bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2021–10–31
48 papers selected by
Catalina Vasilescu, University of Helsinki
  1. It takes two to tango; the essential role of ER-mitochondrial contact sites in mitochondrial dynamics.
  2. SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells.
  3. Regulation of mitochondrial cargo-selective autophagy by post-translational modifications.
  4. Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain.
  5. Multiple variants of the human presequence translocase motor subunit Magmas govern the mitochondrial import.
  6. Mitochondrial calcium exchange in physiology and disease.
  7. Antisense Oligonucleotide-Mediated Silencing of Mitochondrial Fusion and Fission Factors Modulates Mitochondrial Dynamics and Rescues Mitochondrial Dysfunction.
  8. Determining Mitochondrial 3243A>G Heteroplasmy Using an ARMS-ddPCR Strategy.
  9. Mitochondrial metabolism coordinates stage-specific repair processes in macrophages during wound healing.
  10. Bi-allelic variants in the mitochondrial RNase P subunit PRORP cause mitochondrial tRNA processing defects and pleiotropic multisystem presentations.
  11. Temporal proteomics during neurogenesis reveals large-scale proteome and organelle remodeling via selective autophagy.
  12. Novel IBA57 mutations in two chinese patients and literature review of multiple mitochondrial dysfunction syndrome.
  13. Sex-specific genetic regulation of adipose mitochondria and metabolic syndrome by Ndufv2.
  14. Cnm1 mediates nucleus-mitochondria contact site formation in response to phospholipid levels.
  15. SNX14 deficiency-induced defective axonal mitochondrial transport in Purkinje cells underlies cerebellar ataxia and can be reversed by valproate.
  16. High confidence ATFS-1 target genes for quantifying activation of the mitochondrial unfolded protein response.
  17. Mitochondrial phenotypes in purified human immune cell subtypes and cell mixtures.
  18. The mitochondrial permeability transition: Recent progress and open questions.
  19. Adult-onset, isolated respiratory chain complex-IV deficiency with mild manifestations.
  20. The Natural History of Leigh Syndrome: A Study of Disease Burden and Progression.
  21. Intracellular Lipid Accumulation and Mitochondrial Dysfunction Accompanies Endoplasmic Reticulum Stress Caused by Loss of the Co-chaperone DNAJC3.
  22. Cross-species screening platforms identify EPS-8 as a critical link for mitochondrial stress and actin stabilization.
  23. The many roles mitochondria play in mammalian aging.
  24. Physiologic biomechanics enhance reproducible contractile development in a stem cell derived cardiac muscle platform.
  25. Mitochondrial Metabolism in Macrophages.
  26. Inhibition of glucose transport synergizes with chemical or genetic disruption of mitochondrial metabolism and suppresses TCA cycle-deficient tumors.
  27. The function of Scox in glial cells is essential for locomotive ability in Drosophila.
  28. Investigation of USP30 inhibition to enhance Parkin-mediated mitophagy: tools and approaches.
  29. Disease variant prediction with deep generative models of evolutionary data.
  30. Current and Future Treatment Approaches for Barth Syndrome.
  31. Glutamate metabolism directs energetic trade-offs to shape host-pathogen susceptibility in Drosophila.
  32. Muscle-generated BDNF (brain derived neurotrophic factor) maintains mitochondrial quality control in female mice.
  33. Clinical relevance of testing for metabolic vitamin B12 deficiency in patients with polyneuropathy.
  34. Visualization of sparsely-populated lower-order oligomeric states of human mitochondrial Hsp60 by cryo-electron microscopy.
  35. Heme-dependent recognition of 5-aminolevulinate synthase by the human mitochondrial molecular chaperone ClpX.
  36. In Vivo RNA Structure Probing with DMS-MaPseq.
  37. Exercise prevents fatty liver by modifying the compensatory response of mitochondrial metabolism to excess substrate availability.
  38. Mitoepigenetics: An intriguing regulatory layer in aging and metabolic-related diseases.
  39. Phase separation drives the self-assembly of mitochondrial nucleoids for transcriptional modulation.
  40. Health-related out-of-pocket expenses for children living with rare diseases - tuberous sclerosis and mitochondrial disorders: A prospective pilot study in Australian families.
  41. A non-canonical, interferon-independent signaling activity of cGAMP triggers DNA damage response signaling.
  42. An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci.
  43. Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram.
  44. Cytoplasmic DNA: sources, sensing, and role in aging and disease.
  45. Bioorthogonal Photocatalytic Decaging-Enabled Mitochondrial Proteomics.
  46. Expanding the electro-clinical phenotype of CARS2associated neuroregression.
  47. Rapamycin recruits SIRT2 for FKBP12 deacetylation during mTOR activity modulation in innate immunity.
  48. Somatic mosaicism detected by genome-wide sequencing in 500 parent-child trios with suspected genetic disease: Clinical and genetic counseling implications.
  1. Int J Biochem Cell Biol. 2021 Oct 22. pii: S1357-2725(21)00182-5. [Epub ahead of print] 106101
    It takes two to tango; the essential role of ER-mitochondrial contact sites in mitochondrial dynamics.
    Irene M G M Hemel, Rita Sarantidou, Mike Gerards.
      Mitochondria change their shape, size and number, in response to cellular demand, through mitochondrial dynamics. The interaction between mitochondria and the ER, through ER-mitochondrial contact sites, is crucial in mitochondrial dynamics. Several protein complexes tethering mitochondria to the ER include proteins involved in fission or fusion but also proteins involved in calcium homeostasis, which is known to affect mitochondrial dynamics. The formation of these contact sites are especially important for mitochondrial fission as these contact sites induce both outer and inner membrane constriction, prior to recruitment of Drp1. While the exact molecular mechanisms behind these constrictions remain uncertain, several hypotheses have been proposed. In this review, we discuss the involvement of tethering complexes in mitochondrial dynamics and provide an overview of the current knowledge and hypotheses on the constriction of the outer and inner mitochondrial membrane at ER-mitochondrial contact sites.
    Keywords:  ER-mitochondrial contact; Mitochondrial dynamics; Mitochondrial membrane constriction
    DOI:  https://doi.org/10.1016/j.biocel.2021.106101
  2. Nature. 2021 Oct 27.
    SLC25A39 is necessary for mitochondrial glutathione import in mammalian cells.
    Ying Wang, Frederick S Yen, Xiphias Ge Zhu, Rebecca C Timson, Ross Weber, Changrui Xing, Yuyang Liu, Benjamin Allwein, Hanzhi Luo, Hsi-Wen Yeh, Søren Heissel, Gokhan Unlu, Eric R Gamazon, Michael G Kharas, Richard Hite, Kıvanç Birsoy.
      Glutathione (GSH) is a small-molecule thiol that is abundant in all eukaryotes and has key roles in oxidative metabolism1. Mitochondria, as the major site of oxidative reactions, must maintain sufficient levels of GSH to perform protective and biosynthetic functions2. GSH is synthesized exclusively in the cytosol, yet the molecular machinery involved in mitochondrial GSH import remains unknown. Here, using organellar proteomics and metabolomics approaches, we identify SLC25A39, a mitochondrial membrane carrier of unknown function, as a regulator of GSH transport into mitochondria. Loss of SLC25A39 reduces mitochondrial GSH import and abundance without affecting cellular GSH levels. Cells lacking both SLC25A39 and its paralogue SLC25A40 exhibit defects in the activity and stability of proteins containing iron-sulfur clusters. We find that mitochondrial GSH import is necessary for cell proliferation in vitro and red blood cell development in mice. Heterologous expression of an engineered bifunctional bacterial GSH biosynthetic enzyme (GshF) in mitochondria enables mitochondrial GSH production and ameliorates the metabolic and proliferative defects caused by its depletion. Finally, GSH availability negatively regulates SLC25A39 protein abundance, coupling redox homeostasis to mitochondrial GSH import in mammalian cells. Our work identifies SLC25A39 as an essential and regulated component of the mitochondrial GSH-import machinery.
    DOI:  https://doi.org/10.1038/s41586-021-04025-w
  3. J Biol Chem. 2021 Oct 21. pii: S0021-9258(21)01145-5. [Epub ahead of print] 101339
    Regulation of mitochondrial cargo-selective autophagy by post-translational modifications.
    Anna Lechado Terradas, Katharina Zittlau, Boris Macek, Milana Fraiberg, Zvulun Elazar, Philipp J Kahle.
      Mitochondria are important organelles in eukaryotes. Turnover and quality control of mitochondria are regulated at the transcriptional and post-translational level by several cellular mechanisms. Removal of defective mitochondrial proteins is mediated by mitochondria resident proteases or by proteasomal degradation of individual proteins. Clearance of bulk mitochondria occurs via a selective form of autophagy termed mitophagy. In yeast and some developing metazoan cells (e.g. oocytes and reticulocytes), mitochondria are largely removed by ubiquitin-independent mechanisms. In such cases the regulation of mitophagy is mediated via phosphorylation of mitochondria-anchored autophagy receptors. On the other hand, ubiquitin-dependent recruitment of cytosolic autophagy receptors occurs in situations of cellular stress or disease, where dysfunctional mitochondria would cause oxidative damage. In mammalian cells, a well-studied ubiquitin-dependent mitophagy pathway induced by mitochondrial depolarization is regulated by the mitochondrial protein kinase PINK1 that upon activation recruits the ubiquitin ligase parkin. Here we review mechanisms of mitophagy with an emphasis on post-translational modifications that regulate various mitophagy pathways. We describe the autophagy components involved with particular emphasis on post-translational modifications. We detail the phosphorylations mediated by PINK1 and parkin-mediated ubiquitylations of mitochondrial proteins that can be modulated by deubiquitylating enzymes. We also discuss the role of accessory factors regulating mitochondrial fission/fusion and the interplay with pro- and anti-apoptotic Bcl-2 family members. Comprehensive knowledge of the processes of mitophagy is essential for the understanding of vital mitochondrial turnover in health and disease.
    Keywords:  autophagy; mitochondria; phosphorylation; protein kinase PINK1; ubiquitin ligase parkin; ubiquitylation
    DOI:  https://doi.org/10.1016/j.jbc.2021.101339
  4. Dev Cell. 2021 Oct 22. pii: S1534-5807(21)00809-1. [Epub ahead of print]
    Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain.
    Shefali Krishna, Rafael Arrojo E Drigo, Juliana S Capitanio, Ranjan Ramachandra, Mark Ellisman, Martin W Hetzer.
      In order to combat molecular damage, most cellular proteins undergo rapid turnover. We have previously identified large nuclear protein assemblies that can persist for years in post-mitotic tissues and are subject to age-related decline. Here, we report that mitochondria can be long lived in the mouse brain and reveal that specific mitochondrial proteins have half-lives longer than the average proteome. These mitochondrial long-lived proteins (mitoLLPs) are core components of the electron transport chain (ETC) and display increased longevity in respiratory supercomplexes. We find that COX7C, a mitoLLP that forms a stable contact site between complexes I and IV, is required for complex IV and supercomplex assembly. Remarkably, even upon depletion of COX7C transcripts, ETC function is maintained for days, effectively uncoupling mitochondrial function from ongoing transcription of its mitoLLPs. Our results suggest that modulating protein longevity within the ETC is critical for mitochondrial proteome maintenance and the robustness of mitochondrial function.
