bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2023‒11‒19
fifty-one papers selected by
Catalina Vasilescu, Helmholz Munich
  1. GTPBP8 is required for mitoribosomal biogenesis and mitochondrial translation.
  2. Teamwork makes the dream work: functional collaborations between families, scientists, and healthcare providers to drive progress in the treatment of Leigh Syndrome.
  3. Genetic analysis and multimodal imaging identify novel mtDNA 12148T>C leading to multisystem dysfunction with tissue-specific heteroplasmy.
  4. Mitochondrial aminoacyl-tRNA synthetases trigger unique compensatory mechanisms in neurons.
  5. Mitochondrial entry gate as regulatory hub.
  6. Heptanoate Improves Compensatory Mechanism of Glucose Homeostasis in Mitochondrial Long-Chain Fatty Acid Oxidation Defect.
  7. 3D reconstruction of murine mitochondria reveals changes in structure during aging linked to the MICOS complex.
  8. The human mitochondrial mRNA structurome reveals mechanisms of gene expression.
  9. Interactions of mitochondrial and skeletal muscle biology in mitochondrial myopathy.
  10. Stimulates Short-Chain Dehydrogenase/Reductase Proteins to Alleviate Heart Failure Independent of Mitochondrial Protein Deacetylation.
  11. NAD+ regulates nucleotide metabolism and genomic DNA replication.
  12. Mitigating aberrant Cdk5 activation alleviates mitochondrial defects and motor neuron disease symptoms in spinal muscular atrophy.
  13. Nicotinamide Riboside, an NAD + Precursor, Protects Against Cardiac Mitochondrial Dysfunction in Fetal Guinea Pigs Exposed to Gestational Hypoxia.
  14. MCUb is an inducible regulator of calcium-dependent mitochondrial metabolism and substrate utilization in muscle.
  15. Integration of FUNDC1-associated mitochondrial protein import and mitochondrial quality control contributes to TDP-43 degradation.
  16. Knockout or inhibition of USP30 protects dopaminergic neurons in a Parkinson's disease mouse model.
  17. Inorganic polyphosphate and the regulation of mitochondrial physiology.
  18. Ketone body β-hydroxybutyrate (BHB) preserves mitochondrial bioenergetics.
  19. Dystonia in ATP Synthase Defects: Reconnecting Mitochondria and Dopamine.
  20. Cristae dynamics is modulated in bioenergetically compromised mitochondria.
  21. Genetic landscape of pediatric acute liver failure of indeterminate origin.
  22. Protocol to study human mitochondrial ribosome using quantitative density gradient analysis by mass spectrometry and complexome profiling analysis.
  23. Keep in touch: a perspective on the mitochondrial social network and its implication in health and disease.
  24. Mitochondrial dysfunction in Parkinson's disease - a key disease hallmark with therapeutic potential.
  25. Accumulation of 8-oxodG within the human mitochondrial genome positively associates with transcription.
  26. Disruption of CFAP418 interaction with lipids causes widespread abnormal membrane-associated cellular processes in retinal degenerations.
  27. Heteroplasmic pathogenic m.12315G>A variant in MT-TL2 presenting with MELAS syndrome and depletion of nitric oxide donors.
  28. Gut microbiota promotes enteroendocrine cell maturation and mitochondrial function.
  29. Circulating Mitochondrial DNA is associated with High Levels of Fatigue in Two Independent Sarcoidosis Cohorts.
  30. Attaining Diagnostic Excellence: How the Structure and Function of a Rare Disease Service Contribute to Ending the Diagnostic Odyssey.
  31. Developmental and epileptic encephalopathy 82 (DEE82) with novel compound heterozygous mutations of GOT2 gene.
  32. Vitamin B12 emerges as key player during cellular reprogramming.
  33. The Impact of Artificial Intelligence on Optimizing Diagnosis and Treatment Plans for Rare Genetic Disorders.
  34. Impact of N221S missense mutation in human ribonucleotide reductase small subunit b on mitochondrial DNA depletion syndrome.
  35. Utility of AlphaMissense predictions in Asparagine Synthetase deficiency variant classification.
  36. Targeted transplantation of engineered mitochondrial compound promotes functional recovery after spinal cord injury by enhancing macrophage phagocytosis.
  37. MAPL loss dysregulates bile and liver metabolism in mice.
  38. Astrocyte and L-lactate in the anterior cingulate cortex modulate schema memory and neuronal mitochondrial biogenesis.
  39. Systems genetics approaches for understanding complex traits with relevance for human disease.
  40. USP18 enhances dengue virus replication by regulating mitochondrial DNA release.
  41. Pathogenesis and Management of Citrin Deficiency.
  42. Vitamin B12 is a limiting factor for induced cellular plasticity and tissue repair.
  43. A tool kit of highly selective and sensitive genetically encoded neuropeptide sensors.
  44. Mitochondria-associated membrane collapse impairs TBK1-mediated proteostatic stress response in ALS.
  45. Combined changes in temperature and pH mimicking exercise results in decreased efficiency in muscle mitochondria.
  46. Targeting mitochondrial shape: at the heart of cardioprotection.
  47. Flashy molecules decode a polymer's lengthening chain.
  48. An in vivo platform to identify clinically relevant pathogenic loci using Drosophila melanogaster.
  49. A drug-like molecule engages nuclear hormone receptor DAF-12/FXR to regulate mitophagy and extend lifespan.
  50. Inflammatory macrophages reprogram to immunosuppression by reducing mitochondrial translation.
  51. Adjusted vascular contractility relies on integrity of progranulin pathway: Insights into mitochondrial function.
  1. Cell Mol Life Sci. 2023 Nov 16. 80(12): 361
    GTPBP8 is required for mitoribosomal biogenesis and mitochondrial translation.
    Liang Wang, Taru Hilander, Xiaonan Liu, Hoi Ying Tsang, Ove Eriksson, Christopher B Jackson, Markku Varjosalo, Hongxia Zhao.
      Mitochondrial translation occurs on the mitochondrial ribosome, also known as the mitoribosome. The assembly of mitoribosomes is a highly coordinated process. During mitoribosome biogenesis, various assembly factors transiently associate with the nascent ribosome, facilitating the accurate and efficient construction of the mitoribosome. However, the specific factors involved in the assembly process, the precise mechanisms, and the cellular compartments involved in this vital process are not yet fully understood. In this study, we discovered a crucial role for GTP-binding protein 8 (GTPBP8) in the assembly of the mitoribosomal large subunit (mt-LSU) and mitochondrial translation. GTPBP8 is identified as a novel GTPase located in the matrix and peripherally bound to the inner mitochondrial membrane. Importantly, GTPBP8 is specifically associated with the mt-LSU during its assembly. Depletion of GTPBP8 leads to an abnormal accumulation of mt-LSU, indicating that GTPBP8 is critical for proper mt-LSU assembly. Furthermore, the absence of GTPBP8 results in reduced levels of fully assembled 55S monosomes. This impaired assembly leads to compromised mitochondrial translation and, consequently, impaired mitochondrial function. The identification of GTPBP8 as an important player in these processes provides new insights into the molecular mechanisms underlying mitochondrial protein synthesis and its regulation.
    Keywords:  GTP binding protein; Mitochondria; Mitochondrial translation; Mitoribosomal protein; Mitoribosome; Mitoribosome assembly; Mitoribosome large subunit
    DOI:  https://doi.org/10.1007/s00018-023-05014-0
  2. Orphanet J Rare Dis. 2023 Nov 16. 18(1): 355
    Teamwork makes the dream work: functional collaborations between families, scientists, and healthcare providers to drive progress in the treatment of Leigh Syndrome.
    Jesse D Moreira, Karan K Smith, Sophia Zilber, Kasey Woleben, Jessica L Fetterman.
      BACKGROUND: Leigh syndrome, an inherited neurometabolic disorder, is estimated to be the most common pediatric manifestation of mitochondrial disease. No treatments are currently available for Leigh syndrome due to many hurdles in drug discovery efforts. Leigh syndrome causal variants span over 110 different genes and likely lead to both unique and shared biochemical alterations, often resulting in overlapping phenotypic features. The mechanisms by which pathogenic variants in mitochondrial genes alter cellular phenotype to promote disease remain poorly understood. The rarity of cases of specific causal variants creates barriers to drug discovery and adequately sized clinical trials. BODY: To address the current challenges in drug discovery and facilitate communication between researchers, healthcare providers, patients, and families, the Boston University integrative Cardiovascular Metabolism and Pathophysiology (iCAMP) Lab and Cure Mito Foundation hosted a Leigh Syndrome Symposium. This symposium brought together expert scientists and providers to highlight the current successes in drug discovery and novel models of mitochondrial disease, and to connect patients to providers and scientists to foster community and communication.CONCLUSION: In this symposium review, we describe the research presented, the hurdles ahead, and strategies to better connect the Leigh syndrome community members to advance treatments for Leigh syndrome.
    Keywords:  Community; Leigh syndrome; Mitochondria; Mitochondrial disease; Mitochondrial genetics; Patient registries; Symposium
    DOI:  https://doi.org/10.1186/s13023-023-02871-7
  3. medRxiv. 2023 Nov 05. pii: 2023.11.03.23297854. [Epub ahead of print]
    Genetic analysis and multimodal imaging identify novel mtDNA 12148T>C leading to multisystem dysfunction with tissue-specific heteroplasmy.
    Kinsley Belle, Alexander Kreymerman, Nirmal Vadgama, Marco H Ji, Sandeep Randhawa, Juan Caicedo, Megan Wong, Stephanie P Muscat, Casey A Gifford, Richard T Lee, Jamal Nasir, Jill L Young, Gregory Enns, Ioannis Karakikes, Mark Mercola, Edward H Wood.
      Patients with mitochondrial disorders present with clinically diverse symptoms, largely driven by heterogeneous mutations in mitochondrial-encoded and nuclear-encoded mitochondrial genes. These mutations ultimately lead to complex biochemical disorders with a myriad of clinical manifestations, often accumulating during childhood on into adulthood, contributing to life-altering and sometimes fatal events. It is therefore important to diagnose and characterize the associated disorders for each mitochondrial mutation as early as possible since medical management might be able to improve the quality and longevity of life in mitochondrial disease patients. Here we identify a novel mitochondrial variant in a mitochondrial transfer RNA for histidine (mt-tRNA-his) [m.12148T>C], that is associated with the development of ocular, aural, neurological, renal, and muscular dysfunctions. We provide a detailed account of a family harboring this mutation, as well as the molecular underpinnings contributing to cellular and mitochondrial dysfunction. In conclusion, this investigation provides clinical, biochemical, and morphological evidence of the pathogenicity of m.12148T>C. We highlight the importance of multiple tissue testing and in vitro disease modeling in diagnosing mitochondrial disease.
    DOI:  https://doi.org/10.1101/2023.11.03.23297854
  4. Hum Mol Genet. 2023 Nov 17. pii: ddad196. [Epub ahead of print]
    Mitochondrial aminoacyl-tRNA synthetases trigger unique compensatory mechanisms in neurons.
    Oliver Podmanicky, Fei Gao, Benjamin Munro, Matthew J Jennings, Veronika Boczonadi, Denisa Hathazi, Juliane S Mueller, Rita Horvath.
