bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2024–08–04
43 papers selected by
Catalina Vasilescu, Helmholz Munich
  1. Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import.
  2. LRPPRC and SLIRP synergize to maintain sufficient and orderly mammalian mitochondrial translation.
  3. Opa1 processing is dispensable in mouse development but is protective in mitochondrial cardiomyopathy.
  4. Significantly reduced, but balanced, rates of mitochondrial fission and fusion are sufficient to maintain the integrity of yeast mitochondrial DNA.
  5. Axonal mitophagy in retinal ganglion cells.
  6. Mitochondrial DNA disorders in neuromuscular diseases in diverse populations.
  7. Mitochondrial bioenergetics and cardiolipin remodeling abnormalities in mitochondrial trifunctional protein deficiency.
  8. Lactate-carried Mitochondrial Energy Overflow.
  9. Novel Imaging Tools to Study Mitochondrial Dynamics in Caenorhabditis elegans.
  10. The Discovery of Mitochondria-Endoplasmic Reticulum Contact Sites (MERCs) as Mitochondria-Associated Membranes (MAMs).
  11. AutoMitoNetwork: Software for analyzing mitochondrial networks in autofluorescence images to enable label-free cell classification.
  12. Homozygosity for a Rare FASTKD2 Variant Resulting in an Adult Onset Autosomal Recessive Mitochondrial Podocytopathy.
  13. Single-mitochondrion sequencing uncovers distinct mutational patterns and heteroplasmy landscape in mouse astrocytes and neurons.
  14. Two novel SUCLA2 variants cause mitochondrial DNA depletion syndrome, type 5 in two siblings.
  15. The TOM complex from an evolutionary perspective and the functions of TOMM70.
  16. Loss of primary cilia and dopaminergic neuroprotection in pathogenic LRRK2-driven and idiopathic Parkinson's disease.
  17. SLC45A4 encodes a mitochondrial putrescine transporter that promotes GABA de novo synthesis.
  18. Maternal age enhances purifying selection on pathogenic mutations in complex I genes of mammalian mtDNA.
  19. Safety and efficacy of deoxycytidine/deoxythymidine combination therapy in POLG-related disorders: 6-month interim results of an open-label, single arm, phase 2 trial.
  20. The subtherapeutic dose of valproic acid induces the activity of cardiolipin-dependent proteins.
  21. Comparative functional analysis reveals differential nucleotide sensitivity between human and mouse UCP1.
  22. Mitochondria-derived vesicles: potential nano-batteries to recharge the cellular powerhouse.
  23. The membrane transporter SLC25A48 enables transport of choline into human mitochondria.
  24. Inhibition of K63 ubiquitination by G-Protein pathway suppressor 2 (GPS2) regulates mitochondria-associated translation.
  25. Mitochondria can substitute for parvalbumin to lower cytosolic calcium levels in the murine fast skeletal muscle.
  26. Tafazzin deficiency causes substantial remodeling in the lipidome of a mouse model of Barth Syndrome cardiomyopathy.
  27. Guidelines for mitochondrial RNA analysis.
  28. Histone β-hydroxybutyrylation is critical in reversal of sarcopenia.
  29. Loss of MEF2C function by enhancer mutation leads to neuronal mitochondria dysfunction and motor deficits in mice.
  30. IMPDH2 filaments protect from neurodegeneration in AMPD2 deficiency.
  31. Development of a functional beige fat cell line uncovers independent subclasses of cells expressing UCP1 and the futile creatine cycle.
  32. Single-nucleus transcriptomics identifies separate classes of UCP1 and futile cycle adipocytes.
  33. RAB12-LRRK2 Complex Suppresses Primary Ciliogenesis and Regulates Centrosome Homeostasis in Astrocytes.
  34. Orthogonal Persulfide Generation through Precision Tools Provides Insights into Mitochondrial Sulfane Sulfur.
  35. Guidance for estimating penetrance of monogenic disease-causing variants in population cohorts.
  36. Natural history of deoxyguanosine kinase deficiency.
  37. The role of heat shock protein B8 in neuronal protection against oxidative stress and mitochondrial dysfunction: A literature review.
  38. Comparing methylation levels assayed in GC-rich regions with current and emerging methods.
  39. Artificial Intelligence in Metabolomics: A Current Review.
  40. Transfer RNA acetylation regulates in vivo mammalian stress signaling.
  41. A replisome-associated histone H3-H4 chaperone required for epigenetic inheritance.
  42. Mitochondria to plasma membrane redox signaling is essential for fatty acid β-oxidation-driven insulin secretion.
  43. Pharmacogenomics polygenic risk score: Ready or not for prime time?
  1. bioRxiv. 2024 Jul 19. pii: 2024.07.17.604013. [Epub ahead of print]
    Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import.
    Ya-Ting Chang, Benjamin A Barad, Hamidreza Rahmani, Brian M Zid, Danielle A Grotjahn.
      Most of the mitochondria proteome is nuclear-encoded, synthesized by cytoplasmic ribosomes, and targeted to mitochondria post-translationally. However, a subset of mitochondrial-targeted proteins is imported co-translationally, although the molecular mechanisms governing this process remain unclear. We employ cellular cryo-electron tomography to visualize interactions between cytoplasmic ribosomes and mitochondria in Saccharomyces cerevisiae. We use surface morphometrics tools to identify a subset of ribosomes optimally oriented on mitochondrial membranes for protein import. This allows us to establish the first subtomogram average structure of a cytoplasmic ribosome on the surface of the mitochondria in the native cellular context, which showed three distinct connections with the outer mitochondrial membrane surrounding the peptide exit tunnel. Further, this analysis demonstrated that cytoplasmic ribosomes primed for mitochondrial protein import cluster on the outer mitochondrial membrane at sites of local constrictions of the outer and inner mitochondrial membrane. Overall, our study reveals the architecture and the spatial organization of cytoplasmic ribosomes at the mitochondrial surface, providing a native cellular context to define the mechanisms that mediate efficient mitochondrial co-translational protein import.
    DOI:  https://doi.org/10.1101/2024.07.17.604013
  2. Nucleic Acids Res. 2024 Aug 01. pii: gkae662. [Epub ahead of print]
    LRPPRC and SLIRP synergize to maintain sufficient and orderly mammalian mitochondrial translation.
    Diana Rubalcava-Gracia, Kristina Bubb, Fredrik Levander, Stephen P Burr, Amelie V August, Patrick F Chinnery, Camilla Koolmeister, Nils-Göran Larsson.
      In mammals, the leucine-rich pentatricopeptide repeat protein (LRPPRC) and the stem-loop interacting RNA-binding protein (SLIRP) form a complex in the mitochondrial matrix that is required throughout the life cycle of most mitochondrial mRNAs. Although pathogenic mutations in the LRPPRC and SLIRP genes cause devastating human mitochondrial diseases, the in vivo function of the corresponding proteins is incompletely understood. We show here that loss of SLIRP in mice causes a decrease of complex I levels whereas other OXPHOS complexes are unaffected. We generated knock-in mice to study the in vivo interdependency of SLIRP and LRPPRC by mutating specific amino acids necessary for protein complex formation. When protein complex formation is disrupted, LRPPRC is partially degraded and SLIRP disappears. Livers from Lrpprc knock-in mice had impaired mitochondrial translation except for a marked increase in the synthesis of ATP8. Furthermore, the introduction of a heteroplasmic pathogenic mtDNA mutation (m.C5024T of the tRNAAla gene) into Slirp knockout mice causes an additive effect on mitochondrial translation leading to embryonic lethality and reduced growth of mouse embryonic fibroblasts. To summarize, we report that the LRPPRC/SLIRP protein complex is critical for maintaining normal complex I levels and that it also coordinates mitochondrial translation in a tissue-specific manner.
    DOI:  https://doi.org/10.1093/nar/gkae662
  3. Sci Adv. 2024 Aug 02. 10(31): eadp0443
    Opa1 processing is dispensable in mouse development but is protective in mitochondrial cardiomyopathy.
    Sofia Ahola, Lilli A Pazurek, Fiona Mayer, Philipp Lampe, Steffen Hermans, Lore Becker, Oana V Amarie, Helmut Fuchs, Valerie Gailus-Durner, Martin Hrabe de Angelis, Dietmar Riedel, Hendrik Nolte, Thomas Langer.
      Mitochondrial fusion and fission accompany adaptive responses to stress and altered metabolic demands. Inner membrane fusion and cristae morphogenesis depends on optic atrophy 1 (Opa1), which is expressed in different isoforms and is cleaved from a membrane-bound, long to a soluble, short form. Here, we have analyzed the physiological role of Opa1 isoforms and Opa1 processing by generating mouse lines expressing only one cleavable Opa1 isoform or a non-cleavable variant thereof. Our results show that expression of a single cleavable or non-cleavable Opa1 isoform preserves embryonic development and the health of adult mice. Opa1 processing is dispensable under metabolic and thermal stress but prolongs life span and protects against mitochondrial cardiomyopathy in OXPHOS-deficient Cox10-/- mice. Mechanistically, loss of Opa1 processing disturbs the balance between mitochondrial biogenesis and mitophagy, suppressing cardiac hypertrophic growth in Cox10-/- hearts. Our results highlight the critical regulatory role of Opa1 processing, mitochondrial dynamics, and metabolism for cardiac hypertrophy.
    DOI:  https://doi.org/10.1126/sciadv.adp0443
  4. bioRxiv. 2024 Jul 19. pii: 2024.07.18.604121. [Epub ahead of print]
    Significantly reduced, but balanced, rates of mitochondrial fission and fusion are sufficient to maintain the integrity of yeast mitochondrial DNA.
    Brett T Wisniewski, Laura L Lackner.
