bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2023–08–20
fifty papers selected by
Catalina Vasilescu, Helmholz Munich
  1. Deoxyribonucleoside treatment rescues EtBr-induced mtDNA depletion in iPSC-derived neural stem cells with POLG mutations.
  2. E4 ubiquitin ligase promotes mitofusin turnover and mitochondrial stress response.
  3. Muscle mitochondrial transplantation can rescue and maintain cellular homeostasis.
  4. FAM210A mediates an inter-organelle crosstalk essential for protein synthesis and muscle growth in mouse.
  5. Mitochondrial DNA comes with nuclear strings attached.
  6. Application of Flow Cytometric Analysis for Measuring Multiple Mitochondrial Parameters in 3D Brain Organoids.
  7. Optimization of differential filtration-based mitochondrial isolation for mitochondrial transplant to cerebral organoids.
  8. Cardiovascular aging: the mitochondrial influence.
  9. Nuclear genetic control of mtDNA copy number and heteroplasmy in humans.
  10. Feasibility and impact of haplogroup matching for mitochondrial replacement treatment.
  11. Infantile onset encephalomyopathy, retinopathy, optic atrophy, and mitochondrial DNA depletion associated with a novel pathogenic DHX16 variant.
  12. Dynamics of SLC25A51 reveal preference for oxidized NAD+ and substrate led transport.
  13. NME3 binds to phosphatidic acid and mediates PLD6-induced mitochondrial tethering.
  14. Temporal control of contact site formation reveals a relationship between mitochondrial division and Num1-mediated mitochondrial tethering.
  15. Structure-specific roles for PolG2-DNA complexes in maintenance and replication of mitochondrial DNA.
  16. Mitochondrial Ca 2+ uniporter (MCU) variants form plasma-membrane channels.
  17. PPAR-gamma agonist pioglitazone recovers mitochondrial quality control in fibroblasts from PITRM1-deficient patients.
  18. Expanding the phenotypic and biochemical spectrum of NDUFAF3-related mitochondrial disease.
  19. Glutamine metabolism in diseases associated with mitochondrial dysfunction.
  20. Exploring the therapeutic potential of the mitochondrial transfer-associated enzymatic machinery in brain degeneration.
  21. Cytosolic Ca2+ gradients and mitochondrial Ca2+ uptake in resting muscle fibers: A model analysis.
  22. Mitochondria are secreted in extracellular vesicles when lysosomal function is impaired.
  23. Coenzyme Q10 and nicotinamide nucleotide transhydrogenase: Sentinels for mitochondrial hydrogen peroxide signaling.
  24. Milton assembles large mitochondrial clusters, mitoballs, to sustain spermatogenesis.
  25. Autosomal recessive Leber's hereditary optic neuropathy caused by a homozygous variant in DNAJC30 gene.
  26. The mitochondrial succinate dehydrogenase complex controls the STAT3-IL-10 pathway in inflammatory macrophages.
  27. Defining Mitochondrial Cristae Morphology Changes Induced by Aging in Brown Adipose Tissue.
  28. The mitophagy pathway and its implications in human diseases.
  29. Comprehensive interrogation of human skeletal muscle reveals a dissociation between insulin resistance and mitochondrial capacity.
  30. Lactate activates the mitochondrial electron transport chain independent of its metabolism.
  31. Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project.
  32. Mitochondrial transport of catalytic RNAs and targeting of the organellar transcriptome in human cells.
  33. A novel IBA57 variant is associated with mitochondrial iron-sulfur protein deficiency and necrotizing myelopathy in dogs.
  34. Mitochondrial RNA m3C methyltransferase METTL8 relies on an isoform-specific N-terminal extension and modifies multiple heterogenous tRNAs.
  35. A new perspective on mesenchymal stem cell-based therapy for liver diseases: restoring mitochondrial function.
  36. Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis.
  37. Functional mapping of N-terminal residues in the yeast proteome uncovers novel determinants for mitochondrial protein import.
  38. Discovery of Potent Allosteric DRP1 Inhibitors by Disrupting Protein-Protein Interaction with MiD49.
  39. Presenilins and mitochondria-an intriguing link: mini-review.
  40. Frequency and phenotypic spectrum of spinocerebellar ataxia 27B and other genetic ataxias in a Spanish cohort of late-onset cerebellar ataxia.
  41. A genome-wide association study of blood cell morphology identifies cellular proteins implicated in disease aetiology.
  42. Development of a Highly Potent and Selective Degrader of LRRK2.
  43. Massively Parallel Sequencing of the Mitogenome from Human Hair Shafts in Forensic Investigations.
  44. Mitochondria-targeted melatonin photorelease supports the presence of melatonin MT1 receptors in mitochondria inhibiting respiration.
  45. Rare disease variant curation from literature: assessing gaps with creatine transport deficiency in focus.
  46. Dissecting the brain with spatially resolved multi-omics.
  47. A robust method for measuring aminoacylation through tRNA-Seq.
  48. The seductive allure of spatial biology: accelerating new discoveries in the life sciences.
  49. WASF3 disrupts mitochondrial respiration and may mediate exercise intolerance in myalgic encephalomyelitis/chronic fatigue syndrome.
  50. The AAA-ATPase Yta4/ATAD1 interacts with the mitochondrial divisome to inhibit mitochondrial fission.
  1. FASEB J. 2023 09;37(9): e23139
    Deoxyribonucleoside treatment rescues EtBr-induced mtDNA depletion in iPSC-derived neural stem cells with POLG mutations.
    Cecilie Katrin Kristiansen, Jessica Furriol, Anbin Chen, Gareth John Sullivan, Laurence A Bindoff, Kristina Xiao Liang.
      Mutations in POLG, the gene encoding the catalytic subunit of the mitochondrial DNA (mtDNA) polymerase gamma (Pol-γ), lead to diseases driven by defective mtDNA maintenance. Despite being the most prevalent cause of mitochondrial disease, treatments for POLG-related disorders remain elusive. In this study, we used POLG patient-induced pluripotent stem cell (iPSC)-derived neural stem cells (iNSCs), one homozygous for the POLG mutation c.2243G>C and one compound heterozygous with c.2243G>C and c.1399G>A, and treated these iNSCs with ethidium bromide (EtBr) to study the rate of depletion and repopulation of mtDNA. In addition, we investigated the effect of deoxyribonucleoside (dNs) supplementation on mtDNA maintenance during EtBr treatment and post-treatment repopulation in the same cells. EtBr-induced mtDNA depletion occurred at a similar rate in both patient and control iNSCs, however, restoration of mtDNA levels was significantly delayed in iNSCs carrying the compound heterozygous POLG mutations. In contrast, iNSC with the homozygous POLG mutation recovered their mtDNA at a rate similar to controls. When we treated cells with dNs, we found that this reduced EtBr-induced mtDNA depletion and significantly increased repopulation rates in both patient iNSCs. These observations are consistent with the hypothesis that mutations in POLG impair mtDNA repopulation also within intact neural lineage cells and suggest that those with compound heterozygous mutation have a more severe defect of mtDNA synthesis. Our findings further highlight the potential for dNs to improve mtDNA replication in the presence of POLG mutations, suggesting that this may offer a new therapeutic modality for mitochondrial diseases caused by disturbed mtDNA homeostasis.
    Keywords:  deoxynucleosides; iPSCs; mitochondrial DNA replication; neural stem cells; polymerase γ; therapy
    DOI:  https://doi.org/10.1096/fj.202300650RR
  2. Mol Cell. 2023 Aug 17. pii: S1097-2765(23)00563-4. [Epub ahead of print]83(16): 2976-2990.e9
    E4 ubiquitin ligase promotes mitofusin turnover and mitochondrial stress response.
    Vincent Anton, Ira Buntenbroich, Tânia Simões, Mariana Joaquim, Leonie Müller, Reinhard Buettner, Margarete Odenthal, Thorsten Hoppe, Mafalda Escobar-Henriques.
      Ubiquitin-dependent control of mitochondrial dynamics is important for protein quality and neuronal integrity. Mitofusins, mitochondrial fusion factors, can integrate cellular stress through their ubiquitylation, which is carried out by multiple E3 enzymes in response to many different stimuli. However, the molecular mechanisms that enable coordinated responses are largely unknown. Here we show that yeast Ufd2, a conserved ubiquitin chain-elongating E4 enzyme, is required for mitochondrial shape adjustments. Under various stresses, Ufd2 translocates to mitochondria and triggers mitofusin ubiquitylation. This elongates ubiquitin chains on mitofusin and promotes its proteasomal degradation, leading to mitochondrial fragmentation. Ufd2 and its human homologue UBE4B also target mitofusin mutants associated with Charcot-Marie-Tooth disease, a hereditary sensory and motor neuropathy characterized by progressive loss of the peripheral nerves. This underscores the pathophysiological importance of E4-mediated ubiquitylation in neurodegeneration. In summary, we identify E4-dependent mitochondrial stress adaptation by linking various metabolic processes to mitochondrial fusion and fission dynamics.
    Keywords:  CMT2A; Cdc48/p97; E4; Fzo1; MFN2; UBE4B; Ufd2; fusion; mitochondria; mitofusin; stress; ubiquitin
    DOI:  https://doi.org/10.1016/j.molcel.2023.07.021
  3. Am J Physiol Cell Physiol. 2023 Aug 14.
    Muscle mitochondrial transplantation can rescue and maintain cellular homeostasis.
    Debasmita Bhattacharya, Mikhaela B Slavin, David A Hood.
      Mitochondria control cellular functions through their metabolic role. Recent research that has gained considerable attention is their ability to transfer between cells. This has the potential of improving cellular functions in pathological or energy deficit conditions, but little is known about the role of mitochondrial transfer in sustaining cellular homeostasis. Few studies have investigated the potential of skeletal muscle as a source of healthy mitochondria that can be transferred to other cell types. Thus, we isolated intermyofibrillar mitochondria from murine skeletal muscle and incubated them with host cells. We observed dose- and time-dependent increases in mitochondrial incorporation into myoblasts. This resulted in elongated mitochondrial networks and an enhancement of bioenergetic profile of the host cells. Mitochondrial donation also rejuvenated the functional capacities of the myoblasts when respiration efficiency and lysosomal function were inhibited by complex I inhibitor rotenone and bafilomycin A, respectively. Mitochondrial transfer was accomplished via tunneling nanotubes, extracellular vesicles, gap junctions and by macropinocytosis internalization. Murine muscle mitochondria were also effectively transferred to human fibroblast cells having mitochondrial DNA mutations, resulting in augmented mitochondrial dynamics and metabolic functions. This improved cell function by diminishing ROS emission in the diseased cells. Our findings suggest that mitochondria from donor skeletal muscle can be integrated in both healthy and functionally compromised host cells leading to mitochondrial structural refinement and respiratory boost. This mitochondrial trafficking and bioenergetic reprogramming to maintain and revitalise tissue homeostasis could be a useful therapeutic strategy in treating diseases.
    Keywords:  Lysosome; Mitochondrial DNA Defects; Mitochondrial Dynamics; Mitochondrial Transplantation; Oxygen Consumption
    DOI:  https://doi.org/10.1152/ajpcell.00212.2023
  4. bioRxiv. 2023 Aug 05. pii: 2023.08.03.551853. [Epub ahead of print]
    FAM210A mediates an inter-organelle crosstalk essential for protein synthesis and muscle growth in mouse.
