bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2024‒01‒28
85 papers selected by
Catalina Vasilescu, Helmholz Munich
  1. Phosphate starvation signaling increases mitochondrial membrane potential through respiration-independent mechanisms.
  2. Mitochondrial choline import regulates purine nucleotide pools via SLC25A48.
  3. Functional genomics and small molecules in mitochondrial neurodevelopmental disorders.
  4. Genetic variants affecting NQO1 protein levels impact the efficacy of idebenone treatment in Leber hereditary optic neuropathy.
  5. Characterization of a novel variant in the HR1 domain of MFN2 in a patient with ataxia, optic atrophy and sensorineural hearing loss.
  6. Challenges and opportunities to bridge translational to clinical research for personalized mitochondrial medicine.
  7. Decoding the nature and complexity of extracellular mtDNA: Types and implications for health and disease.
  8. Mitochondrial membrane potential regulates nuclear DNA methylation and gene expression through phospholipid remodeling.
  9. Mitochondrial CISD1/Cisd accumulation blocks mitophagy and genetic or pharmacological inhibition rescues neurodegenerative phenotypes in Pink1/parkin models.
  10. The SIRT3-ATAD3A axis regulates MAM dynamics and mitochondrial calcium homeostasis in cardiac hypertrophy.
  11. The Research Progress of Mitochondrial Transplantation in the Treatment of Mitochondrial Defective Diseases.
  12. Protocol for measuring mitochondrial size in mouse and human liver tissues.
  13. AFG3L2 and ACO2-linked Dominant Optic Atrophy: genotype-phenotype characterization compared to OPA1 patients.
  14. Drosophila MIC10b can polymerize into cristae-shaping filaments.
  15. CLPB disaggregase dysfunction impacts the functional integrity of the proteolytic SPY complex.
  16. Mitochondria in Mesenchymal Stem Cells: Key to Fate Determination and Therapeutic Potential.
  17. Mitochondrial-related microRNAs and their roles in cellular senescence.
  18. A diagnostic framework to identify vestibular involvement in multi-sensory neurological disease.
  19. Multilevel evidence of MECP2-associated mitochondrial dysfunction and its therapeutic implications.
  20. Acetylated tau exacerbates apoptosis by disturbing mitochondrial dynamics in HEK293 cells.
  21. Hereditary Optic Neuropathies: A Systematic Review on the Interplay between Biomaterials and Induced Pluripotent Stem Cells.
  22. Editorial: Mitochondria at the nexus of metabolism, aging, and disease.
  23. From Beach to the Bedside: Harnessing Mitochondrial Function in Human Diseases Using New Marine-Derived Strategies.
  24. Direct neuronal reprogramming of NDUFS4 patient cells identifies the unfolded protein response as a novel general reprogramming hurdle.
  25. Diagnostic utility and reporting recommendations for clinical DNA methylation episignature testing in genetically undiagnosed rare diseases.
  26. Shared structural features of Miro binding control mitochondrial homeostasis.
  27. Caspase-dependent apoptosis in Ribloflavin transporter deficiency iPSCs and derived motor neurons.
  28. Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges.
  29. Lessons Learned from Translating Genome Sequencing to Clinical Routine: Understanding the Accuracy of a Diagnostic Pipeline.
  30. Applications of near-infrared spectroscopy in epilepsy, with a focus on mitochondrial disorders.
  31. Neurological outcome in long-chain hydroxy fatty acid oxidation disorders.
  32. Cardiomyocyte maturation alters molecular stress response capacities and determines cell survival upon mitochondrial dysfunction.
  33. Mitochondrial translocation of TFEB regulates complex I and inflammation.
  34. A comprehensive review on signaling attributes of serine and serine metabolism in health and disease.
  35. Mitochondrial techniques for physiologists.
  36. Epigenetic regulation of the nuclear genome associated with mitochondrial dysfunction in Leber's hereditary optic neuropathy (LHON).