      Mitochondria exist as dynamic tubular networks and the morphology of these networks impacts organelle function and cell health. Mitochondrial morphology is maintained in part by the opposing activities of mitochondrial fission and fusion. Mitochondrial fission and fusion are also required to maintain mitochondrial DNA (mtDNA) integrity. In Saccharomyces cerevisiae , the simultaneous inhibition of mitochondrial fission and fusion results in increased mtDNA mutation and the consequent loss of respiratory competence. The mechanism by which fission and fusion maintain mtDNA integrity is not fully understood. Previous work demonstrates that mtDNA is spatially linked to mitochondrial fission sites. Here, we extend this finding using live-cell imaging to localize mtDNA to mitochondrial fusion sites. While mtDNA is present at sites of mitochondrial fission and fusion, mitochondrial fission and fusion rates are not altered in cells lacking mtDNA. Using alleles that alter mitochondrial fission and fusion rates, we find that mtDNA integrity can be maintained in cells with significantly reduced, but balanced, rates of fission and fusion. In addition, we find that increasing mtDNA copy number reduces the loss of respiratory competence in double mitochondrial fission-fusion mutants. Our findings add novel insights into the relationship between mitochondrial dynamics and mtDNA integrity.
    DOI:  https://doi.org/10.1101/2024.07.18.604121
  5. Cell Commun Signal. 2024 Jul 29. 22(1): 382
    Axonal mitophagy in retinal ganglion cells.
    Yang Liang, Yulin Li, Qing Jiao, Muyang Wei, Yan Wang, Aoteng Cui, Zhihui Li, Guangyu Li.
      Neurons, exhibiting unique polarized structures, rely primarily on the mitochondrial production of ATP to maintain their hypermetabolic energy requirements. To maintain a normal energy supply, mitochondria are transported to the distal end of the axon. When mitochondria within the axon are critically damaged beyond their compensatory capacity, they are cleared via autophagosomal phagocytosis, and the degradation products are recycled to replenish energy. When the mitochondria are dysfunctional or their transport processes are blocked, axons become susceptible to degeneration triggered by energy depletion, resulting in neurodegenerative diseases. As the final checkpoint for mitochondrial quality control, axonal mitophagy is vital for neuronal growth, development, injury, and regeneration. Furthermore, abnormal axonal mitophagy is crucial in the pathogenesis of optic nerve-related diseases such as glaucoma. We review recent studies on axonal mitophagy and summarize the progress of research on axonal mitophagy in optic nerve-related diseases to provide insights into diseases associated with axonal damage in optic ganglion cells.
    Keywords:  Axon; Energy; Mitophagy; Optic nerve
    DOI:  https://doi.org/10.1186/s12964-024-01761-0
  6. Ann Clin Transl Neurol. 2024 Aug 02.
    Mitochondrial DNA disorders in neuromuscular diseases in diverse populations.
    ICGNMD Consortium
      Neuromuscular features are common in mitochondrial DNA (mtDNA) disorders. The genetic architecture of mtDNA disorders in diverse populations is poorly understood. We analysed mtDNA variants from whole-exome sequencing data in neuromuscular patients from South Africa, Brazil, India, Turkey and Zambia. In 998 individuals, there were two definite diagnoses, two possible diagnoses and eight secondary findings. Surprisingly, common pathogenic mtDNA variants found in people of European ancestry were very rare. Whole-exome or -genome sequencing from undiagnosed patients with neuromuscular symptoms should be re-analysed for mtDNA variants, but the landscape of pathogenic mtDNA variants differs around the world.
    DOI:  https://doi.org/10.1002/acn3.52141
  7. JCI Insight. 2024 Aug 01. pii: e176887. [Epub ahead of print]
    Mitochondrial bioenergetics and cardiolipin remodeling abnormalities in mitochondrial trifunctional protein deficiency.
    Eduardo Vieira Neto, Meicheng Wang, Austin J Szuminsky, Lethicia Ferraro, Erik Koppes, Yudong Wang, Clinton Van't Land, Al-Walid Mohsen, Geancarlo Zanatta, Areeg H El-Gharbawy, Tamil S Anthonymuthu, Yulia Y Tyurina, Vladimir A Tyurin, Valerian Kagan, Hülya Bayir, Jerry Vockley.
      Mitochondrial trifunctional protein (TFP) deficiency is an inherited metabolic disorder leading to a block in long-chain fatty acid β-oxidation. Mutations in either HADHA and HADHB, which encode the TFPα and β subunits, respectively, usually result in combined TFP deficiency. A single common mutation, HADHA c.1528G>C (p.E510Q), leads to isolated 3-hydroxyacyl-CoA dehydrogenase (LCHAD) deficiency. TFP also catalyzes a step in the remodeling of cardiolipin (CL), a phospholipid critical to mitochondrial membrane stability and function. We explored the effect of mutations in TFP subunits on CL and other phospholipid content and composition and the consequences of these changes on mitochondrial bioenergetics in patient-derived fibroblasts. Abnormalities in these parameters varied extensively among different fibroblasts, and some cells were able to maintain basal oxygen consumption rates similar to controls. Although CL reduction was universally identified, a simultaneous increase in monolysocardiolipins was discrepant among cells. A similar profile was seen in liver mitochondria isolates from a TFP-deficient mouse model. Response to new potential drugs targeting cardiolipin metabolism might be dependent on patient genotype.
    Keywords:  Fatty acid oxidation; Genetics; Intermediary metabolism; Metabolism; Mitochondria
    DOI:  https://doi.org/10.1172/jci.insight.176887
  8. bioRxiv. 2024 Jul 20. pii: 2024.07.19.604361. [Epub ahead of print]
    Lactate-carried Mitochondrial Energy Overflow.
    Daniela Rauseo, Yasna Contreras-Baeza, Hugo Faurand, Nataly Cárcamo, Raibel Suárez, Alexandra von Faber-Castell, Franco Silva, Valentina Mora-González, Matthias T Wyss, Felipe Baeza-Lehnert, Iván Ruminot, Carlos Alvarez-Navarro, Alejandro San Martín, Bruno Weber, Pamela Y Sandoval, L Felipe Barros.
      We addressed the question of mitochondrial lactate metabolism using genetically-encoded sensors. The organelle was found to contain a dynamic lactate pool that leads to dose- and time-dependent protein lactylation. In neurons, mitochondrial lactate reported blood lactate levels with high fidelity. The exchange of lactate across the inner mitochondrial membrane was found to be mediated by a high affinity H+-coupled transport system involving the mitochondrial pyruvate carrier MPC. Assessment of electron transport chain activity and determination of lactate flux showed that mitochondria are tonic lactate producers, a phenomenon driven by energization and stimulated by hypoxia. We conclude that an overflow mechanism caps the redox level of mitochondria, while saving energy in the form of lactate.
    DOI:  https://doi.org/10.1101/2024.07.19.604361
  9. bioRxiv. 2024 Jul 16. pii: 2024.07.16.603730. [Epub ahead of print]
    Novel Imaging Tools to Study Mitochondrial Dynamics in Caenorhabditis elegans.
    Miriam Valera-Alberni, Pallas Yao, Silvia Romero-Sanz, Anne Lanjuin, William B Mair.
      Mitochondria exhibit a close interplay between their structure and function. Understanding this intricate relationship requires advanced imaging techniques that can capture the dynamic nature of mitochondria and their impact on cellular processes. However, much of the work on mitochondrial dynamics has been done in single celled organisms or in vitro cell culture. Here, we introduce novel genetic tools for live imaging of mitochondrial networks in the nematode Caenorhabditis elegans , addressing a pressing need for advanced techniques in studying organelle dynamics within live intact multicellular organisms. Through a comprehensive analysis, we directly compare our tools with existing methods, demonstrating their advantages for visualizing mitochondrial morphology and contrasting their impact on organismal physiology. We reveal limitations of conventional techniques, while showcasing the utility and versatility of our approaches, including endogenous CRISPR tags and ectopic labeling. By providing a guide for selecting the most suitable tools based on experimental goals, our work advances mitochondrial research in C. elegans and enhances the strategic integration of diverse imaging modalities for a holistic understanding of organelle dynamics in living organisms.
    DOI:  https://doi.org/10.1101/2024.07.16.603730
  10. Contact (Thousand Oaks). 2024 Jan-Dec;7:7 25152564241261228
    The Discovery of Mitochondria-Endoplasmic Reticulum Contact Sites (MERCs) as Mitochondria-Associated Membranes (MAMs).
    Tadashi Makio, Thomas Simmen.
      Mitochondria-endoplasmic reticulum contacts (MERCs), also called endoplasmic reticulum (ER)-mitochondria contact sites (ERMCS), are the membrane domains, where these two organelles exchange lipids, Ca2+ ions, and reactive oxygen species. This crosstalk is a major determinant of cell metabolism, since it allows the ER to control mitochondrial oxidative phosphorylation and the Krebs cycle, while conversely, it allows the mitochondria to provide sufficient ATP to control ER proteostasis. MERC metabolic signaling is under the control of tethers and a multitude of regulatory proteins. Many of these proteins have recently been discovered to give rise to rare diseases if their genes are mutated. Surprisingly, these diseases share important hallmarks and cause neurological defects, sometimes paired with, or replaced by skeletal muscle deficiency. Typical symptoms include developmental delay, intellectual disability, facial dysmorphism and ophthalmologic defects. Seizures, epilepsy, deafness, ataxia, or peripheral neuropathy can also occur upon mutation of a MERC protein. Given that most MERC tethers and regulatory proteins have secondary functions, some MERC protein-based diseases do not fit into this categorization. Typically, however, the proteins affected in those diseases have dominant functions unrelated to their roles in MERCs tethering or their regulation. We are discussing avenues to pharmacologically target genetic diseases leading to MERC defects, based on our novel insight that MERC defects lead to common characteristics in rare diseases. These shared characteristics of MERCs disorders raise the hope that they may allow for similar treatment options.
    Keywords:  endoplasmic reticulum; mitochondria; mutation; rare disease
    DOI:  https://doi.org/10.1177/25152564241261228
  11. Cytometry A. 2024 Jul 30.
    AutoMitoNetwork: Software for analyzing mitochondrial networks in autofluorescence images to enable label-free cell classification.
    Shannon Handley, Ayad G Anwer, Aline Knab, Akanksha Bhargava, Ewa M Goldys.