    Jingjuan Chen, Feng Yue, Kun Ho Kim, Peipei Zhu, Jiamin Qiu, W Andy Tao, Shihuan Kuang.
      Mitochondria are not only essential for energy production in eukaryocytes but also a key regulator of intracellular signaling. Here, we report an unappreciated role of mitochondria in regulating cytosolic protein translation in skeletal muscle cells (myofibers). We show that the expression of mitochondrial protein FAM210A (Family With Sequence Similarity 210 Member A) is positively associated with muscle mass in mice and humans. Muscle-specific Myl1 Cre -driven Fam210a knockout ( Fam210a MKO ) in mice reduces mitochondrial density and function, leading to progressive muscle atrophy and premature death. Metabolomic and biochemical analyses reveal that Fam210a MKO reverses the oxidative TCA cycle towards the reductive direction, resulting in acetyl-CoA accumulation and hyperacetylation of cytosolic proteins. Specifically, hyperacetylation of several ribosomal proteins leads to disassembly of ribosomes and translational defects. Transplantation of Fam210a MKO mitochondria into wildtype myoblasts is sufficient to elevate protein acetylation in recipient cells. These findings reveal a novel crosstalk between the mitochondrion and ribosome mediated by FAM210A.
    DOI:  https://doi.org/10.1101/2023.08.03.551853
  5. Nature. 2023 Aug 16.
    Mitochondrial DNA comes with nuclear strings attached.
    Sonia Boscenco, Ed Reznik.
      
    Keywords:  Genetics
    DOI:  https://doi.org/10.1038/d41586-023-01783-7
  6. J Vis Exp. 2023 Aug 04.
    Application of Flow Cytometric Analysis for Measuring Multiple Mitochondrial Parameters in 3D Brain Organoids.
    Sharika Marjan, Tsering Yangzom, Cecilie Katrin Kristiansen, Anbin Chen, Laurence A Bindoff, Kristina Xiao Liang.
      Mitochondrial dysfunction is a common primary or secondary contributor to many types of neurodegeneration, and changes in mitochondrial mass, mitochondrial respiratory chain (MRC) complexes, and mitochondrial DNA (mtDNA) copy number often feature in these processes. Human brain organoids derived from human induced pluripotent stem cells (iPSCs) recapitulate the brain's three-dimensional (3D) cytoarchitectural arrangement and offer the possibility to study disease mechanisms and screen new therapeutics in a complex human system. Here, we report a unique flow cytometry-based approach to measure multiple mitochondrial parameters in iPSC-derived cortical organoids. This report details a protocol for generating cortical brain organoids from iPSCs, single-cell dissociation of generated organoids, fixation, staining, and subsequent flow cytometric analysis to assess multiple mitochondrial parameters. Double staining with antibodies against the MRC complex subunit NADH: Ubiquinone Oxidoreductase Subunit B10 (NDUFB10) or mitochondrial transcription factor A (TFAM) together with voltage-dependent anion-selective channel 1 (VDAC 1) permits assessment of the amount of these proteins per mitochondrion. Since the quantity of TFAM corresponds to the amount of mtDNA, it provides an indirect estimation of the number of mtDNA copies per mitochondrial content. This entire procedure can be completed within a span of 2-3 h. Crucially, it allows for the concurrent quantification of multiple mitochondrial parameters, including both total and specific levels relative to the mitochondrial mass.
    DOI:  https://doi.org/10.3791/65621
  7. Stem Cell Res Ther. 2023 08 15. 14(1): 202
    Optimization of differential filtration-based mitochondrial isolation for mitochondrial transplant to cerebral organoids.
    David F Bodenstein, Pavel Powlowski, Kassandra A Zachos, Dana El Soufi El Sabbagh, Hyunjin Jeong, Liliana Attisano, Landon Edgar, Douglas C Wallace, Ana Cristina Andreazza.
       BACKGROUND: Mitochondrial dysfunction is involved in several diseases ranging from genetic mitochondrial disorders to chronic metabolic diseases. An emerging approach to potentially treat mitochondrial dysfunction is the transplantation of autologous live mitochondria to promote cell regeneration. We tested the differential filtration-based mitochondrial isolation protocol established by the McCully laboratory for use in cellular models but found whole cell contaminants in the mitochondrial isolate.
    METHODS: Therefore, we explored alternative types of 5-μm filters (filters A and B) for isolation of mitochondria from multiple cell lines including HEK293 cells and induced pluripotent stem cells (iPSCs). MitoTracker™ staining combined with flow cytometry was used to quantify the concentration of viable mitochondria. A proof-of-principle mitochondrial transplant was performed using mitoDsRed2-tagged mitochondria into a H9-derived cerebral organoid.
    RESULTS: We found that filter B provided the highest quality mitochondria as compared to the 5-μm filter used in the original protocol. Using this method, mitochondria were also successfully isolated from induced pluripotent stem cells. To test for viability, mitoDsRed2-tagged mitochondria were isolated and transplanted into H9-derived cerebral organoids and observed that mitochondria were engulfed as indicated by immunofluorescent co-localization of TOMM20 and MAP2.
    CONCLUSIONS: Thus, use of filter B in a differential filtration approach is ideal for isolating pure and viable mitochondria from cells, allowing us to begin evaluating long-term integration and safety of mitochondrial transplant using cellular sources.
    Keywords:  Cerebral organoids; Induced pluripotent stem cells; Mitochondria; Mitochondrial isolation; Mitochondrial transplant
    DOI:  https://doi.org/10.1186/s13287-023-03436-y
  8. J Cardiovasc Aging. 2023 Jul;pii: 33. [Epub ahead of print]3(3):
    Cardiovascular aging: the mitochondrial influence.
    Shakti Sagar, Asa B Gustafsson.
      Age-associated cardiovascular disease is becoming progressively prevalent due to the increased lifespan of the population. However, the fundamental mechanisms underlying the aging process and the corresponding decline in tissue functions are still poorly understood. The heart has a very high energy demand and the cellular energy needed to sustain contraction is primarily generated by mitochondrial oxidative phosphorylation. Mitochondria are also involved in supporting various metabolic processes, as well as activation of the innate immune response and cell death pathways. Given the central role of mitochondria in energy metabolism and cell survival, the heart is highly susceptible to the effects of mitochondrial dysfunction. These key organelles have been implicated as underlying drivers of cardiac aging. Here, we review the evidence demonstrating the mitochondrial contribution to the cardiac aging process and disease susceptibility. We also discuss the potential mechanisms responsible for the age-related decline in mitochondrial function.
    Keywords:  Aging; heart disease; mitochondria
    DOI:  https://doi.org/10.20517/jca.2023.22
  9. Nature. 2023 Aug 16.
    Nuclear genetic control of mtDNA copy number and heteroplasmy in humans.
    Rahul Gupta, Masahiro Kanai, Timothy J Durham, Kristin Tsuo, Jason G McCoy, Anna V Kotrys, Wei Zhou, Patrick F Chinnery, Konrad J Karczewski, Sarah E Calvo, Benjamin M Neale, Vamsi K Mootha.
      Mitochondrial DNA (mtDNA) is a maternally inherited, high-copy-number genome required for oxidative phosphorylation1. Heteroplasmy refers to the presence of a mixture of mtDNA alleles in an individual and has been associated with disease and ageing. Mechanisms underlying common variation in human heteroplasmy, and the influence of the nuclear genome on this variation, remain insufficiently explored. Here we quantify mtDNA copy number (mtCN) and heteroplasmy using blood-derived whole-genome sequences from 274,832 individuals and perform genome-wide association studies to identify associated nuclear loci. Following blood cell composition correction, we find that mtCN declines linearly with age and is associated with variants at 92 nuclear loci. We observe that nearly everyone harbours heteroplasmic mtDNA variants obeying two principles: (1) heteroplasmic single nucleotide variants tend to arise somatically and accumulate sharply after the age of 70 years, whereas (2) heteroplasmic indels are maternally inherited as mixtures with relative levels associated with 42 nuclear loci involved in mtDNA replication, maintenance and novel pathways. These loci may act by conferring a replicative advantage to certain mtDNA alleles. As an illustrative example, we identify a length variant carried by more than 50% of humans at position chrM:302 within a G-quadruplex previously proposed to mediate mtDNA transcription/replication switching2,3. We find that this variant exerts cis-acting genetic control over mtDNA abundance and is itself associated in-trans with nuclear loci encoding machinery for this regulatory switch. Our study suggests that common variation in the nuclear genome can shape variation in mtCN and heteroplasmy dynamics across the human population.
    DOI:  https://doi.org/10.1038/s41586-023-06426-5
  10. EMBO Rep. 2023 Aug 17. e54540
    Feasibility and impact of haplogroup matching for mitochondrial replacement treatment.
    Yuko Takeda, Louise Hyslop, Meenakshi Choudhary, Fiona Robertson, Angela Pyle, Ian Wilson, Mauro Santibanez-Koref, Douglass Turnbull, Mary Herbert, Gavin Hudson.
      Mitochondrial replacement technology (MRT) aims to reduce the risk of serious disease in children born to women who carry pathogenic mitochondrial DNA (mtDNA) variants. By transplanting nuclear genomes from eggs of an affected woman to enucleated eggs from an unaffected donor, MRT creates new combinations of nuclear and mtDNA. Based on sets of shared sequence variants, mtDNA is classified into ~30 haplogroups. Haplogroup matching between egg donors and women undergoing MRT has been proposed as a means of reducing mtDNA sequence divergence between them. Here we investigate the potential effect of mtDNA haplogroup matching on clinical delivery of MRT and on mtDNA sequence divergence between donor/recipient pairs. Our findings indicate that haplogroup matching would limit the availability of egg donors such that women belonging to rare haplogroups may have to wait > 4 years for treatment. Moreover, we find that intra-haplogroup sequence variation is frequently within the range observed between randomly matched mtDNA pairs. We conclude that haplogroup matching would restrict the availability of MRT, without necessarily reducing mtDNA sequence divergence between donor/recipient pairs.
    Keywords:  haplogroup matching; mitochondrial disease; mitochondrial replacement therapy
    DOI:  https://doi.org/10.15252/embr.202154540
  11. Clin Genet. 2023 Aug 13.
    Infantile onset encephalomyopathy, retinopathy, optic atrophy, and mitochondrial DNA depletion associated with a novel pathogenic DHX16 variant.
    Milla-Riikka Hautakangas, Paula Widgren, Paavo Korpelainen, Salla M Kangas, Tuomas Komulainen, Päivi Vieira, Elisa Rahikkala, Katri Pylkäs, Hannu Tuominen, Hannaleena Kokkonen, Ilkka Miinalainen, Javad Nadaf, Jacek Majewski, Reetta Hinttala, Johanna Uusimaa.
      We studied a patient with mitochondrial DNA depletion in skeletal muscle and a multiorgan phenotype, including fatal encephalomyopathy, retinopathy, optic atrophy, and sensorineural hearing loss. Instead of pathogenic variants in the mitochondrial maintenance genes, we identified previously unpublished variant in DHX16 gene, a de novo heterozygous c.1360C>T (p. Arg454Trp). Variants in DHX16 encoding for DEAH-box RNA helicase have previously been reported only in five patients with a phenotype called as neuromuscular oculoauditory syndrome including developmental delay, neuromuscular symptoms, and ocular or auditory defects with or without seizures. We performed functional studies on patient-derived fibroblasts and skeletal muscle revealing, that the DHX16 expression was decreased. Clinical features together with functional data suggest, that our patient's disease is associated with a novel pathogenic DHX16 variant, and mtDNA depletion could be a secondary manifestation of the disease.
