bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2024–11–24
48 papers selected by
Catalina Vasilescu, Helmholz Munich
  1. Pathogenic PDE12 variants impair mitochondrial RNA processing causing neonatal mitochondrial disease.
  2. Respiratory Chain Complex I Deficiency in Leber Hereditary Optic Neuropathy: Insights from Ophthalmologic and Molecular Investigations in Tunisia.
  3. AMPK: Balancing mitochondrial quality and quantity through opposite regulation of mitophagy pathways.
  4. Genotype-specific effects of elamipretide in patients with primary mitochondrial myopathy: a post hoc analysis of the MMPOWER-3 trial.
  5. WDR45-related encephalopathy mimicking Leigh syndrome associated with complex I deficiency: a case report.
  6. Endogenous mitochondrial NAD(P)H fluorescence can predict lifespan.
  7. Mutation of CRYAB encoding a conserved mitochondrial chaperone and anti-apoptotic protein causes hereditary optic atrophy.
  8. Textbook oxidative phosphorylation needs to be rewritten.
  9. Interaction with the cysteine-free protein HAX1 expands the substrate specificity and function of MIA40 beyond protein oxidation.
  10. Inducible and reversible SOD2 knockdown in mouse skeletal muscle drives impaired pyruvate oxidation and reduced metabolic flexibility.
  11. Impact of Ageing and Disuse on Neuromuscular Junction and Mitochondrial Function and Morphology: Current Evidence and Controversies.
  12. Mitochondrial mRNA and the Small Subunit rRNA in Budding Yeasts Undergo 3'-End Processing at Conserved Species-specific Elements.
  13. H 2 S remodels mitochondrial ultrastructure and destabilizes respiratory supercomplexes.
  14. Common genetic variants contribute more to rare diseases than previously thought.
  15. MMFP-Tableau: enabling precision mitochondrial medicine through integration, visualization, and analytics of clinical and research health system electronic data.
  16. PINK1 controls RTN3L-mediated ER autophagy by regulating peripheral tubule junctions.
  17. Implementation of multi-omics in diagnosis of pediatric rare diseases.
  18. Intermittent episodes of acute severe encephalomyopathy and early death in two siblings caused by biallelic likely pathogenic variants in FASTKD2: Expanding phenotype and literature review.
  19. Loss of mitochondrial enzyme GPT2 leads to reprogramming of synaptic glutamate metabolism.
  20. Structure of an ex vivoDrosophila TOM complex determined by single-particle cryoEM.
  21. Mitochondrial NADK2-dependent NADPH controls Tau oligomer uptake in human neurons.
  22. Tak1 licenses mitochondrial transfer from astrocytes to POMC neurons to maintain glucose and cholesterol homeostasis.
  23. VACCINE SAFETY IN CHILDREN WITH GENETICALLY CONFIRMED MITOCHONDRIAL DISEASE.
  24. De novo missense variants in the PP2A regulatory subunit PPP2R2B in a neurodevelopmental syndrome: potential links to mitochondrial dynamics and spinocerebellar ataxias.
  25. The mitochondrial-targeted peptide therapeutic elamipretide improves cardiac and skeletal muscle function during aging without detectable changes in tissue epigenetic or transcriptomic age.
  26. PDE12 mediated pruning of the poly-A tail of mitochondrial DNA-encoded tRNAs is essential for survival.
  27. Human genetics identify convergent signals in mitochondrial LACTB-mediated lipid metabolism in cardiovascular-kidney-metabolic syndrome.
  28. A dynamical systems model for the total fission rate in Drp1-dependent mitochondrial fission.
  29. A mitochondrial redox switch licenses the onset of morphogenesis in animals.
  30. Synaptic composition, activity, mRNA translation and dynamics in combined single-synapse profiling using multimodal imaging.
  31. Mitochondrial plasticity: An emergent concept in neuronal plasticity and memory.
  32. Ferroptosis: mechanisms and therapeutic targets.
  33. MOTS-c modulates skeletal muscle function by directly binding and activating CK2.
  34. NOTCH1 mitochondria localization during heart development promotes mitochondrial metabolism and the endothelial-to-mesenchymal transition in mice.
  35. Cardiac effects of OPA1 protein promotion in a transgenic animal model.
  36. Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes.
  37. Mitochondrial heteroplasmy improves risk prediction for myeloid neoplasms.
  38. TET3 regulates terminal cell differentiation at the metabolic level.
  39. CalDAG-GEFI acts as a guanine nucleotide exchange factor for LRRK2 to regulate LRRK2 function and neurodegeneration.
  40. Toward trustable use of machine learning models of variant effects in the clinic.
  41. Efficient suppression of premature termination codons with alanine by engineered chimeric pyrrolysine tRNAs.
  42. SIngle cell level Genotyping Using scRna Data (SIGURD).
  43. The commitment of the human cell atlas to humanity.
  44. Computational technologies of the Human Cell Atlas.
  45. Type-II kinase inhibitors that target Parkinson's Disease-associated LRRK2.
  46. Human HDAC6 senses valine abundancy to regulate DNA damage.
  47. Predicting cell type-specific epigenomic profiles accounting for distal genetic effects.
  48. Simultaneous determination of cytosolic aminoacyl-tRNA synthetase activities by LC-MS/MS.
  1. EMBO Mol Med. 2024 Nov 20.
    Pathogenic PDE12 variants impair mitochondrial RNA processing causing neonatal mitochondrial disease.
    Lindsey Van Haute, Petra Páleníková, Jia Xin Tang, Pavel A Nash, Mariella T Simon, Angela Pyle, Monika Oláhová, Christopher A Powell, Pedro Rebelo-Guiomar, Alexander Stover, Michael Champion, Charulata Deshpande, Emma L Baple, Karen L Stals, Sian Ellard, Olivia Anselem, Clémence Molac, Giulia Petrilli, Laurence Loeuillet, Sarah Grotto, Tania Attie-Bitach, Jose E Abdenur, Robert W Taylor, Michal Minczuk.
      Pathogenic variants in either the mitochondrial or nuclear genomes are associated with a diverse group of human disorders characterized by impaired mitochondrial function. Within this group, an increasing number of families have been identified, where Mendelian genetic disorders implicate defective mitochondrial RNA biology. The PDE12 gene encodes the poly(A)-specific exoribonuclease, involved in the quality control of mitochondrial non-coding RNAs. Here, we report that disease-causing PDE12 variants in three unrelated families are associated with mitochondrial respiratory chain deficiencies and wide-ranging clinical presentations in utero and within the neonatal period, with muscle and brain involvement leading to marked cytochrome c oxidase (COX) deficiency in muscle and severe lactic acidosis. Whole exome sequencing of affected probands revealed novel, segregating bi-allelic missense PDE12 variants affecting conserved residues. Patient-derived primary fibroblasts demonstrate diminished steady-state levels of PDE12 protein, whilst mitochondrial poly(A)-tail RNA sequencing (MPAT-Seq) revealed an accumulation of spuriously polyadenylated mitochondrial RNA, consistent with perturbed function of PDE12 protein. Our data suggest that PDE12 regulates mitochondrial RNA processing and its loss results in neurological and muscular phenotypes.
    Keywords:  Exome Sequencing; Lactic Acidosis; Mitochondrial Disease; RNA Processing; tRNA
    DOI:  https://doi.org/10.1038/s44321-024-00172-5
  2. BMC Genomics. 2024 Nov 22. 25(1): 1133
    Respiratory Chain Complex I Deficiency in Leber Hereditary Optic Neuropathy: Insights from Ophthalmologic and Molecular Investigations in Tunisia.
    Latifa Chkioua, Yessine Amri, Chayma Sahli, Tawfik Nasri, Mohamed Omar Miladi, Taieb Massoud, Sandrine Laradi, Mohamed Ghorbel, Hassen Ben Abdennebi.
       BACKGROUND: Leber hereditary optic neuropathy (LHON) is a mitochondrial DNA (mtDNA) rare disease due to the pathogenic variant of the NADH dehydrogenase enzyme. LHON is characterized by a sudden central vision loss due to focal degeneration of the retinal ganglion cell layer and optic nerve. Symptoms usually appear between the age of 18 and 35 years. Some individuals present the mtDNA mutations but not presented the LHON clinical features. The heteroplasmic or homoplasmic character of the mutations among patients explains why they develop the disease or not even though they carry the pathogenic variant.
    METHODS: This study was performed in collaboration with the department of ophthalmology of Farhat Hached Hospital, Sousse, Tunisia. Screening for the common mutations in Mt-ND1 gene (m.3460G > A), Mt-ND4 gene (m.11778G > A) and Mt-ND6 gene (m.14484T > C) was performed in five Tunisian families by standard RFLP PCR, followed by direct sequencing of the entire of these genes. Indeed, bioinformatics tools were used to predict the potential functional impact of the identified mutations on the Human mitochondrial respiratory complex I protein.
    RESULTS: one novel p.L601M (m.1413 C > A) and four previously reported mutations were identified in this study including: rs199476112G > A (m.11778G > A); rs202227543G > A (m.14258G > A); rs1603224763 (m.14510 dup) and NC_012920.1: m.3244G > C. In this present report, only one patient was found carrying the primary point mutation (m. 11778G > A). The ophthalmologic findings showing major fundus changes included hyperemic optic discs; disc pseudo-oedema and microangiopathy leading to optic disc atrophy. The analyses of the stability of protein upon identified mutations using DynaMut tool server demonstrated that these variations induce a rigidification in the region where they are located.
    CONCLUSION: This is the first Tunisian report of mtDNA mutations identified in Tunisia causing the LHON. The main factors involved in the pathophysiological mechanisms of this disease are genetic, epigenetic, hormonal and environmental influences.
    Keywords:  Leber hereditary optic neuropathy; Mitochondrial DNA; Mutations; Pathophysiological mechanisms
    DOI:  https://doi.org/10.1186/s12864-024-11060-0
  3. Mol Cell. 2024 Nov 21. pii: S1097-2765(24)00880-3. [Epub ahead of print]84(22): 4261-4263
    AMPK: Balancing mitochondrial quality and quantity through opposite regulation of mitophagy pathways.
    Hui Jiang.
      In this issue of Molecular Cell, Longo et al.1 reveal that AMPK, a regulatory kinase activated by metabolic stress, inhibits NIX/BNIP3-dependent mitophagy to preserve mitochondrial quantity and activates PINK1/Parkin-dependent mitophagy to ensure mitochondrial quality.
    DOI:  https://doi.org/10.1016/j.molcel.2024.10.040
  4. Orphanet J Rare Dis. 2024 Nov 21. 19(1): 431
    Genotype-specific effects of elamipretide in patients with primary mitochondrial myopathy: a post hoc analysis of the MMPOWER-3 trial.