      High-resolution mitochondria imaging in combination with image analysis tools have significantly advanced our understanding of cellular function in health and disease. However, most image analysis tools for mitochondrial studies have been designed to work with fluorescently labeled images only. Additionally, efforts to integrate features describing mitochondrial networks with machine learning techniques for the differentiation of cell types have been limited. Herein, we present AutoMitoNetwork software for image-based assessment of mitochondrial networks in label-free autofluorescence images using a range of interpretable morphological, intensity, and textural features. To demonstrate its utility, we characterized unstained mitochondrial networks in healthy retinal cells and in retinal cells exposed to two types of treatments: rotenone, which directly inhibited mitochondrial respiration and ATP production, and iodoacetic acid, which had a milder impact on mitochondrial networks via the inhibition of anaerobic glycolysis. For both cases, our multi-dimensional feature analysis combined with a support vector machine classifier distinguished between healthy cells and those treated with rotenone or iodoacetic acid. Subtle changes in morphological features were measured including increased fragmentation in the treated retinal cells, pointing to an association with metabolic mechanisms. AutoMitoNetwork opens new options for image-based machine learning in label-free imaging, diagnostics, and mitochondrial disease drug development.
    Keywords:  autofluorescence; biological image analysis; label‐free imaging; machine learning; mitochondria; mitochondria network
    DOI:  https://doi.org/10.1002/cyto.a.24889
  12. Am J Kidney Dis. 2024 Jul 31. pii: S0272-6386(24)00897-7. [Epub ahead of print]
    Homozygosity for a Rare FASTKD2 Variant Resulting in an Adult Onset Autosomal Recessive Mitochondrial Podocytopathy.
    Francisco Pereira Gonçalves, Isabel Tavares, Roberto Silva, Ana Teresa Nunes, Luciano Pereira, Andreia Campos, Joel Pinto, Ana Lopes, Marta Simões, Manuela Grazina, Agnes B Fogo, João Paulo Oliveira.
      Mitochondrial cytopathies can have kidney involvement in up to half of cases. Their diagnosis is challenging due to phenotypic variability, lack of noninvasive tests to assess mitochondrial dysfunction and genetic heterogeneity. We report on a young adult male with hypertrophic cardiomyopathy (HCM) and chronic kidney disease (CKD) with sub-nephrotic proteinuria, who presented to the emergency department with kidney failure and hypervolemia requiring dialysis. A kidney biopsy showed focal segmental and global glomerulosclerosis, extensive foot process effacement, and abnormal mitochondria in podocytes and tubular epithelial cells; the genetic workup identified a rare FASTKD2 exon 2 variant, c.29G>C p.(Ser10Thr), in homozygosity; and functional mitochondrial assays in cultured skin fibroblasts showed reduction in FASTKD2 protein expression and moderate combined impairment in mitochondrial respiratory chain (MRC) assembly and function. This is the first report of a FASTKD2-associated cardiorenal mitochondrial cytopathy, characterized by young adult-onset proteinuric CKD and dilated HCM, in the absence of the severe neurologic manifestations described in patients with biallelic FASTKD2 mutations. We hypothesize that the increased production of reactive oxygen species associated with moderate MRC impairment could result in a smoldering podocytopathy with progressive proteinuric CKD, without overt tubulopathy or encephalomyopathy, which are, instead, pathogenically related to adenosine triphosphate deficiency.
    Keywords:  FASTKD2; chronic kidney disease; hypertrophic cardiomyopathy; mitochondrial disease; podocytopathy
    DOI:  https://doi.org/10.1053/j.ajkd.2024.05.018
  13. BMC Biol. 2024 Jul 29. 22(1): 162
    Single-mitochondrion sequencing uncovers distinct mutational patterns and heteroplasmy landscape in mouse astrocytes and neurons.
    Parnika S Kadam, Zijian Yang, Youtao Lu, Hua Zhu, Yasemin Atiyas, Nishal Shah, Stephen Fisher, Erik Nordgren, Junhyong Kim, David Issadore, James Eberwine.
       BACKGROUND: Mitochondrial (mt) heteroplasmy can cause adverse biological consequences when deleterious mtDNA mutations accumulate disrupting "normal" mt-driven processes and cellular functions. To investigate the heteroplasmy of such mtDNA changes, we developed a moderate throughput mt isolation procedure to quantify the mt single-nucleotide variant (SNV) landscape in individual mouse neurons and astrocytes. In this study, we amplified mt-genomes from 1645 single mitochondria isolated from mouse single astrocytes and neurons to (1) determine the distribution and proportion of mt-SNVs as well as mutation pattern in specific target regions across the mt-genome, (2) assess differences in mtDNA SNVs between neurons and astrocytes, and (3) study co-segregation of variants in the mouse mtDNA.
    RESULTS: (1) The data show that specific sites of the mt-genome are permissive to SNV presentation while others appear to be under stringent purifying selection. Nested hierarchical analysis at the levels of mitochondrion, cell, and mouse reveals distinct patterns of inter- and intra-cellular variation for mt-SNVs at different sites. (2) Further, differences in the SNV incidence were observed between mouse neurons and astrocytes for two mt-SNV 9027:G > A and 9419:C > T showing variation in the mutational propensity between these cell types. Purifying selection was observed in neurons as shown by the Ka/Ks statistic, suggesting that neurons are under stronger evolutionary constraint as compared to astrocytes. (3) Intriguingly, these data show strong linkage between the SNV sites at nucleotide positions 9027 and 9461.
    CONCLUSIONS: This study suggests that segregation as well as clonal expansion of mt-SNVs is specific to individual genomic loci, which is important foundational data in understanding of heteroplasmy and disease thresholds for mutation of pathogenic variants.
    Keywords:  Astrocytes; Heteroplasmy; Neurons; Single mitochondrion; Single-nucleotide variants
    DOI:  https://doi.org/10.1186/s12915-024-01953-7
  14. Front Neurol. 2024 ;15 1394150
    Two novel SUCLA2 variants cause mitochondrial DNA depletion syndrome, type 5 in two siblings.
    Xiaohuan Zhang, Guo Zhang, Li Cao, Wenjing Zhou, Chang Tan, Shi Ma, Jiyun Yang.
      Mitochondrial DNA depletion syndrome (MDS), characterized by succinate-CoA ligase deficiency and loss of mitochondrial DNA (mtDNA), is caused by specific variants in nuclear genes responsible for mtDNA maintenance. SUCLA2-related mitochondrial DNA depletion syndrome, type 5 (MTDPS-5), presents as a rare, severe early progressive encephalomyopathy. This report investigates a new family exhibiting clinical manifestations of MTDPS-5 and elucidates the genetic basis of this disorder. In two affected siblings, a novel maternally inherited nonsense variant [c.1234C>T (p.Arg412*)] in the SUCLA2 gene and a unique paternally inherited indel variant (g.48569263-48571020del1758insATGA) were identified. Additionally, the siblings exhibited blood mtDNA content lower than 33% compared to age-matched controls. These findings underscore the importance of assessing SUCLA2 variants in patients with severe early progressive encephalomyopathy, even in the absence of methylmalonic aciduria or mtDNA loss, thereby broaden the mutational spectrum of this gene.
    Keywords:  MTDPS-5; NGS; SUCLA2; mitochondrial DNA; mitochondrial succinate-CoA ligase; rare disease
    DOI:  https://doi.org/10.3389/fneur.2024.1394150
  15. Biol Chem. 2024 Aug 02.
    The TOM complex from an evolutionary perspective and the functions of TOMM70.
    Metin Özdemir, Sven Dennerlein.
      In humans, up to 1,500 mitochondrial precursor proteins are synthesized at cytosolic ribosomes and must be imported into the organelle. This is not only essential for mitochondrial but also for many cytosolic functions. The majority of mitochondrial precursor proteins are imported over the translocase of the outer membrane (TOM). In recent years, high-resolution structure analyses from different organisms shed light on the composition and arrangement of the TOM complex. Although significant similarities have been found, differences were also observed, which have been favored during evolution and could reflect the manifold functions of TOM with cellular signaling and its response to altered metabolic situations. A key component within these regulatory mechanisms is TOMM70, which is involved in protein import, forms contacts to the ER and the nucleus, but is also involved in cellular defense mechanisms during infections.
    Keywords:  TOM complex; mitochondria; mitochondrial import
    DOI:  https://doi.org/10.1515/hsz-2024-0043
  16. Proc Natl Acad Sci U S A. 2024 Aug 06. 121(32): e2402206121
    Loss of primary cilia and dopaminergic neuroprotection in pathogenic LRRK2-driven and idiopathic Parkinson's disease.
    Shahzad S Khan, Ebsy Jaimon, Yu-En Lin, Jonas Nikoloff, Francesca Tonelli, Dario R Alessi, Suzanne R Pfeffer.
      Activating leucine-rich repeat kinase 2 (LRRK2) mutations cause Parkinson's and phosphorylation of Rab10 by pathogenic LRRK2 blocks primary ciliogenesis in cultured cells. In the mouse brain, LRRK2 blockade of primary cilia is highly cell type specific: For example, cholinergic interneurons and astrocytes but not medium spiny neurons of the dorsal striatum lose primary cilia in LRRK2-pathway mutant mice. We show here that the cell type specificity of LRRK2-mediated cilia loss is also seen in human postmortem striatum from patients with LRRK2 pathway mutations and idiopathic Parkinson's. Single nucleus RNA sequencing shows that cilia loss in mouse cholinergic interneurons is accompanied by decreased glial-derived neurotrophic factor transcription, decreasing neuroprotection for dopamine neurons. Nevertheless, LRRK2 expression differences cannot explain the unique vulnerability of cholinergic neurons to LRRK2 kinase as much higher LRRK2 expression is seen in medium spiny neurons that have normal cilia. In parallel with decreased striatal dopaminergic neurite density, LRRK2 G2019S neurons show increased autism-linked CNTN5 adhesion protein expression; glial cells show significant loss of ferritin heavy chain. These data strongly suggest that loss of cilia in specific striatal cell types decreases neuroprotection for dopamine neurons in mice and human Parkinson's.
    Keywords:  Hedgehog signaling; LRRK2 kinase; Parkinson’s disease; Rab GTPase; primary cilia
    DOI:  https://doi.org/10.1073/pnas.2402206121
  17. bioRxiv. 2024 Jul 24. pii: 2024.07.23.604788. [Epub ahead of print]
    SLC45A4 encodes a mitochondrial putrescine transporter that promotes GABA de novo synthesis.