    Keywords:  DHX16; encephalomyopathy; mitochondrial DNA depletion; optic atrophy; retinopathy
    DOI:  https://doi.org/10.1111/cge.14416
  12. EMBO Rep. 2023 Aug 14. e56596
    Dynamics of SLC25A51 reveal preference for oxidized NAD+ and substrate led transport.
    Shivansh Goyal, Akhilesh Paspureddi, Mu-Jie Lu, Hsin-Ru Chan, Scott N Lyons, Crystal N Wilson, Marc Niere, Mathias Ziegler, Xiaolu A Cambronne.
      SLC25A51 is a member of the mitochondrial carrier family (MCF) but lacks key residues that contribute to the mechanism of other nucleotide MCF transporters. Thus, how SLC25A51 transports NAD+ across the inner mitochondrial membrane remains unclear. To elucidate its mechanism, we use Molecular Dynamics simulations to reconstitute SLC25A51 homology models into lipid bilayers and to generate hypotheses to test. We observe spontaneous binding of cardiolipin phospholipids to three distinct sites on the exterior of SLC25A51's central pore and find that mutation of these sites impairs cardiolipin binding and transporter activity. We also observe that stable formation of the required matrix gate is controlled by a single salt bridge. We identify binding sites in SLC25A51 for NAD+ and show that its selectivity for NAD+ is guided by an electrostatic interaction between the charged nicotinamide ring in the ligand and a negatively charged patch in the pore. In turn, interaction of NAD+ with interior residue E132 guides the ligand to dynamically engage and weaken the salt bridge gate, representing a ligand-induced initiation of transport.
    Keywords:  MCART1; SLC25A51; mitochondrial carrier family; mitochondrial transport; nicotinamide adenine dinucleotide (NAD)
    DOI:  https://doi.org/10.15252/embr.202256596
  13. J Cell Biol. 2023 10 02. pii: e202301091. [Epub ahead of print]222(10):
    NME3 binds to phosphatidic acid and mediates PLD6-induced mitochondrial tethering.
    You-An Su, Hsin-Yi Chiu, Yu-Chen Chang, Chieh-Ju Sung, Chih-Wei Chen, Reika Tei, Xuang-Rong Huang, Shao-Chun Hsu, Shan-Shan Lin, Hsien-Chu Wang, Yu-Chun Lin, Jui-Cheng Hsu, Hermann Bauer, Yuxi Feng, Jeremy M Baskin, Zee-Fen Chang, Ya-Wen Liu.
      Mitochondria are dynamic organelles regulated by fission and fusion processes. The fusion of membranes requires elaborative coordination of proteins and lipids and is particularly crucial for the function and quality control of mitochondria. Phosphatidic acid (PA) on the mitochondrial outer membrane generated by PLD6 facilitates the fusion of mitochondria. However, how PA promotes mitochondrial fusion remains unclear. Here, we show that a mitochondrial outer membrane protein, NME3, is required for PLD6-induced mitochondrial tethering or clustering. NME3 is enriched at the contact interface of two closely positioned mitochondria depending on PLD6, and NME3 binds directly to PA-exposed lipid packing defects via its N-terminal amphipathic helix. The PA binding function and hexamerization confer NME3 mitochondrial tethering activity. Importantly, nutrient starvation enhances the enrichment efficiency of NME3 at the mitochondrial contact interface, and the tethering ability of NME3 contributes to fusion efficiency. Together, our findings demonstrate NME3 as a tethering protein promoting selective fusion between PLD6-remodeled mitochondria for quality control.
    DOI:  https://doi.org/10.1083/jcb.202301091
  14. Mol Biol Cell. 2023 Aug 16. mbcE23050168
    Temporal control of contact site formation reveals a relationship between mitochondrial division and Num1-mediated mitochondrial tethering.
    Clare S Harper, Jason C Casler, Laura L Lackner.
      Mitochondrial division is critical for maintenance of mitochondrial morphology and cellular homeostasis. Previous work has suggested that the mitochondria-ER-cortex anchor (MECA), a tripartite membrane contact site between mitochondria, the ER, and the plasma membrane, is involved in mitochondrial division. However, its role is poorly understood. We developed a system to control MECA formation and depletion, which allowed us to investigate the relationship between MECA-mediated contact sites and mitochondrial division. Num1 is the protein that mediates mitochondria-ER-plasma membrane tethering at MECA sites. Using both rapamycin-inducible dimerization and auxin-inducible degradation components coupled with Num1, we developed systems to temporally control the formation and depletion of the native contact site. Additionally, we designed a regulatable Num1-independant mitochondria-PM tether. We found that mitochondria-PM tethering alone is not sufficient to rescue mitochondrial division and that a specific feature of Num1-mediated tethering is required. This study demonstrates the utility of systems that regulate contact site formation and depletion in studying the biological functions of membrane contact sites. [Media: see text] [Media: see text].
    DOI:  https://doi.org/10.1091/mbc.E23-05-0168
  15. Nucleic Acids Res. 2023 Aug 18. pii: gkad679. [Epub ahead of print]
    Structure-specific roles for PolG2-DNA complexes in maintenance and replication of mitochondrial DNA.
    Jessica L Wojtaszek, Kirsten E Hoff, Matthew J Longley, Parminder Kaur, Sara N Andres, Hong Wang, R Scott Williams, William C Copeland.
      The homodimeric PolG2 accessory subunit of the mitochondrial DNA polymerase gamma (Pol γ) enhances DNA binding and processive DNA synthesis by the PolG catalytic subunit. PolG2 also directly binds DNA, although the underlying molecular basis and functional significance are unknown. Here, data from Atomic Force Microscopy (AFM) and X-ray structures of PolG2-DNA complexes define dimeric and hexameric PolG2 DNA binding modes. Targeted disruption of PolG2 DNA-binding interfaces impairs processive DNA synthesis without diminishing Pol γ subunit affinities. In addition, a structure-specific DNA-binding role for PolG2 oligomers is supported by X-ray structures and AFM showing that oligomeric PolG2 localizes to DNA crossings and targets forked DNA structures resembling the mitochondrial D-loop. Overall, data indicate that PolG2 DNA binding has both PolG-dependent and -independent functions in mitochondrial DNA replication and maintenance, which provide new insight into molecular defects associated with PolG2 disruption in mitochondrial disease.
    DOI:  https://doi.org/10.1093/nar/gkad679
  16. bioRxiv. 2023 Aug 02. pii: 2023.07.31.551242. [Epub ahead of print]
    Mitochondrial Ca 2+ uniporter (MCU) variants form plasma-membrane channels.
    Iuliia Polina, Jyotsna Mishra, Michael W Cypress, Maria Landherr, Nedyalka Valkov, Isabel Chaput, Bridget Nieto, Ulrike Mende, Peng Zhang, Bong Sook Jhun, Jin O-Uchi.
      MCU is widely recognized as a responsible gene for encoding a pore-forming subunit of highly mitochondrial-specific and Ca 2+ -selective channel, mitochondrial Ca 2+ uniporter complex (mtCUC). Here, we report a novel short variant derived from the MCU gene (termed MCU-S) which lacks mitochondria-targeted sequence and forms a Ca 2+ - permeable channel outside of mitochondria. MCU-S was ubiquitously expressed in all cell-types/tissues, with particularly high expression in human platelets. MCU-S formed Ca 2+ channels at the plasma membrane, which exhibited similar channel properties to those observed in mtCUC. MCU-S channels at the plasma membrane served as an additional Ca 2+ influx pathway for platelet activation. Our finding is completely distinct from the originally reported MCU gene function and provides novel insights into the molecular basis of MCU variant-dependent cellular Ca 2+ handling.
    DOI:  https://doi.org/10.1101/2023.07.31.551242
  17. Front Pharmacol. 2023 ;14 1220620
    PPAR-gamma agonist pioglitazone recovers mitochondrial quality control in fibroblasts from PITRM1-deficient patients.
    Alessia Di Donfrancesco, Christian Berlingieri, Marta Giacomello, Chiara Frascarelli, Ana Paula Magalhaes Rebelo, Laurence A Bindoff, Segel Reeval, Paul Renbaum, Filippo M Santorelli, Giulia Massaro, Carlo Viscomi, Massimo Zeviani, Daniele Ghezzi, Emanuela Bottani, Dario Brunetti.
      Introduction: Biallelic variants in PITRM1 are associated with a slowly progressive syndrome characterized by intellectual disability, spinocerebellar ataxia, cognitive decline and psychosis. The pitrilysin metallopeptidase 1 (PITRM1) is a mitochondrial matrix enzyme, which digests diverse oligopeptides, including the mitochondrial targeting sequences (MTS) that are cleaved from proteins imported across the inner mitochondrial membrane by the mitochondrial processing peptidase (MPP). Mitochondrial peptidases also play a role in the maturation of Frataxin, the protein affected in Friedreich's ataxia. Recent studies in yeast indicated that the mitochondrial matrix protease Ste23, which is a homologue of the human insulin-degrading enzyme (IDE), cooperates with Cym1 (homologue of PITRM1) to ensure the proper functioning of the preprotein processing machinery. In humans, IDE could be upregulated by Peroxisome Proliferator-Activated Receptor Gamma (PPARG) agonists. Methods: We investigated preprotein processing, mitochondrial membrane potential and MTS degradation in control and patients' fibroblasts, and we evaluated the pharmacological effect of the PPARG agonist Pioglitazone on mitochondrial proteostasis. Results: We discovered that PITRM1 dysfunction results in the accumulation of MTS, leading to the disruption and dissipation of the mitochondrial membrane potential. This triggers a feedback inhibition of MPP activity, consequently impairing the processing and maturation of Frataxin. Furthermore, we found that the pharmacological stimulation of PPARG by Pioglitazone upregulates IDE and also PITRM1 protein levels restoring the presequence processing machinery and improving Frataxin maturation and mitochondrial function. Discussion: Our findings provide mechanistic insights and suggest a potential pharmacological strategy for this rare neurodegenerative mitochondrial disease.
    Keywords:  cerebellar ataxia; mitochondrial disease; neurodegenaration; pioglitazone; proteostasis
    DOI:  https://doi.org/10.3389/fphar.2023.1220620
  18. Mol Genet Metab. 2023 Aug 04. pii: S1096-7192(23)00305-0. [Epub ahead of print]140(3): 107675
    Expanding the phenotypic and biochemical spectrum of NDUFAF3-related mitochondrial disease.
    Amelie T van der Ven, Alfredo Cabrera-Orefice, Isabell Wente, René G Feichtinger, Konstantinos Tsiakas, Deike Weiss, Tatjana Bierhals, Leila Scholle, Holger Prokisch, Robert Kopajtich, René Santer, Johannes A Mayr, Maja Hempel, Ilka Wittig.