    MMPOWER-3 Trial Investigators
       BACKGROUND: As previously published, the MMPOWER-3 clinical trial did not demonstrate a significant benefit of elamipretide treatment in a genotypically diverse population of adults with primary mitochondrial myopathy (PMM). However, the prespecified subgroup of subjects with disease-causing nuclear DNA (nDNA) pathogenic variants receiving elamipretide experienced an improvement in the six-minute walk test (6MWT), while the cohort of subjects with mitochondrial DNA (mtDNA) pathogenic variants showed no difference versus placebo. These published findings prompted additional genotype-specific post hoc analyses of the MMPOWER-3 trial. Here, we present these analyses to further investigate the findings and to seek trends and commonalities among those subjects who responded to treatment, to build a more precise Phase 3 trial design for further investigation in likely responders.
    RESULTS: Subjects with mtDNA pathogenic variants or single large-scale mtDNA deletions represented 74% of the MMPOWER-3 population, with 70% in the mtDNA cohort having either single large-scale mtDNA deletions or MT-TL1 pathogenic variants. Most subjects in the nDNA cohort had pathogenic variants in genes required for mtDNA maintenance (mtDNA replisome), the majority of which were in POLG and TWNK. The mtDNA replisome post-hoc cohort displayed an improvement on the 6MWT, trending towards significant, in the elamipretide group when compared with placebo (25.2 ± 8.7 m versus 2.0 ± 8.6 m for placebo group; p = 0.06). The 6MWT results at week 24 in subjects with replisome variants showed a significant change in the elamipretide group subjects who had chronic progressive external ophthalmoplegia (CPEO) (37.3 ± 9.5 m versus - 8.0 ± 10.7 m for the placebo group; p = 0.0024). Pharmacokinetic (exposure-response) analyses in the nDNA cohort showed a weak positive correlation between plasma elamipretide concentration and 6MWT improvement.
    CONCLUSIONS: Post hoc analyses indicated that elamipretide had a beneficial effect in PMM patients with mtDNA replisome disorders, underscoring the importance of considering specific genetic subtypes in PMM clinical trials. These data serve as the foundation for a follow-up Phase 3 clinical trial (NuPOWER) which has been designed as described in this paper to determine the efficacy of elamipretide in patients with mtDNA maintenance-related disorders.
    CLASSIFICATION OF EVIDENCE: Class I CLINICALTRIALS.
    GOV IDENTIFIER: NCT03323749.
    Keywords:  Elamipretide; Mitochondria; MtDNA maintenance; MtDNA multiple deletions; PMM; Replisome
    DOI:  https://doi.org/10.1186/s13023-024-03421-5
  5. Eur J Hum Genet. 2024 Nov 22.
    WDR45-related encephalopathy mimicking Leigh syndrome associated with complex I deficiency: a case report.
    Giulia Ferrera, Kevork Derderian, Rossella Izzo, Barbara Gnutti, Andrea Legati, Giovanna Zorzi, Eleonora Lamantea, Arcangela Iuso, Anna Ardissone.
      Pathogenic WDR45 variants cause neurodevelopmental disorders (NDDs) including β-propeller protein-associated neurodegeneration (BPAN), characterized by developmental delay (DD), ataxia and extrapyramidal signs. Our patient, initially presenting at 22 months with DD, now, aged 7, shows intellectual disability, ataxia and rigidity. MRI findings were suggestive of Leigh syndrome, a mitochondrial disorder (MD) phenotype, with no brain iron accumulation. Reduced activity of respiratory chain complex I (cI) and complex II (cII) was identified in muscle and fibroblasts, and a cII reduction in muscle only; however, a primary MD was excluded. Exome sequencing revealed a de novo pathogenic WDR45 variant. Autophagic flux analysis showed a mildly reduced p62 response, with normal autophagy progression. This is the first report linking WDR45 to cI assembly and activity, indicating mitochondrial dysfunction as a potential pathophysiological BPAN mechanism. We recommend considering WDR45-related NDDs when diagnosing early-onset NDDs, particularly Leigh-like encephalopathies with cI deficiency, even without brain iron accumulation.
    DOI:  https://doi.org/10.1038/s41431-024-01745-1
  6. Commun Biol. 2024 Nov 21. 7(1): 1551
    Endogenous mitochondrial NAD(P)H fluorescence can predict lifespan.
    Christopher S Morrow, Pallas Yao, Carlos A Vergani-Junior, Praju Vikas Anekal, Paula Montero Llopis, Jeffrey W Miller, Bérénice A Benayoun, William B Mair.
      Many aging clocks have recently been developed to predict health outcomes and deconvolve heterogeneity in aging. However, existing clocks are limited by technical constraints, such as low spatial resolution, long processing time, sample destruction, and a bias towards specific aging phenotypes. Therefore, here we present a non-destructive, label-free and subcellular resolution approach for quantifying aging through optically resolving age-dependent changes to the biophysical properties of NAD(P)H in mitochondria through fluorescence lifetime imaging (FLIM) of endogenous NAD(P)H fluorescence. We uncover age-dependent changes to mitochondrial NAD(P)H across tissues in C. elegans that are associated with a decline in physiological function and construct non-destructive, label-free and cellular resolution models for prediction of age, which we refer to as "mito-NAD(P)H age clocks." Mito-NAD(P)H age clocks can resolve heterogeneity in the rate of aging across individuals and predict remaining lifespan. Moreover, we spatiotemporally resolve age-dependent changes to mitochondria across and within tissues, revealing multiple modes of asynchrony in aging and show that longevity is associated with a ubiquitous attenuation of these changes. Our data present a high-resolution view of mitochondrial NAD(P)H across aging, providing insights that broaden our understanding of how mitochondria change during aging and approaches which expand the toolkit to quantify aging.
    DOI:  https://doi.org/10.1038/s42003-024-07243-w
  7. JCI Insight. 2024 Nov 19. pii: e182209. [Epub ahead of print]
    Mutation of CRYAB encoding a conserved mitochondrial chaperone and anti-apoptotic protein causes hereditary optic atrophy.
    Chenghui Wang, Liyao Zhang, Zhipeng Nie, Min Liang, Hanqing Liu, Qiuzi Yi, Chunyan Wang, Cheng Ai, Juanjuan Zhang, Yinglong Gao, Yanchun Ji, Min-Xin Guan.
      The degeneration of retinal ganglion cells (RGC) due to mitochondrial dysfunctions manifests optic neuropathy. However, the molecular components of RGC linked to optic neuropathy manifestations remain largely unknown. Here, we identified a novel optic atrophy-causative CRYAB gene encoding a highly conserved major lens protein acting as mitochondrial chaperone and possessing anti-apoptotic activities. The heterozygous CRYAB mutation (c.313G>A, p. Glu105Lys) was cosegregated with autosomal dominant inheritance of optic atrophy in 3 Chinese families. The p.E105K mutation altered the structure and function of CRYAB, including decreased stability, reduced formation of oligomers and decreasing chaperone activity. Coimmunoprecipitation indicated that the p.E105K mutation reduced the interaction of CRYAB with apoptosis-associated cytochrome c and VDAC. The cell lines carrying the p.E105K mutation displayed promoting apoptosis, defective assembly, stability and activities of oxidative phosphorylation system and imbalance of mitochondrial dynamics. Involvement of CRYAB in optic atrophy was confirmed by phenotypic evaluations of Cryabp.E105K knock-in mice. These mutant mice exhibited ocular lesions including changing intra-retina layers, degeneration of RGCs, photoreceptor deficits and abnormal retinal vasculature. Furthermore, Cryab-deficient mice displayed elevated apoptosis and mitochondrial dysfunctions. Our findings provide new insight of pathophysiology of optic atrophy arising from RGC degeneration caused by CRYAB deficiency-induced elevated apoptosis and mitochondrial dysfunctions.
    Keywords:  Apoptosis; Bioenergetics; Genetics; Mitochondria; Ophthalmology
    DOI:  https://doi.org/10.1172/jci.insight.182209
  8. Trends Biochem Sci. 2024 Nov 21. pii: S0968-0004(24)00254-8. [Epub ahead of print]
    Textbook oxidative phosphorylation needs to be rewritten.
    Alicia J Kowaltowski, Fernando Abdulkader.
      Oxidative phosphorylation (OxPhos) is the energy-transfer process that generates most of our ATP, fueled by proton and electrical gradients across the inner mitochondrial membrane. A new surprising finding by Hernansanz-Agustín et al. demonstrates that between one-third and half of this gradient is attributable to Na+, transported in exchange for protons within complex I.
    Keywords:  complex I; ion transport; mitochondria; oxidative phosphorylation; sodium–proton exchange
    DOI:  https://doi.org/10.1016/j.tibs.2024.11.002
  9. FEBS J. 2024 Nov 20.
    Interaction with the cysteine-free protein HAX1 expands the substrate specificity and function of MIA40 beyond protein oxidation.
    Robin Alexander Rothemann, Dylan Stobbe, Michaela Nicole Hoehne-Wiechmann, Lena Maria Murschall, Esra Peker, Lara Katharina Knaup, Julia Racho, Markus Habich, Sarah Gerlich, Kim Jasmin Lapacz, Kathrin Ulrich, Jan Riemer.
      The mitochondrial disulphide relay machinery is essential for the import and oxidative folding of many proteins in the mitochondrial intermembrane space. Its core component, the import receptor MIA40 (also CHCHD4), serves as an oxidoreductase but also as a chaperone holdase, which initially interacts with its substrates non-covalently before introducing disulphide bonds for folding and retaining proteins in the intermembrane space. Interactome studies have identified diverse substrates of MIA40, among them the intrinsically disordered HCLS1-associated protein X-1 (HAX1). Interestingly, this protein does not contain cysteines, raising the question of how and to what end HAX1 can interact with MIA40. Here, we demonstrate that MIA40 non-covalently interacts with HAX1 independent of its redox-active cysteines. While HAX1 import is driven by its weak mitochondrial targeting sequence, its subsequent transient interaction with MIA40 stabilizes the protein in the intermembrane space. HAX1 solely depends on the holdase activity of MIA40, and the absence of MIA40 results in the aggregation, degradation and loss of HAX1. Collectively, our study introduces HAX1 as the first endogenous MIA40 substrate without cysteines and demonstrates the diverse functions of this highly conserved oxidoreductase and import receptor.
    Keywords:  HAX1; IMS; MIA40; mitochondria; mitochondrial disulphide relay
    DOI:  https://doi.org/10.1111/febs.17328
  10. Free Radic Biol Med. 2024 Nov 16. pii: S0891-5849(24)01018-9. [Epub ahead of print]226 237-250
    Inducible and reversible SOD2 knockdown in mouse skeletal muscle drives impaired pyruvate oxidation and reduced metabolic flexibility.