    Keywords:  age mosaicism; aging; electron transport chain; heterogeneity; long-lived proteins; mitochondria; muscle; neurons; protein homeostasis; supercomplexes
    DOI:  https://doi.org/10.1016/j.devcel.2021.10.008
  5. J Biol Chem. 2021 Oct 26. pii: S0021-9258(21)01155-8. [Epub ahead of print] 101349
    Multiple variants of the human presequence translocase motor subunit Magmas govern the mitochondrial import.
    Tejashree Pradip Waingankar, Patrick D'Silva.
      Mitochondrial protein translocation is an intricately regulated process that requires dedicated translocases at the outer and inner membranes. The presequence translocase complex, TIM23, facilitates most of the import of preproteins containing presequences into the mitochondria, and its primary structural organization is highly conserved. As part of the translocase motor, two J-proteins DnaJC15 and DnaJC19, are recruited to form two independent translocation machineries (Translocase A and Translocase B, respectively). On the other hand, the J-like protein subunit of TIM23, Magmas (orthologous to the yeast subunit Pam16), can regulate human import motor activity by forming a heterodimer with DnaJC19 and DnaJC15. However, the precise coordinated regulation of two human import motors by a single Magmas protein is poorly understood. Here we report two additional Magmas variants (Magmas-1 and Magmas-2) constitutively expressed in the mammalian system. Both Magmas variants are functional orthologs of Pam16 with an evolutionarily conserved J-like domain critical for cell survival. Moreover, Magmas variants are peripherally associated with the inner membrane as part of the human import motor for translocation. Our results demonstrate that Magmas-1 is predominantly recruited to translocase B, while Magmas-2 is majorly associated with translocase A. Strikingly, both variants exhibit differential J-protein inhibitory activity in modulating import motor, thereby regulating overall translocase function. Based on our findings, we hypothesize that additional Magmas variants are of evolutionary significance in humans to maximize protein import in familial-linked pathological conditions.
    Keywords:  Magmas; Mitochondria; Mitochondrial translocase of inner membrane; Protein import; Protein translocation
    DOI:  https://doi.org/10.1016/j.jbc.2021.101349
  6. Physiol Rev. 2021 10 26.
    Mitochondrial calcium exchange in physiology and disease.
    Joanne F Garbincius, John W Elrod.
      The uptake of calcium into and extrusion of calcium from the mitochondrial matrix is a fundamental biological process that has critical effects on cellular metabolism, signaling, and survival. Disruption of mitochondrial calcium (mCa2+) cycling is implicated in numerous acquired diseases such as heart failure, stroke, neurodegeneration, diabetes, and cancer, and is genetically linked to several inherited neuromuscular disorders. Understanding the mechanisms responsible for mCa2+ exchange therefore holds great promise for the treatment of these diseases. The past decade has seen the genetic identification of many of the key proteins that mediate mitochondrial calcium uptake and efflux. Here, we present an overview of the phenomenon of mCa2+ transport, and a comprehensive examination of the molecular machinery that mediates calcium flux across the inner mitochondrial membrane: the mitochondrial uniporter complex (consisting of MCU, EMRE, MICU1, MICU2, MICU3, MCUB, and MCUR1), NCLX, LETM1, the mitochondrial ryanodine receptor, and the mitochondrial permeability transition pore. We then consider the physiological implications of mCa2+ flux and evaluate how alterations in mCa2+ homeostasis contribute to human disease. This review concludes by highlighting opportunities and challenges for therapeutic intervention in pathologies characterized by aberrant mCa2+ handling and by summarizing critical unanswered questions regarding the biology of mCa2+ flux.
    Keywords:  calcium; energetics; metabolism; mitochondria; oxidative phosphorylation
    DOI:  https://doi.org/10.1152/physrev.00041.2020
  7. Nucleic Acid Ther. 2021 Oct 25.
    Antisense Oligonucleotide-Mediated Silencing of Mitochondrial Fusion and Fission Factors Modulates Mitochondrial Dynamics and Rescues Mitochondrial Dysfunction.
    Daniel A Garcia, Andrew F Powers, Thomas A Bell, Shuling Guo, Mariam Aghajan.
      Mitochondria are highly dynamic organelles that produce ATP and maintain metabolic, catabolic, and redox homeostasis. Mitochondria owe this dynamic nature to their constant fission and fusion-processes that are regulated, in part, by fusion factors (MFN1 and MFN2) and fission factors (DRP1, FIS1, MFF, MIEF1, MIEF2) located on the outer mitochondrial membrane. While mitochondrial fusion and fission are known to influence mitochondrial morphology and function, a key question is whether rebalancing mitochondrial morphology can ameliorate mitochondrial dysfunction in the context of mitochondrial pathology. In this study, we used antisense oligonucleotides (ASOs) to systematically evaluate the effects of fusion and fission factors in vitro. Free uptake by cells of fusion or fission factor ASOs caused robust decreases in target gene expression and altered a variety of mitochondrial parameters, including mitochondrial size and respiration, which were dose dependent. In Mfn1 knockout mouse embryonic fibroblasts (MEFs) and MFN2-R94Q (Charcot-Marie-Tooth Type 2 Disease-associated mutation) MEFs, two cellular models of mitochondrial dysfunction, we found that ASO-mediated silencing of only Drp1 restored mitochondrial morphology and enhanced mitochondrial respiration. Together, these data demonstrate in vitro proof-of-concept for rebalancing mitochondrial morphology to rescue function using ASOs and suggest that ASO-mediated modulation of mitochondrial dynamics may be a viable therapeutic approach to restore mitochondrial homeostasis in diseases driven by mitochondrial dysfunction.
    Keywords:  antisense; mitochondria; mitochondrial dynamics; oligonucleotides
    DOI:  https://doi.org/10.1089/nat.2021.0029
  8. Am J Clin Pathol. 2021 Oct 26. pii: aqab174. [Epub ahead of print]
    Determining Mitochondrial 3243A>G Heteroplasmy Using an ARMS-ddPCR Strategy.
    Pu Xu, Manli Jia, Jimei Yan, Xiangshu Yuan, Weidong Yu, Zhuohua Zhou, Hezhi Fang, Feng Gao, Lijun Shen.
       OBJECTIVES: Determining mitochondrial DNA (mtDNA) A-to-G substitution at nucleotide 3243 (m.3243A>G) heteroplasmy is essential for both precision diagnosis of m.3243A>G-associated mitochondrial disease and genetic counseling. Precise determination of m.3243A>G heteroplasmy is challenging, however, without appropriate strategies to accommodate heteroplasmic levels ranging from 1% to 100% in samples carrying thousands to millions of mtDNA copies.
    METHODS: We used a combined strategy of amplification-refractory mutation system-quantitative polymerase chain reaction (ARMS-qPCR) and droplet digital PCR (ddPCR) to determine m.3243A>G heteroplasmy. Primers were specifically designed and screened for both ARMS-qPCR and ddPCR to determine m.3243A>G heteroplasmy. An optimized ARMS-qPCR-ddPCR-based strategy was established using artificial standards, with different mixtures of m.3243A-containing and m.3243G-containing plasmids and further tested using clinical samples containing the m.3243A>G mutation.
    RESULTS: One of 20 primer pairs designed in the study was omitted for ARMS-qPCR-ddPCR strategy application according to criteria of 85% to 110%, R2  > 0.98 amplification efficiency, melt curve with a single clear peak, and specificity for m.3243A and m.3243G artificial standards (|CtWt-CtMut|max). Using plasmid standards with various m.3243A>G heteroplasmy (1%-100%) at low, mid, and high copy numbers (3,000, 104, and 105-107, respectively) and DNA from the blood of 20 patients carrying m.3243A>G with mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes, we found that ARMS-qPCR was reliable for determining m.3243A>G at 3% to 100% for low copy number and 1% to 100% for mid to high copy number samples. Meanwhile, ddPCR was reliable for determining m.3243A>G at 1% to 100% at low to mid copy number samples.
    CONCLUSIONS: An ARMS-qPCR-ddPCR-based strategy was successfully established for precise determination of m.3243A>G heteroplasmy in complex clinical samples.
    Keywords:  ARMS-qPCR; Heteroplasmy; Mitochondrial disease; ddPCR; mtDNA copy number
    DOI:  https://doi.org/10.1093/ajcp/aqab174
  9. Cell Metab. 2021 Oct 25. pii: S1550-4131(21)00482-4. [Epub ahead of print]
    Mitochondrial metabolism coordinates stage-specific repair processes in macrophages during wound healing.
    Sebastian Willenborg, David E Sanin, Alexander Jais, Xiaolei Ding, Thomas Ulas, Julian Nüchel, Milica Popović, Thomas MacVicar, Thomas Langer, Joachim L Schultze, Alexander Gerbaulet, Axel Roers, Edward J Pearce, Jens C Brüning, Aleksandra Trifunovic, Sabine A Eming.
      Wound healing is a coordinated process that initially relies on pro-inflammatory macrophages, followed by a pro-resolution function of these cells. Changes in cellular metabolism likely dictate these distinct activities, but the nature of these changes has been unclear. Here, we profiled early- versus late-stage skin wound macrophages in mice at both the transcriptional and functional levels. We found that glycolytic metabolism in the early phase is not sufficient to ensure productive repair. Instead, by combining conditional disruption of the electron transport chain with deletion of tgcqmitochondrial aspartyl-tRNA synthetase, followed by single-cell sequencing analysis, we found that a subpopulation of early-stage wound macrophages are marked by mitochondrial ROS (mtROS) production and HIF1α stabilization, which ultimately drives a pro-angiogenic program essential for timely healing. In contrast, late-phase, pro-resolving wound macrophages are marked by IL-4Rα-mediated mitochondrial respiration and mitohormesis. Collectively, we identify changes in mitochondrial metabolism as a critical control mechanism for macrophage effector functions during wound healing.
    Keywords:  metabolism; mitochondria; mitochondrial repurposing; mitohormesis; monocyte/macrophage; tissue repair; type 2 immunity; wound healing
    DOI:  https://doi.org/10.1016/j.cmet.2021.10.004
  10. Am J Hum Genet. 2021 Oct 25. pii: S0002-9297(21)00379-7. [Epub ahead of print]
    Bi-allelic variants in the mitochondrial RNase P subunit PRORP cause mitochondrial tRNA processing defects and pleiotropic multisystem presentations.
