therapeutic interventions make it difficult to develop an effective treatment strategy against ferroptosis in neurodegeneration conditions. In this study, we explored the use of mitochondrial transplantation as a novel therapeutic approach for preventing ferroptotic neuronal cell death. Our data showed that isolated exogenous mitochondria were incorporated into both healthy and ferroptotic immortalized hippocampal HT-22 cells and primary cortical neurons (PCN). The mitochondrial incorporation was accompanied by increased metabolic activity and cell survival through attenuating lipid peroxidation and mitochondrial superoxide production. Further, the function of mitochondrial complexes I, III and V activities contributed to the neuroprotective activity of exogenous mitochondria. Similarly, we have also showed the internalization of exogenous mitochondria in mouse PCN; these internalized mitochondria were found to effectively preserve the neuronal networks when challenged with ferroptotic stimuli. The administration of exogenous mitochondria into the axonal compartment of a two-compartment microfluidic device induced mitochondrial transportation to the cell body, which prevented fragmentation of the neuronal network in ferroptotic PCN. These findings suggest that mitochondria transplantation may be a promising therapeutic approach for protecting neuronal cells from ferroptotic cell death.
    Keywords:  Ferroptosis; HT-22 cells; Mitochondrial transplantation; Oxidative stress; Primary cortical neurons
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2023.07.034
  49. Cell Mol Life Sci. 2023 Aug 02. 80(8): 237
    The expanding organelle lipidomes: current knowledge and challenges.
    Maria J Sarmento, Alicia Llorente, Toni Petan, Denis Khnykin, Iuliana Popa, Matea Nikolac Perkovic, Marcela Konjevod, Morana Jaganjac.
      Lipids in cell membranes and subcellular compartments play essential roles in numerous cellular processes, such as energy production, cell signaling and inflammation. A specific organelle lipidome is characterized by lipid synthesis and metabolism, intracellular trafficking, and lipid homeostasis in the organelle. Over the years, considerable effort has been directed to the identification of the lipid fingerprints of cellular organelles. However, these fingerprints are not fully characterized due to the large variety and structural complexity of lipids and the great variability in the abundance of different lipid species. The process becomes even more challenging when considering that the lipidome differs in health and disease contexts. This review summarizes the information available on the lipid composition of mammalian cell organelles, particularly the lipidome of the nucleus, mitochondrion, endoplasmic reticulum, Golgi apparatus, plasma membrane and organelles in the endocytic pathway. The lipid compositions of extracellular vesicles and lamellar bodies are also described. In addition, several examples of subcellular lipidome dynamics under physiological and pathological conditions are presented. Finally, challenges in mapping organelle lipidomes are discussed.
    Keywords:  Cellular organelles; Lipidomics; Lipids; Mass spectrometry; Subcellular fractionation
    DOI:  https://doi.org/10.1007/s00018-023-04889-3
  50. Brain. 2023 Jul 31. pii: awad246. [Epub ahead of print]
    The non-specific lethal complex regulates genes and pathways genetically linked to Parkinson's disease.
    Amy R Hicks, Regina H Reynolds, Ben O'Callaghan, Sonia Garcia Ruiz, Ana Luisa Gil Martinez, Juan Botia, Helene Plun-Favreau, Mina Ryten.
      Genetic variants conferring risk for Parkinson's disease have been highlighted through genome-wide association studies, yet exploration of their specific disease mechanisms is lacking. Two Parkinson's disease candidate genes, KAT8 and KANSL1, identified through genome-wide studies and a PINK1-mitophagy screen, encode part of the histone acetylating non-specific lethal complex. This complex localises to the nucleus, where it has a role in transcriptional activation, and to mitochondria, where it has been suggested to have a role in mitochondrial transcription. In this study, we sought to identify whether the non-specific lethal complex has potential regulatory relationships with other genes associated with Parkinson's disease in human brain. Correlation in the expression of non-specific lethal genes and Parkinson's disease-associated genes was investigated in primary gene co-expression networks utilising publicly available transcriptomic data from multiple brain regions (provided by the Genotype-Tissue Expression Consortium and UK Brain Expression Consortium), whilst secondary networks were used to examine cell-type specificity. Reverse engineering of gene regulatory networks generated regulons of the complex, which were tested for heritability using stratified linkage disequilibrium score regression. Prioritised gene targets were then validated in vitro using a QuantiGene multiplex assay and publicly available chromatin immunoprecipitation-sequencing data. Significant clustering of non-specific lethal genes was revealed alongside Parkinson's disease-associated genes in frontal cortex primary co-expression modules, amongst other brain regions. Both primary and secondary co-expression modules containing these genes were enriched for mainly neuronal cell types. Regulons of the complex contained Parkinson's disease-associated genes and were enriched for biological pathways genetically linked to disease. When examined in a neuroblastoma cell line, 41% of prioritised gene targets showed significant changes in mRNA expression following KANSL1 or KAT8 perturbation. KANSL1 and H4K8 chromatin immunoprecipitation-sequencing data demonstrated NSL complex activity at many of these genes. In conclusion, genes encoding the non-specific lethal complex are highly correlated with and regulate genes associated with Parkinson's disease. Overall, these findings reveal a potentially wider role for this protein complex in regulating genes and pathways implicated in Parkinson's disease.