      Mitochondrial aminoacyl-tRNA synthetase (mt-ARS) mutations cause severe, progressive, and often lethal diseases with highly heterogeneous and tissue-specific clinical manifestations. This study investigates the molecular mechanisms triggered by three different mt-ARS defects caused by biallelic mutations in AARS2, EARS2, and RARS2, using an in vitro model of human neuronal cells. We report distinct molecular mechanisms of mitochondrial dysfunction among the mt-ARS defects studied. Our findings highlight the ability of proliferating neuronal progenitor cells (iNPCs) to compensate for mitochondrial translation defects and maintain balanced levels of oxidative phosphorylation (OXPHOS) components, which becomes more challenging in mature neurons. Mutant iNPCs exhibit unique compensatory mechanisms, involving specific branches of the integrated stress response, which may be gene-specific or related to the severity of the mitochondrial translation defect. RNA sequencing revealed distinct transcriptomic profiles showing dysregulation of neuronal differentiation and protein translation. This study provides valuable insights into the tissue-specific compensatory mechanisms potentially underlying the phenotypes of patients with mt-ARS defects. Our novel in vitro model may more accurately represent the neurological presentation of patients and offer an improved platform for future investigations and therapeutic development.
    Keywords:  aminoacyl-tRNA synthetase; mitochondrial biology; neurological disease; protein synthesis
    DOI:  https://doi.org/10.1093/hmg/ddad196
  5. Biochim Biophys Acta Mol Cell Res. 2023 Jul 04. pii: S0167-4889(23)00101-5. [Epub ahead of print] 119529
    Mitochondrial entry gate as regulatory hub.
    Fabian den Brave, Nikolaus Pfanner, Thomas Becker.
      Mitochondria import 1000-1300 different precursor proteins from the cytosol. The main mitochondrial entry gate is formed by the translocase of the outer membrane (TOM complex). Molecular coupling and modification of TOM subunits control and modulate protein import in response to cellular signaling. The TOM complex functions as regulatory hub to integrate mitochondrial protein biogenesis and quality control into the cellular proteostasis network.
    Keywords:  Mitochondria; Protein sorting; Proteostasis; Quality control; Stress response; TOM complex
    DOI:  https://doi.org/10.1016/j.bbamcr.2023.119529
  6. Nutrients. 2023 Nov 05. pii: 4689. [Epub ahead of print]15(21):
    Heptanoate Improves Compensatory Mechanism of Glucose Homeostasis in Mitochondrial Long-Chain Fatty Acid Oxidation Defect.
    Siti Nurjanah, Albert Gerding, Marcel A Vieira-Lara, Bernard Evers, Miriam Langelaar-Makkinje, Ute Spiekerkoetter, Barbara M Bakker, Sara Tucci.
      Defects in mitochondrial fatty acid β-oxidation (FAO) impair metabolic flexibility, which is an essential process for energy homeostasis. Very-long-chain acyl-CoA dehydrogenase (VLCADD; OMIM 609575) deficiency is the most common long-chain mitochondrial FAO disorder presenting with hypoglycemia as a common clinical manifestation. To prevent hypoglycemia, triheptanoin-a triglyceride composed of three heptanoates (C7) esterified with a glycerol backbone-can be used as a dietary treatment, since it is metabolized into precursors for gluconeogenesis. However, studies investigating the effect of triheptanoin on glucose homeostasis are limited. To understand the role of gluconeogenesis in the pathophysiology of long-chain mitochondrial FAO defects, we injected VLCAD-deficient (VLCAD-/-) mice with 13C3-glycerol in the presence and absence of heptanoate (C7). The incorporation of 13C3-glycerol into blood glucose was higher in VLCAD-/- mice than in WT mice, whereas the difference disappeared in the presence of C7. The result correlates with 13C enrichment of liver metabolites in VLCAD-/- mice. In contrast, the C7 bolus significantly decreased the 13C enrichment. These data suggest that the increased contribution of gluconeogenesis to the overall glucose production in VLCAD-/- mice increases the need for gluconeogenesis substrate, thereby avoiding hypoglycemia. Heptanoate is a suitable substrate to induce glucose production in mitochondrial FAO defect.
    Keywords:  VLCAD deficiency; fatty acid oxidation disorder; glucose homeostasis; glycerol; heptanoate; stable isotope; very long-chain acyl-CoA dehydrogenase
    DOI:  https://doi.org/10.3390/nu15214689
  7. Aging Cell. 2023 Nov 13. e14009
    3D reconstruction of murine mitochondria reveals changes in structure during aging linked to the MICOS complex.
    Zer Vue, Edgar Garza-Lopez, Kit Neikirk, Prasanna Katti, Larry Vang, Heather Beasley, Jianqiang Shao, Andrea G Marshall, Amber Crabtree, Alexandria C Murphy, Brenita C Jenkins, Praveena Prasad, Chantell Evans, Brittany Taylor, Margaret Mungai, Mason Killion, Dominique Stephens, Trace A Christensen, Jacob Lam, Benjamin Rodriguez, Mark A Phillips, Nastaran Daneshgar, Ho-Jin Koh, Alice Koh, Jamaine Davis, Nina Devine, Saleem Muhammod, Estevão Scudese, Kenneth Ryan Arnold, Valeria Vanessa Chavarin, Ryan Daniel Robinson, Moumita Chakraborty, Jennifer A Gaddy, Mariya T Sweetwyne, Genesis Wilson, Elma Zaganjor, James Kezos, Cristiana Dondi, Anilkumar K Reddy, Brian Glancy, Annet Kirabo, Anita M Quintana, Dao-Fu Dai, Karen Ocorr, Sandra A Murray, Steven M Damo, Vernat Exil, Blake Riggs, Bret C Mobley, Jose A Gomez, Melanie R McReynolds, Antentor Hinton.
      During aging, muscle gradually undergoes sarcopenia, the loss of function associated with loss of mass, strength, endurance, and oxidative capacity. However, the 3D structural alterations of mitochondria associated with aging in skeletal muscle and cardiac tissues are not well described. Although mitochondrial aging is associated with decreased mitochondrial capacity, the genes responsible for the morphological changes in mitochondria during aging are poorly characterized. We measured changes in mitochondrial morphology in aged murine gastrocnemius, soleus, and cardiac tissues using serial block-face scanning electron microscopy and 3D reconstructions. We also used reverse transcriptase-quantitative PCR, transmission electron microscopy quantification, Seahorse analysis, and metabolomics and lipidomics to measure changes in mitochondrial morphology and function after loss of mitochondria contact site and cristae organizing system (MICOS) complex genes, Chchd3, Chchd6, and Mitofilin. We identified significant changes in mitochondrial size in aged murine gastrocnemius, soleus, and cardiac tissues. We found that both age-related loss of the MICOS complex and knockouts of MICOS genes in mice altered mitochondrial morphology. Given the critical role of mitochondria in maintaining cellular metabolism, we characterized the metabolomes and lipidomes of young and aged mouse tissues, which showed profound alterations consistent with changes in membrane integrity, supporting our observations of age-related changes in muscle tissues. We found a relationship between changes in the MICOS complex and aging. Thus, it is important to understand the mechanisms that underlie the tissue-dependent 3D mitochondrial phenotypic changes that occur in aging and the evolutionary conservation of these mechanisms between Drosophila and mammals.
    Keywords:   Drosophila ; 3D morphometry; MICOS; aging; mitochondria; mitochondrial disease; mitochondrion; reconstruction; reticulum; serial block-face SEM; skeletal muscle
    DOI:  https://doi.org/10.1111/acel.14009
  8. bioRxiv. 2023 Nov 02. pii: 2023.10.31.564750. [Epub ahead of print]
    The human mitochondrial mRNA structurome reveals mechanisms of gene expression.
    J Conor Moran, Amir Brivanlou, Michele Brischigliaro, Flavia Fontanesi, Silvi Rouskin, Antoni Barrientos.
      The mammalian mitochondrial genome encodes thirteen oxidative phosphorylation system proteins, crucial in aerobic energy transduction. These proteins are translated from 9 monocistronic and 2 bicistronic transcripts, whose native structures remain unexplored, leaving fundamental molecular determinants of mitochondrial gene expression unknown. To address this gap, we developed a mitoDMS-MaPseq approach and used DREEM clustering to resolve the native human mitochondrial mt-mRNA structurome. We gained insights into mt-mRNA biology and translation regulatory mechanisms, including a unique programmed ribosomal frameshifting for the ATP8/ATP6 transcript. Furthermore, absence of the mt-mRNA maintenance factor LRPPRC led to a mitochondrial transcriptome structured differently, with specific mRNA regions exhibiting increased or decreased structuredness. This highlights the role of LRPPRC in maintaining mRNA folding to promote mt-mRNA stabilization and efficient translation. In conclusion, our mt-mRNA folding maps reveal novel mitochondrial gene expression mechanisms, serving as a detailed reference and tool for studying them in different physiological and pathological contexts.
    DOI:  https://doi.org/10.1101/2023.10.31.564750
  9. Biochem J. 2023 Nov 15. 480(21): 1767-1789
    Interactions of mitochondrial and skeletal muscle biology in mitochondrial myopathy.
    Valeria Di Leo, Tiago M Bernardino Gomes, Amy E Vincent.
      Mitochondrial dysfunction in skeletal muscle fibres occurs with both healthy aging and a range of neuromuscular diseases. The impact of mitochondrial dysfunction in skeletal muscle and the way muscle fibres adapt to this dysfunction is important to understand disease mechanisms and to develop therapeutic interventions. Furthermore, interactions between mitochondrial dysfunction and skeletal muscle biology, in mitochondrial myopathy, likely have important implications for normal muscle function and physiology. In this review, we will try to give an overview of what is known to date about these interactions including metabolic remodelling, mitochondrial morphology, mitochondrial turnover, cellular processes and muscle cell structure and function. Each of these topics is at a different stage of understanding, with some being well researched and understood, and others in their infancy. Furthermore, some of what we know comes from disease models. Whilst some findings are confirmed in humans, where this is not yet the case, we must be cautious in interpreting findings in the context of human muscle and disease. Here, our goal is to discuss what is known, highlight what is unknown and give a perspective on the future direction of research in this area.
    Keywords:  function; metabolism; mitochondria; mitochondrial dysfunction; structure
    DOI:  https://doi.org/10.1042/BCJ20220233
  10. Circulation. 2023 Nov 15.
    Stimulates Short-Chain Dehydrogenase/Reductase Proteins to Alleviate Heart Failure Independent of Mitochondrial Protein Deacetylation.
    Matthew A Walker, Hongye Chen, Aprajita Yadav, Julia Ritterhoff, Outi Villet, Tim McMillen, Yuliang Wang, Hayley Purcell, Danijel Djukovic, Daniel Raftery, Nina Isoherranen, Rong Tian.
      BACKGROUND: Strategies to increase cellular NAD+ (oxidized nicotinamide adenine dinucleotide) level have prevented cardiac dysfunction in multiple models of heart failure, but molecular mechanisms remain unclear. Little is known about the benefits of NAD+-based therapies in failing hearts after the symptoms of heart failure have appeared. Most pretreatment regimens suggested mechanisms involving activation of sirtuin, especially Sirt3 (sirtuin 3), and mitochondrial protein acetylation.METHODS: We induced cardiac dysfunction by pressure overload in SIRT3-deficient (knockout) mice and compared their response with nicotinamide riboside chloride treatment with wild-type mice. To model a therapeutic approach, we initiated the treatment in mice with established cardiac dysfunction and found nicotinamide riboside chloride improved mitochondrial function and blunted heart failure progression. Similar benefits were observed in wild-type and knockout mice. Boosting NAD+ level improved the function of NAD(H) redox-sensitive SDR (short-chain dehydrogenase/reductase) family proteins. Upregulation of Mrpp2 (mitochondrial ribonuclease P protein 2), a multifunctional SDR protein and a subunit of mitochondrial ribonuclease P, improves mitochondrial DNA transcripts processing and electron transport chain function. Activation of SDRs in the retinol metabolism pathway stimulates RXRα (retinoid X receptor α)/PPARα (proliferator-activated receptor α) signaling and restores mitochondrial oxidative metabolism. Downregulation of Mrpp2 and impaired mitochondrial ribonuclease P were found in human failing hearts, suggesting a shared mechanism of defective mitochondrial biogenesis in mouse and human heart failure.