  37. ChemRAP uncovers specific mRNA translation regulation via RNA 5' phospho-methylation.
  38. A mito-centric view on muscle aging and function.
  39. Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures.
  40. Deep generative modeling of the human proteome reveals over a hundred novel genes involved in rare genetic disorders.
  41. Forward Genetic Screens Identify Mechanisms of Resistance to Small-Molecule Lactate Dehydrogenase Inhibitors.
  42. The potential influence of melatonin on mitochondrial quality control: a review.
  43. Evaluation of Mitochondrial Respiratory Function in Murine Splenocytes.
  44. Mitochondria in Multi-Directional Differentiation of Dental-Derived Mesenchymal Stem Cells.
  45. Advances in crosstalk among innate immune pathways activated by mitochondrial DNA.
  46. Post-translational modification and mitochondrial function in Parkinson's disease.
  47. A biological classification of Parkinson's disease: the SynNeurGe research diagnostic criteria.
  48. Nuclear and mitochondrial genetic variants associated with mitochondrial DNA copy number.
  49. Motion of VAPB molecules reveals ER-mitochondria contact site subdomains.
  50. Deciphering cell states and genealogies of human hematopoiesis.
  51. Complex trait associations in rare diseases and impacts on Mendelian variant interpretation.
  52. Epigenetic Reprogramming as a Key to Reverse Ageing and Increase Longevity.
  53. Impact of genome build on RNA-seq interpretation and diagnostics.
  54. ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism.
  55. The Role of Chorein Deficiency in Late Spermatogenesis.
  56. HDAC1/2 inhibitor therapy improves multiple organ systems in aged mice.
  57. Glutamine Metabolism Promotes Renal Fibrosis through Regulation of Mitochondrial Energy Generation and Mitochondrial Fission.
  58. Mass spectrometry-based proteomics data from thousands of HeLa control samples.
  59. What a Clinician Needs to Know about Genome Editing: Status and Opportunities for Inborn Errors of Immunity.
  60. Variants in the SARS2 gene cause HUPRA syndrome with atypical features: two case reports and review of the literature.
  61. Mitochondrial and Cellular Function in Fibroblasts, Induced Neurons, and Astrocytes Derived from Case Study Patients: Insights into Major Depression as a Mitochondria-Associated Disease.
  62. Lessons learned from rapid exome sequencing for 575 critically ill patients across the broad spectrum of rare disease.
  63. Gene selection for genomic newborn screening: moving towards consensus?
  64. Recent Advances in Electrochemical Detection of Cell Energy Metabolism.
  65. Yeast EndoG prevents genome instability by degrading cytoplasmic DNA.
  66. Sirtuins mediate mitochondrial quality control mechanisms: a novel therapeutic target for osteoporosis.
  67. AIBP: A New Safeguard against Glaucomatous Neuroinflammation.
  68. One carbon metabolism and its implication in health and immune functions.
  69. Seven technologies to watch in 2024.
  70. Metabolic control of induced pluripotency.
  71. High Sucrose Diet-Induced Subunit I Tyrosine 304 Phosphorylation of Cytochrome c Oxidase Leads to Liver Mitochondrial Respiratory Dysfunction in the Cohen Diabetic Rat Model.
  72. Mitochondrial Glutathione in Cellular Redox Homeostasis and Disease Manifestation.
  73. Uniparental Disomy as a Mechanism for Combined Oxidative Phosphorylation Deficiency Associated with MRPS34 Gene.
  74. Whole genome sequencing as a first-tier diagnostic test for infants in neonatal intensive care units: A pilot study in Brazil.
  75. Protein-Protein Interactions of Seryl-tRNA Synthetases with Emphasis on Human Counterparts and Their Connection to Health and Disease.