    Cecilia Colson, Yujue Wang, James Atherton, Xiaoyang Su.
      Solute carriers (SLC) are membrane proteins that facilitate the transportation of ions and metabolites across either the plasma membrane or the membrane of intracellular organelles. With more than 450 human genes annotated as SLCs, many of them are still orphan transporters without known biochemical functions. We developed a metabolomic-transcriptomic association analysis, and we found that the expression of SLC45A4 has a strong positive correlation with the cellular level of γ-aminobutyric acid (GABA). Using mass spectrometry and the stable isotope tracing approach, we demonstrated that SLC45A4 promotes GABA de novo synthesis through the Arginine/Ornithine/Putrescine (AOP) pathway. SLC45A4 functions as a putrescine transporter localized to the mitochondrial membrane to facilitate GABA production. Taken together, our results revealed a new biochemical mechanism where SLC45A4 controls GABA production.
    DOI:  https://doi.org/10.1101/2024.07.23.604788
  18. Nat Aging. 2024 Jul 29.
    Maternal age enhances purifying selection on pathogenic mutations in complex I genes of mammalian mtDNA.
    Yanfei Ru, Xiaoling Deng, Jiatong Chen, Leping Zhang, Zhe Xu, Qunyu Lv, Shiyun Long, Zijian Huang, Minghua Kong, Jing Guo, Min Jiang.
      Mitochondrial diseases, caused mainly by pathogenic mitochondrial DNA (mtDNA) mutations, pose major challenges due to the lack of effective treatments. Investigating the patterns of maternal transmission of mitochondrial diseases could pave the way for preventive approaches. In this study, we used DddA-derived cytosine base editors (DdCBEs) to generate two mouse models, each haboring a single pathogenic mutation in complex I genes (ND1 and ND5), replicating those found in human patients. Our findings revealed that both mutations are under strong purifying selection during maternal transmission and occur predominantly during postnatal oocyte maturation, with increased protein synthesis playing a vital role. Interestingly, we discovered that maternal age intensifies the purifying selection, suggesting that older maternal age may offer a protective effect against the transmission of deleterious mtDNA mutations, contradicting the conventional notion that maternal age correlates with increased transmitted mtDNA mutations. As collecting comprehensive clinical data is needed to understand the relationship between maternal age and transmission patterns in humans, our findings may have profound implications for reproductive counseling of mitochondrial diseases, especially those involving complex I gene mutations.
    DOI:  https://doi.org/10.1038/s43587-024-00672-6
  19. EClinicalMedicine. 2024 Aug;74 102740
    Safety and efficacy of deoxycytidine/deoxythymidine combination therapy in POLG-related disorders: 6-month interim results of an open-label, single arm, phase 2 trial.
    Heather Pekeles, Saoussen Berrahmoune, Christelle Dassi, Anthony C T Cheung, Tommy Gagnon, Paula J Waters, Ralf Eberhard, Daniela Buhas, Kenneth A Myers.
       Background: DNA polymerase gamma (POLG)-related disorders are a group of rare neurodegenerative mitochondrial diseases caused by pathogenic variants in POLG, the gene encoding POLG. Patients may experience a range of signs and symptoms, including seizures, vision loss, myopathy, neuropathy, developmental impairment or regression, and liver failure. The diseases follow a progressive, degenerative course, with most affected individuals dying within 3 months-12 years of diagnosis. At present, there are no effective treatments for POLG-related disorders.
    Methods: In this study we report the interim 6-month data from a long term open-label, single arm phase 2 trial, in which we assessed the safety and efficacy of combination therapy with deoxycytidine and deoxythymidine (dC/dT) in children with POLG-related disorders. dC/dT was given enterally in powder form, dissolved in water. The primary outcome measures included Newcastle Mitochondrial Disease Scale (NMDS) score, serum growth differentiation factor 15 (GDF-15; a biomarker of mitochondrial dysfunction), electroencephalography (EEG), seizure diary, and blood and urine tests to assess end organ and mitochondrial function. Secondary outcome measures included recording of all adverse events to evaluate the safety of the intervention. The trial is registered with ClinicalTrials.gov, NCT04802707 (https://clinicaltrials.gov/ct2/show/NCT04802707). Data were collected from 14 October, 2021 to 13 December, 2023.
    Findings: We present 6-month interim data from the first ten people with POLG-related disorders enrolled in the trial, six with Alpers-Huttenlocher syndrome, two with ataxia-neuropathy spectrum, and two who do not fit into a classical POLG-related phenotype. During the 6 months of treatment, NMDS score improved from a mean of 27.3 at baseline to 20.7 at 6 months (estimated difference 6.0; 95% CI 2.5-∞). GDF-15 values remained stable or decreased in all patients; the mean decreased from 1031 pg/ml to 729 pg/ml (estimated difference 200; 95% CI 12-∞). 8/10 patients had abnormal baseline EEG; improvement in EEG was seen in 5 of these 8. There were no significant changes in other blood and urine testing. Regarding adverse events, two patients experienced diarrhea that spontaneously resolved.
    Interpretation: dC/dT is a promising treatment option for people with POLG-related disorders. Further research is needed to assess the long-term safety and efficacy in POLG-related disorders, as well as safety and efficacy in other mitochondrial DNA depletion disorders.
    Funding: This study was primarily funded by the Liam Foundation, with additional funding from the Savoy Foundation, Grand Défi Pierre Lavoie Foundation, and Fonds de Recherche du Québec - Santé.
    Keywords:  Deoxycytidine; Deoxynucleosides; Deoxythymidine; POLG; Thymidine
    DOI:  https://doi.org/10.1016/j.eclinm.2024.102740
  20. Biochim Biophys Acta Bioenerg. 2024 Jul 29. pii: S0005-2728(24)00471-7. [Epub ahead of print]1865(4): 149501
    The subtherapeutic dose of valproic acid induces the activity of cardiolipin-dependent proteins.
    Paulina Horonyova, Ivana Durisova, Petra Cermakova, Lenka Babelova, Barbora Buckova, Lucia Sofrankova, Martin Valachovic, Yuan-Hao Howard Hsu, Maria Balazova.
      A mood-stabilizing anticonvulsant valproic acid (VPA) is a drug with a pleiotropic effect on cells. Here, we describe the impact of VPA on the metabolic function of human HAP1 cells. We show that VPA altered the biosynthetic pathway of cardiolipin (CL) and affected the activities of mitochondrial enzymes such as pyruvate dehydrogenase, α-ketoglutarate dehydrogenase and NADH dehydrogenase. We demonstrate that a therapeutic dose of VPA (0.6 mM) has a harmful effect on cell growth and increases the production of reactive oxygen species and superoxides. On the contrary, less concentrated VPA (0.06 mM) increased the activities of CL-dependent enzymes leading to an increased level of oxidative phosphorylation and ATP production. The effect of VPA was also tested on the Barth syndrome model, which is characterized by a reduced amount of CL and an increased level of monolyso-CL. In this model, VPA treatment slightly attenuated the mitochondrial defects by altering the activities of CL-dependent enzymes. However, the presence of CL was essential for the increase in ATP production by VPA. Our findings highlight the potential therapeutic role of VPA in normalizing mitochondrial function in BTHS and shed light on the intricate interplay between lipid metabolism and mitochondrial physiology in health and disease. SUMMARY: This study investigates the dose-dependent effect of valproate, a mood-stabilizing drug, on mitochondrial function. The therapeutic concentration reduced overall cellular metabolic activity, while a subtherapeutic concentration notably improved the function of cardiolipin-dependent proteins within mitochondria. These findings shed light on novel aspects of valproate's effect and suggest potential practical applications for its use. By elucidating the differential effects of valproate doses on mitochondrial activity, this research underscores the drug's multifaceted role in cellular metabolism and highlights avenues for further exploration in therapeutic interventions.
    Keywords:  Barth syndrome; Cardiolipin; Krebs cycle; Mitochondria; Respiration; Valproic acid
    DOI:  https://doi.org/10.1016/j.bbabio.2024.149501
  21. Acta Physiol (Oxf). 2024 Jul 29. e14209
    Comparative functional analysis reveals differential nucleotide sensitivity between human and mouse UCP1.
    Eva Musiol, Tobias Fromme, Julia Hau, Antonella Di Pizio, Martin Klingenspor.
       AIM: Mitochondrial uncoupling protein 1 (UCP1) is a unique protein of brown adipose tissue. Upon activation by free fatty acids, UCP1 facilitates a thermogenic net proton flux across the mitochondrial inner membrane. Non-complexed purine nucleotides inhibit this fatty acid-induced activity of UCP1. The most available data have been generated from rodent model systems. In light of its role as a putative pharmacological target for treating metabolic disease, in-depth analyses of human UCP1 activity, regulation, and structural features are essential.
    METHODS: In the present study, we established a doxycycline-regulated cell model with inducible human or murine UCP1 expression and conducted functional studies using respirometry comparing wild-type and mutant variants of human UCP1.
    RESULTS: We demonstrate that human and mouse UCP1 exhibit similar specific fatty acid-induced activity but a different inhibitory potential of purine nucleotides. Mutagenesis of non-conserved residues in human UCP1 revealed structural components in α-helix 56 and α-helix 6 crucial for uncoupling function.
    CONCLUSION: Comparative studies of human UCP1 with other orthologs can provide new insights into the structure-function relationship for this mitochondrial carrier and will be instrumental in searching for new activators.
    Keywords:  brown adipose tissue; fatty acids; mitochondrial carriers; mutagenesis; proton leak; purine nucleotides; thermogenesis; uncoupling proteins
    DOI:  https://doi.org/10.1111/apha.14209
  22. Extracell Vesicles Circ Nucl Acids. 2024 Jun;5(2): 271-275
    Mitochondria-derived vesicles: potential nano-batteries to recharge the cellular powerhouse.
    Shalini Mishra, Gagan Deep.