    CONCLUSIONS: These findings identify SDR proteins as important regulators of mitochondrial function and molecular targets of NAD+-based therapy. Furthermore, the benefit is observed regardless of Sirt3-mediated mitochondrial protein deacetylation, a widely held mechanism for NAD+-based therapy for heart failure. The data also show that NAD+-based therapy can be useful in pre-existing heart failure.
    Keywords:  NAD+; heart failure; mitochondria; nicotinamide riboside; short-chain dehydrogenase; sirtuin
    DOI:  https://doi.org/10.1161/CIRCULATIONAHA.123.066039
  11. Nat Cell Biol. 2023 Nov 13.
    NAD+ regulates nucleotide metabolism and genomic DNA replication.
    Sebastian Howen Nesgaard Munk, Joanna Maria Merchut-Maya, Alba Adelantado Rubio, Arnaldur Hall, George Pappas, Giacomo Milletti, MyungHee Lee, Lea Giørtz Johnsen, Per Guldberg, Jiri Bartek, Apolinar Maya-Mendoza.
      The intricate orchestration of enzymatic activities involving nicotinamide adenine dinucleotide (NAD+) is essential for maintaining metabolic homeostasis and preserving genomic integrity. As a co-enzyme, NAD+ plays a key role in regulating metabolic pathways, such as glycolysis and Kreb's cycle. ADP-ribosyltransferases (PARPs) and sirtuins rely on NAD+ to mediate post-translational modifications of target proteins. The activation of PARP1 in response to DNA breaks leads to rapid depletion of cellular NAD+ compromising cell viability. Therefore, the levels of NAD+ must be tightly regulated. Here we show that exogenous NAD+, but not its precursors, has a direct effect on mitochondrial activity. Short-term incubation with NAD+ boosts Kreb's cycle and the electron transport chain and enhances pyrimidine biosynthesis. Extended incubation with NAD+ results in depletion of pyrimidines, accumulation of purines, activation of the replication stress response and cell cycle arrest. Moreover, a combination of NAD+ and 5-fluorouridine selectively kills cancer cells that rely on de novo pyrimidine synthesis. We propose an integrated model of how NAD+ regulates nucleotide metabolism, with relevance to healthspan, ageing and cancer therapy.
    DOI:  https://doi.org/10.1038/s41556-023-01280-z
  12. Proc Natl Acad Sci U S A. 2023 Nov 21. 120(47): e2300308120
    Mitigating aberrant Cdk5 activation alleviates mitochondrial defects and motor neuron disease symptoms in spinal muscular atrophy.
    Nimrod Miller, Zhaofa Xu, Katharina A Quinlan, Amy Ji, Jered V McGivern, Zhihua Feng, Han Shi, Chien-Ping Ko, Li-Huei Tsai, Charles J Heckman, Allison D Ebert, Yongchao C Ma.
      Spinal muscular atrophy (SMA), the top genetic cause of infant mortality, is characterized by motor neuron degeneration. Mechanisms underlying SMA pathogenesis remain largely unknown. Here, we report that the activity of cyclin-dependent kinase 5 (Cdk5) and the conversion of its activating subunit p35 to the more potent activator p25 are significantly up-regulated in mouse models and human induced pluripotent stem cell (iPSC) models of SMA. The increase of Cdk5 activity occurs before the onset of SMA phenotypes, suggesting that it may be an initiator of the disease. Importantly, aberrant Cdk5 activation causes mitochondrial defects and motor neuron degeneration, as the genetic knockout of p35 in an SMA mouse model rescues mitochondrial transport and fragmentation defects, and alleviates SMA phenotypes including motor neuron hyperexcitability, loss of excitatory synapses, neuromuscular junction denervation, and motor neuron degeneration. Inhibition of the Cdk5 signaling pathway reduces the degeneration of motor neurons derived from SMA mice and human SMA iPSCs. Altogether, our studies reveal a critical role for the aberrant activation of Cdk5 in SMA pathogenesis and suggest a potential target for therapeutic intervention.
    Keywords:  Cdk5; mitochondria; motor neuron; neurodegeneration; spinal muscular atrophy
    DOI:  https://doi.org/10.1073/pnas.2300308120
  13. Reprod Sci. 2023 Nov 13.
    Nicotinamide Riboside, an NAD + Precursor, Protects Against Cardiac Mitochondrial Dysfunction in Fetal Guinea Pigs Exposed to Gestational Hypoxia.
    Loren P Thompson, Hong Song, Jamie Hartnett.
      Gestational hypoxia inhibits mitochondrial function in the fetal heart and placenta contributing to fetal growth restriction and organ dysfunction. NAD + deficiency may contribute to a metabolic deficit by inhibiting oxidative phosphorylation and ATP synthesis. We tested the effects of nicotinamide riboside (NR), an NAD + precursor, as a treatment for reversing known mitochondrial dysfunction in hypoxic fetal hearts. Pregnant guinea pigs were housed in room air (normoxia) or placed in a hypoxic chamber (10.5%O2) for the last 14 days of gestation (term = 65 days) and administered either water or NR (1.6 mg/ml) in the drinking bottle. Fetuses were excised at term, and NAD + levels of maternal liver, placenta, and fetal heart ventricles were measured. Indices of mitochondrial function (complex IV activity, sirtuin 3 activity, protein acetylation) and ATP synthesis were measured in fetal heart ventricles of NR-treated/untreated normoxic and hypoxic animals. Hypoxia reduced fetal body weight in both sexes (p = 0.01), which was prevented by NR. Hypoxia had no effect on maternal liver NAD + levels but decreased (p = 0.04) placenta NAD + levels, the latter normalized with NR treatment. Hypoxia had no effect on fetal heart NAD + but decreased (p < 0.05) mitochondrial complex IV and sirtuin 3 activities, ATP content, and increased mitochondrial acetylation, which were all normalized with maternal NR. Hypoxia increased (p < 0.05) mitochondrial acetylation in female fetal hearts but had no effect on other mitochondrial indices. We conclude that maternal NR is an effective treatment for normalizing mitochondrial dysfunction and ATP synthesis in the hypoxic fetal heart.
    Keywords:  Acetylation; Fetus; Heart; Hypoxia; Mitochondria; NAD; Nicotinamide; Placenta; Sirtuin
    DOI:  https://doi.org/10.1007/s43032-023-01387-6
  14. Cell Rep. 2023 Nov 16. pii: S2211-1247(23)01477-8. [Epub ahead of print]42(11): 113465
    MCUb is an inducible regulator of calcium-dependent mitochondrial metabolism and substrate utilization in muscle.
    Jiuzhou Huo, Vikram Prasad, Kelly M Grimes, Davy Vanhoutte, N Scott Blair, Suh-Chin Lin, Michael J Bround, Donald M Bers, Jeffery D Molkentin.
      Mitochondria use the electron transport chain to generate high-energy phosphate from oxidative phosphorylation, a process also regulated by the mitochondrial Ca2+ uniporter (MCU) and Ca2+ levels. Here, we show that MCUb, an inhibitor of MCU-mediated Ca2+ influx, is induced by caloric restriction, where it increases mitochondrial fatty acid utilization. To mimic the fasted state with reduced mitochondrial Ca2+ influx, we generated genetically altered mice with skeletal muscle-specific MCUb expression that showed greater fatty acid usage, less fat accumulation, and lower body weight. In contrast, mice lacking Mcub in skeletal muscle showed increased pyruvate dehydrogenase activity, increased muscle malonyl coenzyme A (CoA), reduced fatty acid utilization, glucose intolerance, and increased adiposity. Mechanistically, pyruvate dehydrogenase kinase 4 (PDK4) overexpression in muscle of Mcub-deleted mice abolished altered substrate preference. Thus, MCUb is an inducible control point in regulating skeletal muscle mitochondrial Ca2+ levels and substrate utilization that impacts total metabolic balance.
    Keywords:  CP: Metabolism; metabolism; mitochondria; obesity; skeletal muscle; substrate utilization
    DOI:  https://doi.org/10.1016/j.celrep.2023.113465
  15. Cell Death Dis. 2023 11 11. 14(11): 735
    Integration of FUNDC1-associated mitochondrial protein import and mitochondrial quality control contributes to TDP-43 degradation.
    Jinfa Ma, Lei Liu, Lu Song, Jianghong Liu, Lingyao Yang, Quan Chen, Jane Y Wu, Li Zhu.
      Though TDP-43 protein can be translocated into mitochondria and causes mitochondrial damage in TDP-43 proteinopathy, little is known about how TDP-43 is imported into mitochondria. In addition, whether mitochondrial damage is caused by mitochondrial mislocalization of TDP-43 or a side effect of mitochondria-mediated TDP-43 degradation remains to be investigated. Here, our bioinformatical analyses reveal that mitophagy receptor gene FUNDC1 is co-expressed with TDP-43, and both TDP-43 and FUNDC1 expression is correlated with genes associated with mitochondrial protein import pathway in brain samples of patients diagnosed with TDP-43 proteinopathy. FUNDC1 promotes mitochondrial translocation of TDP-43 possibly by promoting TDP-43-TOM70 and DNAJA2-TOM70 interactions, which is independent of the LC3 interacting region of FUNDC1 in cellular experiments. In the transgenic fly model of TDP-43 proteinopathy, overexpressing FUNDC1 enhances TDP-43 induced mitochondrial damage, whereas down-regulating FUNDC1 reverses TDP-43 induced mitochondrial damage. FUNDC1 regulates mitochondria-mediated TDP-43 degradation not only by regulating mitochondrial TDP-43 import, but also by increasing LONP1 level and by activating mitophagy, which plays important roles in cytosolic TDP-43 clearance. Together, this study not only uncovers the mechanism of mitochondrial TDP-43 import, but also unravels the active role played by mitochondria in regulating TDP-43 homeostasis.
    DOI:  https://doi.org/10.1038/s41419-023-06261-6
  16. Nat Commun. 2023 Nov 13. 14(1): 7295
    Knockout or inhibition of USP30 protects dopaminergic neurons in a Parkinson's disease mouse model.
    Tracy-Shi Zhang Fang, Yu Sun, Andrew C Pearce, Simona Eleuteri, Mark Kemp, Christopher A Luckhurst, Rachel Williams, Ross Mills, Sarah Almond, Laura Burzynski, Nóra M Márkus, Christopher J Lelliott, Natasha A Karp, David J Adams, Stephen P Jackson, Jin-Feng Zhao, Ian G Ganley, Paul W Thompson, Gabriel Balmus, David K Simon.
      Mutations in SNCA, the gene encoding α-synuclein (αSyn), cause familial Parkinson's disease (PD) and aberrant αSyn is a key pathological hallmark of idiopathic PD. This α-synucleinopathy leads to mitochondrial dysfunction, which may drive dopaminergic neurodegeneration. PARKIN and PINK1, mutated in autosomal recessive PD, regulate the preferential autophagic clearance of dysfunctional mitochondria ("mitophagy") by inducing ubiquitylation of mitochondrial proteins, a process counteracted by deubiquitylation via USP30. Here we show that loss of USP30 in Usp30 knockout mice protects against behavioral deficits and leads to increased mitophagy, decreased phospho-S129 αSyn, and attenuation of SN dopaminergic neuronal loss induced by αSyn. These observations were recapitulated with a potent, selective, brain-penetrant USP30 inhibitor, MTX115325, with good drug-like properties. These data strongly support further study of USP30 inhibition as a potential disease-modifying therapy for PD.
    DOI:  https://doi.org/10.1038/s41467-023-42876-1
  17. Biochem Soc Trans. 2023 Nov 13. pii: BST20230735. [Epub ahead of print]
    Inorganic polyphosphate and the regulation of mitochondrial physiology.