      Recessive variants in NDUFAF3 are a known cause of complex I (CI)-related mitochondrial disorders (MDs). The seven patients reported to date exhibited severe neurologic symptoms and lactic acidosis, followed by a fatal course and death during infancy in most cases. We present a 10-year-old patient with a neurodevelopmental disorder, progressive exercise intolerance, dystonia, basal ganglia abnormalities, and elevated lactate concentration in blood. Trio-exome sequencing revealed compound-heterozygosity for a pathogenic splice-site and a likely pathogenic missense variant in NDUFAF3. Spectrophotometric analysis of fibroblast-derived mitochondria demonstrated a relatively mild reduction of CI activity. Complexome analyses revealed severely reduced NDUFAF3 as well as CI in patient fibroblasts. Accumulation of early sub-assemblies of the membrane arm of CI associated with mitochondrial complex I intermediate assembly (MCIA) complex was observed. The most striking additional findings were both the unusual occurrence of free monomeric CI holding MCIA and other assembly factors. Here we discuss our patient in context of genotype, phenotype and metabolite data from previously reported NDUFAF3 cases. With the atypical presentation of our patient, we provide further insight into the phenotypic spectrum of NDUFAF3-related MDs. Complexome analysis in our patient confirms the previously defined role of NDUFAF3 within CI biogenesis, yet adds new aspects regarding the correct timing of both the association of soluble and membrane arm modules and CI-maturation as well as respiratory supercomplex formation.
    Keywords:  Complexome profiling; Exome sequencing; Intellectual and developmental disability; Metabolic disorder; Mitochondria
    DOI:  https://doi.org/10.1016/j.ymgme.2023.107675
  19. Mol Cell Neurosci. 2023 Aug 15. pii: S1044-7431(23)00081-7. [Epub ahead of print]126 103887
    Glutamine metabolism in diseases associated with mitochondrial dysfunction.
    Rebecca Bornstein, Michael T Mulholland, Margaret Sedensky, Phil Morgan, Simon C Johnson.
      Mitochondrial dysfunction can arise from genetic defects or environmental exposures and impact a wide range of biological processes. Among these are metabolic pathways involved in glutamine catabolism, anabolism, and glutamine-glutamate cycling. In recent years, altered glutamine metabolism has been found to play important roles in the pathologic consequences of mitochondrial dysfunction. Glutamine is a pleiotropic molecule, not only providing an alternate carbon source to glucose in certain conditions, but also playing unique roles in cellular communication in neurons and astrocytes. Glutamine consumption and catabolic flux can be significantly altered in settings of genetic mitochondrial defects or exposure to mitochondrial toxins, and alterations to glutamine metabolism appears to play a particularly significant role in neurodegenerative diseases. These include primary mitochondrial diseases like Leigh syndrome (subacute necrotizing encephalopathy) and MELAS (mitochondrial myopathy with encephalopathy, lactic acidosis, and stroke-like episodes), as well as complex age-related neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. Pharmacologic interventions targeting glutamine metabolizing and catabolizing pathways appear to provide some benefits in cell and animal models of these diseases, indicating glutamine metabolism may be a clinically relevant target. In this review, we discuss glutamine metabolism, mitochondrial disease, the impact of mitochondrial dysfunction on glutamine metabolic processes, glutamine in neurodegeneration, and candidate targets for therapeutic intervention.
    Keywords:  Glutamine toxicity; Mitochondrial disease; Neurodegenerative disease
    DOI:  https://doi.org/10.1016/j.mcn.2023.103887
  20. Front Physiol. 2023 ;14 1217815
    Exploring the therapeutic potential of the mitochondrial transfer-associated enzymatic machinery in brain degeneration.
    Noymar Luque-Campos, Ricardo Riquelme, Luis Molina, Gisela Canedo-Marroquín, Ana María Vega-Letter, Patricia Luz-Crawford, Felipe A Bustamante-Barrientos.
      Mitochondrial dysfunction is a central event in the pathogenesis of several degenerative brain disorders. It entails fission and fusion dynamics disruption, progressive decline in mitochondrial clearance, and uncontrolled oxidative stress. Many therapeutic strategies have been formulated to reverse these alterations, including replacing damaged mitochondria with healthy ones. Spontaneous mitochondrial transfer is a naturally occurring process with different biological functions. It comprises mitochondrial donation from one cell to another, carried out through different pathways, such as the formation and stabilization of tunneling nanotubules and Gap junctions and the release of extracellular vesicles with mitochondrial cargoes. Even though many aspects of regulating these mechanisms still need to be discovered, some key enzymatic regulators have been identified. This review summarizes the current knowledge on mitochondrial dysfunction in different neurodegenerative disorders. Besides, we analyzed the usage of mitochondrial transfer as an endogenous revitalization tool, emphasizing the enzyme regulators that govern this mechanism. Going deeper into this matter would be helpful to take advantage of the therapeutic potential of mitochondrial transfer.
    Keywords:  cellular therapy; degenerative brain disorders; enzymes; fission and fusion; mitochondrial dysfunction; mitochondrial transfer; mitophagy; oxidative damage
    DOI:  https://doi.org/10.3389/fphys.2023.1217815
  21. Biophys Rep (N Y). 2023 Sep 13. 3(3): 100117
    Cytosolic Ca2+ gradients and mitochondrial Ca2+ uptake in resting muscle fibers: A model analysis.
    Lorenzo Marcucci, Antonio Michelucci, Carlo Reggiani.
      Calcium ions (Ca2+) enter mitochondria via the mitochondrial Ca2+ uniporter, driven by electrical and concentration gradients. In this regard, transgenic mouse models, such as calsequestrin knockout (CSQ-KO) mice, with higher mitochondrial Ca2+ concentrations ([Ca2+]mito), should display higher cytosolic Ca2+ concentrations ([Ca2+]cyto). However, repeated measurements of [Ca2+]cyto in quiescent CSQ-KO fibers never showed a difference between WT and CSQ-KO. Starting from the consideration that fluorescent Ca2+ probes (Fura-2 and Indo-1) measure averaged global cytosolic concentrations, in this report we explored the role of local Ca2+ concentrations (i.e., Ca2+ microdomains) in regulating mitochondrial Ca2+ in resting cells, using a multicompartmental diffusional Ca2+ model. Progressively including the inward and outward fluxes of sarcoplasmic reticulum (SR), extracellular space, and mitochondria, we explored their contribution to the local Ca2+ distribution within the cell. The model predicts Ca2+ concentration gradients with hot spots or microdomains even at rest, minor but similar to those of evoked Ca2+ release. Due to their specific localization close to Ca2+ release units (CRU), mitochondria could take up Ca2+ directly from high-concentration microdomains, thus sensibly raising [Ca2+]mito, despite minor, possibly undetectable, modifications of the average [Ca2+]cyto.
    DOI:  https://doi.org/10.1016/j.bpr.2023.100117
  22. Nat Commun. 2023 Aug 18. 14(1): 5031
    Mitochondria are secreted in extracellular vesicles when lysosomal function is impaired.
    Wenjing Liang, Shakti Sagar, Rishith Ravindran, Rita H Najor, Justin M Quiles, Liguo Chi, Rachel Y Diao, Benjamin P Woodall, Leonardo J Leon, Erika Zumaya, Jason Duran, David M Cauvi, Antonio De Maio, Eric D Adler, Åsa B Gustafsson.
      Mitochondrial quality control is critical for cardiac homeostasis as these organelles are responsible for generating most of the energy needed to sustain contraction. Dysfunctional mitochondria are normally degraded via intracellular degradation pathways that converge on the lysosome. Here, we identified an alternative mechanism to eliminate mitochondria when lysosomal function is compromised. We show that lysosomal inhibition leads to increased secretion of mitochondria in large extracellular vesicles (EVs). The EVs are produced in multivesicular bodies, and their release is independent of autophagy. Deletion of the small GTPase Rab7 in cells or adult mouse heart leads to increased secretion of EVs containing ubiquitinated cargos, including intact mitochondria. The secreted EVs are captured by macrophages without activating inflammation. Hearts from aged mice or Danon disease patients have increased levels of secreted EVs containing mitochondria indicating activation of vesicular release during cardiac pathophysiology. Overall, these findings establish that mitochondria are eliminated in large EVs through the endosomal pathway when lysosomal degradation is inhibited.
    DOI:  https://doi.org/10.1038/s41467-023-40680-5
  23. Free Radic Biol Med. 2023 Aug 12. pii: S0891-5849(23)00587-7. [Epub ahead of print]208 260-271
    Coenzyme Q10 and nicotinamide nucleotide transhydrogenase: Sentinels for mitochondrial hydrogen peroxide signaling.
    Cathryn Grayson, Ryan J Mailloux.
      Mitochondria use hydrogen peroxide (H2O2) as a mitokine for cell communication. H2O2 output for signaling depends on its rate of production and degradation, both of which are strongly affected by the redox state of the coenzyme Q10 (CoQ) pool and NADPH availability. Here, we propose the CoQ pool and nicotinamide nucleotide transhydrogenase (NNT) have evolved to be central modalities for mitochondrial H2O2 signaling. Both factors play opposing yet equally important roles in dictating H2O2 availability because they are connected to one another by two central parameters in bioenergetics: electron supply and Δp. The CoQ pool is the central point of convergence for electrons from various dehydrogenases and the electron transport chain (ETC). The increase in Δp creates a significant amount of protonic backpressure on mitochondria to promote H2O2 genesis through CoQ pool reduction. These same factors also drive the activity of NNT, which uses electrons and the Δp to eliminate H2O2. In this way, electron supply and the magnitude of the Δp manifests as a redox connection between the two sentinels, CoQ and NNT, which serve as opposing yet equally important forces required for budgeting H2O2. Taken together, CoQ and NNT are sentinels linked through mitochondrial bioenergetics to manage H2O2 availability for interorganelle and intercellular redox signaling.
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2023.08.015
  24. Proc Natl Acad Sci U S A. 2023 08 22. 120(34): e2306073120
    Milton assembles large mitochondrial clusters, mitoballs, to sustain spermatogenesis.
    Andy Y Z Li, Ying Di, Sumaera Rathore, Ason C-Y Chiang, Jan Jezek, Hansong Ma.
      Mitochondria are dynamic organelles that undergo frequent remodeling to accommodate developmental needs. Here, we describe a striking organization of mitochondria into a large ball-like structure adjacent to the nucleus in premeiotic Drosophila melanogaster spermatocytes, which we term "mitoball". Mitoballs are transient structures that colocalize with the endoplasmic reticulum, Golgi bodies, and the fusome. We observed similar premeiotic mitochondrial clusters in a wide range of insect species, including mosquitos and cockroaches. Through a genetic screen, we identified that Milton, an adaptor protein that links mitochondria to microtubule-based motors, mediates mitoball formation. Flies lacking a 54 amino acid region in the C terminus of Milton completely lacked mitoballs, had swollen mitochondria in their spermatocytes, and showed reduced male fertility. We suggest that the premeiotic mitochondrial clustering is a conserved feature of insect spermatogenesis that supports sperm development.
    Keywords:  Milton-mediated mitochondrial trafficking; insect spermatogenesis; male fertility; mitoballs; mitochondrial clustering
    DOI:  https://doi.org/10.1073/pnas.2306073120
  25. Eur J Med Genet. 2023 Aug 12. pii: S1769-7212(23)00127-1. [Epub ahead of print]66(9): 104821
    Autosomal recessive Leber's hereditary optic neuropathy caused by a homozygous variant in DNAJC30 gene.
    L Mauring, S Puusepp, M Parik, E Roomets, R Teek, T Reimand, S Pajusalu, K Kaljurand, K Õunap.