    Ethan L Ostrom, Rudy Stuppard, Aurora Mattson-Hughes, David J Marcinek.
       INTRODUCTION: Skeletal muscle mitochondrial dysfunction is a key characteristic of aging muscle and contributes to age related diseases such as sarcopenia, frailty, and type 2 diabetes. Mitochondrial oxidative stress has been implicated as a driving factor in these age-related diseases, however whether it is a cause, or a consequence of mitochondrial dysfunction remains to be determined. The development of flexible genetic models is an important tool to test the mechanistic role of mitochondrial oxidative stress on skeletal muscle metabolic dysfunction. We characterize a new model of inducible and reversible mitochondrial redox stress using a tetracycline controlled skeletal muscle specific short hairpin RNA targeted to superoxide dismutase 2 (iSOD2).
    METHODS: iSOD2 KD and control (CON) animals were administered doxycycline for 3- or 12- weeks and followed for up to 24 weeks and mitochondrial respiration and muscle contraction were measured to define the time course of SOD2 KD and muscle functional changes and recovery.
    RESULTS: Maximum knockdown of SOD2 protein occurred by 6 weeks and recovered by 24 weeks after DOX treatment. Mitochondrial aconitase activity and maximum mitochondrial respiration declined in KD muscle by 12 weeks and recovered by 24 weeks. There were no significant differences in antioxidant or mitochondrial biogenesis genes between groups. Twelve-week KD showed a small, but significant decrease in muscle fatigue resistance. The primary phenotype was reduced metabolic flexibility characterized by impaired pyruvate driven respiration when other substrates are present. The pyruvate dehydrogenase kinase inhibitor dichloroacetate partially restored pyruvate driven respiration, while the thiol reductant DTT did not.
    CONCLUSION: We use a model of inducible and reversible skeletal muscle SOD2 knockdown to demonstrate that elevated matrix superoxide reversibly impairs mitochondrial substrate flexibility characterized by impaired pyruvate oxidation. Despite the bioenergetic effect, the limited change in gene expression suggests that the elevated redox stress in this model is confined to the mitochondrial matrix.
    Keywords:  Inducible SOD2 knockdown; Metabolic inflexibility; Mitochondrial oxidative stress; Mitochondrial respiration; Pyruvate oxidation; Skeletal muscle
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2024.10.310
  11. Ageing Res Rev. 2024 Nov 16. pii: S1568-1637(24)00404-5. [Epub ahead of print] 102586
    Impact of Ageing and Disuse on Neuromuscular Junction and Mitochondrial Function and Morphology: Current Evidence and Controversies.
    Evgeniia Motanova, Marco Pirazzini, Samuele Negro, Ornella Rossetto, Marco Narici.
      Inactivity and ageing can have a detrimental impact on skeletal muscle and the neuromuscular junction (NMJ). Decreased physical activity results in muscle atrophy, impaired mitochondrial function, and NMJ instability. Ageing is associated with a progressive decrease in muscle mass, deterioration of mitochondrial function in the motor axon terminals and in myofibres, NMJ instability and loss of motor units. Focusing on the impact of inactivity and ageing, this review examines the consequences on NMJ stability and the role of mitochondrial dysfunction, delving into their complex relationship with ageing and disuse. Evidence suggests that mitochondrial dysfunction can be a pathogenic driver for NMJ alterations, with studies revealing the role of mitochondrial defects in motor neuron degeneration and NMJ instability. Two perspectives behind NMJ instability are discussed: one is that mitochondrial dysfunction in skeletal muscle triggers NMJ deterioration, the other envisages dysfunction of motor terminal mitochondria as a primary contributor to NMJ instability. While evidence from these studies supports both perspectives on the relationship between NMJ dysfunction and mitochondrial impairment, gaps persist in the understanding of how mitochondrial dysfunction can cause NMJ deterioration. Further research, both in humans and in animal models, is essential for unravelling the mechanisms and potential interventions for age- and inactivity-related neuromuscular and mitochondrial alterations.
    Keywords:  Ageing; Disuse; Mitochondrial Ca(2+); Mitochondrial dysfunction; Neuromuscular junction; Skeletal muscle
    DOI:  https://doi.org/10.1016/j.arr.2024.102586
  12. RNA. 2024 Nov 21. pii: rna.080254.124. [Epub ahead of print]
    Mitochondrial mRNA and the Small Subunit rRNA in Budding Yeasts Undergo 3'-End Processing at Conserved Species-specific Elements.
    Michael Anikin, Michael F Henry, Viktoria Hodorova, Hristo B Houbaviy, Jozef Nosek, Dimitri G Pestov, Dmitriy Markov.
      Respiration in eukaryotes depends on mitochondrial protein synthesis, which is performed by organelle-specific ribosomes translating organelle-encoded mRNAs. Although RNA maturation and stability are central events controlling mitochondrial gene expression, many of the molecular details in this pathway remain elusive. These include cis- and trans-regulatory factors that generate and protect the 3' ends. Here, we mapped the 3' ends of mitochondrial mRNAs of yeasts classified into multiple families of the subphylum Saccharomycotina. We found that the processing of mitochondrial 15S rRNA and mRNAs involves species-specific sequence elements, which we term 3'-end RNA processing elements (3'-RPEs). In Saccharomyces cerevisiae, the 3'-RPE has long been recognized as a conserved dodecamer sequence, which recent studies have shown to specifically interact with the nuclear genome-encoded pentatricopeptide repeat protein Rmd9. We also demonstrate that, analogous to Rmd9 in Saccharomyces cerevisiae, two Rmd9 orthologs from the Debaryomycetaceae family interact with their respective 3'-RPEs found in mRNAs and 15S rRNA. Thus, Rmd9-dependent processing of mitochondrial RNA precursors is a common mechanism among the families of the Saccharomycotina subphylum. This represents an example of mitochondrial-nuclear co-evolution. Surprisingly, we observed that 3'-RPEs often occur upstream of stop codons in complex I subunit mRNAs from yeasts of the CUG-Ser1 clade. We examined two of these mature mRNAs and found that their stop codons are indeed removed. Thus, translation of these transcripts would require a novel termination mechanism. Our findings establish Rmd9 as a key evolutionarily conserved factor in both mitochondrial mRNA metabolism and mitoribosome biogenesis in a variety of yeasts.
    Keywords:  15S rRNA; Rmd9; mRNA maturation; mitochondrial gene expression; yeast mitochondria
    DOI:  https://doi.org/10.1261/rna.080254.124
  13. bioRxiv. 2024 Nov 03. pii: 2024.10.30.621162. [Epub ahead of print]
    H 2 S remodels mitochondrial ultrastructure and destabilizes respiratory supercomplexes.
    David A Hanna, Brandon Chen, Yatrik M Shah, Oleh Khalimonchuk, Brian Cunniff, Ruma Banerjee.
      Mitochondrial form and function are intimately interconnected, responding to cellular stresses and changes in energy demand. Hydrogen sulfide, a product of amino acid metabolism, has dual roles as an electron transport chain substrate and complex IV (CIV) inhibitor, leading to a reductive shift, which has pleiotropic metabolic consequences. Luminal sulfide concentration in colon is high due to microbial activity, and in this study, we demonstrate that chronic sulfide exposure of colonocyte-derived cells leads to lower Mic60 and Mic19 expression that is correlated with a profound loss of cristae and lower mitochondrial networking. Sulfide-induced depolarization of the inner mitochondrial membrane activates Oma1-dependent cleavage of Opa1 and is associated with a profound loss of CI and CIV activities associated with respirasomes. Our study reveals a potential role for sulfide as an endogenous modulator of mitochondrial dynamics and suggests that this regulation is corrupted in hereditary or acquired diseases associated with elevated sulfide.
    Significance Statement: Hydrogen sulfide is a product of host as well as gut microbial metabolism and has the dual capacity for activating respiration as a substrate, and inhibiting it at the level of complex IV. In this study, we report that chronic albeit low-level sulfide exposure elicits profound changes in mitochondrial architecture in cultured human cells. Disruption of mitochondrial networks is reversed upon removal of sulfide from the growth chamber atmosphere. Sulfide-dependent depolarization of the inner mitochondrial membrane is associated with loss of cristae and respiratory supercomplexes. Our study reveals the potential for sulfide to be an endogenous regulator of mitochondrial ultrastructure and function via modulation of electron flux and for this process to be corrupted in sulfide dysregulated diseases.
    DOI:  https://doi.org/10.1101/2024.10.30.621162
  14. Nature. 2024 Nov 20.
    Common genetic variants contribute more to rare diseases than previously thought.
    Gerome Breen.
      
    Keywords:  DNA sequencing; Diseases; Genomics
    DOI:  https://doi.org/10.1038/d41586-024-03554-4
  15. JAMIA Open. 2024 Dec;7(4): ooae134
    MMFP-Tableau: enabling precision mitochondrial medicine through integration, visualization, and analytics of clinical and research health system electronic data.
    Ibrahim George-Sankoh, Laura E MacMullen, Asif T Chinwalla, Deanne Taylor, Rebecca D Ganetzky, Katelynn Stanley, Elizabeth M McCormick, Zarazuela Zolkipli-Cunningham, Marni J Falk.
       Objective: To describe a novel data integration workflow developed to automate clinical and research electronic health system data integration and harmonization from siloed sources for centralized access, visualization and analysis by clinicians and researchers in an end user-friendly customized analytic platform.
    Materials and Methods: A centralized, semi-automated framework provides data provenance and user access to integrated data sources. Data models are implemented leveraging a centralized server (Alteryx) for high-level analytics including scheduling, integration, and modeling. Data are then sent to a secure Tableau instance for end-user visualization and interaction, with minimal software development required.
    Results: MMFP-Tableau, named for its origin in the Mitochondrial Medicine Frontier Program (MMFP) at the Children's Hospital of Philadelphia (CHOP), has advanced efforts to realize precision medicine by facilitating expert clinician and researcher end-user direct access to integrated, highly robust health system datasets. This scalable data solution enables translational researchers to link subject and cohort clinical and research parameters with research samples; enhances external biopharma collaborations for clinical trial design, subject recruitment, and data tracking; accelerates retrospective clinical cohort data analysis; and improves complex data visualization for clinicians and researchers.
    Discussion: MMFP-Tableau promotes complex data integration, visibility, and advanced analytic capabilities to facilitate seamless multidisciplinary research, benefitting clinical care and research in rare disease patients and cohorts.