    Renata T Da Costa, Lindsey M Riggs, Maria E Solesio.
      Inorganic polyphosphate (polyP) is an ancient polymer that is well-conserved throughout evolution. It is formed by multiple subunits of orthophosphates linked together by phosphoanhydride bonds. The presence of these bonds, which are structurally similar to those found in ATP, and the high abundance of polyP in mammalian mitochondria, suggest that polyP could be involved in the regulation of the physiology of the organelle, especially in the energy metabolism. In fact, the scientific literature shows an unequivocal role for polyP not only in directly regulating oxidative a phosphorylation; but also in the regulation of reactive oxygen species metabolism, mitochondrial free calcium homeostasis, and the formation and opening of mitochondrial permeability transitions pore. All these processes are closely interconnected with the status of mitochondrial bioenergetics and therefore play a crucial role in maintaining mitochondrial and cell physiology. In this invited review, we discuss the main scientific literature regarding the regulatory role of polyP in mammalian mitochondrial physiology, placing a particular emphasis on its impact on energy metabolism. Although the effects of polyP on the physiology of the organelle are evident; numerous aspects, particularly within mammalian cells, remain unclear and require further investigation. These aspects encompass, for example, advancing the development of more precise analytical methods, unraveling the mechanism responsible for sensing polyP levels, and understanding the exact molecular mechanism that underlies the effects of polyP on mitochondrial physiology. By increasing our understanding of the biology of this ancient and understudied polymer, we could unravel new pharmacological targets in diseases where mitochondrial dysfunction, including energy metabolism dysregulation, has been broadly described.
    Keywords:  cell biology; energy metabolism; inorganic polyphosphate; mitochondria; mitochondrial physiology; polyP
    DOI:  https://doi.org/10.1042/BST20230735
  18. Sci Rep. 2023 11 11. 13(1): 19664
    Ketone body β-hydroxybutyrate (BHB) preserves mitochondrial bioenergetics.
    I Llorente-Folch, H Düssmann, O Watters, N M C Connolly, Jochen H M Prehn.
      The ketogenic diet is an emerging therapeutic approach for refractory epilepsy, as well as certain rare and neurodegenerative disorders. The main ketone body, β-hydroxybutyrate (BHB), is the primary energy substrate endogenously produced in a ketogenic diet, however, mechanisms of its therapeutic actions remain unknown. Here, we studied the effects of BHB on mitochondrial energetics, both in non-stimulated conditions and during glutamate-mediated hyperexcitation. We found that glutamate-induced hyperexcitation stimulated mitochondrial respiration in cultured cortical neurons, and that this response was greater in cultures supplemented with BHB than with glucose. BHB enabled a stronger and more sustained maximal uncoupled respiration, indicating that BHB enables neurons to respond more efficiently to increased energy demands such as induced during hyperexcitation. We found that cytosolic Ca2+ was required for BHB-mediated enhancement of mitochondrial function, and that this enhancement was independent of the mitochondrial glutamate-aspartate carrier, Aralar/AGC1. Our results suggest that BHB exerts its protective effects against hyperexcitation by enhancing mitochondrial function through a Ca2+-dependent, but Aralar/AGC1-independent stimulation of mitochondrial respiration.
    DOI:  https://doi.org/10.1038/s41598-023-46776-8
  19. Mov Disord. 2023 Nov 14.
    Dystonia in ATP Synthase Defects: Reconnecting Mitochondria and Dopamine.
    Elisabetta Indelicato, Sylvia Boesch, Niccolo' E Mencacci, Daniele Ghezzi, Holger Prokisch, Juliane Winkelmann, Michael Zech.
      
    Keywords:  ATP synthase; dystonia; mitochondrial diseases; movement disorder
    DOI:  https://doi.org/10.1002/mds.29657
  20. Life Sci Alliance. 2024 Feb;pii: e202302386. [Epub ahead of print]7(2):
    Cristae dynamics is modulated in bioenergetically compromised mitochondria.
    Mathias Golombek, Thanos Tsigaras, Yulia Schaumkessel, Sebastian Hänsch, Stefanie Weidtkamp-Peters, Ruchika Anand, Andreas S Reichert, Arun Kumar Kondadi.
      Cristae membranes have been recently shown to undergo intramitochondrial merging and splitting events. Yet, the metabolic and bioenergetic factors regulating them are unclear. Here, we investigated whether and how cristae morphology and dynamics are dependent on oxidative phosphorylation (OXPHOS) complexes, the mitochondrial membrane potential (ΔΨm), and the ADP/ATP nucleotide translocator. Advanced live-cell STED nanoscopy combined with in-depth quantification were employed to analyse cristae morphology and dynamics after treatment of mammalian cells with rotenone, antimycin A, oligomycin A, and CCCP. This led to formation of enlarged mitochondria along with reduced cristae density but did not impair cristae dynamics. CCCP treatment leading to ΔΨm abrogation even enhanced cristae dynamics showing its ΔΨm-independent nature. Inhibition of OXPHOS complexes was accompanied by reduced ATP levels but did not affect cristae dynamics. However, inhibition of ADP/ATP exchange led to aberrant cristae morphology and impaired cristae dynamics in a mitochondrial subset. In sum, we provide quantitative data of cristae membrane remodelling under different conditions supporting an important interplay between OXPHOS, metabolite exchange, and cristae membrane dynamics.
    DOI:  https://doi.org/10.26508/lsa.202302386
  21. Hepatology. 2023 Nov 17.
    Genetic landscape of pediatric acute liver failure of indeterminate origin.
    Dominic Lenz, Lea D Schlieben, Masaru Shimura, Alyssa Bianzano, Dmitrii Smirnov, Robert Kopajtich, Riccardo Berutti, Rüdiger Adam, Denise Aldrian, Ivo Baric, Ulrich Baumann, Neslihan Eksi Bozbulut, Melanie Brugger, Theresa Brunet, Philip Bufler, Birutė Burnytė, Pier Luigi Calvo, Ellen Crushell, Buket Dalgıç, Anibh M Das, Antal Dezsőfi, Felix Distelmaier, Alexander Fichtner, Peter Freisinger, Sven F Garbade, Harald Gaspar, Louise Goujon, Nedim Hadzic, Steffen Hartleif, Bianca Hegen, Maja Hempel, Stephan Henning, Andre Hoerning, Roderick Houwen, Joanne Hughes, Raffaele Iorio, Katarzyna Iwanicka-Pronicka, Martin Jankofsky, Norman Junge, Ino Kanavaki, Aydan Kansu, Sonja Kaspar, Simone Kathemann, Deidre Kelly, Ceyda Tuna Kırsaçlıoğlu, Birgit Knoppke, Martina Kohl, Heike Kölbel, Stefan Kölker, Vassiliki Konstantopoulou, Tatiana Krylova, Zarife Kuloğlu, Alice Kuster, Martin W Laass, Elke Lainka, Eberhard Lurz, Hanna Mandel, Katharina Mayerhanser, Johannes A Mayr, Patrick McKiernan, Patricia McLean, Valerie McLin, Karine Mention, Hanna Müller, Laurent Pasquier, Martin Pavlov, Natalia Pechatnikova, Bianca Peters, Danijela Petković Ramadža, Dorota Piekutowska-Abramczuk, Denisa Pilic, Sanjay Rajwal, Nathalie Rock, Agnès Roetig, René Santer, Wilfried Schenk, Natalia Semenova, Christiane Sokollik, Ekkehard Sturm, Robert W Taylor, Eva Tschiedel, Vaidotas Urbonas, Roser Urreizti, Jan Vermehren, Jerry Vockley, Georg-Friedrich Vogel, Matias Wagner, Wendy van der Woerd, Saskia B Wortmann, Ekaterina Zakharova, Georg Friedrich Hoffmann, Thomas Meitinger, Kei Murayama, Christian Staufner, Holger Prokisch.
      BACKGROUND AIMS: Pediatric acute liver failure (PALF) is a life-threatening condition. In Europe, main causes are viral infections (12-16%) and inherited metabolic diseases (14-28%). Yet, in up to 50% of cases the underlying etiology remains elusive, challenging clinical management, including liver transplantation. We systematically studied indeterminate PALF cases referred for genetic evaluation by whole-exome sequencing (WES), and analyzed phenotypic and biochemical markers, and the diagnostic yield of WES in this condition.METHODS: With this international, multicenter observational study, patients (0-18 y) with indeterminate PALF were analyzed by WES. Data on the clinical and biochemical phenotype were retrieved and systematically analyzed.
    RESULTS: In total, 260 indeterminate PALF patients from 19 countries were recruited between 2011 and 2022, of whom 59 had recurrent PALF (RALF). WES established a genetic diagnosis in 37% of cases (97/260). Diagnostic yield was highest in children with PALF in the first year of life (46%), and in children with RALF (64%). Thirty-six distinct disease genes were identified. Defects in NBAS (n=20), MPV17 (n=8) and DGUOK (n=7) were the most frequent findings. When categorizing, most frequent were mitochondrial diseases (45%), disorders of vesicular trafficking (28%) and cytosolic aminoacyl-tRNA synthetase deficiencies (10%). One-third of patients had a fatal outcome. Fifty-six patients received liver transplants.
    CONCLUSION: This study elucidates a large contribution of genetic causes in PALF of indeterminate origin with an increasing spectrum of disease entities. The high proportion of diagnosed cases and potential treatment implications argue for exome or in future rapid genome sequencing in PALF diagnostics.
    DOI:  https://doi.org/10.1097/HEP.0000000000000684
  22. STAR Protoc. 2023 Nov 15. pii: S2666-1667(23)00572-5. [Epub ahead of print]4(4): 102605
    Protocol to study human mitochondrial ribosome using quantitative density gradient analysis by mass spectrometry and complexome profiling analysis.
    Petra Páleníková, Michal Minczuk, Pedro Rebelo-Guiomar.
      Dynamic macromolecular complexes containing a large number of components are often difficult to study using conventional approaches, such as immunoblotting. Here, we present a protocol for the analysis of macromolecular complexes in near-native conditions using a flexible setup to suit different cellular targets. We describe analysis of human mitochondrial ribosome, composed of 82 proteins, in a standardized way using density gradient ultracentrifugation coupled to quantitative mass spectrometry and subsequent analysis of the generated data (ComPrAn). For complete details on the use and execution of this protocol, please refer to Páleníková et al.1 and Rebelo-Guiomar et al.2.
    Keywords:  Bioinformatics; Protein Expression and Purification; Proteomics
    DOI:  https://doi.org/10.1016/j.xpro.2023.102605
  23. Cell Death Discov. 2023 Nov 16. 9(1): 417
    Keep in touch: a perspective on the mitochondrial social network and its implication in health and disease.
    Silvia Barabino, Silvia Lombardi, Mara Zilocchi.
      Mitochondria have been the focus of extensive research for decades since their dysfunction is linked to more than 150 distinct human disorders. Despite considerable efforts, researchers have only been able to skim the surface of the mitochondrial social complexity and the impact of inter-organelle and inter-organ communication alterations on human health. While some progress has been made in deciphering connections among mitochondria and other cytoplasmic organelles through direct (i.e., contact sites) or indirect (i.e., inter-organelle trafficking) crosstalk, most of these efforts have been restricted to a limited number of proteins involved in specific physiological pathways or disease states. This research bottleneck is further narrowed by our incomplete understanding of the cellular alteration timeline in a specific pathology, which prevents the distinction between a primary organelle dysfunction and the defects occurring due to the disruption of the organelle's interconnectivity. In this perspective, we will (i) summarize the current knowledge on the mitochondrial crosstalk within cell(s) or tissue(s) in health and disease, with a particular focus on neurodegenerative disorders, (ii) discuss how different large-scale and targeted approaches could be used to characterize the different levels of mitochondrial social complexity, and (iii) consider how investigating the different expression patterns of mitochondrial proteins in different cell types/tissues could represent an important step forward in depicting the distinctive architecture of inter-organelle communication.