  76. Precision Medicine in Parkinson's Disease using Induced Pluripotent Stem Cells.
  77. RORα-GABP-TFAM axis alleviates myosteatosis with fatty atrophy through reinforcement of mitochondrial capacity.
  78. Case report: Clinical profile, molecular genetics, and neuroimaging findings presenting in a patient with Kearns-Sayre syndrome associated with inherited thrombophilia.
  79. Challenges and approaches to calibrating patient phenotype as evidence for cancer gene variant classification under ACMG/AMP guidelines.
  80. Lethal phenotypes in Mendelian disorders.
  81. Parkinson's disease is a recognisable and useful diagnostic entity.
  82. A mouse model to study glutathione limitation in vivo.
  83. Are the European reference networks for rare diseases ready to embrace machine learning? A mixed-methods study.
  84. Discovery and engineering of AiEvo2, a novel Cas12a nuclease for human gene editing applications.
  85. User Centered Rare Disease Clinical Trial Knowledge Graph (RCTKG).
  1. Elife. 2024 Jan 22. pii: e84282. [Epub ahead of print]13
    Phosphate starvation signaling increases mitochondrial membrane potential through respiration-independent mechanisms.
    Yeyun Ouyang, Mi-Young Jeong, Corey N Cunningham, Jordan A Berg, Ashish G Toshniwal, Casey E Hughes, Kristina Seiler, Jonathan G Van Vranken, Ahmad A Cluntun, Geanette Lam, Jacob M Winter, Emel Akdoǧan, Katja K Dove, Sara M Nowinski, Matthew West, Greg Odorizzi, Steven P Gygi, Cory D Dunn, Dennis R Winge, Jared Rutter.
      Mitochondrial membrane potential directly powers many critical functions of mitochondria, including ATP production, mitochondrial protein import, and metabolite transport. Its loss is a cardinal feature of aging and mitochondrial diseases, and cells closely monitor membrane potential as an indicator of mitochondrial health. Given its central importance, it is logical that cells would modulate mitochondrial membrane potential in response to demand and environmental cues, but there has been little exploration of this question. We report that loss of the Sit4 protein phosphatase in yeast increases mitochondrial membrane potential, both through inducing the electron transport chain and the phosphate starvation response. Indeed, a similarly elevated mitochondrial membrane potential is also elicited simply by phosphate starvation or by abrogation of the Pho85-dependent phosphate sensing pathway. This enhanced membrane potential is primarily driven by an unexpected activity of the ADP/ATP carrier. We also demonstrate that this connection between phosphate limitation and enhancement of mitochondrial membrane potential is observed in primary and immortalized mammalian cells as well as in Drosophila. These data suggest that mitochondrial membrane potential is subject to environmental stimuli and intracellular signaling regulation and raise the possibility for therapeutic enhancement of mitochondrial function even in defective mitochondria.
    Keywords:  D. melanogaster; S. cerevisiae; cell biology; human
    DOI:  https://doi.org/10.7554/eLife.84282
  2. bioRxiv. 2024 Jan 01. pii: 2023.12.31.573776. [Epub ahead of print]
    Mitochondrial choline import regulates purine nucleotide pools via SLC25A48.
    Anthony R P Verkerke, Xu Shi, Ichitaro Abe, Robert E Gerszten, Shingo Kajimura.
      Choline is an essential nutrient for cellular metabolism, including the biosynthesis of phospholipids, neurotransmitters, and one-carbon metabolism. A critical step of choline catabolism is the mitochondrial import and synthesis of chorine-derived methyl donors, such as betaine. However, the underlying mechanisms and the biological significance of mitochondrial choline catabolism remain insufficiently understood. Here, we report that a mitochondrial inner-membrane protein SLC25A48 controls mitochondrial choline transport and catabolism in vivo . We demonstrate that SLC25A48 is highly expressed in brown adipose tissue and required for whole-body cold tolerance, thermogenesis, and mitochondrial respiration. Mechanistically, choline uptake into the mitochondrial matrix via SLC25A48 facilitates betaine synthesis and one-carbon metabolism. Importantly, cells lacking SLC25A48 exhibited reduced synthesis of purine nucleotides and failed to initiate the G1-to-S phase transition, thereby leading to cell death. Taken together, the present study identified SLC25A48 as a mitochondrial carrier that mediates choline import and plays a critical role in mitochondrial respiratory capacity, purine nucleotide synthesis, and cell survival.Key points: SLC25A48 is required for mitochondrial choline uptake.Mitochondrial choline uptake regulates one-carbon contribution to purine nucleotide synthesis.Brown fat thermogenesis requires mitochondrial choline catabolism for respiratory capacity.Cancer cells require mitochondrial choline uptake for cell survival.