    Conclusion: The MMFP-Tableau data platform integrates multiple data sources across various siloed data platforms to transform complex data into readily accessible datasets. This approach represents a generalizable workflow concept readily adaptable to implement across diverse fields of medicine.
    Keywords:  data integration; data visualization; mitochondrial disease; personalized medicine
    DOI:  https://doi.org/10.1093/jamiaopen/ooae134
  16. J Cell Biol. 2024 Dec 02. pii: e202407193. [Epub ahead of print]223(12):
    PINK1 controls RTN3L-mediated ER autophagy by regulating peripheral tubule junctions.
    Ravi Chidambaram, Kamal Kumar, Smriti Parashar, Gowsalya Ramachandran, Shuliang Chen, Susan Ferro-Novick.
      Here, we report that the RTN3L-SEC24C endoplasmic reticulum autophagy (ER-phagy) receptor complex, the CUL3KLHL12 E3 ligase that ubiquitinates RTN3L, and the FIP200 autophagy initiating protein, target mutant proinsulin (Akita) condensates for lysosomal delivery at ER tubule junctions. When delivery was blocked, Akita condensates accumulated in the ER. In exploring the role of tubulation in these events, we unexpectedly found that loss of the Parkinson's disease protein, PINK1, reduced peripheral tubule junctions and blocked ER-phagy. Overexpression of the PINK1 kinase substrate, DRP1, increased junctions, reduced Akita condensate accumulation, and restored lysosomal delivery in PINK1-depleted cells. DRP1 is a dual-functioning protein that promotes ER tubulation and severs mitochondria at ER-mitochondria contact sites. DRP1-dependent ER tubulating activity was sufficient for suppression. Supporting these findings, we observed PINK1 associating with ER tubules. Our findings show that PINK1 shapes the ER to target misfolded proinsulin for RTN3L-SEC24C-mediated macro-ER-phagy at defined ER sites called peripheral junctions. These observations may have important implications for understanding Parkinson's disease.
    DOI:  https://doi.org/10.1083/jcb.202407193
  17. Pediatr Res. 2024 Nov 19.
    Implementation of multi-omics in diagnosis of pediatric rare diseases.
    Sara S Ali, Qifei Li, Pankaj B Agrawal.
      The rapid and accurate diagnosis of rare diseases is paramount in directing clinical management. In recent years, the integration of multi-omics approaches has emerged as a potential strategy to overcome diagnostic hurdles. This review examines the application of multi-omics technologies, including genomics, epigenomics, transcriptomics, proteomics, and metabolomics, in relation to the diagnostic journey of rare diseases. We explore how these combined approaches enhance the detection of pathogenic genetic variants and decipher molecular mechanisms. This review highlights the groundbreaking potential of multi-omics in advancing the precision medicine paradigm for rare diseases, offering insights into future directions and clinical applications. IMPACT: This review discusses using current tests and emerging technologies to diagnose pediatric rare diseases. We describe the next steps after inconclusive molecular testing and a structure for using multi-omics in further investigations. The use of multi-omics is expanding, and it is essential to incorporate it into clinical practice to enhance individualized patient care.
    DOI:  https://doi.org/10.1038/s41390-024-03728-w
  18. Ann Hum Genet. 2024 Nov 22.
    Intermittent episodes of acute severe encephalomyopathy and early death in two siblings caused by biallelic likely pathogenic variants in FASTKD2: Expanding phenotype and literature review.
    Namanpreet Kaur, Puneeth H Somashekar, Sekar Deepha, Periyasamy Govindaraj, Anju Shukla, Siddaramappa J Patil.
       INTRODUCTION: Combined oxidative phosphorylation (OXPHOS) deficiency 44 (COXPD44; MIM# 618855) is caused by biallelic pathogenic variants in FAS-activated serine-threonine kinase domain 2 (FASTKD2) (MIM# 612322). COXPD44 is characterized by variable clinical features-developmental delay, chronic epileptic encephalopathy, seizure disorder/status epilepticus and cerebellar ataxia. We ascertained one sib with episodic acute encephalomyopathy triggered by acute gastroenteritis and associated with haematological abnormalities, rhabdomyolysis leading to acute kidney injury, hypotensive shock leading to early death and a similarly affected sib with early death. Both siblings were normal neurologically in between the acute episodes.
    MATERIAL AND METHODS: Whole exome sequencing (WES) was performed in the elder sibling. Mitochondrial respiratory chain enzyme activity assaywas performed in fibroblast cells and muscle tissue of the elder sibling. Also, Adenosine triphosphate (ATP) determination assay was done in fibroblast cells of the elder sibling.
    RESULTS: WES revealed compound heterozygous missense likely pathogenic variants in FASTKD2. Mitochondrial respiratory chain enzyme activity in muscle tissue showed reduced complex IV activity and ATP determination assay showed a reduction of ATP in skin fibroblasts.
    CONCLUSION: Herein, we report two siblings with novel clinical phenotype associated with COXPD44. Our report further validates the biallelic variants in FASTKD2 associated with the variable phenotypes and mitochondrial OXPHOS defect.
    Keywords:  FASTKD2; OXPHOS deficiency; acute encephalomyopathy; complex IV deficiency; haematological abnormalities
    DOI:  https://doi.org/10.1111/ahg.12585
  19. bioRxiv. 2024 Nov 07. pii: 2024.11.06.622291. [Epub ahead of print]
    Loss of mitochondrial enzyme GPT2 leads to reprogramming of synaptic glutamate metabolism.
    Ozan Baytas, Shawn M Davidson, Julie A Kauer, Eric M Morrow.
      Recessive loss-of-function mutations in the mitochondrial enzyme Glutamate Pyruvate Transaminase 2 (GPT2) cause intellectual disability in children. Given this cognitive disorder, and because glutamate metabolism is tightly regulated to sustain excitatory neurotransmission, here we investigate the role of GPT2 in synaptic function. GPT2 catalyzes a reversible reaction interconverting glutamate and pyruvate with alanine and alpha-ketoglutarate, a TCA cycle intermediate; thereby, GPT2 may play an important role in linking mitochondrial tricarboxylic acid (TCA) cycle with synaptic transmission. In mouse brain, we find that GPT2 is enriched in mitochondria of synaptosomes (isolated synaptic terminals). Loss of Gpt2 in mouse appears to lead to reprogramming of glutamate and glutamine metabolism, and to decreased glutamatergic synaptic transmission. Whole-cell patch-clamp recordings in pyramidal neurons of CA1 hippocampal slices from Gpt2- null mice reveal decreased excitatory post-synaptic currents (mEPSCs) without changes in mEPSC frequency, or importantly, changes in inhibitory post-synaptic currents (mIPSCs). Additional evidence of defective glutamate release included reduced levels of glutamate released from Gpt2- null synaptosomes measured biochemically. Glutamate release from synaptosomes was rescued to wild-type levels by alpha-ketoglutarate supplementation. Additionally, we observed evidence of altered metabolism in isolated Gpt2- null synaptosomes: decreased TCA cycle intermediates, and increased glutamate dehydrogenase activity. Notably, alterations in the TCA cycle and the glutamine pool were alleviated by alpha-ketoglutarate supplementation. In conclusion, our data support a model whereby GPT2 mitochondrial activity may contribute to glutamate availability in pre-synaptic terminals, thereby highlighting potential interactions between pre-synaptic mitochondrial metabolism and synaptic transmission.
    DOI:  https://doi.org/10.1101/2024.11.06.622291
  20. IUCrJ. 2025 Jan 01.
    Structure of an ex vivoDrosophila TOM complex determined by single-particle cryoEM.
    Agalya Periasamy, Pamela Ornelas, Thomas Bausewein, Naomi Mitchell, Jiamin Zhao, Leonie M Quinn, Werner Kuehlbrandt, Jacqueline M Gulbis.
      Most mitochondrial precursor proteins are encoded in the cell nucleus and synthesized on cytoplasmic ribosomes. The translocase of the outer membrane (TOM) is the main protein-import pore of mitochondria, recognizing nascent precursors of mitochondrially targeted proteins and transferring them across the outer membrane. A 3.3 Å resolution map and molecular model of a TOM complex from Drosophila melanogaster, obtained by single-particle electron cryomicroscopy, is presented. As the first reported structure of a transgenic protein expressed and purified ex vivo from Drosophila, the method provides impetus for parallel structural and genetic analyses of protein complexes linked to human pathology. The core TOM complex extracted from native membranes of the D. melanogaster retina contains transgenic Tom40 co-assembled with four endogenous TOM components: Tom22, Tom5, Tom6 and Tom7. The Drosophila TOM structure presented here shows that the human and Drosophila TOM are very similar, with small conformational changes at two subunit interfaces attributable to variation in lipid-binding residues. The new structure provides an opportunity to pinpoint general features that differentiate the TOM structures of higher and unicellular eukaryotes. While the quaternary fold of the assembly is retained, local nuances of structural elements implicated in precursor import are indicative of subtle evolutionary change.
    Keywords:  Drosophila melanogaster; TOM complex; Tom40; macromolecular machines; membrane proteins; mitochondrial translocases; single-particle cryoEM
    DOI:  https://doi.org/10.1107/S2052252524011011
  21. bioRxiv. 2024 Nov 01. pii: 2024.10.31.621392. [Epub ahead of print]
    Mitochondrial NADK2-dependent NADPH controls Tau oligomer uptake in human neurons.
    Evelyn Pardo, Taylor Kim, Horst Wallrabe, Kristine E Zengeler, Vijay Kumar Sagar, Garnett Mingledorff, Xuehan Sun, Ammasi Periasamy, John R Lukens, George S Bloom, Andrés Norambuena.
      Alterations in NADH and NADPH metabolism are associated with aging, cancer, and Alzheimer's Disease. Using 2P-FLIM imaging of the mitochondrial NAD(P)H in live human neurons and PS19 mouse brains, we show that tau oligomers (TauO) upregulate the mitochondrial de novo NADPH synthesis through NADK2. This process controls LRP1-mediated internalization of TauO, setting a vicious cycle for further TauO internalization. Thus, mitochondrial NADK2-dependent NADPH controls a key step in TauO toxicity.
    DOI:  https://doi.org/10.1101/2024.10.31.621392
  22. Cell Rep. 2024 Nov 19. pii: S2211-1247(24)01334-2. [Epub ahead of print]43(12): 114983
    Tak1 licenses mitochondrial transfer from astrocytes to POMC neurons to maintain glucose and cholesterol homeostasis.
    Kaili Yin, Tingting Zhang, Xiyuan Lu, Qing Shen, Kaiyue Gu, Ying Huang, Chaonan Li, Jingyi Hou, Juxue Li, Guo Zhang.