    DOI:  https://doi.org/10.1038/s41420-023-01710-9
  24. Mol Neurodegener. 2023 Nov 11. 18(1): 83
    Mitochondrial dysfunction in Parkinson's disease - a key disease hallmark with therapeutic potential.
    Martin T Henrich, Wolfgang H Oertel, D James Surmeier, Fanni F Geibl.
      Mitochondrial dysfunction is strongly implicated in the etiology of idiopathic and genetic Parkinson's disease (PD). However, strategies aimed at ameliorating mitochondrial dysfunction, including antioxidants, antidiabetic drugs, and iron chelators, have failed in disease-modification clinical trials. In this review, we summarize the cellular determinants of mitochondrial dysfunction, including impairment of electron transport chain complex 1, increased oxidative stress, disturbed mitochondrial quality control mechanisms, and cellular bioenergetic deficiency. In addition, we outline mitochondrial pathways to neurodegeneration in the current context of PD pathogenesis, and review past and current treatment strategies in an attempt to better understand why translational efforts thus far have been unsuccessful.
    Keywords:  Antioxidants; Electron transport chain; MPTP; Mitochondria; Mitochondrial dysfunction; Neuroprotective therapies; Parkinson’s disease; Synuclein
    DOI:  https://doi.org/10.1186/s13024-023-00676-7
  25. NAR Genom Bioinform. 2023 Dec;5(4): lqad100
    Accumulation of 8-oxodG within the human mitochondrial genome positively associates with transcription.
    Giovanni Scala, Susanna Ambrosio, Margherita Menna, Francesca Gorini, Carmen Caiazza, Marcus S Cooke, Barbara Majello, Stefano Amente.
      Mitochondrial DNA (mtDNA) can be subject to internal and environmental stressors that lead to oxidatively generated damage and the formation of 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxodG). The accumulation of 8-oxodG has been linked to degenerative diseases and aging, as well as cancer. Despite the well-described implications of 8-oxodG in mtDNA for mitochondrial function, there have been no reports of mapping of 8-oxodG across the mitochondrial genome. To address this, we used OxiDIP-Seq and mapped 8-oxodG levels in the mitochondrial genome of human MCF10A cells. Our findings indicated that, under steady-state conditions, 8-oxodG is non-uniformly distributed along the mitochondrial genome, and that the longer non-coding region appeared to be more protected from 8-oxodG accumulation compared with the coding region. However, when the cells have been exposed to oxidative stress, 8-oxodG preferentially accumulated in the coding region which is highly transcribed as H1 transcript. Our data suggest that 8-oxodG accumulation in the mitochondrial genome is positively associated with mitochondrial transcription.
    DOI:  https://doi.org/10.1093/nargab/lqad100
  26. JCI Insight. 2023 Nov 16. pii: e162621. [Epub ahead of print]
    Disruption of CFAP418 interaction with lipids causes widespread abnormal membrane-associated cellular processes in retinal degenerations.
    Anna M Clark, Dongmei Yu, Grace Neiswanger, Daniel Zhu, Junhuang Zou, J Alan Maschek, Thomas Burgoyne, Jun Yang.
      Syndromic ciliopathies and retinal degenerations are large heterogeneous groups of genetic diseases. Pathogenic variants in the CFAP418 gene may cause both disorders, and its protein sequence is evolutionarily conserved. However, the disease mechanism underlying CFAP418 mutations has not been explored. Here, we apply quantitative lipidomic, proteomic, and phosphoproteomic profiling and affinity purification coupled with mass spectrometry to address the molecular function of CFAP418 in retinas. We show that CFAP418 protein binds to lipid metabolism precursor phosphatidic acid (PA) and mitochondrion-specific lipid cardiolipin but does not form a tight and static complex with proteins. Loss of Cfap418 in mice disturbs membrane lipid homeostasis and membrane-protein association, which subsequently causes mitochondrial defects and membrane remodeling abnormalities across multiple vesicular trafficking pathways in photoreceptors, especially the endosomal sorting complexes required for transport (ESCRT) pathway. Ablation of Cfap418 also increases the activity of PA-binding protein kinase Cα in the retina. Overall, our results indicate that membrane lipid imbalance is a pathological mechanism underlying syndromic ciliopathies and retinal degenerations, which is associated with other known causative genes of these diseases.
    Keywords:  Cell Biology; Ophthalmology; Protein traffic; Proteomics; Retinopathy
    DOI:  https://doi.org/10.1172/jci.insight.162621
  27. Am J Med Genet A. 2023 Nov 12.
    Heteroplasmic pathogenic m.12315G>A variant in MT-TL2 presenting with MELAS syndrome and depletion of nitric oxide donors.
    Matthew T Snyder, Joshua Manor, Charul Gijavanekar, Elizabeth Mizerik, Stephen F Kralik, Sarah H Elsea, Keren Machol, Lisa Emrick, Fernando Scaglia.
      The MT-TL2 m.12315G>A pathogenic variant has previously been reported in five individuals with mild clinical phenotypes. Herein we report the case of a 5-year-old child with heteroplasmy for this variant who developed neurological regression and stroke-like episodes similar to those observed in mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS). Biochemical evaluation revealed depletion of arginine on plasma amino acid analysis and low z-scores for citrulline on untargeted plasma metabolomics analysis. These findings suggested that decreased availability of nitric oxide may have contributed to the stroke-like episodes. The use of intravenous arginine during stroke-like episodes and daily enteral L-citrulline supplementation normalized her biochemical values of arginine and citrulline. Untargeted plasma metabolomics showed the absence of nicotinamide and 1-methylnicotinamide, and plasma total glutathione levels were low; thus, nicotinamide riboside and N-acetylcysteine therapies were initiated. This report expands the phenotype associated with the rare mitochondrial variant MT-TL2 m.12315G>A to include neurological regression and a MELAS-like phenotype. Individuals with this variant should undergo in-depth biochemical analysis to include untargeted plasma metabolomics, plasma amino acids, and glutathione levels to help guide a targeted approach to treatment.
    Keywords:  MELAS; MT-TL2; arginine; citrulline; nitric oxide; stroke-like episodes
    DOI:  https://doi.org/10.1002/ajmg.a.63461
  28. bioRxiv. 2023 Nov 05. pii: 2023.09.27.558332. [Epub ahead of print]
    Gut microbiota promotes enteroendocrine cell maturation and mitochondrial function.
    Alfahdah Alsudayri, Shane Perelman, Annika Chura, Melissa Brewer, Madelyn McDevitt, Catherine Drerup, Lihua Ye.
      The enteroendocrine cells (EECs) in the intestine are crucial for sensing ingested nutrients and regulating feeding behavior. The means by which gut microbiota regulates the nutrient-sensing EEC activity is unclear. Our transcriptomic analysis of the EECs from germ-free (GF) and conventionalized (CV) zebrafish revealed that commensal microbiota colonization significantly increased the expression of many genes that are associated with mitochondrial function. Using in vivo imaging and 3D automated cell tracking approach, we developed new methods to image and analyze the EECs' cytoplasmic and mitochondrial calcium activity at cellular resolution in live zebrafish. Our data revealed that during the development, shortly after gut microbiota colonization, EECs briefly increased cytoplasm and mitochondrial Ca 2+ , a phenomenon we referred to as "EEC awakening". Following the EEC awakening, cytoplasmic Ca 2+ levels but not mitochondrial Ca 2+ level in the EECs decreased, resulting in a consistent increase in the mitochondrial-to-cytoplasmic Ca 2+ ratio. The increased mitochondrial-to-cytoplasmic Ca 2+ ratio is associated with the EEC maturation process. In immature EECs, we further discovered that their mitochondria are evenly distributed in the cytoplasm. When EECs mature, their mitochondria are highly localized in the basal lateral membrane where EEC vesicle secretion occurs. Furthermore, CV EECs, but not GF EECs, exhibit spontaneous low-amplitude calcium fluctuation. The mitochondrial-to-cytoplasm Ca 2+ ratio is significantly higher in CV EECs. When stimulating the CV zebrafish with nutrients like fatty acids, nutrient stimulants increase cytoplasmic Ca 2+ in a subset of EECs and promote a sustained mitochondrial Ca 2+ increase. However, the nutrient induced EEC mitochondrial activation is nearly abolished in GF zebrafish. Together, our study reveals that commensal microbiota are critical in supporting EEC mitochondrial function and maturation. Selectively manipulating gut microbial signals to alter EEC mitochondrial function will provide new opportunities to change gut-brain nutrient sensing efficiency and feeding behavior.
    DOI:  https://doi.org/10.1101/2023.09.27.558332
  29. Chest. 2023 Nov 15. pii: S0012-3692(23)05793-8. [Epub ahead of print]
    Circulating Mitochondrial DNA is associated with High Levels of Fatigue in Two Independent Sarcoidosis Cohorts.
    Vitória Fiorini, Buqu Hu, Ying Sun, Sheeline Yu, John McGovern, Shifa Gandhi, Samuel Woo, Sara Jean Turcotte-Foster, Taylor Pivarnik, Zara Khan, Taylor Adams, Erica Herzog, Naftali Kaminski, Mridu Gulati, Changwan Ryu.
      BACKGROUND: Sarcoidosis patients who develop severe clinical phenotypes of pulmonary fibrosis or multi-organ disease experience debilitating symptoms, with fatigue being a common chief complaint. Studies investigating this patient-related outcome measure (PROM) have employed the Fatigue Assessment Scale (FAS), a self-reported questionnaire that reflects mental and physical domains. Despite extensive work, its etiology is unknown and treatment options remain limited. Previously, we showed that the plasma of sarcoidosis patients with extrapulmonary disease endorsing fatigue was enriched for mitochondrial DNA (mtDNA), a ligand for the innate immune receptor Toll-like Receptor 9 (TLR9). Through our cross-disciplinary platform, we investigated a relationship between sarcoidosis-induced fatigue and circulating mtDNA.RESEARCH QUESTION: Is there a psychobiologic mechanism connecting sarcoidosis-induced fatigue and mtDNA-mediated TLR9 activation?
    STUDY DESIGN AND METHODS: Using a local cohort of patients at Yale (discovery cohort) and the NIH-sponsored GRADS study (validation cohort), we scored the FAS and quantified in the plasma mtDNA concentrations, TLR9 activation, and cytokine levels.
    RESULTS: While FAS scores were independent of corticosteroid use and Scadding Stage, we observed a robust association between FAS scores, including mental and physical domains, and multi-organ sarcoidosis. Subsequently, we identified a significant correlation between plasma mtDNA concentrations and all domains of fatigue. Additionally, we found that TLR9 activation is associated with all aspects of the FAS and partially mediates this PROM through mtDNA. Lastly, we found that TLR9 associated soluble mediators in the plasma are independent of all facets of fatigue.
    INTERPRETATION: Through our cross-disciplinary translational platform, we identified a previously unrecognized psychobiologic connection between sarcoidosis-induced fatigue and circulating mtDNA concentrations potentially mediated by TLR9 activation. Mechanistic work investigating the contribution of mtDNA-mediated innate immune activation in this PROM, and clinical studies with prospective cohorts, has the potential to catalyze novel therapeutic strategies for this patient population and those with similar conditions.
    Keywords:  (1) Sarcoidosis; (2) Fatigue Assessment Scale; (3) Patient-related outcome measures; (4) Mitochondrial DNA; (5) Toll-like receptor 9
    DOI:  https://doi.org/10.1016/j.chest.2023.11.020
  30. Med Clin North Am. 2024 Jan;pii: S0025-7125(23)00095-0. [Epub ahead of print]108(1): 1-14
    Attaining Diagnostic Excellence: How the Structure and Function of a Rare Disease Service Contribute to Ending the Diagnostic Odyssey.