    Genomics England Research Consortium
      Human mitochondrial RNase P (mt-RNase P) is responsible for 5' end processing of mitochondrial precursor tRNAs, a vital step in mitochondrial RNA maturation, and is comprised of three protein subunits: TRMT10C, SDR5C1 (HSD10), and PRORP. Pathogenic variants in TRMT10C and SDR5C1 are associated with distinct recessive or x-linked infantile onset disorders, resulting from defects in mitochondrial RNA processing. We report four unrelated families with multisystem disease associated with bi-allelic variants in PRORP, the metallonuclease subunit of mt-RNase P. Affected individuals presented with variable phenotypes comprising sensorineural hearing loss, primary ovarian insufficiency, developmental delay, and brain white matter changes. Fibroblasts from affected individuals in two families demonstrated decreased steady state levels of PRORP, an accumulation of unprocessed mitochondrial transcripts, and decreased steady state levels of mitochondrial-encoded proteins, which were rescued by introduction of the wild-type PRORP cDNA. In mt-tRNA processing assays performed with recombinant mt-RNase P proteins, the disease-associated variants resulted in diminished mitochondrial tRNA processing. Identification of disease-causing variants in PRORP indicates that pathogenic variants in all three subunits of mt-RNase P can cause mitochondrial dysfunction, each with distinct pleiotropic clinical presentations.
    Keywords:  MRPP3; PRORP; Perrault syndrome; RNase P; leukodystrophy; mitochondria; primary ovarian insufficiency; rare disease; sensorineural hearing loss
    DOI:  https://doi.org/10.1016/j.ajhg.2021.10.002
  11. Mol Cell. 2021 Oct 15. pii: S1097-2765(21)00800-5. [Epub ahead of print]
    Temporal proteomics during neurogenesis reveals large-scale proteome and organelle remodeling via selective autophagy.
    Alban Ordureau, Felix Kraus, Jiuchun Zhang, Heeseon An, Sookhee Park, Tim Ahfeldt, Joao A Paulo, J Wade Harper.
      Cell state changes are associated with proteome remodeling to serve newly emergent cell functions. Here, we show that NGN2-driven conversion of human embryonic stem cells to induced neurons (iNeurons) is associated with increased PINK1-independent mitophagic flux that is temporally correlated with metabolic reprogramming to support oxidative phosphorylation. Global multiplex proteomics during neurogenesis revealed large-scale remodeling of functional modules linked with pluripotency, mitochondrial metabolism, and proteostasis. Differentiation-dependent mitophagic flux required BNIP3L and its LC3-interacting region (LIR) motif, and BNIP3L also promoted mitophagy in dopaminergic neurons. Proteomic analysis of ATG12-/- iNeurons revealed accumulation of endoplasmic reticulum, Golgi, and mitochondria during differentiation, indicative of widespread organelle remodeling during neurogenesis. This work reveals broad organelle remodeling of membrane-bound organelles during NGN2-driven neurogenesis via autophagy, identifies BNIP3L's central role in programmed mitophagic flux, and provides a proteomic resource for elucidating how organelle remodeling and autophagy alter the proteome during changes in cell state.
    Keywords:  autophagy; iNeurons; mitophagy; proteomics
    DOI:  https://doi.org/10.1016/j.molcel.2021.10.001
  12. Metab Brain Dis. 2021 Oct 28.
    Novel IBA57 mutations in two chinese patients and literature review of multiple mitochondrial dysfunction syndrome.
    Feixia Zhan, Xiaoli Liu, Ruilong Ni, Taotao Liu, Yuwen Cao, Jingying Wu, Wotu Tian, Xinghua Luan, Li Cao.
      Multiple mitochondrial dysfunction syndrome (MMDS) refers to a class of mitochondrial diseases caused by nuclear gene mutations, which usually begins in early infancy and is classically characterized by markedly impaired neurological development, generalized muscle weakness, lactic acidosis, and hyperglycinemia, cavitating leukoencephalopathy, respiratory failure, as well as early fatality resulted from dysfunction of energy metabolism in multiple systems. So far, six types of MMDS have been identified based on different genotypes, which are caused by mutations in NFU1, BOLA3, IBA57, ISCA2, ISCA1 and PMPCB, respectively. IBA57 encodes a protein involved in the mitochondrial Fe/S cluster assembly process, which plays a vital role in the activity of multiple mitochondrial enzymes. Herein, detailed clinical investigation of 2 Chinese patients from two unrelated families were described, both of them showed mildly delay in developmental milestone before disease onset, the initial symptoms were all presented with acute motor and mental retrogression, and brain MRI showed diffused leukoencephalopathy with cavities, dysplasia of corpus callosum and cerebral atrophy. Exome sequencing revealed three IBA57 variants, one shared variant (c.286T>C) has been previously reported, the remaining two (c.189delC and c.580 A>G) are novel. To enhance the understanding of this rare disease, we further made a literature review about the current progress in clinical, genetic and treatment of the disorder. Due to the rapid progress of MMDS, early awareness is crucial to prompt and proper administration, as well as genetic counseling.
    Keywords:  IBA57; Leukoencephalopathy; MMDS; Mitochondrial disorders; Multiple mitochondrial dysfunction syndrome
    DOI:  https://doi.org/10.1007/s11011-021-00856-8
  13. Nat Metab. 2021 Oct 25.
    Sex-specific genetic regulation of adipose mitochondria and metabolic syndrome by Ndufv2.
    Karthickeyan Chella Krishnan, Laurent Vergnes, Rebeca Acín-Pérez, Linsey Stiles, Michael Shum, Lijiang Ma, Etienne Mouisel, Calvin Pan, Timothy M Moore, Miklós Péterfy, Casey E Romanoski, Karen Reue, Johan L M Björkegren, Markku Laakso, Marc Liesa, Aldons J Lusis.
      We have previously suggested a central role for mitochondria in the observed sex differences in metabolic traits. However, the mechanisms by which sex differences affect adipose mitochondrial function and metabolic syndrome are unclear. Here we show that in both mice and humans, adipose mitochondrial functions are elevated in females and are strongly associated with adiposity, insulin resistance and plasma lipids. Using a panel of diverse inbred strains of mice, we identify a genetic locus on mouse chromosome 17 that controls mitochondrial mass and function in adipose tissue in a sex- and tissue-specific manner. This locus contains Ndufv2 and regulates the expression of at least 89 mitochondrial genes in females, including oxidative phosphorylation genes and those related to mitochondrial DNA content. Overexpression studies indicate that Ndufv2 mediates these effects by regulating supercomplex assembly and elevating mitochondrial reactive oxygen species production, which generates a signal that increases mitochondrial biogenesis.
    DOI:  https://doi.org/10.1038/s42255-021-00481-w
  14. J Cell Biol. 2021 Nov 01. pii: e202104100. [Epub ahead of print]220(11):
    Cnm1 mediates nucleus-mitochondria contact site formation in response to phospholipid levels.
    Michal Eisenberg-Bord, Naama Zung, Javier Collado, Layla Drwesh, Emma J Fenech, Amir Fadel, Nili Dezorella, Yury S Bykov, Doron Rapaport, Ruben Fernandez-Busnadiego, Maya Schuldiner.
      Mitochondrial functions are tightly regulated by nuclear activity, requiring extensive communication between these organelles. One way by which organelles can communicate is through contact sites, areas of close apposition held together by tethering molecules. While many contacts have been characterized in yeast, the contact between the nucleus and mitochondria was not previously identified. Using fluorescence and electron microscopy in S. cerevisiae, we demonstrate specific areas of contact between the two organelles. Using a high-throughput screen, we uncover a role for the uncharacterized protein Ybr063c, which we have named Cnm1 (contact nucleus mitochondria 1), as a molecular tether on the nuclear membrane. We show that Cnm1 mediates contact by interacting with Tom70 on mitochondria. Moreover, Cnm1 abundance is regulated by phosphatidylcholine, enabling the coupling of phospholipid homeostasis with contact extent. The discovery of a molecular mechanism that allows mitochondrial crosstalk with the nucleus sets the ground for better understanding of mitochondrial functions in health and disease.
    DOI:  https://doi.org/10.1083/jcb.202104100
  15. Natl Sci Rev. 2021 Jul;8(7): nwab024
    SNX14 deficiency-induced defective axonal mitochondrial transport in Purkinje cells underlies cerebellar ataxia and can be reversed by valproate.
    Hongfeng Zhang, Yujuan Hong, Weijie Yang, Ruimin Wang, Ting Yao, Jian Wang, Ke Liu, Huilong Yuan, Chaoqun Xu, Yuanyuan Zhou, Guanxian Li, Lishan Zhang, Hong Luo, Xian Zhang, Dan Du, Hao Sun, Qiuyang Zheng, Yun-Wu Zhang, Yingjun Zhao, Ying Zhou, Huaxi Xu, Xin Wang.
      Loss-of-function mutations in sorting nexin 14 (SNX14) cause autosomal recessive spinocerebellar ataxia 20, which is a form of early-onset cerebellar ataxia that lacks molecular mechanisms and mouse models. We generated Snx14-deficient mouse models and observed severe motor deficits and cell-autonomous Purkinje cell degeneration. SNX14 deficiency disrupted microtubule organization and mitochondrial transport in axons by destabilizing the microtubule-severing enzyme spastin, which is implicated in dominant hereditary spastic paraplegia with cerebellar ataxia, and compromised axonal integrity and mitochondrial function. Axonal transport disruption and mitochondrial dysfunction further led to degeneration of high-energy-demanding Purkinje cells, which resulted in the pathogenesis of cerebellar ataxia. The antiepileptic drug valproate ameliorated motor deficits and cerebellar degeneration in Snx14-deficient mice via the restoration of mitochondrial transport and function in Purkinje cells. Our study revealed an unprecedented role for SNX14-dependent axonal transport in cerebellar ataxia, demonstrated the convergence of SNX14 and spastin in mitochondrial dysfunction, and suggested valproate as a potential therapeutic agent.
    Keywords:  Purkinje cell degeneration; axonal transport; cerebellar ataxia; mitochondrial dysfunction; sorting nexin 14; valproate
    DOI:  https://doi.org/10.1093/nsr/nwab024
  16. MicroPubl Biol. 2021 ;2021
    High confidence ATFS-1 target genes for quantifying activation of the mitochondrial unfolded protein response.
    Sonja K Soo, Jeremy M Van Raamsdonk.
      The mitochondrial unfolded protein response (mitoUPR) is an evolutionarily conserved pathway that restores homeostasis to the mitochondria after various disturbances. This pathway has roles in both resistance to exogenous stressors and longevity. The mitoUPR is mediated by the transcription factor ATFS-1/ATF-5, which modulates the expression of genes involved in protein folding, metabolism and stress resistance. MitoUPR activation in C. elegans is most commonly evaluated through transcriptional reporter strains for the mitochondrial chaperones HSP-6 and HSP-60. In order to obtain a more comprehensive view of transcriptional changes resulting from activation of the mitoUPR, we compared gene expression changes from three different mitoUPR-activating interventions: mutation of nuo-6, RNA interference (RNAi) knockdown of spg-7,and constitutive activation of ATFS-1. We specifically focused on gene expression changes that are dependent on ATFS-1. From this comparison, we identified 61 high confidence target genes that can be used to monitor mitoUPR activation. Notably, neither hsp-6 nor hsp-60 were significantly upregulated under all three mitoUPR activating conditions. We ranked the 61 genes according to the magnitude of upregulation and identify multiple genes that may serve as robust readouts of mitoUPR activation.
    DOI:  https://doi.org/10.17912/micropub.biology.000484
  17. Elife. 2021 Oct 26. pii: e70899. [Epub ahead of print]10
    Mitochondrial phenotypes in purified human immune cell subtypes and cell mixtures.