      It remains incompletely understood how the astrocytes in the mediobasal hypothalamus (MBH) regulate systemic glucose and cholesterol metabolism. Here, we show that MBH astrocytic Tak1 (transforming growth factor β [TGF-β]-activated kinase 1) controls the metabolism of glucose and cholesterol. Tak1 is expressed in MBH astrocytes and activated after a short-term nutritional excess. In chow-fed mice, astrocytic deletion of Tak1 across the brain or its suppression in the MBH impairs glucose tolerance, reduces insulin sensitivity, and results in hypercholesterolemia. Astrocytic Tak1 activation in the MBH alleviates these symptoms in mice fed a high-fat diet (HFD). We show that astrocytic Tak1 modulates the activity of proopiomelanocortin (POMC) neurons and enables the transport of mitochondria from astrocytes to POMC neurons. In astrocytic Tak1 knockout mice, supplementation of CD38, a molecule that is crucial in mitochondrial transfer, restores glucose and cholesterol homeostasis. Overall, these findings highlight an important role of MBH astrocytic Tak1 in glucose and cholesterol metabolism.
    Keywords:  CP: Metabolism; CP: Neuroscience; Tak1; astrocyte; glucose homeostasis; hypothalamus; mitochondrial transfer
    DOI:  https://doi.org/10.1016/j.celrep.2024.114983
  23. Immunol Lett. 2024 Nov 16. pii: S0165-2478(24)00120-2. [Epub ahead of print] 106946
    VACCINE SAFETY IN CHILDREN WITH GENETICALLY CONFIRMED MITOCHONDRIAL DISEASE.
    Annemarie de Vreugd, Franz A Zimmermann, Katja Steinbrücker, Maaike C de Vries, Lonneke de Boer, Mirian Ch Janssen, Martina Huemer, Saskia B Wortmann.
      We here explore adverse events following immunization (AEFI) in children with mitochondrial disease (MD) recruited from two expertise centers in Austria (SALK) and The Netherlands (RUMC). Parents completed a questionnaire on the type of immunizations received and AEFI in a post-vaccination exposure period of seven days. 95 individuals were invited to this study, of whom 30 (median age 13.4 years) participated. Together these individuals had received 376 immunizations with a median of 12 vaccinations each. In 316 of 376 (84%) vaccinations no AEFI occurred, 22 patients (73%) never experienced any AEFI. Eight patients experienced 76 AEFI after 60 vaccinations, these were mild (redness (n=9) /pain at injection site (n=21), fever (n=44), gastrointestinal complaints (n= 2)). None had a metabolic deterioration or seizures, no patient was admitted to the hospital. Although our data is limited by the small sample size, this may aid in discussing responsible immunization decisions with parents.
    Keywords:  adverse effect; adverse events following immunization (AEFI); epilepsy; immunization; metabolic deterioration; seizure; side effect; vaccination
    DOI:  https://doi.org/10.1016/j.imlet.2024.106946
  24. Hum Mol Genet. 2024 Nov 20. pii: ddae166. [Epub ahead of print]
    De novo missense variants in the PP2A regulatory subunit PPP2R2B in a neurodevelopmental syndrome: potential links to mitochondrial dynamics and spinocerebellar ataxias.
    Priyanka Sandal, Chian Ju Jong, Ronald A Merrill, Grace J Kollman, Austin H Paden, Eric G Bend, Jennifer Sullivan, Rebecca C Spillmann, Vandana Shashi, Anneke T Vulto-van Silfhout, Rolph Pfundt, Bert B A de Vries, Pan P Li, Louise S Bicknell, Stefan Strack.
      The heterotrimeric protein phosphatase 2A (PP2A) complex catalyzes about half of Ser/Thr dephosphorylations in eukaryotic cells. A CAG repeat expansion in the neuron-specific protein PP2A regulatory subunit PPP2R2B gene causes spinocerebellar ataxia type 12 (SCA12). We established five monoallelic missense variants in PPP2R2B (four confirmed as de novo) as a cause of intellectual disability with developmental delay (R149P, T246K, N310K, E37K, I427T). In addition to moderate to severe intellectual disability and developmental delay, affected individuals presented with seizures, microcephaly, aggression, hypotonia, as well as broad-based or stiff gait. We used biochemical and cellular assays, including a novel luciferase complementation assay to interrogate PP2A holoenzyme assembly and activity, as well as deregulated mitochondrial dynamics as possible pathogenic mechanisms. Cell-based assays documented impaired ability of PPP2R2B missense variants to incorporate into the PP2A holoenzyme, localize to mitochondria, induce fission of neuronal mitochondria, and dephosphorylate the mitochondrial fission enzyme dynamin-related protein 1. AlphaMissense-based pathogenicity prediction suggested that an additional seven unreported missense variants may be pathogenic. In conclusion, our studies identify loss-of-function at the PPP2R2B locus as the basis for syndromic intellectual disability with developmental delay. They also extend PPP2R2B-related pathologies from neurodegenerative (SCA12) to neurodevelopmental disorders and suggests that altered mitochondrial dynamics may contribute to mechanisms.
    Keywords:  cerebellar ataxias; dynamin-related protein 1; mitochondrial dynamics; neurodevelopmental disorders; protein phosphatase 2A
    DOI:  https://doi.org/10.1093/hmg/ddae166
  25. bioRxiv. 2024 Oct 31. pii: 2024.10.30.620676. [Epub ahead of print]
    The mitochondrial-targeted peptide therapeutic elamipretide improves cardiac and skeletal muscle function during aging without detectable changes in tissue epigenetic or transcriptomic age.
    Wayne Mitchell, Gavin Pharaoh, Alexander Tyshkovskiy, Matthew Campbell, David J Marcinek, Vadim N Gladyshev.
      Aging-related decreases in cardiac and skeletal muscle function are strongly associated with various comorbidities. Elamipretide (ELAM), a novel mitochondrial-targeted peptide, has demonstrated broad therapeutic efficacy in ameliorating disease conditions associated with mitochondrial dysfunction across both clinical and pre-clinical models. ELAM is proposed to restore mitochondrial bioenergetic function by stabilizing inner membrane structure and increasing oxidative phosphorylation coupling and efficiency. Although ELAM treatment effectively attenuates physiological declines in multiple tissues in rodent aging models, it remains unclear whether these functional improvements correlate with favorable changes in molecular biomarkers of aging. Herein, we investigated the impact of 8-week ELAM treatment on pre- and post-measures of C57BL/6J mice frailty, skeletal muscle, and cardiac muscle function, coupled with post-treatment assessments of biological age and affected molecular pathways. We found that health status, as measured by frailty index, cardiac strain, diastolic function, and skeletal muscle force are significantly diminished with age, with skeletal muscle force changing in a sex-dependent manner. Conversely, ELAM mitigated frailty accumulation and was able to partially reverse these declines, as evidenced by treatment-induced increases in cardiac strain and muscle fatigue resistance. Despite these improvements, we did not detect statistically significant changes in gene expression or DNA methylation profiles indicative of molecular reorganization or reduced biological age in most ELAM-treated groups. However, pathway analyses revealed that ELAM treatment showed pro-longevity shifts in gene expression such as upregulation of genes involved in fatty acid metabolism, mitochondrial translation and oxidative phosphorylation, and downregulation of inflammation. Together, these results indicate that ELAM treatment is effective at mitigating signs of sarcopenia and heart failure in an aging mouse model, but that these functional improvements occur independently of detectable changes in epigenetic and transcriptomic age. Thus, some age-related changes in function may be uncoupled from changes in molecular biological age.
    DOI:  https://doi.org/10.1101/2024.10.30.620676
  26. EMBO Mol Med. 2024 Nov 20.
    PDE12 mediated pruning of the poly-A tail of mitochondrial DNA-encoded tRNAs is essential for survival.
    Chenxiao Yu, Marco Tigano, Erin L Seifert.
      
    DOI:  https://doi.org/10.1038/s44321-024-00171-6
  27. Cell Metab. 2024 Nov 14. pii: S1550-4131(24)00403-0. [Epub ahead of print]
    Human genetics identify convergent signals in mitochondrial LACTB-mediated lipid metabolism in cardiovascular-kidney-metabolic syndrome.
    Shen Li, Hongbo Liu, Hailong Hu, Eunji Ha, Praveena Prasad, Brenita C Jenkins, Ujjalkumar Subhash Das, Sarmistha Mukherjee, Kyosuke Shishikura, Renming Hu, Daniel J Rader, Liming Pei, Joseph A Baur, Megan L Matthews, Garret A FitzGerald, Melanie R McReynolds, Katalin Susztak.
      The understanding of cardiovascular-kidney-metabolic syndrome remains difficult despite recently performed large scale genome-wide association studies. Here, we identified beta-lactamase (LACTB), a novel gene whose expression is targeted by genetic variations causing kidney dysfunction and hyperlipidemia. Mice with LACTB deletion developed impaired glucose tolerance, elevated lipid levels, and increased sensitivity to kidney disease, while mice with tubule-specific overexpression of LACTB were protected from kidney injury. We show that LACTB is a novel mitochondrial protease cleaving and activating phospholipase A2 group VI (PLA2G6), a kidney-metabolic risk gene itself. Genetic deletion of PLA2G6 in tubule-specific LACTB-overexpressing mice abolished the protective function of LACTB. Via mouse and human lipidomic studies, we show that LACTB and downstream PLA2G6 convert oxidized phosphatidylethanolamine to lyso-phosphatidylethanolamine and thereby regulate mitochondrial function and ferroptosis. In summary, we identify a novel gene and a core targetable pathway for kidney-metabolic disorders.
    Keywords:  GWAS; cardiovascular-kidney-metabolic syndrome; ferroptosis; genetics; kidney disease; mitochondria; phospholipase; phospholipid; serine protease
    DOI:  https://doi.org/10.1016/j.cmet.2024.10.007
  28. PLoS Comput Biol. 2024 Nov 18. 20(11): e1012596
    A dynamical systems model for the total fission rate in Drp1-dependent mitochondrial fission.
    Anna K Leinheiser, Colleen C Mitchell, Ethan Rooke, Stefan Strack, Chad E Grueter.