    Brett J Bordini, Ryan D Walsh, Donald Basel, Tejaswini Deshmukh.
      Patients with rare or otherwise undiagnosed disorders frequently find themselves on a diagnostic odyssey, the often-prolonged journey toward diagnosis that can be characterized by significant physical, emotional, and financial hardship, as well as by diagnostic errors and delays. The wider availability of clinical exome sequencing has helped end many diagnostic odysseys, though diagnostic success rates of around 35% for exome sequencing leave many patients undiagnosed. Diagnostic yields can be improved via the implementation of advanced genetic testing modalities, though both these modalities and exome sequencing perform significantly better when paired with high-quality phenotypic data. Diagnostic centers of excellence can improve outcomes for patients on a diagnostic odyssey by providing a process and environment that address shortfalls in diagnostic access while providing high-quality phenotyping. Features of successful undiagnosed and rare disease evaluation teams are discussed and an illustrative case is provided.
    Keywords:  Diagnostic access; Diagnostic odyssey; Phenotyping; Rare diseases; Undiagnosed diseases
    DOI:  https://doi.org/10.1016/j.mcna.2023.06.013
  31. Seizure. 2023 Nov 09. pii: S1059-1311(23)00290-X. [Epub ahead of print]
    Developmental and epileptic encephalopathy 82 (DEE82) with novel compound heterozygous mutations of GOT2 gene.
    Özlem Yalçın Çapan, Dilşad Türkdoğan, Sertaç Atalay, Hande S Çağlayan.
      PURPOSE: Developmental and Epileptic Encephalopathies (DEEs) are rare neurological disorders characterized by early-onset medically resistant epileptic seizures, structural brain malformations, and severe developmental delays. These disorders can arise from mutations in genes involved in vital metabolic pathways, including those within the brain. Recent studies have implicated defects in the mitochondrial malate aspartate shuttle (MAS) as potential contributors to the clinical manifestation of infantile epileptic encephalopathy. Although rare, mutations in MDH1, MDH2, AGC1, or GOT2 genes have been reported in patients exhibiting neurological symptoms such as global developmental delay, epilepsy, and progressive microcephaly.METHOD: In this study, we employed exome data analysis of a patient diagnosed with DEE, focusing on the screening of 1896 epilepsy-related genes listed in the HPO and ClinVar databases. Sanger sequencing was subsequently conducted to validate and assess the inheritance pattern of the identified variants within the family. The evolutionary conservation scores of the mutated residues were evaluated using the ConSurf Database. Furthermore, the impacts of the causative variations on protein stability were analyzed through I-Mutant and MuPro bioinformatic tools. Structural comparisons between wild-type and mutant proteins were performed using PyMOL, and the physicochemical effects of the mutations were assessed using Project Hope.
    RESULTS: Exome data analysis unveiled the presence of novel compound heterozygous mutations in the GOT2 gene coding for mitochondrial glutamate aspartate transaminase. Sanger sequencing confirmed the paternal inheritance of the p.Asp257Asn mutation and the maternal inheritance of the p.Arg262Cys mutation. The affected individual exhibited plasma metabolic disturbances, including hyperhomocysteinemia, hyperlactatemia, and reduced levels of methionine and arginine. Detailed bioinformatic analysis indicated that the mutations were located within evolutionarily conserved domains of the enzyme, resulting in disruptions to protein stability and structure.
    CONCLUSION: Herein, we describe a case with DEE82 (MIM: # 618721) with pathologic novel biallelic mutations in the GOT2 gene. Early genetic diagnosis of metabolic epilepsies is crucial for long-term neurodevelopmental improvements and seizure control as targeted treatments can be administered based on the affected metabolic pathways.
    Keywords:  Aspartate aminotransferase; Developmental and epileptic encephalopathies; GOT2 enzyme; Inborn error of metabolism; Malate-aspartate shuttle; Metabolic epilepsy; Vitamin B6 therapy; Whole exome sequencing
    DOI:  https://doi.org/10.1016/j.seizure.2023.11.003
  32. Nat Metab. 2023 Nov 16.
    Vitamin B12 emerges as key player during cellular reprogramming.
    Alba Vílchez-Acosta, Gabriela Desdín-Micó, Alejandro Ocampo.
      
    DOI:  https://doi.org/10.1038/s42255-023-00917-5
  33. Cureus. 2023 Oct;15(10): e46860
    The Impact of Artificial Intelligence on Optimizing Diagnosis and Treatment Plans for Rare Genetic Disorders.
    Shenouda Abdallah, Mouhammad Sharifa, Mohammed Khaleel I Kh Almadhoun, Muhammad Muneeb Khawar, Unzla Shaikh, Khaled M Balabel, Inam Saleh, Amima Manzoor, Arun Kumar Mandal, Osatohanmwen Ekomwereren, Wai Mon Khine, Oluwaseyi T Oyelaja.
      Rare genetic disorders (RDs), characterized by their low prevalence and diagnostic complexities, present significant challenges to healthcare systems. This article explores the transformative impact of artificial intelligence (AI) and machine learning (ML) in addressing these challenges. It emphasizes the need for accurate and early diagnosis of RDs, often hindered by genetic and clinical heterogeneity. This article discusses how AI and ML are reshaping healthcare, providing examples of their effectiveness in disease diagnosis, prognosis, image analysis, and drug repurposing. It highlights AI's ability to efficiently analyze extensive datasets and expedite diagnosis, showcasing case studies like Face2Gene. Furthermore, the article explores how AI tailors treatment plans for RDs, leveraging ML and deep learning (DL) to create personalized therapeutic regimens. It emphasizes AI's role in drug discovery, including the identification of potential candidates for rare disease treatments. Challenges and limitations related to AI in healthcare, including ethical, legal, technical, and human aspects, are addressed. This article underscores the importance of data ethics, privacy, and algorithmic fairness, as well as the need for standardized evaluation techniques and transparency in AI research. It highlights second-generation AI systems that prioritize patient-centric care, efficient patient recruitment for clinical trials, and the significance of high-quality data. The integration of AI with telemedicine, the growth of health databases, and the potential for personalized therapeutic recommendations are identified as promising directions for the field. In summary, this article provides a comprehensive exploration of how AI and ML are revolutionizing the diagnosis and treatment of RDs, addressing challenges while considering ethical implications in this rapidly evolving healthcare landscape.
    Keywords:  deep learning artificial intelligence; genetic basis of congenital heart disease; genetic syndromes; genetic variant; rare genetic diseases
    DOI:  https://doi.org/10.7759/cureus.46860
  34. Sci Rep. 2023 Nov 14. 13(1): 19899
    Impact of N221S missense mutation in human ribonucleotide reductase small subunit b on mitochondrial DNA depletion syndrome.
    Leila Su, Xin Wang, Jianghai Wang, Frank Luh, Yun Yen.
      The impact of N221S mutation in hRRM2B gene, which encodes the small subunit of human ribonucleotide reductase (RNR), on RNR activity and the pathogenesis of mitochondrial DNA depletion syndrome (MDDS) was investigated. Our results demonstrate that N221 mutations significantly reduce RNR activity, suggesting its role in the development of MDDS. We proposed an allosteric regulation pathway involving a chain of three phenylalanine residues on the αE helix of RNR small subunit β. This pathway connects the C-terminal loop of β2, transfers the activation signal from the large catalytic subunit α to β active site, and controls access of oxygen for radical generation. N221 is near this pathway and likely plays a role in regulating RNR activity. Mutagenesis studies on residues involved in the phenylalanine chain and the regulation pathway were conducted to confirm our proposed mechanism. We also performed molecular dynamic simulation and protein contact network analysis to support our findings. This study sheds new light on RNR small subunit regulation and provides insight on the pathogenesis of MDDS.
    DOI:  https://doi.org/10.1038/s41598-023-47284-5
  35. bioRxiv. 2023 Nov 02. pii: 2023.10.30.564808. [Epub ahead of print]
    Utility of AlphaMissense predictions in Asparagine Synthetase deficiency variant classification.
    Stephen J Staklinski, Armin Scheben, Adam Siepel, Michael S Kilberg.
      AlphaMissense is a recently developed method that is designed to classify missense variants into pathogenic, benign, or ambiguous categories across the entire human proteome. Asparagine Synthetase Deficiency (ASNSD) is a developmental disorder associated with severe symptoms, including congenital microcephaly, seizures, and premature death. Diagnosing ASNSD relies on identifying mutations in the asparagine synthetase (ASNS) gene through DNA sequencing and determining whether these variants are pathogenic or benign. Pathogenic ASNS variants are predicted to disrupt the protein's structure and/or function, leading to asparagine depletion within cells and inhibition of cell growth. AlphaMissense offers a promising solution for the rapid classification of ASNS variants established by DNA sequencing and provides a community resource of pathogenicity scores and classifications for newly diagnosed ASNSD patients. Here, we assessed AlphaMissense's utility in ASNSD by benchmarking it against known critical residues in ASNS and evaluating its performance against a list of previously reported ASNSD-associated variants. We also present a pipeline to calculate AlphaMissense scores for any protein in the UniProt database. AlphaMissense accurately attributed a high average pathogenicity score to known critical residues within the two ASNS active sites and the connecting intramolecular tunnel. The program successfully categorized 78.9% of known ASNSD-associated missense variants as pathogenic. The remaining variants were primarily labeled as ambiguous, with a smaller proportion classified as benign. This study underscores the potential role of AlphaMissense in classifying ASNS variants in suspected cases of ASNSD, potentially providing clarity to patients and their families grappling with ongoing diagnostic uncertainty.
    DOI:  https://doi.org/10.1101/2023.10.30.564808
  36. Bioact Mater. 2024 Feb;32 427-444
    Targeted transplantation of engineered mitochondrial compound promotes functional recovery after spinal cord injury by enhancing macrophage phagocytosis.
    Jiaqi Xu, Chaoran Shi, Feifei Yuan, Yinghe Ding, Yong Xie, Yudong Liu, Fengzhang Zhu, Hongbin Lu, Chunyue Duan, Jianzhong Hu, Liyuan Jiang.
      Mitochondria are crucial in sustaining and orchestrating cellular functions. Capitalizing on this, we explored mitochondrial transplantation as an innovative therapeutic strategy for acute spinal cord injury (SCI). In our study, we developed an engineered mitochondrial compound tailored to target macrophages within the SCI region. Sourced from IL-10-induced Mertkhi bone marrow-derived macrophages, we conjugated a peptide sequence, cations-cysteine-alanine-glutamine-lysine (CAQK), with the mitochondria, optimizing its targeting affinity for the injury site. Our data demonstrated that these compounds significantly enhanced macrophage phagocytosis of myelin debris, curtailed lipid buildup, ameliorated mitochondrial dysfunction, and attenuated pro-inflammatory profiles in macrophages, both in vitro and in vivo. The intravenously delivered mitochondrial compounds targeted the SCI epicenter, with macrophages being the primary recipients. Critically, they promoted tissue regeneration and bolstered functional recovery in SCI mice. This study heralds a transformative approach to mitochondrial transplantation in SCI, spotlighting the modulation of macrophage activity, phagocytosis, and phenotype.
    Keywords:  Macrophage; Mitochondrial transplantation; Phagocytosis; Spinal cord injury (SCI); Targeted therapy
    DOI:  https://doi.org/10.1016/j.bioactmat.2023.10.016
  37. EMBO Rep. 2023 Nov 14. e57972
    MAPL loss dysregulates bile and liver metabolism in mice.