      Mitochondria dysfunction is increasingly recognized as a critical factor in various pathogenic processes. The mechanism governing mitochondrial quality control serves as an adaptive response, ensuring the preservation of mitochondrial morphology, quantity, and overall function, crucial for cell survival. The generation of mitochondria-derived vesicles (MDVs) is one of the processes of mitochondrial quality control. Recent literature has suggested MDV heterogeneity; however, the detailed characteristics of various MDV subtypes still need to be studied better. Recent studies have shown that MDVs also play a role in inter-organelle communication for mitochondria besides quality control. For instance, Hazan et al. demonstrated that functional mitochondria from Saccharomyces cerevisiae release vesicles independent of the fission machinery. These vesicles, falling within the typical size range of MDVs, were selectively loaded with mitochondrial proteins, especially with functional ATP synthase subunits. Intriguingly, these MDVs maintained membrane potential and could generate ATP. Moreover, MDVs could fuse with naïve mitochondria, transferring their ATP generation machinery. Lastly, this study revealed a potential delivery mechanism of ATP-producing vesicles, presenting a promising avenue to rejuvenate ATP-deficient mitochondria. Overall, this study unveils a novel mechanism for inter-organelle communication by vesicles, which is crucial for maintaining cellular homeostasis and could also be important in pathological conditions.
    Keywords:  F1-F0 ATP synthase; Mitochondria; inter-organelle communication; mitochondria-derived vesicle
    DOI:  https://doi.org/10.20517/evcna.2023.71
  23. Kidney Int. 2024 Jul 29. pii: S0085-2538(24)00526-X. [Epub ahead of print]
    The membrane transporter SLC25A48 enables transport of choline into human mitochondria.
    Suraj Patil, Oleg Borisov, Nora Scherer, Christophe Wirth, Pascal Schlosser, Matthias Wuttke, Sandra Ehret, Luciana Hannibal, Kai-Uwe Eckardt, Carola Hunte, Björn Neubauer, Anna Köttgen, Michael Köttgen.
      Choline has important physiological functions as a precursor for essential cell components, signaling molecules, phospholipids, and the neurotransmitter acetylcholine. Choline is a water-soluble charged molecule requiring transport proteins to cross biological membranes. Although transporters continue to be identified, membrane transport of choline is incompletely understood and knowledge about choline transport into intracellular organelles such as mitochondria remains limited. Here we show that SLC25A48 imports choline into human mitochondria. Human loss-of-function mutations in SLC25A48 show impaired choline transport into mitochondria and are associated with elevated urine and plasma choline levels. Thus, our studies may have implications for understanding and treating conditions related to choline metabolism.
    Keywords:  Choline transport; SLC25A48; deorphanization; mGWAS; mitochondria
    DOI:  https://doi.org/10.1016/j.kint.2024.06.022
  24. Pharmacol Res. 2024 Jul 31. pii: S1043-6618(24)00281-0. [Epub ahead of print] 107336
    Inhibition of K63 ubiquitination by G-Protein pathway suppressor 2 (GPS2) regulates mitochondria-associated translation.
    Yuan Gao, Julian Kwan, Joseph Orofino, Giulia Burrone, Sahana Mitra, Ting-Yu Fan, Justin English, Ryan Hekman, Andrew Emili, Shawn M Lyons, Maria Dafne Cardamone, Valentina Perissi.
      G-Protein Pathway Suppressor 2 (GPS2) is an inhibitor of non-proteolytic K63 ubiquitination mediated by the E2 ubiquitin-conjugating enzyme Ubc13. Previous studies have associated GPS2-mediated restriction of ubiquitination with the regulation of insulin signaling, inflammatory responses and mitochondria-nuclear communication across different tissues and cell types. However, a detailed understanding of the targets of GPS2/Ubc13 activity is lacking. Here, we have dissected the GPS2-regulated K63 ubiquitome in mouse embryonic fibroblasts and human breast cancer cells, unexpectedly finding an enrichment for proteins involved in RNA binding and translation on the outer mitochondrial membrane. Validation of selected targets of GPS2-mediated regulation, including the RNA-binding protein PABPC1 and translation factors RPS1, RACK1 and eIF3M, revealed a mitochondrial-specific strategy for regulating the translation of nuclear-encoded mitochondrial proteins via non-proteolytic ubiquitination. Removal of GPS2-mediated inhibition, either via genetic deletion or stress-induced nuclear translocation, promotes the import-coupled translation of selected mRNAs leading to the increased expression of an adaptive antioxidant program. In light of GPS2 role in nuclear-mitochondria communication, these findings reveal an exquisite regulatory network for modulating mitochondrial gene expression through spatially coordinated transcription and translation.
    Keywords:  FCCP; GPS2; Homo-harringtonine; NSC697923; PABPC1; Puromycin; Tamoxifen; Ubiquitin; mitochondria; mitochondria stress response (MSR); translation
    DOI:  https://doi.org/10.1016/j.phrs.2024.107336
  25. Acta Physiol (Oxf). 2024 Jul 30. e14208
    Mitochondria can substitute for parvalbumin to lower cytosolic calcium levels in the murine fast skeletal muscle.
    Lorenzo Marcucci, Leonardo Nogara, Marta Canato, Elena Germinario, Anna Raffaello, Michela Carraro, Paolo Bernardi, Laura Pietrangelo, Simona Boncompagni, Feliciano Protasi, Nazareno Paolocci, Carlo Reggiani.
       AIM: Parvalbumin (PV) is a primary calcium buffer in mouse fast skeletal muscle fibers. Previous work showed that PV ablation has a limited impact on cytosolic Ca2+ ([Ca2+]cyto) transients and contractile response, while it enhances mitochondrial density and mitochondrial matrix-free calcium concentration ([Ca2+]mito). Here, we aimed to quantitatively test the hypothesis that mitochondria act to compensate for PV deficiency.
    METHODS: We determined the free Ca2+ redistribution during a 2 s 60 Hz tetanic stimulation in the sarcoplasmic reticulum, cytosol, and mitochondria. Via a reaction-diffusion Ca2+ model, we quantitatively evaluated mitochondrial uptake and storage capacity requirements to compensate for PV lack and analyzed possible extracellular export.
    RESULTS: [Ca2+]mito during tetanic stimulation is greater in knock-out (KO) (1362 ± 392 nM) than in wild-type (WT) (855 ± 392 nM), p < 0.05. Under the assumption of a non-linear intramitochondrial buffering, the model predicts an accumulation of 725 μmoles/Lfiber (buffering ratio 1:11 000) in KO, much higher than in WT (137 μmoles/Lfiber, ratio 1:4500). The required transport rate via mitochondrial calcium uniporter (MCU) reaches 3 mM/s, compatible with available literature. TEM images of calcium entry units and Mn2+ quenching showed a greater capacity of store-operated calcium entry in KO compared to WT. However, levels of [Ca2+]cyto during tetanic stimulation were not modulated to variations of extracellular calcium.
    CONCLUSIONS: The model-based analysis of experimentally determined calcium distribution during tetanic stimulation showed that mitochondria can act as a buffer to compensate for the lack of PV. This result contributes to a better understanding of mitochondria's role in modulating [Ca2+]cyto in skeletal muscle fibers.
    Keywords:  calcium; mitochondria; mouse skeletal muscle fibers; parvalbumin; reaction–diffusion model
    DOI:  https://doi.org/10.1111/apha.14208
  26. Front Mol Med. 2024 ;4 1389456
    Tafazzin deficiency causes substantial remodeling in the lipidome of a mouse model of Barth Syndrome cardiomyopathy.
    Malte Hachmann, Güntas Gülcan, Ranjithkumar Rajendran, Marcus Höring, Gerhard Liebisch, Akash Bachhuka, Michael Kohlhaas, Christoph Maack, Süleyman Ergün, Jan Dudek, Srikanth Karnati.
      Barth Syndrome (BTHS) is a rare X-linked disease, characterized clinically by cardiomyopathy, skeletal myopathy, neutropenia, and growth retardation. BTHS is caused by mutations in the phospholipid acyltransferase tafazzin (Gene: TAFAZZIN, TAZ). Tafazzin catalyzes the final step in the remodeling of cardiolipin (CL), a glycerophospholipid located in the inner mitochondrial membrane. As the phospholipid composition strongly determines membrane properties, correct biosynthesis of CL and other membrane lipids is essential for mitochondrial function. Mitochondria provide 95% of the energy demand in the heart, particularly due to their role in fatty acid oxidation. Alterations in lipid homeostasis in BTHS have an impact on mitochondrial membrane proteins and thereby contribute to cardiomyopathy. We analyzed a transgenic TAFAZZIN-knockdown (TAZ-KD) BTHS mouse model and determined the distribution of 193 individual lipid species in TAZ-KD and WT hearts at 10 and 50 weeks of age, using electrospray ionization tandem mass spectrometry (ESI-MS/MS). Our results revealed significant lipid composition differences between the TAZ-KD and WT groups, indicating genotype-dependent alterations in most analyzed lipid species. Significant changes in the myocardial lipidome were identified in both young animals without cardiomyopathy and older animals with heart failure. Notable alterations were found in phosphatidylcholine (PC), phosphatidylethanolamine (PE), lysophosphatidylethanolamine (LPE), lysophosphatidylcholine (LPC) and plasmalogen species. PC species with 2-4 double bonds were significantly increased, while polyunsaturated PC species showed a significant decrease in TAZ-KD mice. Furthermore, Linoleic acid (LA, 18:2) containing PC and PE species, as well as arachidonic acid (AA, 20:4) containing PE 38:4 species are increased in TAZ-KD. We found higher levels of AA containing LPE and PE-based plasmalogens (PE P-). Furthermore, we are the first to show significant changes in sphingomyelin (SM) and ceramide (Cer) lipid species Very long-chained SM species are accumulating in TAZ-KD hearts, whereas long-chained Cer and several hexosyl ceramides (HexCer) species accumulate only in 50-week-old TAZ-KD hearts These findings offer potential avenues for the diagnosis and treatment of BTHS, presenting new possibilities for therapeutic approaches.