      Recently, Stenton et al. (2021) described a new, autosomal recessive inheritance pattern of Leber's hereditary optic neuropathy (LHON) caused by missense variants in the DNAJC30 gene. The DNAJC30 c.152A > G, p.(Tyr51Cys) variant was by far the most common variant reported in patients originating from Eastern Europe, therefore, it is believed to be a founder variant in these populations. We report the first two cases of DNAJC30-linked autosomal recessive LHON in a young male and a female originating from Estonia. The patients presented severe loss of central vision and clinical features indistinguishable from mitochondrial LHON. The whole exome sequencing carried out in the male patient and the next-generation sequencing panel in the young female patient identified the same homozygous missense variant in the DNAJC30 gene. Our cases further reinforce the pathogenicity of c.152A > G, p.(Tyr51Cys) DNAJC30 variant causing autosomal recessive LHON. According to the gnomAD database, the allele frequency of this variant in the Estonian population is 0.8%, translating into a prevalence of carriers of 1:60. It is the highest among different gnomAD populations. Applying the Hardy-Weinberg equation, an estimated 92 persons in the Estonian population carry the homozygous variant c.152A > G, p.(Tyr51Cys) in DNAJC30. In patients with LHON, we advise sequencing both the DNAJC30 gene and mitochondrial DNA simultaneously.
    Keywords:  Autosomal recessive LHON; DNAJC30; DNAJC30 c.152A>G; Homozygote; Leber's hereditary optic neuropathy; arLHON; p.(Tyr51Cys) variant
    DOI:  https://doi.org/10.1016/j.ejmg.2023.104821
  26. iScience. 2023 Aug 18. 26(8): 107473
    The mitochondrial succinate dehydrogenase complex controls the STAT3-IL-10 pathway in inflammatory macrophages.
    Dino Gobelli, Pablo Serrano-Lorenzo, María J Esteban-Amo, Julia Serna, M Teresa Pérez-García, Antonio Orduña, Alexis A Jourdain, Miguel Á Martín-Casanueva, Miguel Á de la Fuente, María Simarro.
      The functions of macrophages are tightly regulated by their metabolic state. However, the role of the mitochondrial electron transport chain (ETC) in macrophage functions remains understudied. Here, we provide evidence that the succinate dehydrogenase (SDH)/complex II (CII) is required for respiration and plays a role in controlling effector responses in macrophages. We find that the absence of the catalytic subunits Sdha and Sdhb in macrophages impairs their ability to effectively stabilize HIF-1α and produce the pro-inflammatory cytokine IL-1β in response to LPS stimulation. We also arrive at the novel result that both subunits are essential for the LPS-driven production of IL-10, a potent negative feedback regulator of the macrophage inflammatory response. This phenomenon is explained by the fact that the absence of Sdha and Sdhb leads to the inhibition of Stat3 tyrosine phosphorylation, caused partially by the excessive accumulation of mitochondrial reactive oxygen species (mitoROS) in the knockout cells.
    Keywords:  Biological sciences; Cell biology; Immunology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2023.107473
  27. bioRxiv. 2023 Aug 02. pii: 2023.05.12.540609. [Epub ahead of print]
    Defining Mitochondrial Cristae Morphology Changes Induced by Aging in Brown Adipose Tissue.
    Amber Crabtree, Kit Neikirk, Andrea G Marshall, Larry Vang, Aaron J Whiteside, Qiana Williams, Christopher T Altamura, Trinity Celeste Owens, Dominique Stephens, Bryanna Shao, Alice Koh, Mason Killion, Edgar Garza Lopez, Jacob Lam, Ben Rodriguez, Margaret Mungai, Jade Stanley, E Danielle Dean, Ho-Jin Koh, Jennifer A Gaddy, Estevão Scudese, Mariya Sweetwyne, Jamaine Davis, Elma Zaganjor, Sandra A Murray, Prasanna Katti, Steven M Damo, Zer Vue, Antentor Hinton.
      Mitochondria are required for energy production and even give brown adipose tissue (BAT) its characteristic color due to their high iron content and abundance. The physiological function and bioenergetic capacity of mitochondria are connected to the structure, folding, and organization of its inner-membrane cristae. During the aging process, mitochondrial dysfunction is observed, and the regulatory balance of mitochondrial dynamics is often disrupted, leading to increased mitochondrial fragmentation in aging cells. Therefore, we hypothesized that significant morphological changes in BAT mitochondria and cristae would be present with aging. We developed a quantitative three-dimensional (3D) electron microscopy approach to map cristae network organization in mouse BAT to test this hypothesis. Using this methodology, we investigated the 3D morphology of mitochondrial cristae in adult (3-month) and aged (2-year) murine BAT tissue via serial block face-scanning electron microscopy (SBF-SEM) and 3D reconstruction software for manual segmentation, analysis, and quantification. Upon investigation, we found increases in mitochondrial volume, surface area, and complexity and decreased sphericity in aged BAT, alongside significant decreases in cristae volume, area, perimeter, and score. Overall, these data define the nature of the mitochondrial structure in murine BAT across aging.
    Abstract Figure:
    DOI:  https://doi.org/10.1101/2023.05.12.540609
  28. Signal Transduct Target Ther. 2023 08 16. 8(1): 304
    The mitophagy pathway and its implications in human diseases.
    Shouliang Wang, Haijiao Long, Lianjie Hou, Baorong Feng, Zihong Ma, Ying Wu, Yu Zeng, Jiahao Cai, Da-Wei Zhang, Guojun Zhao.
      Mitochondria are dynamic organelles with multiple functions. They participate in necrotic cell death and programmed apoptotic, and are crucial for cell metabolism and survival. Mitophagy serves as a cytoprotective mechanism to remove superfluous or dysfunctional mitochondria and maintain mitochondrial fine-tuning numbers to balance intracellular homeostasis. Growing evidences show that mitophagy, as an acute tissue stress response, plays an important role in maintaining the health of the mitochondrial network. Since the timely removal of abnormal mitochondria is essential for cell survival, cells have evolved a variety of mitophagy pathways to ensure that mitophagy can be activated in time under various environments. A better understanding of the mechanism of mitophagy in various diseases is crucial for the treatment of diseases and therapeutic target design. In this review, we summarize the molecular mechanisms of mitophagy-mediated mitochondrial elimination, how mitophagy maintains mitochondrial homeostasis at the system levels and organ, and what alterations in mitophagy are related to the development of diseases, including neurological, cardiovascular, pulmonary, hepatic, renal disease, etc., in recent advances. Finally, we summarize the potential clinical applications and outline the conditions for mitophagy regulators to enter clinical trials. Research advances in signaling transduction of mitophagy will have an important role in developing new therapeutic strategies for precision medicine.
    DOI:  https://doi.org/10.1038/s41392-023-01503-7
  29. Am J Physiol Endocrinol Metab. 2023 Aug 16.
    Comprehensive interrogation of human skeletal muscle reveals a dissociation between insulin resistance and mitochondrial capacity.
    Katie L Whytock, Maria F Pino, Yifei Sun, Gongxin Yu, Flavia G De Carvalho, Reichelle X Yeo, Rick B Vega, Parmar Gaganvir, Adeline Divoux, Nidhi Kapoor, Fanchao Yi, Heather H Cornnell, David A Patten, Mary-Ellen Harper, Stephen J Gardell, Steven R Smith, Martin J Walsh, Lauren M Sparks.
      Insulin resistance and blunted mitochondrial capacity in skeletal muscle are often synonymous; however, this association remains controversial. The aim of this study was to perform an in-depth multi-factorial comparison of skeletal muscle mitochondrial capacity between individuals who were lean and active (Active- n = 9), individuals with obesity (Obese- n = 9) and individuals with Obesity, insulin resistance and type 2 diabetes (T2D- n = 22). Mitochondrial capacity was assessed by ex vivo mitochondrial respiration with fatty-acid and glycolytic supported protocols adjusted for mitochondrial content (mtDNA and citrate synthase activity). Supercomplex assembly was measured by BN-PAGE and immunoblot. TCA cycle intermediates were assessed with targeted metabolomics. Exploratory transcriptomics and DNA methylation analyses were performed to uncover molecular differences affecting mitochondrial function among the three groups. We reveal no discernable differences in skeletal muscle mitochondrial content, mitochondrial capacity, supercomplex assembly, TCA cycle intermediates and mitochondrial molecular profiles between obese individuals with and without T2D that had comparable levels of confounding factors (BMI, age, aerobic capacity). We highlight that lean, active individuals have greater; mitochondrial content, mitochondrial capacity, supercomplex assembly and TCA cycle intermediates. These phenotypical changes are reflected at the level of DNA methylation and gene transcription. The collective observation of comparable muscle mitochondrial capacity in individuals with obesity and T2D (vs. individuals without T2D) underscores a dissociation from skeletal muscle insulin resistance.
    Keywords:  Insulin Resistance; Mitochondrial Capacity; Skeletal Muscle; Transcriptomics; Type 2 Diabetes
    DOI:  https://doi.org/10.1152/ajpendo.00143.2023
  30. bioRxiv. 2023 Aug 04. pii: 2023.08.02.551712. [Epub ahead of print]
    Lactate activates the mitochondrial electron transport chain independent of its metabolism.
    Xin Cai, Charles C Ng, Olivia Jones, Tak Shun Fung, Keunwoo Ryu, Dayi Li, Craig B Thompson.
      Lactate has long been considered a cellular waste product. However, we found that as extracellular lactate accumulates, it also enters the mitochondrial matrix and stimulates mitochondrial electron transport chain (ETC) activity. The resulting increase in mitochondrial ATP synthesis suppresses glycolysis and increases the utilization of pyruvate and/or alternative respiratory substrates. The ability of lactate to increase oxidative phosphorylation does not depend on its metabolism. Both L- and D-lactate are effective at enhancing ETC activity and suppressing glycolysis. Furthermore, the selective induction of mitochondrial oxidative phosphorylation by unmetabolized D-lactate reversibly suppressed aerobic glycolysis in both cancer cell lines and proliferating primary cells in an ATP-dependent manner and enabled cell growth on respiratory-dependent bioenergetic substrates. In primary T cells, D-lactate enhanced cell proliferation and effector function. Together, these findings demonstrate that lactate is a critical regulator of the ability of mitochondrial oxidative phosphorylation to suppress glucose fermentation.
    DOI:  https://doi.org/10.1101/2023.08.02.551712
  31. medRxiv. 2023 Aug 04. pii: 2023.08.02.23293212. [Epub ahead of print]
    Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project.
    Sarah L Stenton, Melanie O'Leary, Gabrielle Lemire, Grace E VanNoy, Stephanie DiTroia, Vijay S Ganesh, Emily Groopman, Emily O'Heir, Brian Mangilog, Ikeoluwa Osei-Owusu, Lynn S Pais, Jillian Serrano, Moriel Singer-Berk, Ben Weisburd, Michael Wilson, Christina Austin-Tse, Marwa Abdelhakim, Azza Althagafi, Giulia Babbi, Riccardo Bellazzi, Samuele Bovo, Maria Giulia Carta, Rita Casadio, Pieter-Jan Coenen, Federica De Paoli, Matteo Floris, Manavalan Gajapathy, Robert Hoehndorf, Julius O B Jacobsen, Thomas Joseph, Akash Kamandula, Panagiotis Katsonis, Cyrielle Kint, Olivier Lichtarge, Ivan Limongelli, Yulan Lu, Paolo Magni, Tarun Karthik Kumar Mamidi, Pier Luigi Martelli, Marta Mulargia, Giovanna Nicora, Keith Nykamp, Vikas Pejaver, Yisu Peng, Thi Hong Cam Pham, Maurizio S Podda, Aditya Rao, Ettore Rizzo, Vangala G Saipradeep, Castrense Savojardo, Peter Schols, Yang Shen, Naveen Sivadasan, Damian Smedley, Dorian Soru, Rajgopal Srinivasan, Yuanfei Sun, Uma Sunderam, Wuwei Tan, Naina Tiwari, Xiao Wang, Yaqiong Wang, Amanda Williams, Elizabeth A Worthey, Rujie Yin, Yuning You, Daniel Zeiberg, Susanna Zucca, Constantina Bakolitsa, Steven E Brenner, Stephanie M Fullerton, Predrag Radivojac, Heidi L Rehm, Anne O'Donnell-Luria.