      Mitochondrial hyperfission in response to cellular insult is associated with reduced energy production and programmed cell death. Thus, there is a critical need to understand the molecular mechanisms coordinating and regulating the complex process of mitochondrial fission. We develop a nonlinear dynamical systems model of dynamin related protein one (Drp1)-dependent mitochondrial fission and use it to identify parameters which can regulate the total fission rate (TFR) as a function of time. The TFR defined from a nondimensionalization of the model undergoes a Hopf bifurcation with bifurcation parameter [Formula: see text] where [Formula: see text] is the total concentration of mitochondrial fission factor (Mff) and k+ and k- are the association and dissociation rate constants between oligomers on the outer mitochondrial membrane. The variable μ can be thought of as the maximum build rate over the disassembling rate of oligomers. Though the nondimensionalization of the system results in four dimensionless parameters, we found the TFR and the cumulative total fission (TF) depend strongly on only one, μ. Interestingly, the cumulative TF does not monotonically increase as μ increases. Instead it increases with μ to a certain point and then begins to decrease as μ continues to increase. This non-monotone dependence on μ suggests interventions targeting k+, k-, or [Formula: see text] may have a non-intuitive impact on the fission mechanism. Thus understanding the impact of regulatory parameters, such as μ, may assist future therapeutic target selection.
    DOI:  https://doi.org/10.1371/journal.pcbi.1012596
  29. bioRxiv. 2024 Oct 29. pii: 2024.10.28.620733. [Epub ahead of print]
    A mitochondrial redox switch licenses the onset of morphogenesis in animals.
    Updip Kahlon, Francesco Dalla Ricca, Saraswathi J Pillai, Marine Olivetta, Kevin M Tharp, Li-En Jao, Omaya Dudin, Kent McDonald, Mustafa G Aydogan.
      Embryos undergo pre-gastrulation cleavage cycles to generate a critical cell mass before transitioning to morphogenesis. The molecular underpinnings of this transition have traditionally centered on zygotic chromatin remodeling and genome activation1,2, as their repression can prevent downstream processes of differentiation and organogenesis. Despite precedents that oxygen depletion can similarly suspend development in early embryos3-6, hinting at a pivotal role for oxygen metabolism in this transition, whether there is a bona fide chemical switch that licenses the onset of morphogenesis remains unknown. Here we discover that a mitochondrial oxidant acts as a metabolic switch to license the onset of animal morphogenesis. Concomitant with the instatement of mitochondrial membrane potential, we found a burst-like accumulation of mitochondrial superoxide (O2 -) during fly blastoderm formation. In vivo chemistry experiments revealed that an electron leak from site IIIQo at ETC Complex III is responsible for O2 - production. Importantly, depleting mitochondrial O2 - fully mimics anoxic conditions and, like anoxia, induces suspended animation prior to morphogenesis, but not after. Specifically, H2O2, and not ONOO-, NO, or HO•, can single-handedly account for this mtROS-based response. We demonstrate that depleting mitochondrial O2 - similarly prevents the onset of morphogenetic events in vertebrate embryos and ichthyosporea, close relatives of animals. We postulate that such redox-based metabolic licensing of morphogenesis is an ancient trait of holozoans that couples the availability of oxygen to development, conserved from early-diverging animal relatives to vertebrates.
    DOI:  https://doi.org/10.1101/2024.10.28.620733
  30. bioRxiv. 2024 Oct 28. pii: 2024.10.28.620504. [Epub ahead of print]
    Synaptic composition, activity, mRNA translation and dynamics in combined single-synapse profiling using multimodal imaging.
    Reuven Falkovich, Sameer Aryal, Jasmine Wang, Morgan Sheng, Mark Bathe.
      The function of neuronal circuits, and its perturbation by psychoactive molecules or disease-associated genetic variants, is governed by the interplay between synapse activity and synaptic protein localization and synthesis across a heterogeneous synapse population. Here, we combine in situ measurement of synaptic multiprotein compositions and activation states, synapse activity in calcium traces or glutamate spiking, and local translation of specific genes, across the same individual synapses. We demonstrate how this high-dimensional data enables identification of interdependencies in the multiprotein-activity network, and causal dissection of complex synaptic phenotypes in disease-relevant chemical and genetic NMDAR loss of function that translate in vivo . We show how this method generalizes to other subcellular systems by deriving mitochondrial protein networks, and, using support vector machines, its value in overcoming animal variability in phenotyping. Integrating multiple synapse information modalities enables deep structure-function characterization of synapse populations and their responses to genetic and chemical perturbations.
    DOI:  https://doi.org/10.1101/2024.10.28.620504
  31. Neurobiol Dis. 2024 Nov 16. pii: S0969-9961(24)00342-5. [Epub ahead of print] 106740
    Mitochondrial plasticity: An emergent concept in neuronal plasticity and memory.
    Typhaine Comyn, Thomas Preat, Alice Pavlowsky, Pierre-Yves Plaçais.
      Mitochondria are classically viewed as 'on demand' energy suppliers to neurons in support of their activity. In order to adapt to a wide range of demands, mitochondria need to be highly dynamic and capable of adjusting their metabolic activity, shape, and localization. Although these plastic properties give them a central support role in basal neuronal physiology, recent lines of evidence point toward a role for mitochondria in the regulation of high-order cognitive functions such as memory formation. In this review, we discuss the interplay between mitochondrial function and neural plasticity in sustaining memory formation at the molecular and cellular levels. First, we explore the global significance of mitochondria in memory formation. Then, we will detail the memory-relevant cellular and molecular mechanisms of mitochondrial plasticity. Finally, we focus on those mitochondrial functions, including but not limited to ATP production, that give mitochondria their pivotal role in memory formation. Altogether, this review highlights the central role of mitochondrial structural and functional plasticity in supporting and regulating neuronal plasticity and memory.
    Keywords:  Energy; Glia; Memory; Mitochondria dynamics; TCA cycle
    DOI:  https://doi.org/10.1016/j.nbd.2024.106740
  32. MedComm (2020). 2024 Dec;5(12): e70010
    Ferroptosis: mechanisms and therapeutic targets.
    Qian Zhou, Yu Meng, Jiayuan Le, Yuming Sun, Yating Dian, Lei Yao, Yixiao Xiong, Furong Zeng, Xiang Chen, Guangtong Deng.
      Ferroptosis is a nonapoptotic form of cell death characterized by iron-dependent lipid peroxidation in membrane phospholipids. Since its identification in 2012, extensive research has unveiled its involvement in the pathophysiology of numerous diseases, including cancers, neurodegenerative disorders, organ injuries, infectious diseases, autoimmune conditions, metabolic disorders, and skin diseases. Oxidizable lipids, overload iron, and compromised antioxidant systems are known as critical prerequisites for driving overwhelming lipid peroxidation, ultimately leading to plasma membrane rupture and ferroptotic cell death. However, the precise regulatory networks governing ferroptosis and ferroptosis-targeted therapy in these diseases remain largely undefined, hindering the development of pharmacological agonists and antagonists. In this review, we first elucidate core mechanisms of ferroptosis and summarize its epigenetic modifications (e.g., histone modifications, DNA methylation, noncoding RNAs, and N6-methyladenosine modification) and nonepigenetic modifications (e.g., genetic mutations, transcriptional regulation, and posttranslational modifications). We then discuss the association between ferroptosis and disease pathogenesis and explore therapeutic approaches for targeting ferroptosis. We also introduce potential clinical monitoring strategies for ferroptosis. Finally, we put forward several unresolved issues in which progress is needed to better understand ferroptosis. We hope this review will offer promise for the clinical application of ferroptosis-targeted therapies in the context of human health and disease.
    Keywords:  epigenetics; ferroptosis; human disease; lipid peroxidation
    DOI:  https://doi.org/10.1002/mco2.70010
  33. iScience. 2024 Nov 15. 27(11): 111212
    MOTS-c modulates skeletal muscle function by directly binding and activating CK2.
    Hiroshi Kumagai, Su-Jeong Kim, Brendan Miller, Hirofumi Zempo, Kumpei Tanisawa, Toshiharu Natsume, Shin Hyung Lee, Junxiang Wan, Naphada Leelaprachakul, Michi Emma Kumagai, Ricardo Ramirez, Hemal H Mehta, Kevin Cao, Tae Jung Oh, James A Wohlschlegel, Jihui Sha, Yuichiro Nishida, Noriyuki Fuku, Shohei Dobashi, Eri Miyamoto-Mikami, Mizuki Takaragawa, Mizuho Fuku, Toshinori Yoshihara, Hisashi Naito, Ryoko Kawakami, Suguru Torii, Taishi Midorikawa, Koichiro Oka, Megumi Hara, Chiharu Iwasaka, Yosuke Yamada, Yasuki Higaki, Keitaro Tanaka, Kelvin Yen, Pinchas Cohen.
      MOTS-c is a mitochondrial microprotein that improves metabolism. Here, we demonstrate CK2 is a direct and functional target of MOTS-c. MOTS-c directly binds to CK2 and activates it in cell-free systems. MOTS-c administration to mice prevented skeletal muscle atrophy and enhanced muscle glucose uptake, which were blunted by suppressing CK2 activity. Interestingly, the effects of MOTS-c are tissue-specific. Systemically administered MOTS-c binds to CK2 in fat and muscle, yet stimulates CK2 activity in muscle while suppressing it in fat by differentially modifying CK2-interacting proteins. Notably, a naturally occurring MOTS-c variant, K14Q MOTS-c, has reduced binding to CK2 and does not activate it or elicit its effects. Male K14Q MOTS-c carriers exhibited a higher risk of sarcopenia and type 2 diabetes (T2D) in an age- and physical-activity-dependent manner, whereas females had an age-specific reduced risk of T2D. Altogether, these findings provide evidence that CK2 is required for MOTS-c effects.
    Keywords:  Physiology; cell biology
    DOI:  https://doi.org/10.1016/j.isci.2024.111212
  34. Nat Commun. 2024 Nov 16. 15(1): 9945
    NOTCH1 mitochondria localization during heart development promotes mitochondrial metabolism and the endothelial-to-mesenchymal transition in mice.
    Jie Wang, Rui Zhao, Sha Xu, Xiang-Yu Zhou, Ke Cai, Yu-Ling Chen, Ze-Yu Zhou, Xin Sun, Yan Shi, Feng Wang, Yong-Hao Gui, Hui Tao, Jian-Yuan Zhao.
      Notch signaling activation drives an endothelial-to-mesenchymal transition (EndMT) critical for heart development, although evidence suggests that the reprogramming of endothelial cell metabolism can regulate endothelial function independent of canonical cell signaling. Herein, we investigated the crosstalk between Notch signaling and metabolic reprogramming in the EndMT process. Biochemically, we find that the NOTCH1 intracellular domain (NICD1) localizes to endothelial cell mitochondria, where it interacts with and activates the complex to enhance mitochondrial metabolism. Targeting NICD1 to mitochondria induces more EndMT compared with wild-type NICD1, and small molecule activation of PDH during pregnancy improves the phenotype in a mouse model of congenital heart defect. A NOTCH1 mutation observed in non-syndromic tetralogy of Fallot patients decreases NICD1 mitochondrial localization and subsequent PDH activity in heart tissues. Altogether, our findings demonstrate NICD1 enrichment in mitochondria of the developing mouse heart, which induces EndMT by activating PDH and subsequently improving mitochondrial metabolism.