    Keywords:  Barth Syndrome; electrospray ionization-tandem mass spectrometry (ESI-MS/MS); heart failure; lipidome; lipids; tafazzin
    DOI:  https://doi.org/10.3389/fmmed.2024.1389456
  27. Mol Ther Nucleic Acids. 2024 Sep 10. 35(3): 102262
    Guidelines for mitochondrial RNA analysis.
    EU-CardioRNA COST Action CA17129
      Mitochondria are the energy-producing organelles of mammalian cells with critical involvement in metabolism and signaling. Studying their regulation in pathological conditions may lead to the discovery of novel drugs to treat, for instance, cardiovascular or neurological diseases, which affect high-energy-consuming cells such as cardiomyocytes, hepatocytes, or neurons. Mitochondria possess both protein-coding and noncoding RNAs, such as microRNAs, long noncoding RNAs, circular RNAs, and piwi-interacting RNAs, encoded by the mitochondria or the nuclear genome. Mitochondrial RNAs are involved in anterograde-retrograde communication between the nucleus and mitochondria and play an important role in physiological and pathological conditions. Despite accumulating evidence on the presence and biogenesis of mitochondrial RNAs, their study continues to pose significant challenges. Currently, there are no standardized protocols and guidelines to conduct deep functional characterization and expression profiling of mitochondrial RNAs. To overcome major obstacles in this emerging field, the EU-CardioRNA and AtheroNET COST Action networks summarize currently available techniques and emphasize critical points that may constitute sources of variability and explain discrepancies between published results. Standardized methods and adherence to guidelines to quantify and study mitochondrial RNAs in normal and disease states will improve research outputs, their reproducibility, and translation potential to clinical application.
    Keywords:  MT: Non-coding RNAs; gene expression; guidelines; microRNAs; mitochondria; noncoding RNAs
    DOI:  https://doi.org/10.1016/j.omtn.2024.102262
  28. Aging Cell. 2024 Jul 30. e14284
    Histone β-hydroxybutyrylation is critical in reversal of sarcopenia.
    Qiquan Wang, Xinqiang Lan, Hao Ke, Siman Xu, Chunping Huang, Jiali Wang, Xiang Wang, Tiane Huang, Xia Wu, Mengxin Chen, Yingqi Guo, Lin Zeng, Xiao-Li Tian, Yang Xiang.
      Sarcopenia, a leading cause for global disability and mortality, is an age-related muscular disorder, characterized by accelerated muscle mass loss and functional decline. It is known that caloric restriction (CR), ketogenic diet or endurance exercise lessen sarcopenia and elevate circulating β-hydroxybutyrate (β-HB) levels. Whether the elevated β-HB is essential to the reversal of sarcopenia, however, remains unclear. Here we show in both Caenorhabditis elegans and mouse models that an increase of β-HB reverse myofiber atrophy and improves motor functions at advanced ages. β-HB-induced histone lysine β-hydroxybutyrylation (Kbhb) is indispensable for the reversal of sarcopenia. Histone Kbhb enhances transcription of genes associated with mitochondrial pathways, including oxidative phosphorylation, ATP metabolic process and aerobic respiration. This ultimately leads to improve mitochondrial integrity and enhance mitochondrial respiration. The histone Kbhb are validated in mouse model with CR. Thus, we demonstrate that β-HB induces histone Kbhb, increases mitochondrial function, and reverses sarcopenia.
    Keywords:  mitochondria; sarcopenia; skeletal muscle; β‐hydroxybutyrate; β‐hydroxybutyrylation
    DOI:  https://doi.org/10.1111/acel.14284
  29. bioRxiv. 2024 Jul 17. pii: 2024.07.15.603186. [Epub ahead of print]
    Loss of MEF2C function by enhancer mutation leads to neuronal mitochondria dysfunction and motor deficits in mice.
    Ali Yousefian-Jazi, Suhyun Kim, Seung-Hye Choi, Jiyeon Chu, Phuong Thi-Thanh Nguyen, Uiyeol Park, Kayeong Lim, Hongik Hwang, Kyungeun Lee, Yeyun Kim, Seung Jae Hyeon, Hyewhon Rhim, Hannah L Ryu, Grewo Lim, Thor D Stein, Hoon Ryu, Junghee Lee.
      Genetic changes and epigenetic modifications are associated with neuronal dysfunction in the pathogenesis of neurodegenerative disorders. However, the mechanism behind genetic mutations in the non-coding region of genes that affect epigenetic modifications remains unclear. Here, we identified an ALS-associated SNP located in the intronic region of MEF2C (rs304152), residing in a putative enhancer element, using convolutional neural network. The enhancer mutation of MEF2C reduces own gene expression and consequently impairs mitochondrial function in motor neurons. MEF2C localizes and binds to the mitochondria DNA, and directly modulates mitochondria-encoded gene expression. CRISPR/Cas-9-induced mutation of the MEF2C enhancer decreases expression of mitochondria-encoded genes. Moreover, MEF2C mutant cells show reduction of mitochondrial membrane potential, ATP level but elevation of oxidative stress. MEF2C deficiency in the upper and lower motor neurons of mice impairs mitochondria-encoded genes, and leads to mitochondrial metabolic disruption and progressive motor behavioral deficits. Together, MEF2C dysregulation by the enhancer mutation leads to mitochondrial dysfunction and oxidative stress, which are prevalent features in motor neuronal damage and ALS pathogenesis. This genetic and epigenetic crosstalk mechanism provides insights for advancing our understanding of motor neuron disease and developing effective treatments.
    DOI:  https://doi.org/10.1101/2024.07.15.603186
  30. EMBO Rep. 2024 Jul 29.
    IMPDH2 filaments protect from neurodegeneration in AMPD2 deficiency.
    Marco Flores-Mendez, Laura Ohl, Thomas Roule, Yijing Zhou, Jesus A Tintos-Hernández, Kelsey Walsh, Xilma R Ortiz-González, Naiara Akizu.
      Metabolic dysregulation is one of the most common causes of pediatric neurodegenerative disorders. However, how the disruption of ubiquitous and essential metabolic pathways predominantly affect neural tissue remains unclear. Here we use mouse models of a childhood neurodegenerative disorder caused by AMPD2 deficiency to study cellular and molecular mechanisms that lead to selective neuronal vulnerability to purine metabolism imbalance. We show that mouse models of AMPD2 deficiency exhibit predominant degeneration of the hippocampal dentate gyrus, despite a general reduction of brain GTP levels. Neurodegeneration-resistant regions accumulate micron-sized filaments of IMPDH2, the rate limiting enzyme in GTP synthesis, while these filaments are barely detectable in the hippocampal dentate gyrus. Furthermore, we show that IMPDH2 filament disassembly reduces GTP levels and impairs growth of neural progenitor cells derived from individuals with human AMPD2 deficiency. Together, our findings suggest that IMPDH2 polymerization prevents detrimental GTP deprivation, opening the possibility of exploring the induction of IMPDH2 assembly as a therapy for neurodegeneration.
    Keywords:  Ampd2; Impdh2 Filaments; Metabolons; Pontocerebellar Hypoplasia; Purine Nucleotides
    DOI:  https://doi.org/10.1038/s44319-024-00218-2
  31. Cell Metab. 2024 Jul 24. pii: S1550-4131(24)00273-0. [Epub ahead of print]
    Development of a functional beige fat cell line uncovers independent subclasses of cells expressing UCP1 and the futile creatine cycle.
    Ariana Vargas-Castillo, Yizhi Sun, Amanda L Smythers, Louisa Grauvogel, Phillip A Dumesic, Margo P Emont, Linus T Tsai, Evan D Rosen, Nathan W Zammit, Sydney M Shaffer, Martha Ordonez, Edward T Chouchani, Steven P Gygi, Tongtong Wang, Anand K Sharma, Miroslav Balaz, Christian Wolfrum, Bruce M Spiegelman.
      Although uncoupling protein 1 (UCP1) is established as a major contributor to adipose thermogenesis, recent data have illustrated an important role for alternative pathways, particularly the futile creatine cycle (FCC). How these pathways co-exist in cells and tissues has not been explored. Beige cell adipogenesis occurs in vivo but has been difficult to model in vitro; here, we describe the development of a murine beige cell line that executes a robust respiratory response, including uncoupled respiration and the FCC. The key FCC enzyme, tissue-nonspecific alkaline phosphatase (TNAP), is localized almost exclusively to mitochondria in these cells. Surprisingly, single-cell cloning from this cell line shows that cells with the highest levels of UCP1 express little TNAP, and cells with the highest expression of TNAP express little UCP1. Immunofluorescence analysis of subcutaneous fat from cold-exposed mice confirms that the highest levels of these critical thermogenic components are expressed in distinct fat cell populations.
    Keywords:  Alpl gene; SV40 large T antigen; TNAP; UCP1; aP2-Prdm16 transgenic mice; functional beige cell line; futile creatine cycle; immortalized beige adipocytes; thermogenesis
    DOI:  https://doi.org/10.1016/j.cmet.2024.07.002
  32. Cell Metab. 2024 Jul 26. pii: S1550-4131(24)00276-6. [Epub ahead of print]
    Single-nucleus transcriptomics identifies separate classes of UCP1 and futile cycle adipocytes.
    Tongtong Wang, Anand Kumar Sharma, Chunyan Wu, Claudia Irene Maushart, Adhideb Ghosh, Wu Yang, Patrik Stefanicka, Zuzana Kovanicova, Jozef Ukropec, Jing Zhang, Myrtha Arnold, Manuel Klug, Katrien De Bock, Ulrich Schneider, Cristina Popescu, Bo Zheng, Lianggong Ding, Fen Long, Revati Sumukh Dewal, Caroline Moser, Wenfei Sun, Hua Dong, Martin Takes, Dominique Suelberg, Alexander Mameghani, Antonio Nocito, Christoph Johannes Zech, Alin Chirindel, Damian Wild, Irene A Burger, Michael R Schön, Arne Dietrich, Min Gao, Markus Heine, Yizhi Sun, Ariana Vargas-Castillo, Susanna Søberg, Camilla Scheele, Miroslav Balaz, Matthias Blüher, Matthias Johannes Betz, Bruce M Spiegelman, Christian Wolfrum.