       Background: A major obstacle faced by rare disease families is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years, and causal variants are identified in under 50%. The Rare Genomes Project (RGP) is a direct-to-participant research study on the utility of genome sequencing (GS) for diagnosis and gene discovery. Families are consented for sharing of sequence and phenotype data with researchers, allowing development of a Critical Assessment of Genome Interpretation (CAGI) community challenge, placing variant prioritization models head-to-head in a real-life clinical diagnostic setting.
    Methods: Predictors were provided a dataset of phenotype terms and variant calls from GS of 175 RGP individuals (65 families), including 35 solved training set families, with causal variants specified, and 30 test set families (14 solved, 16 unsolved). The challenge tasked teams with identifying the causal variants in as many test set families as possible. Ranked variant predictions were submitted with estimated probability of causal relationship (EPCR) values. Model performance was determined by two metrics, a weighted score based on rank position of true positive causal variants and maximum F-measure, based on precision and recall of causal variants across EPCR thresholds.
    Results: Sixteen teams submitted predictions from 52 models, some with manual review incorporated. Top performing teams recalled the causal variants in up to 13 of 14 solved families by prioritizing high quality variant calls that were rare, predicted deleterious, segregating correctly, and consistent with reported phenotype. In unsolved families, newly discovered diagnostic variants were returned to two families following confirmatory RNA sequencing, and two prioritized novel disease gene candidates were entered into Matchmaker Exchange. In one example, RNA sequencing demonstrated aberrant splicing due to a deep intronic indel in ASNS , identified in trans with a frameshift variant, in an unsolved proband with phenotype overlap with asparagine synthetase deficiency.
    Conclusions: By objective assessment of variant predictions, we provide insights into current state-of-the-art algorithms and platforms for genome sequencing analysis for rare disease diagnosis and explore areas for future optimization. Identification of diagnostic variants in unsolved families promotes synergy between researchers with clinical and computational expertise as a means of advancing the field of clinical genome interpretation.
    DOI:  https://doi.org/10.1101/2023.08.02.23293212
  32. J Mol Cell Biol. 2023 Aug 17. pii: mjad051. [Epub ahead of print]
    Mitochondrial transport of catalytic RNAs and targeting of the organellar transcriptome in human cells.
    Paweł Głodowicz, Konrad Kuczyński, Romain Val, André Dietrich, Katarzyna Rolle.
      Mutations in the small genome present in mitochondria often result in severe pathologies. Different genetic strategies have been explored, aiming to contribute to rescue such mutations. A number of these were based on the capacity of human mitochondria to import RNAs from the cytosol and were designed to repress the replication of the mutated genomes or to provide the organelles with wild-type versions of mutant transcripts. However, the mutant RNAs present in mitochondria turned out to be an obstacle to therapy and little attention has been devoted so far to their elimination. Here, we present the development of a strategy to knockdown mitochondrial RNAs in human cells using the transfer RNA-like structure of the Brome mosaic virus or the Tobacco mosaic virus as a shuttle to drive trans-cleaving ribozymes into the organelles in human cell lines. We obtained a specific knockdown of the targeted mitochondrial ATP6 mRNA, followed by a deep drop in ATP6 protein and a functional impairment of the oxidative phosphorylation chain. Our strategy opens a powerful approach to eliminate mutant organellar transcripts and to analyze the control and communication of the human organellar genetic system.
    Keywords:  RNA trafficking; human cells; mitochondria; ribozyme; tRNA-like structure; transcriptome manipulation
    DOI:  https://doi.org/10.1093/jmcb/mjad051
  33. Front Genet. 2023 ;14 1190222
    A novel IBA57 variant is associated with mitochondrial iron-sulfur protein deficiency and necrotizing myelopathy in dogs.
    Paul J J Mandigers, Oliver Stehling, Manon Vos-Loohuis, Frank G Van Steenbeek, Roland Lill, Peter A Leegwater.
      Introduction: Hereditary necrotizing myelopathy (HNM) in young Kooiker dogs is characterized by progressive ataxia and paralysis with autosomal recessive inheritance. The basic genetic defect is unknown. We investigated the possible cause by a genome-wide analysis using six affected and 17 unrelated unaffected Kooiker dogs and by functional follow-up studies. Method: The HNM locus was mapped by a case-control study using a dense SNP array and confirmed by linkage analysis of two pedigrees. The gene exons in the critical region were analyzed by next-generation sequencing. The functional effect of the candidate canine IBA57 pathogenic variant was biochemically examined in an established HeLa cell culture model in which the endogenous IBA75 gene product was depleted by RNAi. Results: The basic defect was localized in the centromeric 5 Mb region of canine chromosome 14. The most associated SNP co-segregated fully with HNM and reached an LOD score of 6.1. A candidate pathogenic mutation was found in the iron-sulfur cluster assembly gene IBA57 and led to the amino acid substitution R147W. The expression of human IBA57 harboring the canine R147W exchange could only partially restore the biochemical defects of several mitochondrial [4Fe-4S] proteins upon IBA57 depletion, showing that the mutant protein is functionally impaired. Discussion: Pathogenic variants in human IBA57 cause multiple mitochondrial dysfunction syndrome 3 (MMDS3), a neurodegenerative disorder with distant similarities to HNM. The incomplete functional complementation of IBA57-depleted human cells by IBA57-R147W identifies the DNA mutation in affected Kooiker dogs as the genetic cause of HNM. Our findings further expand the phenotypic spectrum of pathogenic IBA57 variants.
    Keywords:  IBA57-R147W; Kooiker dog; Kooikerhondje; canine; leukodystrophy; lipoyl synthase; respiratory complexes; spinal cord
    DOI:  https://doi.org/10.3389/fgene.2023.1190222
  34. Sci Bull (Beijing). 2023 Aug 02. pii: S2095-9273(23)00517-0. [Epub ahead of print]
    Mitochondrial RNA m3C methyltransferase METTL8 relies on an isoform-specific N-terminal extension and modifies multiple heterogenous tRNAs.
    Meng-Han Huang, Jin-Tao Wang, Jian-Hui Zhang, Xue-Ling Mao, Gui-Xin Peng, Xiuying Lin, Daizhu Lv, Chen Yuan, Huan Lin, En-Duo Wang, Xiao-Long Zhou.
      Methyltransferase-like 8 (METTL8) encodes a mitochondria-localized METTL8-Iso1 and a nucleolus-distributed METTL8-Iso4 isoform, which differ only in their N-terminal extension (N-extension), by mRNA alternative splicing. METTL8-Iso1 generates 3-methylcytidine at position 32 (m3C32) of mitochondrial tRNAThr and tRNASer(UCN). Whether METTL8-Iso4 is an active m3C32 methyltransferase and the role of the N-extension in mitochondrial tRNA m3C32 formation remain unclear. Here, we revealed that METTL8-Iso4 was inactive in m3C32 generation due to the lack of N-extension, which contains several absolutely conserved modification-critical residues; the counterparts were likewise essential in cytoplasmic m3C32 biogenesis by methyltransferase-like 2A (METTL2A) or budding yeasts tRNA N3-methylcytidine methyltransferase (Trm140), in vitro and in vivo. Cross-compartment/species tRNA modification assays unexpectedly found that METTL8-Iso1 efficiently introduced m3C32 to several cytoplasmic or even bacterial tRNAs in vitro. m3C32 did not influence tRNAThrN6-threonylcarbamoyladenosine (t6A) modification or aminoacylation. In addition to its interaction with mitochondrial seryl-tRNA synthetase (SARS2), we further discovered an interaction between mitochondrial threonyl-tRNA synthetase (TARS2) and METTL8-Iso1. METTL8-Iso1 substantially stimulated the aminoacylation activities of SARS2 and TARS2 in vitro, suggesting a functional connection between mitochondrial tRNA modification and charging. Altogether, our results deepen the mechanistic insights into mitochondrial m3C32 biogenesis and provide a valuable route to prepare cytoplasmic/bacterial tRNAs with only a m3C32 moiety, aiding in future efforts to investigate its effects on tRNA structure and function.
    Keywords:  3-methylcytidine; Aminoacylation; Methyltransferase; tRNA
    DOI:  https://doi.org/10.1016/j.scib.2023.08.002
  35. Cell Commun Signal. 2023 Aug 18. 21(1): 214
    A new perspective on mesenchymal stem cell-based therapy for liver diseases: restoring mitochondrial function.
    Yelei Cen, Guohua Lou, Jinjin Qi, Min Zheng, Yanning Liu.
      Mesenchymal stem cells (MSCs) have emerged as a promising alternative treatment for liver disease due to their roles in regeneration, fibrosis inhibition, and immunoregulation. Mitochondria are crucial in maintaining hepatocyte integrity and function. Mitochondrial dysfunction, such as impaired synthesis of adenosine triphosphate (ATP), decreased activity of respiratory chain complexes, and altered mitochondrial dynamics, is observed in most liver diseases. Accumulating evidence has substantiated that the therapeutic potential of MSCs is mediated not only through their cell replacement and paracrine effects but also through their regulation of mitochondrial dysfunction in liver disease. Here, we comprehensively review the involvement of mitochondrial dysfunction in the development of liver disease and how MSCs can target mitochondrial dysfunction. We also discuss recent advances in a novel method that modifies MSCs to enhance their functions in liver disease. A full understanding of MSC restoration of mitochondrial function and the underlying mechanisms will provide innovative strategies for clinical applications. Video Abstract.
    Keywords:  Liver disease; MSC therapy; Mesenchymal stem cell; Mitochondria; Mitochondrial dysfunction
    DOI:  https://doi.org/10.1186/s12964-023-01230-0
  36. Brief Bioinform. 2023 Aug 14. pii: bbad284. [Epub ahead of print]
    Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis.
    Robert Wang, Ingo Helbig, Andrew C Edmondson, Lan Lin, Yi Xing.
      Genomic variants affecting pre-messenger RNA splicing and its regulation are known to underlie many rare genetic diseases. However, common workflows for genetic diagnosis and clinical variant interpretation frequently overlook splice-altering variants. To better serve patient populations and advance biomedical knowledge, it has become increasingly important to develop and refine approaches for detecting and interpreting pathogenic splicing variants. In this review, we will summarize a few recent developments and challenges in using RNA sequencing technologies for rare disease investigation. Moreover, we will discuss how recent computational splicing prediction tools have emerged as complementary approaches for revealing disease-causing variants underlying splicing defects. We speculate that continuous improvements to sequencing technologies and predictive modeling will not only expand our understanding of splicing regulation but also bring us closer to filling the diagnostic gap for rare disease patients.
    Keywords:  RNA sequencing; diagnostics; machine learning; rare disease; splicing; variant interpretation
    DOI:  https://doi.org/10.1093/bib/bbad284
  37. PLoS Genet. 2023 Aug 16. 19(8): e1010848
    Functional mapping of N-terminal residues in the yeast proteome uncovers novel determinants for mitochondrial protein import.