    Keywords:  GWAS; NSL complex; Parkinson’s disease; gene co-expression networks
    DOI:  https://doi.org/10.1093/brain/awad246
  51. Mol Biol Rep. 2023 Aug 04.
    NAD+ metabolism and eye diseases: current status and future directions.
    Siyuan Liu, Wenfang Zhang.
      Currently, there are no truly effective treatments for a variety of eye diseases, such as glaucoma, age-related macular degeneration (AMD), and inherited retinal degenerations (IRDs). These conditions have a significant impact on patients' quality of life and can be a burden on society. However, these diseases share a common pathological process of NAD+ metabolism disorders. They are either associated with genetically induced primary NAD+ synthase deficiency, decreased NAD+ levels due to aging, or enhanced NAD+ consuming enzyme activity during disease pathology. In this discussion, we explore the role of NAD+ metabolic disorders in the development of associated ocular diseases and the potential advantages and disadvantages of various methods to increase NAD+ levels. It is essential to carefully evaluate the possible adverse effects of these methods and conduct a more comprehensive and objective assessment of their function before considering their use.
    Keywords:  Eye Diseases; NAD+; NAD+ homeostasis; Therapy
    DOI:  https://doi.org/10.1007/s11033-023-08692-y
  52. J Cell Biol. 2023 09 04. pii: e202304076. [Epub ahead of print]222(9):
    Convergent and divergent mechanisms of peroxisomal and mitochondrial division.
    Suresh Subramani, Nandini Shukla, Jean-Claude Farre.
      Organelle division and segregation are important in cellular homeostasis. Peroxisomes (POs) and mitochondria share a core division machinery and mechanism of membrane scission. The division of each organelle is interdependent not only on the other but also on other organelles, reflecting the dynamic communication between subcellular compartments, even as they coordinate the exchange of metabolites and signals. We highlight common and unique mechanisms involved in the fission of these organelles under the premise that much can be gleaned regarding the division of one organelle based on information available for the other.
    DOI:  https://doi.org/10.1083/jcb.202304076
  53. Chem Commun (Camb). 2023 Aug 04.
    A water-soluble fluorescent organic nano-photosensitizer for the ratiometric detection of mitochondrial G-quadruplexes with photodynamic therapy potential.
    Qing-Yu Ma, Xiang Li, Wei Zhou, Xia-Fen Li, Yi-Chen Liu, Gai-Li Feng, Hongwei Tan, Yuan Zhang, Guo-Wen Xing.
      We report a water-soluble AIEgen (TPAL) that can self-assemble into fluorescent organic nanoparticles for the ratiometric detection of mitochondrial DNA (mtDNA) parallel G-quadruplexes (G4s) with high selectivity, a low detection limit and photodynamic therapy (PDT) potential.
    DOI:  https://doi.org/10.1039/d3cc02788k
  54. Gene. 2023 Aug 01. pii: S0378-1119(23)00525-5. [Epub ahead of print] 147684
    An integrative analysis of genotype-phenotype correlation in Charcot Marie Tooth type 2A disease with MFN2 variants: a case and systematic review.
    Yuanzhu Zhang, Daxin Pang, Ziru Wang, Lerong Ma, Yiwu Chen, Lin Yang, Wenyu Xiao, Hongming Yuan, Fei Chang, Hongsheng Ouyang.
      Dominant genetic variants in the mitofusin 2 (MFN2) gene lead to Charcot-Marie-Tooth type 2A (CMT2A), a neurodegenerative disease caused by genetic defects that directly damage axons. In this study, we reported a proband with a pathogenic variant in the GTPase domain of MFN2, c.494A>G (p.His165Arg). To date, at least 184 distinct MFN2 variants identified in 944 independent probands have been reported in 131 references. However, the field of medical genetics has long been challenged by how genetic variation in the MFN2 gene is associated with disease phenotypes. Here, by collating the MFN2 variant data and patient clinical information from Leiden Open Variant Database 3.0, NCBI clinvar database, and available related references in PubMed, we determined the mutation frequency, age of onset, sex ratio, and geographical distribution. Furthermore, the results of an analysis examining the relationship between variants and phenotypes from multiple genetic perspectives indicated that insertion and deletions (indels), copy number variants (CNVs), duplication variants, and nonsense mutations in single nucleotide variants (SNVs) tend to be pathogenic, and the results emphasized the importance of the GTPase domain to the structure and function of MFN2. Overall, three reliable classification methods of MFN2 genotype-phenotype associations provide insights into the prediction of CMT2A disease severity. Of course, there are still many MFN2 variants that have not been given clear clinical significance, which requires clinicians to make more accurate clinical diagnoses.
    Keywords:  CMT2A; MFN2; genotype; phenotype; variants
    DOI:  https://doi.org/10.1016/j.gene.2023.147684
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