      Adipose tissue can recruit catabolic adipocytes that utilize chemical energy to dissipate heat. This process occurs either by uncoupled respiration through uncoupling protein 1 (UCP1) or by utilizing ATP-dependent futile cycles (FCs). However, it remains unclear how these pathways coexist since both processes rely on the mitochondrial membrane potential. Utilizing single-nucleus RNA sequencing to deconvolute the heterogeneity of subcutaneous adipose tissue in mice and humans, we identify at least 2 distinct subpopulations of beige adipocytes: FC-adipocytes and UCP1-beige adipocytes. Importantly, we demonstrate that the FC-adipocyte subpopulation is highly metabolically active and utilizes FCs to dissipate energy, thus contributing to thermogenesis independent of Ucp1. Furthermore, FC-adipocytes are important drivers of systemic energy homeostasis and linked to glucose metabolism and obesity resistance in humans. Taken together, our findings identify a noncanonical thermogenic adipocyte subpopulation, which could be an important regulator of energy homeostasis in mammals.
    Keywords:  energy homeostasis; futile cycling; human metabolism; single-nucleus RNA sequencing; thermogenesis
    DOI:  https://doi.org/10.1016/j.cmet.2024.07.005
  33. bioRxiv. 2024 Jul 19. pii: 2024.07.17.603999. [Epub ahead of print]
    RAB12-LRRK2 Complex Suppresses Primary Ciliogenesis and Regulates Centrosome Homeostasis in Astrocytes.
    Xingjian Li, Hanwen Zhu, Bik Tzu Huang, Xianting Li, Heesoo Kim, Haiyan Tan, Yuanxi Zhang, Insup Choi, Junmin Peng, Pingyi Xu, Ji Sun, Zhenyu Yue.
      Leucine-rich repeat kinase 2 (LRRK2) phosphorylates a subset of RAB GTPases, and the phosphorylation levels are elevated by Parkinson's disease (PD)-linked mutations of LRRK2. However, the precise function of the specific RAB GTPase targeted by LRRK2 signaling in the brain remains to be elucidated. Here, we identify RAB12 as a robust LRRK2 substrate in the mouse brains through phosphoproteomics profiling and solve the structure of RAB12-LRRK2 protein complex through Cryo-EM analysis. Mechanistically, RAB12 cooperates with LRRK2 to inhibit primary ciliogenesis and regulate centrosome homeostasis in astrocytes through enhancing the phosphorylation of RAB10 and recruiting Rab interacting lysosomal protein like 1 (RILPL1), while the functions of RAB12 require a direct interaction with LRRK2 and LRRK2 kinase activity. Furthermore, the ciliary deficits and centrosome alteration caused by the PD-linked LRRK2-G2019S mutation are prevented by the deletion of Rab12 in astrocytes. Thus, our study reveals a physiological function of the RAB12-LRRK2 complex in regulating ciliogenesis and centrosome homeostasis. The RAB12-LRRK2 structure offers a guidance in the therapeutic development of PD by targeting the RAB12-LRRK2 interaction.
    DOI:  https://doi.org/10.1101/2024.07.17.603999
  34. Angew Chem Int Ed Engl. 2024 Aug 02. e202411133
    Orthogonal Persulfide Generation through Precision Tools Provides Insights into Mitochondrial Sulfane Sulfur.
    Suman Manna, Ragini Agrawal, Tarun Yadav, T Anand Kumar, Pooja Kumari, Aadishakti Dalai, Shaunak Kanade, Nagaraj Balasubramanian, Amit Singh, Harinath Chakrapani.
      The sulfane sulfur pool, comprised of persulfide (RS-SH) and polysulfide (RS-SnH) derived from hydrogen sulfide (H2S), has emerged as a major player in redox biochemistry. Mitochondria, besides energy generation, serve as significant cellular redox hubs, mediate stress response and cellular health. However, the effects of endogenous mitochondrial sulfane sulfur (MSS) remain largely uncharacterized as compared with their cytosolic counterparts, cytosolic sulfane sulfur (CSS). To investigate this, we designed a novel artificial substrate for mitochondrial 3-mercaptopyruvate sulfurtransferase (3-MST), a key enzyme involved in MSS biosynthesis. Using cells expressing a mitochondrion-localized persulfide biosensor, we demonstrate this tool's ability to selectively enhance MSS. While H2S was previously known to suppress human immunodeficiency virus (HIV-1), we found that MSS profoundly affected the HIV-1 life cycle, mediating viral reactivation from latency. Additionally, we provide evidence for the role of the host's mitochondrial redox state, membrane potential, apoptosis, and respiration rates in managing HIV-1 latency and reactivation. Together, dynamic fluctuations in the MSS pool have a significant and possibly conflicting effect on HIV-1 viral latency. The precision tools developed herein allow for orthogonal generation of persulfide within both mitochondria and the cytosol and will be useful in interrogating disease biology.
    Keywords:  3-Mercaptopyruvate sulfurtransferase; HIV-1; Hydrogen sulfide; Mitochondrial sulfane sulfur; redox biology
    DOI:  https://doi.org/10.1002/anie.202411133
  35. Nat Genet. 2024 Jul 29.
    Guidance for estimating penetrance of monogenic disease-causing variants in population cohorts.
    Caroline F Wright, Luke N Sharp, Leigh Jackson, Anna Murray, James S Ware, Daniel G MacArthur, Heidi L Rehm, Kashyap A Patel, Michael N Weedon.
      Penetrance is the probability that an individual with a pathogenic genetic variant develops a specific disease. Knowing the penetrance of variants for monogenic disorders is important for counseling of individuals. Until recently, estimates of penetrance have largely relied on affected individuals and their at-risk family members being clinically referred for genetic testing, a 'phenotype-first' approach. This approach substantially overestimates the penetrance of variants because of ascertainment bias. The recent availability of whole-genome sequencing data in individuals from very-large-scale population-based cohorts now allows 'genotype-first' estimates of penetrance for many conditions. Although this type of population-based study can underestimate penetrance owing to recruitment biases, it provides more accurate estimates of penetrance for secondary or incidental findings. Here, we provide guidance for the conduct of penetrance studies to ensure that robust genotypes and phenotypes are used to accurately estimate penetrance of variants and groups of similarly annotated variants from population-based studies.
    DOI:  https://doi.org/10.1038/s41588-024-01842-3
  36. Mol Genet Metab. 2024 Jul 24. pii: S1096-7192(24)00438-4. [Epub ahead of print]143(1-2): 108554
    Natural history of deoxyguanosine kinase deficiency.
    Nandaki Keshavan, Shamima Rahman.
       BACKGROUND AND OBJECTIVES: Deoxyguanosine kinase deficiency is one genetic cause of mtDNA depletion syndrome. Its major phenotypes include neonatal/infantile-onset hepatocerebral disease, isolated hepatic disease and myopathic disease. In this retrospective study, we seek to describe the natural history of deoxyguanosine kinase deficiency and identify any genotype-phenotype correlations.
    METHODS: Retrospective literature search and collation of data from genetically confirmed cases of deoxyguanosine kinase deficiency.
    RESULTS: 173 cases of DGUOK deficiency were identified. Neonatal/infantile-onset hepatocerebral disease accounted for 128 (74%) of cases. Isolated liver disease was seen in 36 (21%) and myopathic disease in 9 (5%) of cases. The most frequently involved systems were liver (98%), brain (75%), growth (46%) and gastrointestinal tract (26%). Infantile-onset disease typically presented with cholestatic jaundice and lactic acidosis. Neurological involvement included hypotonia, nystagmus and developmental delay with MRI brain abnormalities in about half of cases. Missense variants accounted for 48% of all pathogenic variants while variants resulting in truncated transcripts accounted for 39%. Prognosis was poor, especially for neonatal/ infantile-onset hepatocerebral disease for which 1 year survival was 11%. Twenty-three patients received liver transplants, of whom 12 died within 2 years of transplant. Patients with two truncating variants had a higher risk of death and were more likely to have the neonatal/infantile-onset hepatocerebral disease phenotype. No blood biomarker predictive of neurological involvement was identified. Earlier onset correlated with increased mortality.
    CONCLUSIONS: There is a narrow window for therapeutic intervention. For the hepatocerebral disease phenotype, median age of onset was 1 month while the median age of death was 6.5 months implying rapid disease progression.
    Keywords:  DGK; DGUOK; Deoxyguanosine kinase; Mitochondrial DNA depletion syndrome; Mitochondrial disease; Natural history; Outcome measures
    DOI:  https://doi.org/10.1016/j.ymgme.2024.108554
  37. Int Immunopharmacol. 2024 Aug 01. pii: S1567-5769(24)01357-2. [Epub ahead of print]140 112836
    The role of heat shock protein B8 in neuronal protection against oxidative stress and mitochondrial dysfunction: A literature review.
    Yanqing Wu, Feng Xiong, Jianmin Ling.
      Excessive oxidative stress triggers cerebrovascular and neurodegenerative diseases resulting in acute and chronic brain injury. However, the underlying mechanisms remain unknown. Levels of small heat shock protein B8 (HSPB8), which is highly expressed in the brain, are known to be significantly elevated in cerebral injury models. Exogenous HSPB8 protects the brain against mitochondrial damage. One potential mechanism underlying this protection is that HSPB8 overexpression alleviates the mitochondria-dependent pathways of apoptosis; mitochondrial biogenesis, fission, and mitophagy. Overexpression of HSPB8 may therefore have potential as a clinical therapy for cerebrovascular and neurodegenerative diseases. This review provides an overview of advances in the protective effects of HSPB8 against excessive cerebral oxidative stress, including the modulation of mitochondrial dysfunction and potent signaling pathways.
    Keywords:  HSPB8; Mitochondria; Mitophagy; Neurological diseases; Oxidative stress
    DOI:  https://doi.org/10.1016/j.intimp.2024.112836
  38. BMC Genomics. 2024 Jul 30. 25(1): 741
    Comparing methylation levels assayed in GC-rich regions with current and emerging methods.
    Dominic Guanzon, Jason P Ross, Chenkai Ma, Oliver Berry, Yi Jin Liew.