    Salomé Nashed, Houssam El Barbry, Médine Benchouaia, Angélie Dijoux-Maréchal, Thierry Delaveau, Nadia Ruiz-Gutierrez, Lucie Gaulier, Déborah Tribouillard-Tanvier, Guillaume Chevreux, Stéphane Le Crom, Benoit Palancade, Frédéric Devaux, Elodie Laine, Mathilde Garcia.
      N-terminal ends of polypeptides are critical for the selective co-translational recruitment of N-terminal modification enzymes. However, it is unknown whether specific N-terminal signatures differentially regulate protein fate according to their cellular functions. In this work, we developed an in-silico approach to detect functional preferences in cellular N-terminomes, and identified in S. cerevisiae more than 200 Gene Ontology terms with specific N-terminal signatures. In particular, we discovered that Mitochondrial Targeting Sequences (MTS) show a strong and specific over-representation at position 2 of hydrophobic residues known to define potential substrates of the N-terminal acetyltransferase NatC. We validated mitochondrial precursors as co-translational targets of NatC by selective purification of translating ribosomes, and found that their N-terminal signature is conserved in Saccharomycotina yeasts. Finally, systematic mutagenesis of the position 2 in a prototypal yeast mitochondrial protein confirmed its critical role in mitochondrial protein import. Our work highlights the hydrophobicity of MTS N-terminal residues and their targeting by NatC as important features for the definition of the mitochondrial proteome, providing a molecular explanation for mitochondrial defects observed in yeast or human NatC-depleted cells. Functional mapping of N-terminal residues thus has the potential to support the discovery of novel mechanisms of protein regulation or targeting.
    DOI:  https://doi.org/10.1371/journal.pgen.1010848
  38. ACS Med Chem Lett. 2023 Aug 10. 14(8): 1095-1099
    Discovery of Potent Allosteric DRP1 Inhibitors by Disrupting Protein-Protein Interaction with MiD49.
    Takeru Furuya, Jean Lin, Arina Afanaseva, Lisa Molz, Bharat Lagu, Bin Ma.
      Mitochondrial dysfunction has been attributed to many disease indications, including metabolic, cardiovascular, neoplastic, and neurodegenerative diseases. Dynamin related protein 1 (DRP1) is crucial in regulating mitochondrial fission and maintaining mitochondrial homeostasis. MiD49 is a dynamic peripheral protein receptor on the surface of the mitochondrial membrane that recruits DRP1 protein to induce mitochondrial binary fission. By targeting the protein-protein interaction of DRP1/MiD49, we have discovered a novel and potent allosteric DRP1 inhibitor that inhibits mitochondria fragmentation in vitro. X-ray cocrystal structure revealed that it locked the closed DRP1 conformation by induced dimerization.
    DOI:  https://doi.org/10.1021/acsmedchemlett.3c00223
  39. Front Neurosci. 2023 ;17 1249815
    Presenilins and mitochondria-an intriguing link: mini-review.
    Mark Makarov, Liliia Kushnireva, Michele Papa, Eduard Korkotian.
      This review uncovers the intricate relationship between presenilins, calcium, and mitochondria in the context of Alzheimer's disease (AD), with a particular focus on the involvement of presenilin mutations in mitochondrial dysfunction. So far, it is unclear whether the impairment of mitochondrial function arises primarily from damage inflicted by β-amyloid upon mitochondria or from the disruption of calcium homeostasis due to presenilins dysfunctions. The roles of presenilins in mitophagy, autophagy, mitochondrial dynamics, and many other functions, non-γ-secretase related, also require close attention in future research. Resolution of contradictions in understanding of presenilins cellular functions are needed for new effective therapeutic strategies for AD.
    Keywords:  Alzheimer’s disease; mitochondria associated membranes; neurodegeneration; presenilins; spine apparatus
    DOI:  https://doi.org/10.3389/fnins.2023.1249815
  40. Eur J Neurol. 2023 Aug 14.
    Frequency and phenotypic spectrum of spinocerebellar ataxia 27B and other genetic ataxias in a Spanish cohort of late-onset cerebellar ataxia.
    Pablo Iruzubieta, David Pellerin, Alberto Bergareche, Inés Albajar, Elisabet Mondragón, Ana Vinagre, Roberto Fernández-Torrón, Fermín Moreno, Jon Equiza, David Campo-Caballero, Juan José Poza, Marta Ruibal, Alessandro Formica, Marie-Josée Dicaire, Matt C Danzi, Stephan Zuchner, Ioana Croitoru, Montserrat Ruiz, Agatha Schlüter, Carlos Casasnovas, Aurora Pujol, Bernard Brais, Henry Houlden, Adolfo López de Munain, Javier Ruiz-Martínez.
       BACKGROUND: Dominantly inherited GAA repeat expansions in the fibroblast growth factor 14 (FGF14) gene have recently been shown to cause spinocerebellar ataxia 27B (SCA27B). We aimed to study the frequency and phenotype of SCA27B in a cohort of patients with unsolved late-onset cerebellar ataxia (LOCA). We also assessed the frequency of SCA27B relative to other genetically defined LOCAs.
    METHODS: We recruited a consecutive series of 107 patients with LOCA. 64 remained genetically undiagnosed. We screened these 64 patients for the FGF14 GAA repeat expansion. We next analysed the frequency of SCA27B relative to other genetically-defined forms of LOCA in the cohort of 107 patients.
    RESULTS: Eighteen of 64 patients (28%) carried an FGF14 (GAA)≥250 expansion. The median age at onset was 62.5 years (range, 39-72). The most common clinical features included gait ataxia (100%) and mild cerebellar dysarthria (67%). In addition, episodic symptoms and downbeat nystagmus were present in 39% (7/18) and 37% (6/16) of patients, respectively. SCA27B was the most common cause of LOCA in our cohort (17%, 18/107). Among patients with genetically defined LOCA, SCA27B was the main cause of pure ataxia, RFC1-related disease of ataxia with neuropathy, and SPG7 of ataxia with spasticity.
    CONCLUSION: We showed that SCA27B is the most common cause of LOCA in our cohort. Our results support the use of FGF14 GAA repeat expansion screening as a first-tier genetic test in patients with LOCA.
    Keywords:  FGF14; RFC1; SCA27B; ataxia; late-onset cerebellar ataxia; neurogenetics; repeat expansion disorder; GAA-FGF14 ataxia
    DOI:  https://doi.org/10.1111/ene.16039
  41. Nat Commun. 2023 Aug 18. 14(1): 5023
    A genome-wide association study of blood cell morphology identifies cellular proteins implicated in disease aetiology.
    Parsa Akbari, Dragana Vuckovic, Luca Stefanucci, Tao Jiang, Kousik Kundu, Roman Kreuzhuber, Erik L Bao, Janine H Collins, Kate Downes, Luigi Grassi, Jose A Guerrero, Stephen Kaptoge, Julian C Knight, Stuart Meacham, Jennifer Sambrook, Denis Seyres, Oliver Stegle, Jeffrey M Verboon, Klaudia Walter, Nicholas A Watkins, John Danesh, David J Roberts, Emanuele Di Angelantonio, Vijay G Sankaran, Mattia Frontini, Stephen Burgess, Taco Kuijpers, James E Peters, Adam S Butterworth, Willem H Ouwehand, Nicole Soranzo, William J Astle.
      Blood cells contain functionally important intracellular structures, such as granules, critical to immunity and thrombosis. Quantitative variation in these structures has not been subjected previously to large-scale genetic analysis. We perform genome-wide association studies of 63 flow-cytometry derived cellular phenotypes-including cell-type specific measures of granularity, nucleic acid content and reactivity-in 41,515 participants in the INTERVAL study. We identify 2172 distinct variant-trait associations, including associations near genes coding for proteins in organelles implicated in inflammatory and thrombotic diseases. By integrating with epigenetic data we show that many intracellular structures are likely to be determined in immature precursor cells. By integrating with proteomic data we identify the transcription factor FOG2 as an early regulator of platelet formation and α-granularity. Finally, we show that colocalisation of our associations with disease risk signals can suggest aetiological cell-types-variants in IL2RA and ITGA4 respectively mirror the known effects of daclizumab in multiple sclerosis and vedolizumab in inflammatory bowel disease.
    DOI:  https://doi.org/10.1038/s41467-023-40679-y
  42. Bioorg Med Chem Lett. 2023 Aug 15. pii: S0960-894X(23)00327-X. [Epub ahead of print] 129449
    Development of a Highly Potent and Selective Degrader of LRRK2.
    John M Hatcher, Monika Zwirek, Adil R Sarhan, Prasanna S Vatsan, Francesca Tonelli, Dario R Alessi, Paul Davies, Nathanael S Gray.
      The discovery of disease-modifying therapies for Parkinson's Disease (PD) represents a critical need in neurodegenerative medicine. Genetic mutations in leucine-rich repeat kinase 2 (LRRK2) are risk factors for the development of PD, and some of these mutations have been linked to increased LRRK2 kinase activity and neuronal toxicity in cellular and animal models. Furthermore, LRRK2 function as a scaffolding protein in several pathways has been implicated as a plausible mechanism underlying neurodegeneration caused by LRRK2 mutations. Given that both the kinase activity and scaffolding function of LRRK2 have been linked to neurodegeneration, we developed proteolysis-targeting chimeras (PROTACs) targeting LRRK2. The degrader molecule JH-XII-03-02 (6) displayed high potency and remarkable selectivity for LRKK2 when assessed in a of 468 panel kinases and serves the dual purpose of eliminating both the kinase activity as well as the scaffolding function of LRRK2.
    Keywords:  LRRK2; LRRK2 degrader; MLi-2; PROTAC
    DOI:  https://doi.org/10.1016/j.bmcl.2023.129449
  43. Curr Protoc. 2023 Aug;3(8): e865
    Massively Parallel Sequencing of the Mitogenome from Human Hair Shafts in Forensic Investigations.
    Jade T Korber, Lauren C Canale, Mitchell M Holland.
      This article highlights methods used to perform DNA extraction, mitochondrial DNA quantification, multiplex PCR amplification, amplicon-based massively parallel sequencing, and data analysis of the mitochondrial genome (mitogenome) from human hair shafts. The focus is on applications to forensic casework, but this set of protocols can be used for any purpose involving small cuttings (as small as 1 to 5 mm) of human hair shafts up to 40 years from the time of collection. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Extraction of mitochondrial DNA from human hair shafts Basic Protocol 2: Quantification of mitochondrial DNA (copies/μl) Basic Protocol 3: Multiplex amplification of the mitogenome Basic Protocol 4: Library preparation and sequencing of mitogenome amplicons Basic Protocol 5: Data analysis of mitogenome haplotypes.
    Keywords:  DNA extraction of human hair; MPS; forensic genetics; mitochondrial genome; multiplex PCR
    DOI:  https://doi.org/10.1002/cpz1.865
  44. Cell Chem Biol. 2023 Aug 09. pii: S2451-9456(23)00237-4. [Epub ahead of print]
    Mitochondria-targeted melatonin photorelease supports the presence of melatonin MT1 receptors in mitochondria inhibiting respiration.
    Gloria Somalo-Barranco, Antonio C Pagano Zottola, Abdulrasheed O Abdulrahman, Rami M El Zein, Astrid Cannich, Lourdes Muñoz, Carme Serra, Atsuro Oishi, Giovanni Marsicano, Bernard Masri, Luigi Bellocchio, Amadeu Llebaria, Ralf Jockers.