    DOI:  https://doi.org/10.1038/s41467-024-54407-7
  35. PLoS One. 2024 ;19(11): e0310394
    Cardiac effects of OPA1 protein promotion in a transgenic animal model.
    Kitti Bruszt, Orsolya Horvath, Katalin Ordog, Szilard Toth, Kata Juhasz, Eszter Vamos, Katalin Fekete, Ferenc Gallyas, Kalman Toth, Robert Halmosi, Laszlo Deres.
      Mitochondria form a dynamic network in cells, regulated by the balance between mitochondrial fusion and fission. The inhibition of mitochondrial fission can have positive effects in acute ischemic/reperfusion injury models by preventing the fall in mitochondrial membrane potential associated with fission processes. However, inhibition of fission in chronic models is disadvantageous because it obstructs the elimination of damaged mitochondrial fragments. OPA1, in view of previous results, is a possible therapeutic target as a fusion promoter and structure stabilizer protein. We used transgenic mice in which the OMA1 cleavage sites of OPA1 were deleted. This resulted in a higher representation of L-OPA1 compared to S-OPA1. After genotyping and model validation, all animals were examined by echocardiograph on two occasions, at weeks 11 and 36. Histological samples were taken from hearts to examine mitochondrial morphology and structure remodeling. The signaling pathways related to mitochondrial dynamic processes were evaluated. Cardiomyocytes were isolated from neonatal mice to determine the efficiency of mitochondrial respiration using the SeaHorse assay method. OPA1 protein promotion has a negative effect on systolic function during aging. We confirmed that volume overload and ventricular remodeling did not manifest. The reason behind the loss of pump function might be, at least partly, due to the energy deficit caused by mitochondrial respiratory failure and damage in mitochondrial quality control pathways.
    DOI:  https://doi.org/10.1371/journal.pone.0310394
  36. Mol Cell. 2024 Nov 13. pii: S1097-2765(24)00869-4. [Epub ahead of print]
    Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes.
    Kyusik Q Kim, Jeffrey J Li, Ankanahalli N Nanjaraj Urs, Miguel E Pacheco, Victor Lasehinde, Timo Denk, Petr Tesina, Shota Tomomatsu, Yoshitaka Matsuo, Elesa McDonald, Roland Beckmann, Toshifumi Inada, Rachel Green, Hani S Zaher.
      In yeast, multiprotein bridging factor 1 (Mbf1) has been proposed to function in the integrated stress response (ISR) as a transcriptional coactivator by mediating a direct interaction between general transcription machinery and the process's key effector, Gcn4. However, mounting evidence has demonstrated that Mbf1 (and its human homolog EDF1) is recruited to collided ribosomes, a known activator of the ISR. In this study, we connect these otherwise seemingly disparate functions of Mbf1. Our biochemical and structural analyses reveal that Mbf1 functions as a core ISR factor by interacting with collided ribosomes to mediate Gcn2 activation. We further show that Mbf1 serves no role as a transcriptional coactivator of Gcn4. Instead, Mbf1 is required for optimal stress-induced eukaryotic initiation factor 2α (eIF2α) phosphorylation and downstream de-repression of GCN4 translation. Collectively, our data establish that Mbf1 functions in ISR signaling by acting as a direct sensor of stress-induced ribosome collisions.
    Keywords:  Gcn2; Gcn4; Mbf1; integrated stress response; ribosome; ribosome collisions; translation
    DOI:  https://doi.org/10.1016/j.molcel.2024.10.029
  37. Nat Commun. 2024 Nov 22. 15(1): 10133
    Mitochondrial heteroplasmy improves risk prediction for myeloid neoplasms.
    Yun Soo Hong, Sergiu Pasca, Wen Shi, Daniela Puiu, Nicole J Lake, Monkol Lek, Meng Ru, Megan L Grove, Anna Prizment, Corinne E Joshu, Elizabeth A Platz, Eliseo Guallar, Dan E Arking, Lukasz P Gondek.
      Clonal hematopoiesis of indeterminate potential is the primary pathogenic risk factor for myeloid neoplasms, while heteroplasmy (mutations in a subset of cellular mitochondrial DNA) is another marker of clonal expansion associated with hematological malignancies. We explore how these two markers relate and influence myeloid neoplasms incidence, and their role in risk stratification. We find that heteroplasmy is more common in individuals with clonal hematopoiesis of indeterminate potential, particularly those with higher variant allele fractions, multiple mutations, or spliceosome machinery mutations. Individuals with both markers have a higher risk of myeloid neoplasms than those with either alone. Furthermore, heteroplasmic variants with higher predicted deleteriousness increase the risk of myeloid neoplasms. Incorporating heteroplasmy in an existing risk score model for individuals with clonal hematopoiesis of indeterminate potential significantly improves sensitivity and better identifies high-risk groups. This suggests heteroplasmy as a clonal expansion marker and potentially as a biomarker for myeloid neoplasms development.
    DOI:  https://doi.org/10.1038/s41467-024-54443-3
  38. Nat Commun. 2024 Nov 18. 15(1): 9749
    TET3 regulates terminal cell differentiation at the metabolic level.
    Isabel Mulet, Carmen Grueso-Cortina, Mireia Cortés-Cano, Daniela Gerovska, Guangming Wu, Stefania Alexandra Iakab, Daniel Jimenez-Blasco, Andrea Curtabbi, Pablo Hernansanz-Agustín, Harmony Ketchum, Israel Manjarrés-Raza, F Thomas Wunderlich, Juan Pedro Bolaños, Meelad M Dawlaty, Carsten Hopf, José Antonio Enríquez, Marcos J Araúzo-Bravo, Natalia Tapia.
      TET-family members play a critical role in cell fate commitment. Indeed, TET3 is essential to postnatal development due to yet unknown reasons. To define TET3 function in cell differentiation, we have profiled the intestinal epithelium at single-cell level from wild-type and Tet3 knockout mice. We have found that Tet3 is mostly expressed in differentiated enterocytes. In the absence of TET3, enterocytes exhibit an aberrant differentiation trajectory and do not acquire a physiological cell identity due to an impairment in oxidative phosphorylation, specifically due to an ATP synthase assembly deficiency. Moreover, spatial metabolomics analysis has revealed that Tet3 knockout enterocytes exhibit an unphysiological metabolic profile when compared with their wild-type counterparts. In contrast, no metabolic differences have been observed between both genotypes in the stem cell compartment where Tet3 is mainly not expressed. Collectively, our findings suggest a mechanism by which TET3 regulates mitochondrial function and, thus, terminal cell differentiation at the metabolic level.
    DOI:  https://doi.org/10.1038/s41467-024-54044-0
  39. Sci Adv. 2024 Nov 22. 10(47): eadn5417
    CalDAG-GEFI acts as a guanine nucleotide exchange factor for LRRK2 to regulate LRRK2 function and neurodegeneration.
    Qinfang Liu, Bingxu Huang, Noah Guy Lewis Guiberson, Shifan Chen, Dong Zhu, Gang Ma, Xin-Ming Ma, Jill R Crittenden, Jianzhong Yu, Ann M Graybiel, Ted M Dawson, Valina L Dawson, Yulan Xiong.
      Mutations in LRRK2 are the most common genetic cause of Parkinson's disease (PD). LRRK2 protein contains two enzymatic domains: a GTPase (Roc-COR) and a kinase domain. Disease-causing mutations are found in both domains. Now, studies have focused largely on LRRK2 kinase activity, while attention to its GTPase function is limited. LRRK2 is a guanine nucleotide-binding protein, but the mechanism of direct regulation of its GTPase activity remains unclear and its physiological GEF is not known. Here, we identified CalDAG-GEFI (CDGI) as a physiological GEF for LRRK2. CDGI interacts with LRRK2 and increases its GDP to GTP exchange activity. CDGI modulates LRRK2 cellular functions and LRRK2-induced neurodegeneration in both LRRK2 Drosophila and mouse models. Together, this study identified the physiological GEF for LRRK2 and provides strong evidence that LRRK2 GTPase is regulated by GAPs and GEFs. The LRRK2 GTPase, GAP, or GEF activities have the potential to serve as therapeutic targets, which is distinct from the direct LRRK2 kinase inhibition.
    DOI:  https://doi.org/10.1126/sciadv.adn5417
  40. Am J Hum Genet. 2024 Nov 13. pii: S0002-9297(24)00380-X. [Epub ahead of print]
    Toward trustable use of machine learning models of variant effects in the clinic.
    Mafalda Dias, Rose Orenbuch, Debora S Marks, Jonathan Frazer.
      There has been considerable progress in building models to predict the effect of missense substitutions in protein-coding genes, fueled in large part by progress in applying deep learning methods to sequence data. These models have the potential to enable clinical variant annotation on a large scale and hence increase the impact of patient sequencing in guiding diagnosis and treatment. To realize this potential, it is essential to provide reliable assessments of model performance, scope of applicability, and robustness. As a response to this need, the ClinGen Sequence Variant Interpretation Working Group, Pejaver et al., recently proposed a strategy for validation and calibration of in-silico predictions in the context of guidelines for variant annotation. While this work marks an important step forward, the strategy presented still has important limitations. We propose core principles and recommendations to overcome these limitations that can enable both more reliable and more impactful use of variant effect prediction models in the future.
    DOI:  https://doi.org/10.1016/j.ajhg.2024.10.011
  41. Nucleic Acids Res. 2024 Nov 18. pii: gkae1048. [Epub ahead of print]
    Efficient suppression of premature termination codons with alanine by engineered chimeric pyrrolysine tRNAs.
    Aya Awawdeh, Alejandro Tapia, Sarah A Alshawi, Olabode Dawodu, Sarah A Gaier, Caitlin Specht, Jean-Denis Beaudoin, Jeffery M Tharp, Oscar Vargas-Rodriguez.