    Shannon Rausser, Caroline Trumpff, Marlon A McGill, Alex Junker, Wei Wang, Siu-Hong Ho, Anika Mitchell, Kalpita R Karan, Catherine E Monk, Suzanne C Segerstrom, Rebecca G Reed, Martin Picard.
      Using a high-throughput mitochondrial phenotyping platform to quantify multiple mitochondrial features among molecularly-defined immune cell subtypes, we quantify the natural variation in citrate synthase, mitochondrial DNA copy number (mtDNAcn), and respiratory chain enzymatic activities in human neutrophils, monocytes, B cells, and naïve and memory T lymphocyte subtypes. In mixed peripheral blood mononuclear cells (PBMCs) from the same individuals, we show to what extent mitochondrial measures are confounded by both cell type distributions and contaminating platelets. Cell subtype-specific measures among women and men spanning 4 decades of life indicate potential age- and sex-related differences, including an age-related elevation in mtDNAcn, which are masked or blunted in mixed PBMCs. Finally, a proof-of-concept, repeated-measures study in a single individual validates cell type differences and also reveals week-to-week changes in mitochondrial activities. Larger studies are required to validate and mechanistically extend these findings. These mitochondrial phenotyping data build upon established immunometabolic differences among leukocyte sub-populations, and provide foundational quantitative knowledge to develop interpretable blood-based assays of mitochondrial health.
    Keywords:  cell biology; human; immunology; inflammation
    DOI:  https://doi.org/10.7554/eLife.70899
  18. FEBS J. 2021 Oct 28.
    The mitochondrial permeability transition: Recent progress and open questions.
    Paolo Bernardi, Michela Carraro, Giovanna Lippe.
      Major progress has been made in defining the basis of the mitochondrial permeability transition, a Ca2+ -dependent permeability increase of the inner membrane that has puzzled mitochondrial research for almost 70 years. Initially considered an artifact of limited biological interest by most, over the years the permeability transition has raised to the status of regulator of mitochondrial ion homeostasis and of druggable effector mechanism of cell death. The permeability transition is mediated by opening of channel(s) modulated by matrix cyclophilin D, the permeability transition pore(s) (PTP). The field has received new impulse (i) from the hypothesis that the PTP may originate from a Ca2+ -dependent conformational change of F-ATP synthase; and (ii) from the reevaluation of the long-standing hypothesis that it originates from the adenine nucleotide translocator (ANT). Here, we provide a synthetic account of the structure of ANT and F-ATP synthase in order to discuss potential and controversial mechanisms through which they may form high-conductance channels; and review some intriguing findings from the wealth of early studies of PTP modulation that still await an explanation. We hope that this review will stimulate new experiments addressing the many outstanding problems, and thus contribute to the eventual solution of the puzzle of the permeability transition.
    Keywords:  ATP synthase; Mitochondria; adenine nucleotide translocator; calcium transport; channels; cyclophilin; cyclosporin; permeability transition
    DOI:  https://doi.org/10.1111/febs.16254
  19. Pol J Pathol. 2021 ;pii: 45313. [Epub ahead of print]72(2): 185-189
    Adult-onset, isolated respiratory chain complex-IV deficiency with mild manifestations.
    Josef Finsterer, Michael Winklehner.
      Isolated respiratory chain complex-IV deficiency (ICIVD) usually manifests clinically as an early-onset, severe, multisystem mitochondrial disorder (MID) and only rarely with mild manifestations. Here we present an adult patient with late onset ICIVD with slowly progressive, mild clinical manifestations. In a 57-years old Caucasian male with exercise-induced myalgia, muscle cramps, ptosis, and recurrent creatine-kinase (CK) elevation, muscle biopsy and biochemical investigations of the left lateral vastus muscle revealed ICIVD. He additionally had developed diabetes, arterial hypertension, hyperlipidemia, retinal detachment, transient hypothyroidism, and a hearing fall. The family history was positive for diabetes, Parkinsonism, and dementia in the mother and myopathy in the brother, suggesting maternal transmission of the MID. Conclusions: ICIVD may manifest in adulthood with only mild manifestations and may take a slowly progressive course. Patients with mild hyper-CKemia and mild multisystem manifestations, including the muscle, profit from muscle biopsy and biochemical investigations.
    Keywords:   mitochondrial; multisystem; myopathy.; respiratory chain; mtDNA
    DOI:  https://doi.org/10.5114/pjp.2021.109523
  20. Ann Neurol. 2021 Oct 30.
    The Natural History of Leigh Syndrome: A Study of Disease Burden and Progression.
    Albert Z Lim, Yi Shiau Ng, Alasdair Blain, Cecilia Jiminez-Moreno, Charlotte L Alston, Victoria Nesbitt, Louise Simmons, Saikat Santra, Evangeline Wassmer, Emma L Blakely, Doug M Turnbull, Robert W Taylor, Gráinne S Gorman, Robert McFarland.
       OBJECTIVE: This observational cohort study aims to quantify disease burden over time, establish disease progression rates and identify factors that may determine the disease course of Leigh syndrome.
    METHODS: Seventy-two Leigh syndrome children who completed the Newcastle Paediatric Mitochondrial Disease Scales (NPMDS) at baseline 3.7 years (IQR 2.0-7.6) and follow-up assessments 7.5 years (IQR 3.7-11.0) in clinics were enrolled. 82% of this cohort had a confirmed genetic diagnosis with pathogenic variants in the MT-ATP6 and SURF1 genes being the most common cause. The total NPMDS scores denoted mild (0-14), moderate (15-25) and severe (>25) disease burden. Detailed clinical, neuroradiological and molecular genetic findings were also analysed.
    RESULTS: The median total NPMDS scores rose significantly (Z=-6.9, p<0.001) and the percentage of children with severe disease burden doubled (22%→42%) over 2.6 years of follow-up. Poor function (especially mobility, self-care, communication, feeding and education) and extrapyramidal features contributed significantly to the disease burden (τb ≈0.45-0.68, p<0.001). These children also deteriorated to wheelchair dependence (31%→57%), exclusive enteral feeding (22%→46%) and one-to-one assistance for self-care (25%→43%) during the study period. Twelve children (17%) died after their last NPMDS scores were recorded. These children had higher follow-up NPMDS scores (disease burden) (p<0.001) and steeper increase in NPMDS score per annum (disease progression) (p<0.001). Other predictors of poor outcomes include SURF1 gene variants (p<0.001) and bilateral caudate changes on neuroimaging (p<0.01).
    INTERPRETATION: This study has objectively defined the disease burden and progression of Leigh syndrome. Our analysis has also uncovered potential influences on the trajectory of this neurodegenerative condition. This article is protected by copyright. All rights reserved.
    DOI:  https://doi.org/10.1002/ana.26260
  21. Front Cell Dev Biol. 2021 ;9 710247
    Intracellular Lipid Accumulation and Mitochondrial Dysfunction Accompanies Endoplasmic Reticulum Stress Caused by Loss of the Co-chaperone DNAJC3.
    Matthew J Jennings, Denisa Hathazi, Chi D L Nguyen, Benjamin Munro, Ute Münchberg, Robert Ahrends, Annette Schenck, Ilse Eidhof, Erik Freier, Matthis Synofzik, Rita Horvath, Andreas Roos.
      Recessive mutations in DNAJC3, an endoplasmic reticulum (ER)-resident BiP co-chaperone, have been identified in patients with multisystemic neurodegeneration and diabetes mellitus. To further unravel these pathomechanisms, we employed a non-biased proteomic approach and identified dysregulation of several key cellular pathways, suggesting a pathophysiological interplay of perturbed lipid metabolism, mitochondrial bioenergetics, ER-Golgi function, and amyloid-beta processing. Further functional investigations in fibroblasts of patients with DNAJC3 mutations detected cellular accumulation of lipids and an increased sensitivity to cholesterol stress, which led to activation of the unfolded protein response (UPR), alterations of the ER-Golgi machinery, and a defect of amyloid precursor protein. In line with the results of previous studies, we describe here alterations in mitochondrial morphology and function, as a major contributor to the DNAJC3 pathophysiology. Hence, we propose that the loss of DNAJC3 affects lipid/cholesterol homeostasis, leading to UPR activation, β-amyloid accumulation, and impairment of mitochondrial oxidative phosphorylation.
    Keywords:  DNAJC3; cholesterol-stress; mitochondria; proteomics; unfolded protein response (UPR)
    DOI:  https://doi.org/10.3389/fcell.2021.710247
  22. Sci Adv. 2021 Oct 29. 7(44): eabj6818
    Cross-species screening platforms identify EPS-8 as a critical link for mitochondrial stress and actin stabilization.
    Erica A Moehle, Ryo Higuchi-Sanabria, C Kimberly Tsui, Stefan Homentcovschi, Kevin M Tharp, Hanlin Zhang, Hannah Chi, Larry Joe, Mattias de Los Rios Rogers, Arushi Sahay, Naame Kelet, Camila Benitez, Raz Bar-Ziv, Gilberto Garcia, Koning Shen, Phillip A Frankino, Robert T Schinzel, Ophir Shalem, Andrew Dillin.
      [Figure: see text].
    DOI:  https://doi.org/10.1126/sciadv.abj6818
  23. Antioxid Redox Signal. 2021 Oct 29.
    The many roles mitochondria play in mammalian aging.
    Caio M P F Batalha, Anibal Eugênio Vercesi, Nadja C Souza-Pinto.
       SIGNIFICANCE: Aging is a natural process that affects most living organisms, resulting in increased mortality. As the world population ages, the prevalence of age-associated diseases, and their associated healthcare costs, has increased sharply. A better understanding of the molecular mechanisms that lead to cellular dysfunction may provide important targets for interventions to prevent or treat these diseases. Recent Advances: Although the mitochondrial theory of aging has been proposed over 40 years ago, recent new data has given stronger support for a central role for mitochondrial dysfunction in several pathways that are deregulated during normal aging and age-associated disease.
    CRITICAL ISSUES: Several of the experimental evidence linking mitochondrial alterations to age-associated loss of function are correlative and mechanistic insight are still elusive. Here, we review how mitochondrial dysfunction may be involved in many of the known hallmarks of aging, and how these pathways interact in an intricate net of molecular relationships.
    FUTURE DIRECTIONS: As it has become clear that mitochondrial dysfunction plays causative roles in normal aging and age-associated diseases, it is necessary to better define the molecular interactions and the temporal and causal relations between these changes and the relevant phenotypes seen during the aging process.
    DOI:  https://doi.org/10.1089/ars.2021.0074
  24. Nat Commun. 2021 Oct 25. 12(1): 6167
    Physiologic biomechanics enhance reproducible contractile development in a stem cell derived cardiac muscle platform.
    Yao-Chang Tsan, Samuel J DePalma, Yan-Ting Zhao, Adela Capilnasiu, Yu-Wei Wu, Brynn Elder, Isabella Panse, Kathryn Ufford, Daniel L Matera, Sabrina Friedline, Thomas S O'Leary, Nadab Wubshet, Kenneth K Y Ho, Michael J Previs, David Nordsletten, Lori L Isom, Brendon M Baker, Allen P Liu, Adam S Helms.
      Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) allow investigations in a human cardiac model system, but disorganized mechanics and immaturity of hPSC-CMs on standard two-dimensional surfaces have been hurdles. Here, we developed a platform of micron-scale cardiac muscle bundles to control biomechanics in arrays of thousands of purified, independently contracting cardiac muscle strips on two-dimensional elastomer substrates with far greater throughput than single cell methods. By defining geometry and workload in this reductionist platform, we show that myofibrillar alignment and auxotonic contractions at physiologic workload drive maturation of contractile function, calcium handling, and electrophysiology. Using transcriptomics, reporter hPSC-CMs, and quantitative immunofluorescence, these cardiac muscle bundles can be used to parse orthogonal cues in early development, including contractile force, calcium load, and metabolic signals. Additionally, the resultant organized biomechanics facilitates automated extraction of contractile kinetics from brightfield microscopy imaging, increasing the accessibility, reproducibility, and throughput of pharmacologic testing and cardiomyopathy disease modeling.
    DOI:  https://doi.org/10.1038/s41467-021-26496-1
  25. Am J Physiol Cell Physiol. 2021 Oct 27.
    Mitochondrial Metabolism in Macrophages.
    Mohamed Zakaria Nassef, Jasmin E Hanke, Karsten Hiller.
      Mitochondria are considered to be the powerhouse of the cell. Normal functioning of the mitochondria is not only essential for cellular energy production but also for several immunomodulatory processes. Macrophages operate in metabolic niches and rely on rapid adaptation to specific metabolic conditions such as hypoxia, nutrient limitations or reactive oxygen species to neutralize pathogens. In this regard, the fast reprogramming of mitochondrial metabolism is indispensable to provide the cells with the necessary energy and intermediates to efficiently mount the inflammatory response. Moreover, mitochondria act as a physical scaffold for several proteins involved in immune signaling cascades and their dysfunction is immediately associated with a dampened immune response. In this review, we put special focus on mitochondrial function in macrophages and highlight how mitochondrial metabolism is involved in macrophage activation.
    Keywords:  Itaconic acid; Macrophages; Metabolism; Mitochondira
    DOI:  https://doi.org/10.1152/ajpcell.00126.2021
  26. Cell Chem Biol. 2021 Oct 22. pii: S2451-9456(21)00441-4. [Epub ahead of print]
    Inhibition of glucose transport synergizes with chemical or genetic disruption of mitochondrial metabolism and suppresses TCA cycle-deficient tumors.
    Kellen Olszewski, Anthony Barsotti, Xiao-Jiang Feng, Milica Momcilovic, Kevin G Liu, Ji-In Kim, Koi Morris, Christophe Lamarque, Jack Gaffney, Xuemei Yu, Jeegar P Patel, Joshua D Rabinowitz, David B Shackelford, Masha V Poyurovsky.
      Efforts to target glucose metabolism in cancer have been limited by the poor potency and specificity of existing anti-glycolytic agents and a poor understanding of the glucose dependence of cancer subtypes in vivo. Here, we present an extensively characterized series of potent, orally bioavailable inhibitors of the class I glucose transporters (GLUTs). The representative compound KL-11743 specifically blocks glucose metabolism, triggering an acute collapse in NADH pools and a striking accumulation of aspartate, indicating a dramatic shift toward oxidative phosphorylation in the mitochondria. Disrupting mitochondrial metabolism via chemical inhibition of electron transport, deletion of the malate-aspartate shuttle component GOT1, or endogenous mutations in tricarboxylic acid cycle enzymes, causes synthetic lethality with KL-11743. Patient-derived xenograft models of succinate dehydrogenase A (SDHA)-deficient cancers are specifically sensitive to KL-11743, providing direct evidence that TCA cycle-mutant tumors are vulnerable to GLUT inhibitors in vivo.
    Keywords:  GLUT inhibitor; PDX models; electron transport chain inhibitors; glycolysis; imaging; malate-aspartate shuttle; mitochondrial inhibitors; pharmacology; redox biology; toxicology
    DOI:  https://doi.org/10.1016/j.chembiol.2021.10.007
  27. Sci Rep. 2021 Oct 27. 11(1): 21207
    The function of Scox in glial cells is essential for locomotive ability in Drosophila.
    Ryosuke Kowada, Atsushi Kodani, Hiroyuki Ida, Masamitsu Yamaguchi, Im-Soon Lee, Yasushi Okada, Hideki Yoshida.
      Synthesis of cytochrome c oxidase (Scox) is a Drosophila homolog of human SCO2 encoding a metallochaperone that transports copper to cytochrome c, and is an essential protein for the assembly of cytochrome c oxidase in the mitochondrial respiratory chain complex. SCO2 is highly conserved in a wide variety of species across prokaryotes and eukaryotes, and mutations in SCO2 are known to cause mitochondrial diseases such as fatal infantile cardioencephalomyopathy, Leigh syndrome, and Charcot-Marie-Tooth disease, a neurodegenerative disorder. These diseases have a common symptom of locomotive dysfunction. However, the mechanisms of their pathogenesis remain unknown, and no fundamental medications or therapies have been established for these diseases. In this study, we demonstrated that the glial cell-specific knockdown of Scox perturbs the mitochondrial morphology and function, and locomotive behavior in Drosophila. In addition, the morphology and function of synapses were impaired in the glial cell-specific Scox knockdown. Furthermore, Scox knockdown in ensheathing glia, one type of glial cell in Drosophila, resulted in larval and adult locomotive dysfunction. This study suggests that the impairment of Scox in glial cells in the Drosophila CNS mimics the pathological phenotypes observed by mutations in the SCO2 gene in humans.
    DOI:  https://doi.org/10.1038/s41598-021-00663-2
  28. Biochem J. 2021 Oct 27. pii: BCJ20210508. [Epub ahead of print]
    Investigation of USP30 inhibition to enhance Parkin-mediated mitophagy: tools and approaches.
    Eliona Tsefou, Alison S Walker, Emily H Clark, Amy Rose Hicks, Christin Luft, Kunitoshi Takeda, Toru Watanabe, Bianca Ramazio, James M Staddon, Thomas Briston, Robin Ketteler.
      Mitochondrial dysfunction is implicated in Parkinson disease (PD). Mutations in Parkin, an E3 ubiquitin ligase, can cause juvenile-onset Parkinsonism probably through impairment of mitophagy. Inhibition of the de-ubiquitinating enzyme USP30 may counter this effect to enhance mitophagy. Using different tools and cellular approaches, we wanted to independently confirm this claimed role for USP30. Pharmacological characterization of additional tool compounds that selectively inhibit USP30 are reported. The consequence of USP30 inhibition by these compounds, siRNA knockdown and overexpression of dominant-negative USP30 in the mitophagy pathway in different disease-relevant cellular models was explored. Knockdown and inhibition of USP30 showed increased p-Ser65-ubiquitin levels and mitophagy in neuronal cell models. Furthermore, patient-derived fibroblasts carrying pathogenic mutations in Parkin showed reduced p-Ser65-ubiquitin levels compared to wild-type cells, levels that could be restored using either USP30 inhibitor or dominant-negative USP30 expression. Our data provide additional support for USP30 inhibition as a regulator of the mitophagy pathway.
    Keywords:  Parkinsons disease; USP30; USP30 inhibitors; mitoKeima; mitophagy; p-Ser65-ubiquitin
    DOI:  https://doi.org/10.1042/BCJ20210508
  29. Nature. 2021 Oct 27.
    Disease variant prediction with deep generative models of evolutionary data.
    Jonathan Frazer, Pascal Notin, Mafalda Dias, Aidan Gomez, Joseph K Min, Kelly Brock, Yarin Gal, Debora S Marks.
      Quantifying the pathogenicity of protein variants in human disease-related genes would have a marked effect on clinical decisions, yet the overwhelming majority (over 98%) of these variants still have unknown consequences1-3. In principle, computational methods could support the large-scale interpretation of genetic variants. However, state-of-the-art methods4-10 have relied on training machine learning models on known disease labels. As these labels are sparse, biased and of variable quality, the resulting models have been considered insufficiently reliable11. Here we propose an approach that leverages deep generative models to predict variant pathogenicity without relying on labels. By modelling the distribution of sequence variation across organisms, we implicitly capture constraints on the protein sequences that maintain fitness. Our model EVE (evolutionary model of variant effect) not only outperforms computational approaches that rely on labelled data but also performs on par with, if not better than, predictions from high-throughput experiments, which are increasingly used as evidence for variant classification12-16. We predict the pathogenicity of more than 36 million variants across 3,219 disease genes and provide evidence for the classification of more than 256,000 variants of unknown significance. Our work suggests that models of evolutionary information can provide valuable independent evidence for variant interpretation that will be widely useful in research and clinical settings.
    DOI:  https://doi.org/10.1038/s41586-021-04043-8
  30. J Inherit Metab Dis. 2021 Oct 29.
    Current and Future Treatment Approaches for Barth Syndrome.
    Reid Thompson, John Jefferies, Suya Wang, William T Pu, Clifford Takemoto, Brittany Hornby, Andrea Heyman, Michael T Chin, Hilary Vernon.
      Barth Syndrome is an X-linked disorder of mitochondrial cardiolipin metabolism caused by pathogenic variants in TAFAZZIN with pleiotropic effects including cardiomyopathy, neutropenia, growth delay, and skeletal myopathy. Management requires a multidisciplinary approach to the organ-specific manifestations including specialists from cardiology, hematology, nutrition, physical therapy, genetics, and metabolism. Currently, treatment is centered on management of specific clinical features, and is not targeted towards remediating the underlying biochemical defect. However, two clinical trials have been recently undertaken which target the mitochondrial pathology of this disease: a study to examine the effects of elamipretide, a cardiolipin targeted agent, and a study to examine the effects of bezafibrate, a peroxisome proliferator-activated receptor (PPAR) agonist. Treatments to directly target the defective TAFAZZIN pathway are under development, including enzyme and gene therapies. This article is protected by copyright. All rights reserved.
    Keywords:  Barth Syndrome; Cardiolipin; Cardiomyopathy; TAFAZZIN
    DOI:  https://doi.org/10.1002/jimd.12453
  31. Cell Metab. 2021 Oct 22. pii: S1550-4131(21)00481-2. [Epub ahead of print]
    Glutamate metabolism directs energetic trade-offs to shape host-pathogen susceptibility in Drosophila.
    Xiao Zhao, Jason Karpac.