    Vanessa Goyon, Aurèle Besse-Patin, Rodolfo Zunino, Olesia Ignatenko, Mai Nguyen, Étienne Coyaud, Jonathan M Lee, Bich N Nguyen, Brian Raught, Heidi M McBride.
      Mitochondrial and peroxisomal anchored protein ligase (MAPL) is a dual ubiquitin and small ubiquitin-like modifier (SUMO) ligase with roles in mitochondrial quality control, cell death and inflammation in cultured cells. Here, we show that MAPL function in the organismal context converges on metabolic control, as knockout mice are viable, insulin-sensitive, and protected from diet-induced obesity. MAPL loss leads to liver-specific activation of the integrated stress response, inducing secretion of stress hormone FGF21. MAPL knockout mice develop fully penetrant spontaneous hepatocellular carcinoma. Mechanistically, the peroxisomal bile acid transporter ABCD3 is a primary MAPL interacting partner and SUMOylated in a MAPL-dependent manner. MAPL knockout leads to increased bile acid production coupled with defective regulatory feedback in liver in vivo and in isolated primary hepatocytes, suggesting cell-autonomous function. Together, our findings establish MAPL function as a regulator of bile acid synthesis whose loss leads to the disruption of bile acid feedback mechanisms. The consequences of MAPL loss in liver, along with evidence of tumor suppression through regulation of cell survival pathways, ultimately lead to hepatocellular carcinogenesis.
    Keywords:  MUL1; PMP70; SUMO; hepatocellular carcinoma; peroxisome
    DOI:  https://doi.org/10.15252/embr.202357972
  38. Elife. 2023 11 14. pii: e85751. [Epub ahead of print]12
    Astrocyte and L-lactate in the anterior cingulate cortex modulate schema memory and neuronal mitochondrial biogenesis.
    Mastura Akter, Mahadi Hasan, Aruna Surendran Ramkrishnan, Zafar Iqbal, Xianlin Zheng, Zhongqi Fu, Zhuogui Lei, Anwarul Karim, Ying Li.
      Astrocyte-derived L-lactate was shown to confer beneficial effects on synaptic plasticity and cognitive functions. However, how astrocytic Gi signaling in the anterior cingulate cortex (ACC) modulates L-lactate levels and schema memory is not clear. Here, using chemogenetic approach and well-established behavioral paradigm, we demonstrate that astrocytic Gi pathway activation in the ACC causes significant impairments in flavor-place paired associates (PAs) learning, schema formation, and PA memory retrieval in rats. It also impairs new PA learning even if a prior associative schema exists. These impairments are mediated by decreased L-lactate in the ACC due to astrocytic Gi activation. Concurrent exogenous L-lactate administration bilaterally into the ACC rescues these impairments. Furthermore, we show that the impaired schema memory formation is associated with a decreased neuronal mitochondrial biogenesis caused by decreased L-lactate level in the ACC upon astrocytic Gi activation. Our study also reveals that L-lactate-mediated mitochondrial biogenesis is dependent on monocarboxylate transporter 2 (MCT2) and NMDA receptor activity - discovering a previously unrecognized signaling role of L-lactate. These findings expand our understanding of the role of astrocytes and L-lactate in the brain functions.
    Keywords:  DREADD; anterior cingulate cortex; astrocyte; lactate; mitochondrial biogenesis; neuroscience; rat; schema
    DOI:  https://doi.org/10.7554/eLife.85751
  39. Elife. 2023 11 14. pii: e91004. [Epub ahead of print]12
    Systems genetics approaches for understanding complex traits with relevance for human disease.
    Hooman Allayee, Charles R Farber, Marcus M Seldin, Evan Graehl Williams, David E James, Aldons J Lusis.
      Quantitative traits are often complex because of the contribution of many loci, with further complexity added by environmental factors. In medical research, systems genetics is a powerful approach for the study of complex traits, as it integrates intermediate phenotypes, such as RNA, protein, and metabolite levels, to understand molecular and physiological phenotypes linking discrete DNA sequence variation to complex clinical and physiological traits. The primary purpose of this review is to describe some of the resources and tools of systems genetics in humans and rodent models, so that researchers in many areas of biology and medicine can make use of the data.
    Keywords:  complex traits; computational biology; genetics; genomics; human populations; mouse models; omics; systems biology; systems genetics
    DOI:  https://doi.org/10.7554/eLife.91004
  40. Sci Rep. 2023 Nov 17. 13(1): 20126
    USP18 enhances dengue virus replication by regulating mitochondrial DNA release.
    Jenn-Haung Lai, De-Wei Wu, Chien-Hsiang Wu, Li-Feng Hung, Chuan-Yueh Huang, Shuk-Man Ka, Ann Chen, Ling-Jun Ho.
      Dengue virus (DENV) infection remains a challenging health threat worldwide. Ubiquitin-specific protease 18 (USP18), which preserves the anti-interferon (IFN) effect, is an ideal target through which DENV mediates its own immune evasion. However, much of the function and mechanism of USP18 in regulating DENV replication remains incompletely understood. In addition, whether USP18 regulates DENV replication merely by causing IFN hyporesponsiveness is not clear. In the present study, by using several different approaches to block IFN signaling, including IFN neutralizing antibodies (Abs), anti-IFN receptor Abs, Janus kinase inhibitors and IFN alpha and beta receptor subunit 1 (IFNAR1)knockout cells, we showed that USP18 may regulate DENV replication in IFN-associated and IFN-unassociated manners. Localized in mitochondria, USP18 regulated the release of mitochondrial DNA (mtDNA) to the cytosol to affect viral replication, and mechanisms such as mitochondrial reactive oxygen species (mtROS) production, changes in mitochondrial membrane potential, mobilization of calcium into mitochondria, 8-oxoguanine DNA glycosylase 1 (OGG1) expression, oxidation and fragmentation of mtDNA, and opening of the mitochondrial permeability transition pore (mPTP) were involved in USP18-regulated mtDNA release to the cytosol. We therefore identify mitochondrial machineries that are regulated by USP18 to affect DENV replication and its association with IFN effects.
    DOI:  https://doi.org/10.1038/s41598-023-47584-w
  41. Intern Med. 2023 Nov 13.
    Pathogenesis and Management of Citrin Deficiency.
    Kiyoshi Hayasaka.
      Citrin deficiency (CD) is a hereditary disorder caused by SLC25A13 mutations that manifests as neonatal intrahepatic cholestasis caused by CD (NICCD), failure to thrive and dyslipidemia caused by CD (FTTDCD), and adult-onset type 2 citrullinemia (CTLN2). Citrin, an aspartate-glutamate carrier primarily expressed in the liver, is a component of the malate-aspartate shuttle, which is essential for glycolysis. Citrin-deficient hepatocytes have primary defects in glycolysis and de novo lipogenesis and exhibit secondarily downregulated PPARα, leading to impaired β-oxidation. They are unable to utilize glucose and free fatty acids as energy sources, resulting in energy deficiencies. Medium-chain triglyceride (MCT) supplements are effective for treating CD by providing energy to hepatocytes, increasing lipogenesis, and activating the malate-citrate shuttle. However, patients with CD often exhibit growth impairment and irreversible brain and/or liver damage. To improve the quality of life and prevent irreversible damage, MCT supplementation with a diet containing minimal carbohydrates is recommended promptly after the diagnosis.
    Keywords:  SLC25A13; adult-onset type 2 citrullinemia; citrin; medium-chain triglycerides; neonatal intrahepatic cholestasis caused by citrin deficiency
    DOI:  https://doi.org/10.2169/internalmedicine.2595-23
  42. Nat Metab. 2023 Nov 16.
    Vitamin B12 is a limiting factor for induced cellular plasticity and tissue repair.
    Marta Kovatcheva, Elena Melendez, Dafni Chondronasiou, Federico Pietrocola, Raquel Bernad, Adrià Caballe, Alexandra Junza, Jordi Capellades, Adrián Holguín-Horcajo, Neus Prats, Sylvere Durand, Meritxell Rovira, Oscar Yanes, Camille Stephan-Otto Attolini, Guido Kroemer, Manuel Serrano.
      Transient reprogramming by the expression of OCT4, SOX2, KLF4 and MYC (OSKM) is a therapeutic strategy for tissue regeneration and rejuvenation, but little is known about its metabolic requirements. Here we show that OSKM reprogramming in mice causes a global depletion of vitamin B12 and molecular hallmarks of methionine starvation. Supplementation with vitamin B12 increases the efficiency of reprogramming both in mice and in cultured cells, the latter indicating a cell-intrinsic effect. We show that the epigenetic mark H3K36me3, which prevents illegitimate initiation of transcription outside promoters (cryptic transcription), is sensitive to vitamin B12 levels, providing evidence for a link between B12 levels, H3K36 methylation, transcriptional fidelity and efficient reprogramming. Vitamin B12 supplementation also accelerates tissue repair in a model of ulcerative colitis. We conclude that vitamin B12, through its key role in one-carbon metabolism and epigenetic dynamics, improves the efficiency of in vivo reprogramming and tissue repair.
    DOI:  https://doi.org/10.1038/s42255-023-00916-6
  43. Science. 2023 Nov 17. 382(6672): eabq8173
    A tool kit of highly selective and sensitive genetically encoded neuropeptide sensors.
    Huan Wang, Tongrui Qian, Yulin Zhao, Yizhou Zhuo, Chunling Wu, Takuya Osakada, Peng Chen, Zijun Chen, Huixia Ren, Yuqi Yan, Lan Geng, Shengwei Fu, Long Mei, Guochuan Li, Ling Wu, Yiwen Jiang, Weiran Qian, Li Zhang, Wanling Peng, Min Xu, Ji Hu, Man Jiang, Liangyi Chen, Chao Tang, Yingjie Zhu, Dayu Lin, Jiang-Ning Zhou, Yulong Li.
      Neuropeptides are key signaling molecules in the endocrine and nervous systems that regulate many critical physiological processes. Understanding the functions of neuropeptides in vivo requires the ability to monitor their dynamics with high specificity, sensitivity, and spatiotemporal resolution. However, this has been hindered by the lack of direct, sensitive, and noninvasive tools. We developed a series of GRAB (G protein-coupled receptor activation‒based) sensors for detecting somatostatin (SST), corticotropin-releasing factor (CRF), cholecystokinin (CCK), neuropeptide Y (NPY), neurotensin (NTS), and vasoactive intestinal peptide (VIP). These fluorescent sensors, which enable detection of specific neuropeptide binding at nanomolar concentrations, establish a robust tool kit for studying the release, function, and regulation of neuropeptides under both physiological and pathophysiological conditions.
    DOI:  https://doi.org/10.1126/science.abq8173
  44. Proc Natl Acad Sci U S A. 2023 Nov 21. 120(47): e2315347120
    Mitochondria-associated membrane collapse impairs TBK1-mediated proteostatic stress response in ALS.
    Seiji Watanabe, Yuri Murata, Yasuyoshi Oka, Kotaro Oiwa, Mai Horiuchi, Yohei Iguchi, Okiru Komine, Akira Sobue, Masahisa Katsuno, Tomoo Ogi, Koji Yamanaka.
      The organelle contact site of the endoplasmic reticulum and mitochondria, known as the mitochondria-associated membrane (MAM), is a multifunctional microdomain in cellular homeostasis. We previously reported that MAM disruption is a common pathological feature in amyotrophic lateral sclerosis (ALS); however, the precise role of MAM in ALS was uncovered. Here, we show that the MAM is essential for TANK-binding kinase 1 (TBK1) activation under proteostatic stress conditions. A MAM-specific E3 ubiquitin ligase, autocrine motility factor receptor, ubiquitinated nascent proteins to activate TBK1 at the MAM, which results in ribosomal protein degradation. MAM or TBK1 deficiency under proteostatic stress conditions resulted in increased cellular vulnerability in vitro and motor impairment in vivo. Thus, MAM disruption exacerbates proteostatic stress via TBK1 inactivation in ALS. Our study has revealed a proteostatic mechanism mediated by the MAM-TBK1 axis, highlighting the physiological importance of the organelle contact sites.