      The presence of signaling-competent G protein-coupled receptors in intracellular compartments is increasingly recognized. Recently, the presence of Gi/o protein-coupled melatonin MT1 receptors in mitochondria has been revealed, in addition to the plasma membrane. Melatonin is highly cell permeant, activating plasma membrane and mitochondrial receptors equally. Here, we present MCS-1145, a melatonin derivative bearing a triphenylphosphonium cation for specific mitochondrial targeting and a photocleavable o-nitrobenzyl group releasing melatonin upon illumination. MCS-1145 displayed low affinity for MT1 and MT2 but spontaneously accumulated in mitochondria, where it was resistant to washout. Uncaged MCS-1145 and exogenous melatonin recruited β-arrestin 2 to MT1 in mitochondria and inhibited oxygen consumption in mitochondria isolated from HEK293 cells only when expressing MT1 and from mouse cerebellum of WT mice but not from MT1-knockout mice. Overall, we developed the first mitochondria-targeted photoactivatable melatonin ligand and demonstrate that melatonin inhibits mitochondrial respiration through mitochondrial MT1 receptors.
    Keywords:  G protein-coupled receptors; intracellular signaling; melatonin; melatonin receptors; mitochondria; mitochondria-targeted caged melatonin ligand; mitochondrial respiration; photopharmacology
    DOI:  https://doi.org/10.1016/j.chembiol.2023.07.009
  45. BMC Genomics. 2023 Aug 16. 24(1): 460
    Rare disease variant curation from literature: assessing gaps with creatine transport deficiency in focus.
    Erica L Lyons, Daniel Watson, Mohammad S Alodadi, Sharie J Haugabook, Gregory J Tawa, Fady Hannah-Shmouni, Forbes D Porter, Jack R Collins, Elizabeth A Ottinger, Uma S Mudunuri.
       BACKGROUND: Approximately 4-8% of the world suffers from a rare disease. Rare diseases are often difficult to diagnose, and many do not have approved therapies. Genetic sequencing has the potential to shorten the current diagnostic process, increase mechanistic understanding, and facilitate research on therapeutic approaches but is limited by the difficulty of novel variant pathogenicity interpretation and the communication of known causative variants. It is unknown how many published rare disease variants are currently accessible in the public domain.
    RESULTS: This study investigated the translation of knowledge of variants reported in published manuscripts to publicly accessible variant databases. Variants, symptoms, biochemical assay results, and protein function from literature on the SLC6A8 gene associated with X-linked Creatine Transporter Deficiency (CTD) were curated and reported as a highly annotated dataset of variants with clinical context and functional details. Variants were harmonized, their availability in existing variant databases was analyzed and pathogenicity assignments were compared with impact algorithm predictions. 24% of the pathogenic variants found in PubMed articles were not captured in any database used in this analysis while only 65% of the published variants received an accurate pathogenicity prediction from at least one impact prediction algorithm.
    CONCLUSIONS: Despite being published in the literature, pathogenicity data on patient variants may remain inaccessible for genetic diagnosis, therapeutic target identification, mechanistic understanding, or hypothesis generation. Clinical and functional details presented in the literature are important to make pathogenicity assessments. Impact predictions remain imperfect but are improving, especially for single nucleotide exonic variants, however such predictions are less accurate or unavailable for intronic and multi-nucleotide variants. Developing text mining workflows that use natural language processing for identifying diseases, genes and variants, along with impact prediction algorithms and integrating with details on clinical phenotypes and functional assessments might be a promising approach to scale literature mining of variants and assigning correct pathogenicity. The curated variants list created by this effort includes context details to improve any such efforts on variant curation for rare diseases.
    Keywords:  CTD; Gene variant; Literature curation; Rare disease; SLC6A8; Text mining; Variant database
    DOI:  https://doi.org/10.1186/s12864-023-09561-5
  46. J Pharm Anal. 2023 Jul;13(7): 694-710
    Dissecting the brain with spatially resolved multi-omics.
    Yijia Fangma, Mengting Liu, Jie Liao, Zhong Chen, Yanrong Zheng.
      Recent studies have highlighted spatially resolved multi-omics technologies, including spatial genomics, transcriptomics, proteomics, and metabolomics, as powerful tools to decipher the spatial heterogeneity of the brain. Here, we focus on two major approaches in spatial transcriptomics (next-generation sequencing-based technologies and image-based technologies), and mass spectrometry imaging technologies used in spatial proteomics and spatial metabolomics. Furthermore, we discuss their applications in neuroscience, including building the brain atlas, uncovering gene expression patterns of neurons for special behaviors, deciphering the molecular basis of neuronal communication, and providing a more comprehensive explanation of the molecular mechanisms underlying central nervous system disorders. However, further efforts are still needed toward the integrative application of multi-omics technologies, including the real-time spatial multi-omics analysis in living cells, the detailed gene profile in a whole-brain view, and the combination of functional verification.
    Keywords:  Central nervous system disorders; Multi-omics; Spatial metabolomics; Spatial proteomics; Spatial transcriptomics
    DOI:  https://doi.org/10.1016/j.jpha.2023.04.003
  47. bioRxiv. 2023 Aug 01. pii: 2023.07.31.551363. [Epub ahead of print]
    A robust method for measuring aminoacylation through tRNA-Seq.
    Kristian Davidsen, Lucas B Sullivan.
      Current methods to quantify the fraction of aminoacylated tRNAs, also known as the tRNA charge, are limited by issues with either low throughput, precision, and/or accuracy. Here, we present an optimized charge tRNA-Seq method that combines previous developments with newly described approaches to establish a protocol for precise and accurate tRNA charge measurements. We verify that this protocol provides robust quantification of tRNA aminoacylation and we provide an end-to-end method that scales to hundreds of samples including software for data processing. Additionally, we show that this method supports measurements of relative tRNA expression levels and can be used to infer tRNA modifications through reverse transcription misincorporations, thereby supporting multipurpose applications in tRNA biology.
    DOI:  https://doi.org/10.1101/2023.07.31.551363
  48. Immunol Cell Biol. 2023 Aug 12.
    The seductive allure of spatial biology: accelerating new discoveries in the life sciences.
    Arutha Kulasinghe, Fiona Wood, Gabrielle Belz.
      Spatial biology is a rapidly developing field which enables the visualization of protein and transcriptomic data while preserving tissue context and architecture. Initially used in discovery, there is growing promise for translational and diagnostic assay developments. Immediate applications are in precision medicine, such as being able to match patients to optimal therapies through better understanding the tumor microenvironment. However, it also has ramifications for many other disciplines (e.g. immunology, cancer, infectious disease and digital pathology). With increasingly massive data sets being generated, data storage, curation, analysis and sharing require more computational approaches and artificial intelligence-powered tools to fully utilize spatial tools. Here, we discuss spatial biology as an important convergent science approach to tackling complex global challenges in areas such as health.
    Keywords:  Cancer; convergence science; emerging technologies; funding models; genomics; health care; spatial biology; spatial omics
    DOI:  https://doi.org/10.1111/imcb.12669
  49. Proc Natl Acad Sci U S A. 2023 08 22. 120(34): e2302738120
    WASF3 disrupts mitochondrial respiration and may mediate exercise intolerance in myalgic encephalomyelitis/chronic fatigue syndrome.
    Ping-Yuan Wang, Jin Ma, Young-Chae Kim, Annie Y Son, Abu Mohammad Syed, Chengyu Liu, Mateus P Mori, Rebecca D Huffstutler, JoEllyn L Stolinski, S Lalith Talagala, Ju-Gyeong Kang, Brian T Walitt, Avindra Nath, Paul M Hwang.
      Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is characterized by various disabling symptoms including exercise intolerance and is diagnosed in the absence of a specific cause, making its clinical management challenging. A better understanding of the molecular mechanism underlying this apparent bioenergetic deficiency state may reveal insights for developing targeted treatment strategies. We report that overexpression of Wiskott-Aldrich Syndrome Protein Family Member 3 (WASF3), here identified in a 38-y-old woman suffering from long-standing fatigue and exercise intolerance, can disrupt mitochondrial respiratory supercomplex formation and is associated with endoplasmic reticulum (ER) stress. Increased expression of WASF3 in transgenic mice markedly decreased their treadmill running capacity with concomitantly impaired respiratory supercomplex assembly and reduced complex IV levels in skeletal muscle mitochondria. WASF3 induction by ER stress using endotoxin, well known to be associated with fatigue in humans, also decreased skeletal muscle complex IV levels in mice, while decreasing WASF3 levels by pharmacologic inhibition of ER stress improved mitochondrial function in the cells of the patient with chronic fatigue. Expanding on our findings, skeletal muscle biopsy samples obtained from a cohort of patients with ME/CFS showed increased WASF3 protein levels and aberrant ER stress activation. In addition to revealing a potential mechanism for the bioenergetic deficiency in ME/CFS, our study may also provide insights into other disorders associated with fatigue such as rheumatic diseases and long COVID.
    Keywords:  ER stress; WASF3; fatigue; mitochondria; supercomplex
    DOI:  https://doi.org/10.1073/pnas.2302738120
  50. PLoS Biol. 2023 Aug 17. 21(8): e3002247
    The AAA-ATPase Yta4/ATAD1 interacts with the mitochondrial divisome to inhibit mitochondrial fission.
    Jiajia He, Ke Liu, Yifan Wu, Chenhui Zhao, Shuaijie Yan, Jia-Hui Chen, Lizhu Hu, Dongmei Wang, Fan Zheng, Wenfan Wei, Chao Xu, Chengdong Huang, Xing Liu, Xuebiao Yao, Lijun Ding, Zhiyou Fang, Ai-Hui Tang, Chuanhai Fu.
      Mitochondria are in a constant balance of fusion and fission. Excessive fission or deficient fusion leads to mitochondrial fragmentation, causing mitochondrial dysfunction and physiological disorders. How the cell prevents excessive fission of mitochondria is not well understood. Here, we report that the fission yeast AAA-ATPase Yta4, which is the homolog of budding yeast Msp1 responsible for clearing mistargeted tail-anchored (TA) proteins on mitochondria, plays a critical role in preventing excessive mitochondrial fission. The absence of Yta4 leads to mild mitochondrial fragmentation in a Dnm1-dependent manner but severe mitochondrial fragmentation upon induction of mitochondrial depolarization. Overexpression of Yta4 delocalizes the receptor proteins of Dnm1, i.e., Fis1 (a TA protein) and Mdv1 (the bridging protein between Fis1 and Dnm1), from mitochondria and reduces the localization of Dnm1 to mitochondria. The effect of Yta4 overexpression on Fis1 and Mdv1, but not Dnm1, depends on the ATPase and translocase activities of Yta4. Moreover, Yta4 interacts with Dnm1, Mdv1, and Fis1. In addition, Yta4 competes with Dnm1 for binding Mdv1 and decreases the affinity of Dnm1 for GTP and inhibits Dnm1 assembly in vitro. These findings suggest a model, in which Yta4 inhibits mitochondrial fission by inhibiting the function of the mitochondrial divisome composed of Fis1, Mdv1, and Dnm1. Therefore, the present work reveals an uncharacterized molecular mechanism underlying the inhibition of mitochondrial fission.
    DOI:  https://doi.org/10.1371/journal.pbio.3002247
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