      Individual hosts within populations often show inter-individual variation in their susceptibility to bacterial pathogen-related diseases. Utilizing Drosophila, we highlight that phenotypic variation in host-pathogen susceptibility within populations is driven by energetic trade-offs, facilitated by infection-mediated changes in glutamate metabolism. Furthermore, host-pathogen susceptibility is conditioned by life history, which adjusts immunometabolic sensing in muscles to direct vitamin-dependent reallocation of host energy substrates from the adipose tissue (i.e., a muscle-adipose tissue axis). Life history conditions inter-individual variation in the activation strength of intra-muscular NF-κB signaling. Limited intra-muscular NF-κB signaling activity allows for enhanced infection-mediated mitochondrial biogenesis and function, which stimulates glutamate dehydrogenase-dependent synthesis of glutamate. Muscle-derived glutamate acts as a systemic metabolite to promote lipid mobilization through modulating vitamin B enzymatic cofactor transport and function in the adipose tissue. This energy substrate reallocation improves pathogen clearance and boosts host survival. Finally, life history events that adjust energetic trade-offs can shape inter-individual variation in host-pathogen susceptibility after infection.
    Keywords:  Smvt; glutamate; glutamate dehydrogenase; immunometabolism; innate immunity; life history; lipid metabolism; mitochondria; muscle; vitamin
    DOI:  https://doi.org/10.1016/j.cmet.2021.10.003
  32. Autophagy. 2021 Oct 25. 1-18
    Muscle-generated BDNF (brain derived neurotrophic factor) maintains mitochondrial quality control in female mice.
    Palak Ahuja, Chun Fai Ng, Brian Pak Shing Pang, Wing Suen Chan, Margaret Chui Ling Tse, Xinyi Bi, Hiu-Lam Rachel Kwan, Daniel Brobst, Oana Herlea-Pana, Xiuying Yang, Guanhua Du, Suchaorn Saengnipanthkul, Hye Lim Noh, Baowei Jiao, Jason K Kim, Chi Wai Lee, Keqiang Ye, Chi Bun Chan.
      Mitochondrial remodeling is dysregulated in metabolic diseases but the underlying mechanism is not fully understood. We report here that BDNF (brain derived neurotrophic factor) provokes mitochondrial fission and clearance in skeletal muscle via the PRKAA/AMPK-PINK1-PRKN/Parkin and PRKAA-DNM1L/DRP1-MFF pathways. Depleting Bdnf expression in myotubes reduced fatty acid-induced mitofission and mitophagy, which was associated with mitochondrial elongation and impaired lipid handling. Muscle-specific bdnf knockout (MBKO) mice displayed defective mitofission and mitophagy, and accumulation of dysfunctional mitochondria in the muscle when they were fed with a high-fat diet (HFD). These animals also have exacerbated body weight gain, increased intramyocellular lipid deposition, reduced energy expenditure, poor metabolic flexibility, and more insulin resistance. In contrast, consuming a BDNF mimetic (7,8-dihydroxyflavone) increased mitochondrial content, and enhanced mitofission and mitophagy in the skeletal muscles. Hence, BDNF is an essential myokine to maintain mitochondrial quality and function, and its repression in obesity might contribute to impaired metabolism.Abbreviation: 7,8-DHF: 7,8-dihydroxyflavone; ACACA/ACC: acetyl Coenzyme A carboxylase alpha; ACAD: acyl-Coenzyme A dehydrogenase family; ACADVL: acyl-Coenzyme A dehydrogenase, very long chain; ACOT: acyl-CoA thioesterase; CAMKK2: calcium/calmodulin-dependent protein kinase kinase 2, beta; BDNF: brain derived neurotrophic factor; BNIP3: BCL2/adenovirus E1B interacting protein 3; BNIP3L/NIX: BCL2/adenovirus E1B interacting protein 3-like; CCL2/MCP-1: chemokine (C-C motif) ligand 2; CCL5: chemokine (C-C motif) ligand 5; CNS: central nervous system; CPT1B: carnitine palmitoyltransferase 1b, muscle; Cpt2: carnitine palmitoyltransferase 2; CREB: cAMP responsive element binding protein; DNM1L/DRP1: dynamin 1-like; E2: estrogen; EHHADH: enoyl-CoenzymeA hydratase/3-hydroxyacyl CoenzymeA dehydrogenase; ESR1/ER-alpha: estrogen receptor 1 (alpha); FA: fatty acid; FAO: fatty acid oxidation; FCCP: carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone; FFA: free fatty acids; FGF21: fibroblast growth factor 21; FUNDC1: FUN14 domain containing 1; HADHA: hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha; HFD: high-fat diet; iWAT: inguinal white adipose tissues; MAP1LC3A/LC3A: microtubule-associated protein 1 light chain 3 alpha; MBKO; muscle-specific bdnf knockout; IL6/IL-6: interleukin 6; MCEE: methylmalonyl CoA epimerase; MFF: mitochondrial fission factor; NTRK2/TRKB: neurotrophic tyrosine kinase, receptor, type 2; OPTN: optineurin; PA: palmitic acid; PARL: presenilin associated, rhomboid-like; PDH: pyruvate dehydrogenase; PINK1: PTEN induced putative kinase 1; PPARGC1A/PGC-1α: peroxisome proliferative activated receptor, gamma, coactivator 1 alpha; PRKAA/AMPK: protein kinase, AMP-activated, alpha 2 catalytic subunit; ROS: reactive oxygen species; TBK1: TANK-binding kinase 1; TG: triacylglycerides; TNF/TNFα: tumor necrosis factor; TOMM20: translocase of outer mitochondrial membrane 20; ULK1: unc-51 like kinase 1.
    Keywords:  BDNF; mitochondria; mitophagy; muscle; obesity
    DOI:  https://doi.org/10.1080/15548627.2021.1985257
  33. Nutr Neurosci. 2021 Oct 25. 1-11
    Clinical relevance of testing for metabolic vitamin B12 deficiency in patients with polyneuropathy.
    Janna K Warendorf, Perry T C van Doormaal, Alexander F J E Vrancken, Nanda M Verhoeven-Duif, Ruben P A van Eijk, Leonard H van den Berg, Nicolette C Notermans.
       OBJECTIVE: Determine vitamin B12 threshold levels below which additional testing of methylmalonic acid (MMA) and/or homocysteine (Hcy) is useful to diagnose metabolic vitamin B12 deficiency in patients with polyneuropathy, and how vitamin B12, MMA and Hcy levels relate to the effect of supplementation therapy.
    METHODS: In a retrospective cohort study of 331 patients with polyneuropathy, vitamin B12, MMA and Hcy were measured. Linear regression models with vitamin B12 as dependent and Hcy or MMA as covariate were compared, to assess which was best related to vitamin B12. Threshold vitamin B12 levels for metabolic deficiency (defined as elevatede metabolites) were determined using logistic regression with elevated metabolites as dependent and vitamin B12 as covariate.. A structured interview was conducted in 42 patients to evaluate response to vitamin B12 supplementation.
    RESULTS: MMA was best related to vitamin B12. Using elevated MMA for metabolic deficiency, we found 90% sensitivity at a vitamin B12 threshold level <264 pmol/L (358 pg/mL) and 95% sensitivity at <304 pmol/L (412 pg/mL). Improvement after supplementation was reported by 19% patients and stabilization by 24%. 88% of patients with improvement and 90% with stabilization either had absolute deficiency (Vitamin B12 < 148 pmol/L) or metabolic deficiency (elevated MMA and vitamin B12 ≥ 148 pmol/L). There were no additional patients with improvement or stabilization with isolated elevated Hcy.
    CONCLUSION: Testing of MMA has additional value in identifying patients with clinically relevant metabolic deficiency when vitamin B12 is below 304 pmol/L (412 pg/mL). Supplementation can be effective in patients with absolute and metabolic deficiency.
    Keywords:  Metabolic deficiency‌; Vitamin deficiency; Vitamin supplementation‌; homocystein‌; methylmalonic acid; neuropathy; polyneuropathy; vitamin B12
    DOI:  https://doi.org/10.1080/1028415X.2021.1985751
  34. J Mol Biol. 2021 Oct 21. pii: S0022-2836(21)00559-3. [Epub ahead of print] 167322
    Visualization of sparsely-populated lower-order oligomeric states of human mitochondrial Hsp60 by cryo-electron microscopy.
    Marielle A Wälti, Bertram Canagarajah, Charles D Schwieters, G Marius Clore.
      Human mitochondrial Hsp60 (mtHsp60) is a class I chaperonin, 51% identical in sequence to the prototypical E. coli chaperonin GroEL. mtHsp60 maintains the proteome within the mitochondrion and is associated with various neurodegenerative diseases and cancers. The oligomeric assembly of mtHsp60 into heptameric ring structures that enclose a folding chamber only occurs upon addition of ATP and is significantly more labile than that of GroEL, where the only oligomeric species is a tetradecamer. The lability of the mtHsp60 heptamer provides an opportunity to detect and visualize lower-order oligomeric states that may represent intermediates along the assembly/disassembly pathway. Using cryo-electron microscopy we show that, in addition to the fully-formed heptamer and an "inverted" tetradecamer in which the two heptamers associate via their apical domains, thereby blocking protein substrate access, well-defined lower-order oligomeric species, populated at less than 6% of the total particles, are observed. Specifically, we observe open trimers, tetramers, pentamers and hexamers (comprising ∼4% of the total particles) with rigid body rotations from one subunit to the next within ∼1.5-3.5° of that for the heptamer, indicating that these may lie directly on the assembly/disassembly pathway. We also observe a closed-ring hexamer (∼2% of the particles) which may represent an off-pathway species in the assembly/disassembly process in so far that conversion to the mature heptamer would require the closed-ring hexamer to open to accept an additional subunit. Lastly, we observe several classes of tetramers where additional subunits characterized by fuzzy electron density are caught in the act of oligomer extension.
    Keywords:  chaperones; class I chaperonins; cryo-electron microscopy; human mitochondrial Hsp60; sparsely-populated lower-order oligomeric states
    DOI:  https://doi.org/10.1016/j.jmb.2021.167322
  35. FEBS Lett. 2021 Oct 26.
    Heme-dependent recognition of 5-aminolevulinate synthase by the human mitochondrial molecular chaperone ClpX.
    Kazumi Nomura, Yu Kitagawa, Marina Aihara, Yusuke Ohki, Kazumichi Furuyama, Takatsugu Hirokawa.
      The caseinolytic mitochondrial matrix peptidase chaperone subunit (ClpX) plays an important role in the heme-dependent regulation of 5-aminolevulinate synthase (ALAS1), a key enzyme in heme biosynthesis. However, the mechanisms underlying the role of ClpX in this process remain unclear. In this in vitro study, we confirmed the direct binding between ALAS1 and ClpX in a heme-dependent manner. The substitution of C108 P109 (CP motif 3 [CP3]) with A108 A109 in ALAS1 resulted in a loss of ability to bind ClpX. Computational disorder analyses revealed that CP3 was located in a potential intrinsically disordered protein region (IDPR). Thus, we propose that conditional disorder-to-order transitions in the IDPRs of ALAS1 may represent key mechanisms underlying the heme-dependent recognition of ALAS1 by ClpX.
    Keywords:  ALAS1; ClpP; ClpX; ClpXP proteolytic machinery; heme-regulated proteins; intrinsically disordered protein regions; ligand-induced protein degradation; molecular chaperone
    DOI:  https://doi.org/10.1002/1873-3468.14214
  36. Methods Mol Biol. 2022 ;2404 299-310
    In Vivo RNA Structure Probing with DMS-MaPseq.
    Paromita Gupta, Silvia Rouskin.