    Keywords:  TANK-binding kinase 1; amyotrophic lateral sclerosis; mitochondria-associated membrane; sigma-1 receptor; stress granules
    DOI:  https://doi.org/10.1073/pnas.2315347120
  45. J Appl Physiol (1985). 2023 Nov 16.
    Combined changes in temperature and pH mimicking exercise results in decreased efficiency in muscle mitochondria.
    Mathias Flensted-Jensen, Ann-Sofie Kleis-Olsen, Rasmus Kinimond Hassø, Søren Lindtofte, Juan Corral-Pérez, Sonia Ortega-Gómez, Steen Larsen.
      It is well known that exercise efficiency declines at intensities above the lactate threshold, yet the underlying mechanisms are poorly understood. Some have suggested it is due to a decline in mitochondrial efficiency, but this is difficult to examine in vivo. Therefore, the aim of the current study was to examine how changes in temperature and pH, mimicking those that occur during exercise, affect mitochondrial efficiency in skeletal muscle mitochondria. The study was performed on quadriceps muscle of 20 wild type mice. Muscle tissue was dissected and either permeabilized (n = 10) or homogenized for isolation of mitochondria (n = 10), and oxidative phosphorylation capacity and P/O ratio was assessed using high-resolution respirometry. Samples from each muscle was analyzed in both normal physiological conditions (37℃, pH 7.4), decreased pH (6.8), increased temperature (40℃) and a combination of both. The combination of increased temperature and decreased pH resulted in a significantly lower P/O ratio, mirrored by an increase in leak respiration and a decrease in respiratory control ratio (RCR), in isolated mitochondria. In permeabilized fibers, RCR and leak was relatively unaffected, though a main effect of temperature was observed. Oxidative phosphorylation capacity was unaffected by changes in pH and temperature in both isolated mitochondria and permeabilized fibers. These results indicate that exercise-like changes in temperature and pH leads to impaired mitochondrial efficiency. These findings offer some degree of support to the concept of decreased mitochondrial efficiency during exercise, and may have implications for the assessment of mitochondrial function related to exercise.
    Keywords:  Exercise; Mitochondria; Mitochondrial efficiency; Temperature; pH
    DOI:  https://doi.org/10.1152/japplphysiol.00293.2023
  46. Basic Res Cardiol. 2023 Nov 13. 118(1): 49
    Targeting mitochondrial shape: at the heart of cardioprotection.
    Sauri Hernandez-Resendiz, Aishwarya Prakash, Sze Jie Loo, Martina Semenzato, Kroekkiat Chinda, Gustavo E Crespo-Avilan, Linh Chi Dam, Shengjie Lu, Luca Scorrano, Derek J Hausenloy.
      There remains an unmet need to identify novel therapeutic strategies capable of protecting the myocardium against the detrimental effects of acute ischemia-reperfusion injury (IRI), to reduce myocardial infarct (MI) size and prevent the onset of heart failure (HF) following acute myocardial infarction (AMI). In this regard, perturbations in mitochondrial morphology with an imbalance in mitochondrial fusion and fission can disrupt mitochondrial metabolism, calcium homeostasis, and reactive oxygen species production, factors which are all known to be critical determinants of cardiomyocyte death following acute myocardial IRI. As such, therapeutic approaches directed at preserving the morphology and functionality of mitochondria may provide an important strategy for cardioprotection. In this article, we provide an overview of the alterations in mitochondrial morphology which occur in response to acute myocardial IRI, and highlight the emerging therapeutic strategies for targeting mitochondrial shape to preserve mitochondrial function which have the future therapeutic potential to improve health outcomes in patients presenting with AMI.
    Keywords:  Acute myocardial infarction; Acute myocardial ischemia–reperfusion injury; Cardioprotection; Cardiovascular diseases; Heart failure; Mitochondrial morphology
    DOI:  https://doi.org/10.1007/s00395-023-01019-9
  47. Nature. 2023 Nov 09.
    Flashy molecules decode a polymer's lengthening chain.
      
    Keywords:  Chemistry
    DOI:  https://doi.org/10.1038/d41586-023-03497-2
  48. bioRxiv. 2023 Nov 04. pii: 2023.11.01.565153. [Epub ahead of print]
    An in vivo platform to identify clinically relevant pathogenic loci using Drosophila melanogaster.
    Shigehiro Yamada, Tiffany Ou, Sibani Nachadalingam, Shuo Yang, Aaron N Johnson.
      Rare genetic disease discovery efforts typically lead to the identification of new disease genes. While there is inherent value in uncovering the genetic basis of disease for diagnosis, there is also significant opportunity to gain deep mechanistic or biological insights into disease pathogenesis. PreMIER ( Pre cision M edicine Integrated E xperimental R esources) is a collaborative platform among Washington University faculty designed to facilitate functional evaluation of human genetic variants in model systems. The PreMIER platform has identified seven cases could be effectively modeled in fruit flies. A survey of recent, high-impact disease-modeling studies in Drosophila identified six commonly used physiological assays that assess viability, longevity, behavior, and motor function. We knocked down each of the seven genes in neurons and in muscle throughout development and into adulthood, and assessed physiological phenotypes in adults. Tissue-specific knockdown of each gene caused significant changes in adult physiology in multiple assays, arguing that a set of six physiological assays can be used to show a candidate GUS is required for normal viability, longevity, behavior, or motor function. This study lays the foundation for our ongoing GUS screens, which may provide the first genephenotype correlations for patients with idiopathic genetic disorders.
    DOI:  https://doi.org/10.1101/2023.11.01.565153
  49. Nat Aging. 2023 Nov 13.
    A drug-like molecule engages nuclear hormone receptor DAF-12/FXR to regulate mitophagy and extend lifespan.
    Manish Chamoli, Anand Rane, Anna Foulger, Shankar J Chinta, Azar Asadi Shahmirzadi, Caroline Kumsta, Dhanya K Nambiar, David Hall, Angelina Holcom, Suzanne Angeli, Minna Schmidt, Sharon Pitteri, Malene Hansen, Gordon J Lithgow, Julie K Andersen.
      Autophagy-lysosomal function is crucial for maintaining healthy lifespan and preventing age-related diseases. The transcription factor TFEB plays a key role in regulating this pathway. Decreased TFEB expression is associated with various age-related disorders, making it a promising therapeutic target. In this study, we screened a natural product library and discovered mitophagy-inducing coumarin (MIC), a benzocoumarin compound that enhances TFEB expression and lysosomal function. MIC robustly increases the lifespan of Caenorhabditis elegans in an HLH-30/TFEB-dependent and mitophagy-dependent manner involving DCT-1/BNIP3 while also preventing mitochondrial dysfunction in mammalian cells. Mechanistically, MIC acts by inhibiting ligand-induced activation of the nuclear hormone receptor DAF-12/FXR, which, in turn, induces mitophagy and extends lifespan. In conclusion, our study uncovers MIC as a promising drug-like molecule that enhances mitochondrial function and extends lifespan by targeting DAF-12/FXR. Furthermore, we discovered DAF-12/FXR as a previously unknown upstream regulator of HLH-30/TFEB and mitophagy.
    DOI:  https://doi.org/10.1038/s43587-023-00524-9
  50. Nat Commun. 2023 Nov 17. 14(1): 7471
    Inflammatory macrophages reprogram to immunosuppression by reducing mitochondrial translation.
    Marlies Cortés, Agnese Brischetto, M C Martinez-Campanario, Chiara Ninfali, Verónica Domínguez, Sara Fernández, Raquel Celis, Anna Esteve-Codina, Juan J Lozano, Julia Sidorova, Gloria Garrabou, Anna-Maria Siegert, Carlos Enrich, Belén Pintado, Manuel Morales-Ruiz, Pedro Castro, Juan D Cañete, Antonio Postigo.
      Acute inflammation can either resolve through immunosuppression or persist, leading to chronic inflammation. These transitions are driven by distinct molecular and metabolic reprogramming of immune cells. The anti-diabetic drug Metformin inhibits acute and chronic inflammation through mechanisms still not fully understood. Here, we report that the anti-inflammatory and reactive-oxygen-species-inhibiting effects of Metformin depend on the expression of the plasticity factor ZEB1 in macrophages. Using mice lacking Zeb1 in their myeloid cells and human patient samples, we show that ZEB1 plays a dual role, being essential in both initiating and resolving inflammation by inducing macrophages to transition into an immunosuppressed state. ZEB1 mediates these diverging effects in inflammation and immunosuppression by modulating mitochondrial content through activation of autophagy and inhibition of mitochondrial protein translation. During the transition from inflammation to immunosuppression, Metformin mimics the metabolic reprogramming of myeloid cells induced by ZEB1. Mechanistically, in immunosuppression, ZEB1 inhibits amino acid uptake, leading to downregulation of mTORC1 signalling and a decrease in mitochondrial translation in macrophages. These results identify ZEB1 as a driver of myeloid cell metabolic plasticity, suggesting that targeting its expression and function could serve as a strategy to modulate dysregulated inflammation and immunosuppression.
    DOI:  https://doi.org/10.1038/s41467-023-42277-4
  51. bioRxiv. 2023 Nov 01. pii: 2023.10.27.564485. [Epub ahead of print]
    Adjusted vascular contractility relies on integrity of progranulin pathway: Insights into mitochondrial function.
    Shubhnita Singh, Ariane Bruder-Nascimento, Rafael M Costa, Juliano V Alves, Sivakama Bharathi, Eric S Goetzman, Thiago Bruder-Nascimento.
      Objective: Cardiovascular disease (CVD) is a global health crisis and a leading cause of mortality. The intricate interplay between vascular contractility and mitochondrial function is central to CVD pathogenesis. The progranulin gene (GRN) encodes glycoprotein progranulin (PGRN), a ubiquitous molecule with known anti-inflammatory property. However, the role of PGRN in CVD remains enigmatic. In this study, we sought to dissect the significance of PGRN in the regulation vascular contractility and investigate the interface between PGRN and mitochondrial quality.Method: Our investigation utilized aortae from male and female C57BL6/J wild-type (PGRN+/+) and B6(Cg)-Grntm1.1Aidi/J (PGRN-/-) mice, encompassing wire myograph assays to assess vascular contractility and primary aortic vascular smooth muscle cells (VSMCs) for mechanistic insights.
    Results: Our results showed suppression of contractile activity in PGRN-/- VSMCs and aorta, followed by reduced α-smooth muscle actin expression. Mechanistically, PGRN deficiency impaired mitochondrial oxygen consumption rate (OCR), complex I activity, mitochondrial turnover, and mitochondrial redox signaling, while restoration of PGRN levels in aortae from PGRN-/- mice via lentivirus delivery ameliorated contractility and boosted OCR. In addition, VSMC overexpressing PGRN displayed higher mitochondrial respiration and complex I activity accompanied by cellular hypercontractility. Furthermore, increased PGRN triggered lysosome biogenesis by regulating transcription factor EB and accelerated mitophagy flux in VSMC, while treatment with spermidine, an autophagy inducer, improved mitochondrial phenotype and enhanced vascular contractility. Finally, angiotensin II failed to induce vascular contractility in PGRN-/- suggesting a key role of PGRN to maintain the vascular tone.
    Conclusion: Our findings suggest that PGRN preserves the vascular contractility via regulating mitophagy flux, mitochondrial complex I activity, and redox signaling. Therefore, loss of PGRN function appears as a pivotal risk factor in CVD development.
    DOI:  https://doi.org/10.1101/2023.10.27.564485
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