      DNA methylation is an epigenetic mechanism that regulates gene expression, and for mammals typically occurs on cytosines within CpG dinucleotides. A significant challenge for methylation detection methods is accurately measuring methylation levels within GC-rich regions such as gene promoters, as inaccuracies compromise downstream biological interpretation of the data. To address this challenge, we compared methylation levels assayed using four different Methods Enzymatic Methyl-seq (EM-seq), whole genome bisulphite sequencing (WGBS), Infinium arrays (Illumina MethylationEPIC, "EPIC"), and Oxford Nanopore Technologies nanopore sequencing (ONT) applied to human DNA. Overall, all methods produced comparable and consistent methylation readouts across the human genome. The flexibility offered by current gold standard WGBS in interrogating genome-wide cytosines is surpassed technically by both EM-seq and ONT, as their coverages and methylation readouts are less prone to GC bias. These advantages are tempered by increased laboratory time (EM-seq) and higher complexity (ONT). We further assess the strengths and weaknesses of each method, and provide recommendations in choosing the most appropriate methylation method for specific scientific questions or translational needs.
    Keywords:  DNA methylation; EM-seq; GC-rich loci; Infinium arrays; ONT; WGBS
    DOI:  https://doi.org/10.1186/s12864-024-10605-7
  39. Trends Analyt Chem. 2024 Sep;pii: 117852. [Epub ahead of print]178
    Artificial Intelligence in Metabolomics: A Current Review.
    Jinhua Chi, Jingmin Shu, Ming Li, Rekha Mudappathi, Yan Jin, Freeman Lewis, Alexandria Boon, Xiaoyan Qin, Li Liu, Haiwei Gu.
      Metabolomics and artificial intelligence (AI) form a synergistic partnership. Metabolomics generates large datasets comprising hundreds to thousands of metabolites with complex relationships. AI, aiming to mimic human intelligence through computational modeling, possesses extraordinary capabilities for big data analysis. In this review, we provide a recent overview of the methodologies and applications of AI in metabolomics studies in the context of systems biology and human health. We first introduce the AI concept, history, and key algorithms for machine learning and deep learning, summarizing their strengths and weaknesses. We then discuss studies that have successfully used AI across different aspects of metabolomic analysis, including analytical detection, data preprocessing, biomarker discovery, predictive modeling, and multi-omics data integration. Lastly, we discuss the existing challenges and future perspectives in this rapidly evolving field. Despite limitations and challenges, the combination of metabolomics and AI holds great promises for revolutionary advancements in enhancing human health.
    Keywords:  Artificial Intelligence; Deep Learning; Disease Diagnosis; Drug Discovery; Machine Learning; Metabolomics; Precision Medicine; Systems Biology
    DOI:  https://doi.org/10.1016/j.trac.2024.117852
  40. bioRxiv. 2024 Jul 28. pii: 2024.07.25.605208. [Epub ahead of print]
    Transfer RNA acetylation regulates in vivo mammalian stress signaling.
    Supuni Thalalla Gamage, Roxane Khoogar, Shereen Howpay Manage, McKenna C Crawford, Joe Georgeson, Bogdan V Polevoda, Chelsea Sanders, Kendall A Lee, Kellie D Nance, Vinithra Iyer, Anatoly Kustanovich, Minervo Perez, Chu T Thu, Sam R Nance, Ruhul Amin, Christine N Miller, Ronald J Holewinski, Thomas Meyer, Vishal Koparde, Acong Yang, Parthav Jailwala, Joe T Nguyen, Thorkell Andresson, Kent Hunter, Shuo Gu, Beverly A Mock, Elijah F Edmondson, Simone Difilippantonio, Raj Chari, Schraga Schwartz, Mitchell R O'Connell, Colin Chih-Chien Wu, Jordan L Meier.
      Transfer RNA (tRNA) modifications are crucial for protein synthesis, but their position-specific physiological roles remain poorly understood. Here we investigate the impact of N4-acetylcytidine (ac 4 C), a highly conserved tRNA modification, using a Thumpd1 knockout mouse model. We find that loss of Thumpd1-dependent tRNA acetylation leads to reduced levels of tRNA Leu , increased ribosome stalling, and activation of eIF2α phosphorylation. Thumpd1 knockout mice exhibit growth defects and sterility. Remarkably, concurrent knockout of Thumpd1 and the stress-sensing kinase Gcn2 causes penetrant postnatal lethality, indicating a critical genetic interaction. Our findings demonstrate that a modification restricted to a single position within type II cytosolic tRNAs can regulate ribosome-mediated stress signaling in mammalian organisms, with implications for our understanding of translation control as well as therapeutic interventions.
    DOI:  https://doi.org/10.1101/2024.07.25.605208
  41. Cell. 2024 Jul 25. pii: S0092-8674(24)00766-9. [Epub ahead of print]
    A replisome-associated histone H3-H4 chaperone required for epigenetic inheritance.
    Juntao Yu, Yujie Zhang, Yimeng Fang, Joao A Paulo, Dadmehr Yaghoubi, Xu Hua, Gergana Shipkovenska, Takenori Toda, Zhiguo Zhang, Steven P Gygi, Songtao Jia, Qing Li, Danesh Moazed.
      Faithful transfer of parental histones to newly replicated daughter DNA strands is critical for inheritance of epigenetic states. Although replication proteins that facilitate parental histone transfer have been identified, how intact histone H3-H4 tetramers travel from the front to the back of the replication fork remains unknown. Here, we use AlphaFold-Multimer structural predictions combined with biochemical and genetic approaches to identify the Mrc1/CLASPIN subunit of the replisome as a histone chaperone. Mrc1 contains a conserved histone-binding domain that forms a brace around the H3-H4 tetramer mimicking nucleosomal DNA and H2A-H2B histones, is required for heterochromatin inheritance, and promotes parental histone recycling during replication. We further identify binding sites for the FACT histone chaperone in Swi1/TIMELESS and DNA polymerase α that are required for heterochromatin inheritance. We propose that Mrc1, in concert with FACT acting as a mobile co-chaperone, coordinates the distribution of parental histones to newly replicated DNA.
    Keywords:  CLASPIN; FACT; chromatin replication; epigenetics; fork protection complex; heterochromatin; histone inheritance; parental histone transfer; replisome, Mrc1
    DOI:  https://doi.org/10.1016/j.cell.2024.07.006
  42. Redox Biol. 2024 Jul 23. pii: S2213-2317(24)00261-1. [Epub ahead of print]75 103283
    Mitochondria to plasma membrane redox signaling is essential for fatty acid β-oxidation-driven insulin secretion.
    Martin Jabůrek, Eduardo Klöppel, Pavla Průchová, Oleksandra Mozheitova, Jan Tauber, Hana Engstová, Petr Ježek.
      We asked whether acute redox signaling from mitochondria exists concomitantly to fatty acid- (FA-) stimulated insulin secretion (FASIS) at low glucose by pancreatic β-cells. We show that FA β-oxidation produces superoxide/H2O2, providing: i) mitochondria-to-plasma-membrane redox signaling, closing KATP-channels synergically with elevated ATP (substituting NADPH-oxidase-4-mediated H2O2-signaling upon glucose-stimulated insulin secretion); ii) activation of redox-sensitive phospholipase iPLA2γ/PNPLA8, cleaving mitochondrial FAs, enabling metabotropic GPR40 receptors to amplify insulin secretion (IS). At fasting glucose, palmitic acid stimulated IS in wt mice; palmitic, stearic, lauric, oleic, linoleic, and hexanoic acids also in perifused pancreatic islets (PIs), with suppressed 1st phases in iPLA2γ/PNPLA8-knockout mice/PIs. Extracellular/cytosolic H2O2-monitoring indicated knockout-independent redox signals, blocked by mitochondrial antioxidant SkQ1, etomoxir, CPT1 silencing, and catalase overexpression, all inhibiting FASIS, keeping ATP-sensitive K+-channels open, and diminishing cytosolic [Ca2+]-oscillations. FASIS in mice was a postprandially delayed physiological event. Redox signals of FA β-oxidation are thus documented, reaching the plasma membrane, essentially co-stimulating IS.
    Keywords:  Fatty acid-stimulated insulin secretion; GPR40; Mitochondrial fatty acids; Pancreatic β-cells; Redox signaling; Redox-activated phospholipase iPLA2γ
    DOI:  https://doi.org/10.1016/j.redox.2024.103283
  43. Clin Transl Sci. 2024 Aug;17(8): e13893
    Pharmacogenomics polygenic risk score: Ready or not for prime time?
    Sonal Singh, Gabriele Stocco, Katherine N Theken, Alyson Dickson, QiPing Feng, Jason H Karnes, Jonathan D Mosley, Nihal El Rouby.
      Pharmacogenomic Polygenic Risk Scores (PRS) have emerged as a tool to address the polygenic nature of pharmacogenetic phenotypes, increasing the potential to predict drug response. Most pharmacogenomic PRS have been extrapolated from disease-associated variants identified by genome wide association studies (GWAS), although some have begun to utilize genetic variants from pharmacogenomic GWAS. As pharmacogenomic PRS hold the promise of enabling precision medicine, including stratified treatment approaches, it is important to assess the opportunities and challenges presented by the current data. This assessment will help determine how pharmacogenomic PRS can be advanced and transitioned into clinical use. In this review, we present a summary of recent evidence, evaluate the current status, and identify several challenges that have impeded the progress of pharmacogenomic PRS. These challenges include the reliance on extrapolations from disease genetics and limitations inherent to pharmacogenomics research such as low sample sizes, phenotyping inconsistencies, among others. We finally propose recommendations to overcome the challenges and facilitate the clinical implementation. These recommendations include standardizing methodologies for phenotyping, enhancing collaborative efforts, developing new statistical methods to capitalize on drug-specific genetic associations for PRS construction. Additional recommendations include enhancing the infrastructure that can integrate genomic data with clinical predictors, along with implementing user-friendly clinical decision tools, and patient education. Ethical and regulatory considerations should address issues related to patient privacy, informed consent and safe use of PRS. Despite these challenges, ongoing research and large-scale collaboration is likely to advance the field and realize the potential of pharmacogenomic PRS.
    DOI:  https://doi.org/10.1111/cts.13893
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