      RNA has an extraordinary capacity to fold and form intrinsic secondary structures that play a central role in maintaining its functionality. It is crucial to have ways to study RNA structures and identify their functions in their biological environment. In the last few decades, a number of different chemical probing methods have been used to study RNA secondary structure. Here, we present a dimethyl sulfate-based (DMS) chemical probing method coupled with Next Generation sequencing (DMS-MaPseq) to study RNA secondary structure in vivo.DMS modifies unpaired adenine and cytosine bases which are then converted to mutations/mismatches using a thermostable group II intron reverse transcriptase (TGIRT) and further analyzed using sequencing. We validated the technique in model systems ranging from Drosophila to human cell lines, thus increasing the technique's broad range of applications. DMS-MaPseq provides high quality data and can be used for both gene-targeted as well as genome-wide analysis.
    Keywords:  DMS; DMS-MaPseq; In vivo; RNA; RNA structure; Reverse transcription; Sequencing; TGIRT
    DOI:  https://doi.org/10.1007/978-1-0716-1851-6_16
  37. Mol Metab. 2021 Oct 22. pii: S2212-8778(21)00206-4. [Epub ahead of print] 101359
    Exercise prevents fatty liver by modifying the compensatory response of mitochondrial metabolism to excess substrate availability.
    Miriam Hoene, Lisa Kappler, Laxmikanth Kollipara, Chunxiu Hu, Martin Irmler, Daniel Bleher, Christoph Hoffmann, Johannes Beckers, Martin Hrabě de Angelis, Hans-Ulrich Häring, Andreas L Birkenfeld, Andreas Peter, Albert Sickmann, Guowang Xu, Rainer Lehmann, Cora Weigert.
       OBJECTIVE: Liver mitochondria adapt to high calorie intake. We investigated how exercise alters the early compensatory response of mitochondria and thus prevents fatty liver disease as a long-term consequence of overnutrition.
    METHODS: We compared the effects of a steatogenic high-energy diet (HED, for 6 weeks) on mitochondrial metabolism of sedentary and treadmill-trained C57BL/6N mice. We applied multi-OMICs analyses to study the alterations in the proteome, transcriptome and lipids in isolated mitochondria of liver and skeletal muscle as well as in whole tissue and examined the functional consequences by high resolution respirometry.
    RESULTS: HED increased the respiratory capacity of isolated liver mitochondria, both in sedentary and in trained mice. However, proteomics analysis of the mitochondria and transcriptomics indicated that training modified the adaptation of the hepatic metabolism to HED on the level of respiratory complex I, glucose oxidation, pyruvate and acetyl-CoA metabolism and lipogenesis. Training also counteracted the HED-induced increase in fasting insulin, glucose tolerance, and liver fat. This was accompanied by lower diacylglycerol species and JNK phosphorylation in the livers of trained HED-fed mice, two mechanisms that can reverse hepatic insulin resistance. In skeletal muscle, the combination of HED and training improved the oxidative capacity to a greater extent than training alone by increasing respiration of isolated mitochondria and total mitochondrial protein content.
    CONCLUSION: We provide a comprehensive insight into the early adaptations of mitochondria in liver and skeletal muscle to HED and endurance training. Our results suggest that exercise disconnects the HED-induced increase in mitochondrial substrate oxidation from pyruvate and acetyl-CoA-driven lipid synthesis. This could contribute to the prevention of deleterious long-term effects of high fat and sugar intake on hepatic mitochondrial function and insulin sensitivity.
    Keywords:  MAFLD; acetyl-CoA; exercise; lipidomics; mitochondrial supercomplexes; proteomics
    DOI:  https://doi.org/10.1016/j.molmet.2021.101359
  38. Free Radic Biol Med. 2021 Oct 26. pii: S0891-5849(21)00781-4. [Epub ahead of print]
    Mitoepigenetics: An intriguing regulatory layer in aging and metabolic-related diseases.
    Ke Cao, Zhihui Feng, Feng Gao, Weijin Zang, Jiankang Liu.
      As a key organelle in eukaryotic cells, mitochondria play a central role in maintaining normal cellular functions. Mitochondrial dysfunction is reported to be closely related with aging and various diseases. Epigenetic modifications in nuclear genome provide a substantial layer for the modulation of nuclear-encoded gene expression. However, whether mitochondria could also be subjected to such similar epigenetic alterations and the involved mechanisms remain largely obscure and controversial. Recently, accumulating evidence has suggested that mitochondrial epigenetics, also known as mitoepigenetics may serve as an intriguing regulatory layer in mitochondrial DNA (mtDNA)-encoded gene expression. Given the potential regulatory role of mitoepigenetics, mitochondrial dysfunction derived from mitoepigenetics-induced abnormal gene expression could also be closely associated with aging and disease development. In this review, we summarized the recent advances in mitoepigenetics, with a special focus on mtDNA methylation in aging and metabolic-related diseases as well as the new methods and technologies for the study of mitoepigenetics. Uncovering the regulatory role of mitoepigenetics will help to understand the underlying mechanisms of mitochondrial dysfunction and provide novel strategies for delaying aging and preventing metabolic-related diseases.
    Keywords:  Mitochondrial DNA (mtDNA) methylation; Mitochondrial epigenetics (mitoepigenetics); Mitochondrial non-coding RNAs (ncRNAs); Post-translational modifications (PTMs); mtDNA-associated proteins
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2021.10.031
  39. Nat Struct Mol Biol. 2021 Oct 28.
    Phase separation drives the self-assembly of mitochondrial nucleoids for transcriptional modulation.
    Qi Long, Yanshuang Zhou, Hao Wu, Shiwei Du, Mingli Hu, Juntao Qi, Wei Li, Jingyi Guo, Yi Wu, Liang Yang, Ge Xiang, Liang Wang, Shouhua Ye, Jiayuan Wen, Heng Mao, Junwei Wang, Hui Zhao, Wai-Yee Chan, Jinsong Liu, Yonglong Chen, Pilong Li, Xingguo Liu.
      Mitochondria, the only semiautonomous organelles in mammalian cells, possess a circular, double-stranded genome termed mitochondrial DNA (mtDNA). While nuclear genomic DNA compaction, chromatin compartmentalization and transcription are known to be regulated by phase separation, how the mitochondrial nucleoid, a highly compacted spherical suborganelle, is assembled and functions is unknown. Here we assembled mitochondrial nucleoids in vitro and show that mitochondrial transcription factor A (TFAM) undergoes phase separation with mtDNA to drive nucleoid self-assembly. Moreover, nucleoid droplet formation promotes recruitment of the transcription machinery via a special, co-phase separation that concentrates transcription initiation, elongation and termination factors, and retains substrates to facilitate mtDNA transcription. We propose a model of mitochondrial nucleoid self-assembly driven by phase separation, and a pattern of co-phase separation involved in mitochondrial transcriptional regulation, which orchestrates the roles of TFAM in both mitochondrial nucleoid organization and transcription.
    DOI:  https://doi.org/10.1038/s41594-021-00671-w
  40. J Paediatr Child Health. 2021 Oct 27.
    Health-related out-of-pocket expenses for children living with rare diseases - tuberous sclerosis and mitochondrial disorders: A prospective pilot study in Australian families.
    Marie Deverell, Amy Phu, Elizabeth J Elliott, Suzy M Teutsch, Guy D Eslick, Clare Stuart, Sean Murray, Rebecca Davis, Troy Dalkeith, John Christodoulou, Yvonne A Zurynski.
       AIM: We aimed to describe health-related out-of-pocket (OOP) expenses incurred by Australian families living with children with chronic and complex diseases.
    METHODS: A prospective pilot study of OOP expenses in families with children with tuberous sclerosis (TS) or mitochondrial disorders (MD) in 2016-2017. An initial survey assessed the family's financial situation, child's health functioning and estimated previous 6 months' and lifetime OOP expenses. Thereafter, families completed a survey each month for 6 months, prospectively tracking OOP expenses.
    RESULTS: Initial surveys were completed by 13 families with 15 children; median age 7 years (range: 1-12); 5 with MD, 10 with TS. All families reported OOP expenses: 38% paid $2000 per annum, more than double the annual per-capita OOP costs reported for Australia by the Organisation for Economic Co-operation and Development. Eight families estimated $5000-$25 000 in OOP expenses over their child's lifetime and 62% of mothers reduced or stopped work due to caring responsibilities. Eleven families paid annual private health insurance premiums of $2000-$5122, but 72% said this was poor value-for-money. Prospective tracking by eight families (9 children) identified the median OOP expenditure was $863 (range $55-$1398) per family for 6 months. OOP spending was associated with visits to allied health professionals, non-prescription medicines, special foods, supplements and disposable items. Eight families paid for 91 prescription medications over 6 months.
    CONCLUSION: All families caring for children with TS or MD reported OOP expenses. A larger study is needed to explore the affordability of health care for children living with a broader range of chronic diseases.
    Keywords:  health expenditure; mitochondrial disease; rare disease; tuberous sclerosis
    DOI:  https://doi.org/10.1111/jpc.15784
  41. Nat Commun. 2021 Oct 27. 12(1): 6207
    A non-canonical, interferon-independent signaling activity of cGAMP triggers DNA damage response signaling.
    Daipayan Banerjee, Kurt Langberg, Salar Abbas, Eric Odermatt, Praveen Yerramothu, Martin Volaric, Matthew A Reidenbach, Kathy J Krentz, C Dustin Rubinstein, David L Brautigan, Tarek Abbas, Bradley D Gelfand, Jayakrishna Ambati, Nagaraj Kerur.
      Cyclic guanosine monophosphate-adenosine monophosphate (cGAMP), produced by cyclic GMP-AMP synthase (cGAS), stimulates the production of type I interferons (IFN). Here we show that cGAMP activates DNA damage response (DDR) signaling independently of its canonical IFN pathways. Loss of cGAS dampens DDR signaling induced by genotoxic insults. Mechanistically, cGAS activates DDR in a STING-TBK1-dependent manner, wherein TBK1 stimulates the autophosphorylation of the DDR kinase ATM, with the consequent activation of the CHK2-p53-p21 signal transduction pathway and the induction of G1 cell cycle arrest. Despite its stimulatory activity on ATM, cGAMP suppresses homology-directed repair (HDR) through the inhibition of polyADP-ribosylation (PARylation), in which cGAMP reduces cellular levels of NAD+; meanwhile, restoring NAD+ levels abrogates cGAMP-mediated suppression of PARylation and HDR. Finally, we show that cGAMP also activates DDR signaling in invertebrate species lacking IFN (Crassostrea virginica and Nematostella vectensis), suggesting that the genome surveillance mechanism of cGAS predates metazoan interferon-based immunity.
    DOI:  https://doi.org/10.1038/s41467-021-26240-9
  42. Nat Genet. 2021 Oct 28.
    An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci.
    Edward Mountjoy, Ellen M Schmidt, Miguel Carmona, Jeremy Schwartzentruber, Gareth Peat, Alfredo Miranda, Luca Fumis, James Hayhurst, Annalisa Buniello, Mohd Anisul Karim, Daniel Wright, Andrew Hercules, Eliseo Papa, Eric B Fauman, Jeffrey C Barrett, John A Todd, David Ochoa, Ian Dunham, Maya Ghoussaini.