      Mutations that introduce premature termination codons (PTCs) within protein-coding genes are associated with incurable and severe genetic diseases. Many PTC-associated disorders are life-threatening and have no approved medical treatment options. Suppressor transfer RNAs (sup-tRNAs) with the capacity to translate PTCs represent a promising therapeutic strategy to treat these conditions; however, developing novel sup-tRNAs with high efficiency and specificity often requires extensive engineering and screening. Moreover, these efforts are not always successful at producing more efficient sup-tRNAs. Here we show that a pyrrolysine (Pyl) tRNA (tRNAPyl), which naturally translates the UAG stop codon, offers a favorable scaffold for developing sup-tRNAs that restore protein synthesis from PTC-containing genes. We created a series of rationally designed Pyl tRNAScaffold Suppressor-tRNAs (PASS-tRNAs) that are substrates of bacterial and human alanyl-tRNA synthetase. Using a PTC-containing fluorescent reporter gene, PASS-tRNAs restore protein synthesis to wild-type levels in bacterial cells. In human cells, PASS-tRNAs display robust and consistent PTC suppression in multiple reporter genes, including pathogenic mutations in the tumor suppressor gene BRCA1 associated with breast and ovarian cancer. Moreover, PTC suppression occurred with high codon specificity and no observed cellular dysregulation. Collectively, these results unveil a new class of sup-tRNAs with encouraging potential for tRNA-based therapeutic applications.
    DOI:  https://doi.org/10.1093/nar/gkae1048
  42. Brief Bioinform. 2024 Sep 23. pii: bbae604. [Epub ahead of print]25(6):
    SIngle cell level Genotyping Using scRna Data (SIGURD).
    Martin Grasshoff, Milena Kalmer, Nicolas Chatain, Kim Kricheldorf, Angela Maurer, Ralf Weiskirchen, Steffen Koschmieder, Ivan G Costa.
       MOTIVATION: By accounting for variants within measured transcripts, it is possible to evaluate the status of somatic variants using single-cell RNA-sequencing (scRNA-seq) and to characterize their clonality. However, the sparsity (very few reads per transcript) or bias in protocols (favoring 3' ends of the transcripts) makes the chance of capturing somatic variants very unlikely. This can be overcome by targeted sequencing or the use of mitochondrial variants as natural barcodes for clone identification. Currently, available computational tools focus on genotyping, but do not provide functionality for combined analysis of somatic and mitochondrial variants and functional analysis such as characterization of gene expression changes in detected clones.
    RESULTS: Here, we propose SIGURD (SIngle cell level Genotyping Using scRna Data) (SIGURD), which is an R-based pipeline for the clonal analysis of scRNA-seq data. This allows the quantification of clones by leveraging both somatic and mitochondrial variants. SIGURD also allows for functional analysis after clonal detection: association of clones with cell populations, detection of differentially expressed genes across clones, and association of somatic and mitochondrial variants. Here, we demonstrate the power of SIGURD by analyzing single-cell data of colony-forming cells derived from patients with myeloproliferative neoplasms.
    Keywords:  clonality; leukemia; myeloproliferative neoplasms; single-cell RNA-seq; single-cell genotyping
    DOI:  https://doi.org/10.1093/bib/bbae604
  43. Nat Commun. 2024 Nov 20. 15(1): 10019
    The commitment of the human cell atlas to humanity.
    Ido Amit, Kristin Ardlie, Fabiana Arzuaga, Gordon Awandare, Gary Bader, Alexander Bernier, Piero Carninci, Stacey Donnelly, Roland Eils, Alistair R R Forrest, Henry T Greely, Roderic Guigo, Nir Hacohen, Muzlifah Haniffa, Emily Sarah Kirby, Bartha Maria Knoppers, Arnold Kriegstein, Ed S Lein, Sten Linnarsson, Partha P Majumder, Miriam Merad, Kerstin Meyer, Musa M Mhlanga, Garry Nolan, Ntobeko A B Ntusi, Dana Pe'er, Shyam Prabhakar, Maili Raven-Adams, Aviv Regev, Orit Rozenblatt-Rosen, Senjuti Saha, Andrea Saltzman, Alex K Shalek, Jay W Shin, Henk Stunnenberg, Sarah A Teichmann, Timothy Tickle, Alexandra-Chloe Villani, Christine Wells, Barbara Wold, Huanming Yang, Xiaowei Zhuang.
      The Human Cell Atlas (HCA) is a global partnership "to create comprehensive reference maps of all human cells-the fundamental units of life - as a basis for both understanding human health and diagnosing, monitoring, and treating disease." ( https://www.humancellatlas.org/ ) The atlas shall characterize cells from diverse individuals across the globe to better understand human biology. HCA proactively considers the priorities of, and benefits accrued to, contributing communities. Here, we lay out principles and action items that have been adopted to affirm HCA's commitment to equity so that the atlas is beneficial to all of humanity.
    DOI:  https://doi.org/10.1038/s41467-024-54306-x
  44. Nature. 2024 Nov;635(8039): 773-775
    Computational technologies of the Human Cell Atlas.
    Amber Dance.
      
    Keywords:  Biological techniques; Computational biology and bioinformatics; Genomics; Machine learning; Technology
    DOI:  https://doi.org/10.1038/d41586-024-03762-y
  45. bioRxiv. 2024 Oct 31. pii: 2024.09.17.613365. [Epub ahead of print]
    Type-II kinase inhibitors that target Parkinson's Disease-associated LRRK2.
    Nicolai D Raig, Katherine J Surridge, Marta Sanz-Murillo, Verena Dederer, Andreas Krämer, Martin P Schwalm, Lewis Elson, Deep Chatterjee, Sebastian Mathea, Thomas Hanke, Andres E Leschziner, Samara L Reck-Peterson, Stefan Knapp.
      Aberrant increases in kinase activity of leucine-rich repeat kinase 2 (LRRK2) are associated with Parkinson's disease (PD). Numerous LRRK2-selective type-I kinase inhibitors have been developed and some have entered clinical trials. In this study, we present the first LRRK2-selective type-II kinase inhibitors. Targeting the inactive conformation of LRRK2 is functionally distinct from targeting the active-like conformation using type-I inhibitors. We designed these inhibitors using a combinatorial chemistry approach fusing selective LRRK2 type-I and promiscuous type-II inhibitors by iterative cycles of synthesis supported by structural biology and activity testing. Our current lead structures are selective and potent LRRK2 inhibitors. Through cellular assays, cryo-electron microscopy structural analysis, and in vitro motility assays, we show that our inhibitors stabilize the open, inactive kinase conformation. These new conformation-specific compounds will be invaluable as tools to study LRRK2's function and regulation, and expand the potential therapeutic options for PD.
    DOI:  https://doi.org/10.1101/2024.09.17.613365
  46. Nature. 2024 Nov 20.
    Human HDAC6 senses valine abundancy to regulate DNA damage.
    Jiali Jin, Tong Meng, Yuanyuan Yu, Shuheng Wu, Chen-Chen Jiao, Sihui Song, Ya-Xu Li, Yu Zhang, Yuan-Yuan Zhao, Xinran Li, Zixin Wang, Yu-Fan Liu, Runzhi Huang, Jieling Qin, Yihua Chen, Hao Cao, Xiao Tan, Xin Ge, Cong Jiang, Jianhuang Xue, Jian Yuan, Dianqing Wu, Wei Wu, Ci-Zhong Jiang, Ping Wang.
      As an essential branched amino acid, valine is pivotal for protein synthesis, neurological behaviour, haematopoiesis and leukaemia progression1-3. However, the mechanism by which cellular valine abundancy is sensed for subsequent cellular functions remains undefined. Here we identify that human histone deacetylase 6 (HDAC6) serves as a valine sensor by directly binding valine through a primate-specific SE14 repeat domain. The nucleus and cytoplasm shuttling of human, but not mouse, HDAC6 is tightly controlled by the intracellular levels of valine. Valine deprivation leads to HDAC6 retention in the nucleus and induces DNA damage. Mechanistically, nuclear-localized HDAC6 binds and deacetylates ten-eleven translocation 2 (TET2) to initiate active DNA demethylation, which promotes DNA damage through thymine DNA glycosylase-driven excision. Dietary valine restriction inhibits tumour growth in xenograft and patient-derived xenograft models, and enhances the therapeutic efficacy of PARP inhibitors. Collectively, our study identifies human HDAC6 as a valine sensor that mediates active DNA demethylation and DNA damage in response to valine deprivation, and highlights the potential of dietary valine restriction for cancer treatment.
    DOI:  https://doi.org/10.1038/s41586-024-08248-5
  47. Nat Commun. 2024 Nov 16. 15(1): 9951
    Predicting cell type-specific epigenomic profiles accounting for distal genetic effects.
    Alan E Murphy, William Beardall, Marek Rei, Mike Phuycharoen, Nathan G Skene.
      Understanding how genetic variants affect the epigenome is key to interpreting GWAS, yet profiling these effects across the non-coding genome remains challenging due to experimental scalability. This necessitates accurate computational models. Existing machine learning approaches, while progressively improving, are confined to the cell types they were trained on, limiting their applicability. Here, we introduce Enformer Celltyping, a deep learning model which incorporates distal effects of DNA interactions, up to 100,000 base-pairs away, to predict epigenetic signals in previously unseen cell types. Using DNA and chromatin accessibility data for epigenetic imputation, Enformer Celltyping outperforms current best-in-class approaches and generalises across cell types and biological regions. Moreover, we propose a framework for evaluating models on genetic variant effect prediction using regulatory quantitative trait loci mapping studies, highlighting current limitations in genomic deep learning models. Despite this, Enformer Celltyping can also be used to study cell type-specific genetic enrichment of complex traits.
    DOI:  https://doi.org/10.1038/s41467-024-54441-5
  48. Nucleic Acids Res. 2024 Nov 22. pii: gkae1134. [Epub ahead of print]
    Simultaneous determination of cytosolic aminoacyl-tRNA synthetase activities by LC-MS/MS.
    Marisa I Mendes, Nicole I Wolf, Joëlle Rudinger-Thirion, Dominic Lenz, Magali Frugier, Patrick Verloo, Hanna Mandel, Joshua Manor, Rachel Kassel, Willemijn E Corpeleijn, Sanne van der Rijt, Elsbeth M Schroor, Silvy J M van Dooren, Christian Staufner, Gajja S Salomons, Desirée E C Smith.
      In recent years, pathogenic variants in ARS genes, encoding aminoacyl-tRNA synthetases (aaRSs), have been associated with human disease. Patients harbouring pathogenic variants in ARS genes have clinical signs partly unique to certain aaRSs defects, partly overlapping between the different aaRSs defects. Diagnosis relies mostly on genetics and remains challenging, often requiring functional validation of new ARS variants. In this study, we present the development and validation of a method to simultaneously determine aminoacylation activities of all cytosolic aaRSs (encoded by ARS1 genes) in one single cell lysate, improving diagnosis in suspected ARS1 disorders and facilitating functional characterization of ARS1 variants of unknown significance. As proof of concept, we show enzyme activities of five individuals with variants in different ARS1 genes, demonstrating the usability and convenience of the presented method.
    DOI:  https://doi.org/10.1093/nar/gkae1134
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