      Genome-wide association studies (GWASs) have identified many variants associated with complex traits, but identifying the causal gene(s) is a major challenge. In the present study, we present an open resource that provides systematic fine mapping and gene prioritization across 133,441 published human GWAS loci. We integrate genetics (GWAS Catalog and UK Biobank) with transcriptomic, proteomic and epigenomic data, including systematic disease-disease and disease-molecular trait colocalization results across 92 cell types and tissues. We identify 729 loci fine mapped to a single-coding causal variant and colocalized with a single gene. We trained a machine-learning model using the fine-mapped genetics and functional genomics data and 445 gold-standard curated GWAS loci to distinguish causal genes from neighboring genes, outperforming a naive distance-based model. Our prioritized genes were enriched for known approved drug targets (odds ratio = 8.1, 95% confidence interval = 5.7, 11.5). These results are publicly available through a web portal ( http://genetics.opentargets.org ), enabling users to easily prioritize genes at disease-associated loci and assess their potential as drug targets.
    DOI:  https://doi.org/10.1038/s41588-021-00945-5
  43. Nat Methods. 2021 Oct 28.
    Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram.
    Tommaso Biancalani, Gabriele Scalia, Lorenzo Buffoni, Raghav Avasthi, Ziqing Lu, Aman Sanger, Neriman Tokcan, Charles R Vanderburg, Åsa Segerstolpe, Meng Zhang, Inbal Avraham-Davidi, Sanja Vickovic, Mor Nitzan, Sai Ma, Ayshwarya Subramanian, Michal Lipinski, Jason Buenrostro, Nik Bear Brown, Duccio Fanelli, Xiaowei Zhuang, Evan Z Macosko, Aviv Regev.
      Charting an organs' biological atlas requires us to spatially resolve the entire single-cell transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and single-nucleus RNA-seq (sc/snRNA-seq) can profile cells comprehensively, but lose spatial information. Spatial transcriptomics allows for spatial measurements, but at lower resolution and with limited sensitivity. Targeted in situ technologies solve both issues, but are limited in gene throughput. To overcome these limitations we present Tangram, a method that aligns sc/snRNA-seq data to various forms of spatial data collected from the same region, including MERFISH, STARmap, smFISH, Spatial Transcriptomics (Visium) and histological images. Tangram can map any type of sc/snRNA-seq data, including multimodal data such as those from SHARE-seq, which we used to reveal spatial patterns of chromatin accessibility. We demonstrate Tangram on healthy mouse brain tissue, by reconstructing a genome-wide anatomically integrated spatial map at single-cell resolution of the visual and somatomotor areas.
    DOI:  https://doi.org/10.1038/s41592-021-01264-7
  44. Cell. 2021 Oct 28. pii: S0092-8674(21)01117-X. [Epub ahead of print]184(22): 5506-5526
    Cytoplasmic DNA: sources, sensing, and role in aging and disease.
    Karl N Miller, Stella G Victorelli, Hanna Salmonowicz, Nirmalya Dasgupta, Tianhui Liu, João F Passos, Peter D Adams.
      Endogenous cytoplasmic DNA (cytoDNA) species are emerging as key mediators of inflammation in diverse physiological and pathological contexts. Although the role of endogenous cytoDNA in innate immune activation is well established, the cytoDNA species themselves are often poorly characterized and difficult to distinguish, and their mechanisms of formation, scope of function and contribution to disease are incompletely understood. Here, we summarize current knowledge in this rapidly progressing field with emphases on similarities and differences between distinct cytoDNAs, their underlying molecular mechanisms of formation and function, interactions between cytoDNA pathways, and therapeutic opportunities in the treatment of age-associated diseases.
    Keywords:  aging; cancer; cytoplasmic DNA; cytoplasmic chromatin fragment; micronucleus; mitochondrial DNA; retrotransposon; senescence
    DOI:  https://doi.org/10.1016/j.cell.2021.09.034
  45. J Am Chem Soc. 2021 Oct 28.
    Bioorthogonal Photocatalytic Decaging-Enabled Mitochondrial Proteomics.
    Zongyu Huang, Ziqi Liu, Xiao Xie, Ruxin Zeng, Zujie Chen, Linghao Kong, Xinyuan Fan, Peng R Chen.
      Spatiotemporally resolved dissection of subcellular proteome is crucial to our understanding of cellular functions in health and disease. We herein report a bioorthogonal and photocatalytic decaging-enabled proximity labeling strategy (CAT-Prox) for spatiotemporally resolved mitochondrial proteome profiling in living cells. Our systematic survey of the photocatalysts has led to the identification of Ir(ppy)2bpy as a bioorthogonal and mitochondria-targeting catalyst that allowed photocontrolled, rapid rescue of azidobenzyl-caged quinone methide as a highly reactive Michael acceptor for proximity-based protein labeling in mitochondria of live cells. Upon careful validation through in vitro labeling, mitochondria-targeting specificity, in situ catalytic activity as well as protein tagging, we applied CAT-Prox for mitochondria proteome profiling in living Hela cells as well as hard-to-transfect macrophage RAW264.7 cells with approximately 70% mitochondria specificity observed from up to 300 proteins enriched. Finally, CAT-Prox was further applied to the dynamic dissection of mitochondria proteome of macrophage cells upon lipopolysaccharide stimulation. By integrating photocatalytic decaging chemistry with proximity-based protein labeling, CAT-Prox offers a general, catalytic, and nongenetic alternative to the enzyme-based proximity labeling strategies for diverse live cell settings.
    DOI:  https://doi.org/10.1021/jacs.1c09171
  46. Epilepsy Behav Rep. 2021 ;16 100485
    Expanding the electro-clinical phenotype of CARS2associated neuroregression.
    Dipti Kapoor, Purvi Majethia, Aakanksha Anand, Anju Shukla, Suvasini Sharma.
      Biallelic variants in CARS2 (Cysteinyl-tRNA synthetase 2; MIM*612800), are known to cause combined oxidative phosphorylation deficiency 27 (MIM#616672), characterized by severe myoclonic epilepsy, neuroregression and complex movement disorders. To date, six individuals from five families have been reported with variants in CARS2. Herein, we present an 11-year-old boy who presented with neuroregression, dysfluent speech, aggressive behavior and tremors for 2 years. An electroencephalogram (EEG) revealed a highly abnormal background with generalized spike-and-wave discharges suggestive of Electrical Status Epilepticus during Sleep (ESES). A known homozygous c.655G > A(p.Ala219Thr) pathogenic variant in exon 6 of the CARS2(NM_024537.4) was identified on exome sequencing. Our report expands the electro-clinical spectrum of the phenotype with presence of severe behavioral abnormalities, continuous tremors and ESES pattern on EEG, not previously reported.
    Keywords:  Behavioural changes; Neuroregression; Tremors; Whole exome Sequencing
    DOI:  https://doi.org/10.1016/j.ebr.2021.100485
  47. iScience. 2021 Nov 19. 24(11): 103177
    Rapamycin recruits SIRT2 for FKBP12 deacetylation during mTOR activity modulation in innate immunity.
    Lin Hu, Fuxian Chen, Chao Wu, Jun Wang, Si-Si Chen, Xiang-Rong Li, Jing Wang, Linpeng Wu, Jian-Ping Ding, Jian-Chuan Wang, Chao Huang, Hui Zheng, Yu Rao, Yu Sun, Zhijie Chang, Wei Deng, Cheng Luo, Y Eugene Chin.
      The mammalian target of rapamycin (mTOR) is a serine-threonine kinase involved in cellular innate immunity, metabolism, and senescence. FK506-binding protein 12 (FKBP12) inhibits mTOR kinase activity via direct association. The FKBP12-mTOR association can be strengthened by the immunosuppressant rapamycin, but the underlying mechanism remains elusive. We show here that the FKBP12-mTOR association is tightly regulated by an acetylation-deacetylation cycle. FKBP12 is acetylated on the lysine cluster (K45/K48/K53) by CREB-binding protein (CBP) in mammalian cells in response to nutrient treatment. Acetyl-FKBP12 associates with CBP acetylated Rheb. Rapamycin recruits SIRT2 with a high affinity for FKBP12 association and deacetylation. SIRT2-deacetylated FKBP12 then switches its association from Rheb to mTOR. Nutrient-activated mTOR phosphorylates IRF3S386 for the antiviral response. In contrast, rapamycin strengthening FKBP12-mTOR association blocks mTOR antiviral activity by recruiting SIRT2 to deacetylate FKBP12. Hence, on/off mTOR activity in response to environmental nutrients relies on FKBP12 acetylation and deacetylation status in mammalian cells.
    Keywords:  Biochemistry; Molecular biology; Protein
    DOI:  https://doi.org/10.1016/j.isci.2021.103177
  48. Cold Spring Harb Mol Case Stud. 2021 Oct 25. pii: mcs.a006125. [Epub ahead of print]
    Somatic mosaicism detected by genome-wide sequencing in 500 parent-child trios with suspected genetic disease: Clinical and genetic counseling implications.
    Courtney B Cook, Linlea Armstrong, Cornelius F Boerkoel, Lorne A Clarke, Christele du Souich, Michelle K Demos, William T Gibson, Harinder Gill, Elena Lopez, Millan S Patel, Kathryn Selby, Ziad Abu-Sharar, Causes Study, Alison M Elliott, Jan M Friedman.
      Identifying genetic mosaicism is important in establishing a diagnosis, assessing recurrence risk, and providing accurate genetic counseling. Next-generation sequencing has allowed for the identification of mosaicism at levels below those detectable by conventional Sanger sequencing or chromosomal microarray analysis. The CAUSES Clinic was a pediatric translational trio-based genome-wide (exome or genome) sequencing study of 500 families (531 children) with suspected genetic disease at BC Children's and Women's Hospitals. Here we present 12 cases of apparent mosaicism identified in the CAUSES cohort: 9 cases of parental mosaicism for a disease-causing variant found in a child and 3 cases of mosaicism in the proband for a de novo variant. In 6 of these cases, there was no evidence of mosaicism on Sanger sequencing; the variant was not detected on Sanger sequencing in 3 cases, and it appeared to be heterozygous in 3 others. These cases are examples of 6 clinical manifestations of mosaicism: a proband with classical clinical features of mosaicism (e.g., segmental abnormalities of skin pigmentation or asymmetrical growth of bilateral body parts), a proband with unusually mild manifestations of a disease, a mosaic proband who is clinically indistinguishable from the constitutive phenotype, a mosaic parent with no clinical features of the disease, a mosaic parent with mild manifestations of the disease and a family in which both parents are unaffected and two siblings have the same disease-causing constitutional mutation. Our data demonstrates the importance of considering the possibility of mosaicism whenever exome or genome sequencing is performed and that its detection via genome-wide sequencing can permit more accurate genetic counseling.
    Keywords:  Intellectual disability, mild; Intellectual disability, moderate; Intellectual disability, profound
    DOI:  https://doi.org/10.1101/mcs.a006125
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