    DOI:  https://doi.org/10.1101/2023.12.31.573776
  3. Neurotherapeutics. 2024 Jan 19. pii: S1878-7479(24)00002-3. [Epub ahead of print]21(1): e00316
    Functional genomics and small molecules in mitochondrial neurodevelopmental disorders.
    Daniel G Calame, Lisa T Emrick.
      Mitochondria are critical for brain development and homeostasis. Therefore, pathogenic variation in the mitochondrial or nuclear genome which disrupts mitochondrial function frequently results in developmental disorders and neurodegeneration at the organismal level. Large-scale application of genome-wide technologies to individuals with mitochondrial diseases has dramatically accelerated identification of mitochondrial disease-gene associations in humans. Multi-omic and high-throughput studies involving transcriptomics, proteomics, metabolomics, and saturation genome editing are providing deeper insights into the functional consequence of mitochondrial genomic variation. Integration of deep phenotypic and genomic data through allelic series continues to uncover novel mitochondrial functions and permit mitochondrial gene function dissection on an unprecedented scale. Finally, mitochondrial disease-gene associations illuminate disease mechanisms and thereby direct therapeutic strategies involving small molecules and RNA-DNA therapeutics. This review summarizes progress in functional genomics and small molecule therapeutics in mitochondrial neurodevelopmental disorders.
    Keywords:  Functional genomics; Mitochondrial disease; Neurodevelopmental disorders; Small molecules; Therapeutics
    DOI:  https://doi.org/10.1016/j.neurot.2024.e00316
  4. Cell Rep Med. 2024 Jan 17. pii: S2666-3791(23)00612-2. [Epub ahead of print] 101383
    Genetic variants affecting NQO1 protein levels impact the efficacy of idebenone treatment in Leber hereditary optic neuropathy.
    Serena Jasmine Aleo, Valentina Del Dotto, Martina Romagnoli, Claudio Fiorini, Giada Capirossi, Camille Peron, Alessandra Maresca, Leonardo Caporali, Mariantonietta Capristo, Concetta Valentina Tropeano, Claudia Zanna, Fred N Ross-Cisneros, Alfredo A Sadun, Maria Gemma Pignataro, Carla Giordano, Chiara Fasano, Andrea Cavaliere, Anna Maria Porcelli, Gaia Tioli, Francesco Musiani, Alessia Catania, Costanza Lamperti, Stefania Bianchi Marzoli, Annamaria De Negri, Maria Lucia Cascavilla, Marco Battista, Piero Barboni, Michele Carbonelli, Giulia Amore, Chiara La Morgia, Dmitrii Smirnov, Catalina Vasilescu, Aiman Farzeen, Beryll Blickhaeuser, Holger Prokisch, Claudia Priglinger, Bettina Livonius, Claudia B Catarino, Thomas Klopstock, Valeria Tiranti, Valerio Carelli, Anna Maria Ghelli.
      Idebenone, the only approved treatment for Leber hereditary optic neuropathy (LHON), promotes recovery of visual function in up to 50% of patients, but we can neither predict nor understand the non-responders. Idebenone is reduced by the cytosolic NAD(P)H oxidoreductase I (NQO1) and directly shuttles electrons to respiratory complex III, bypassing complex I affected in LHON. We show here that two polymorphic variants drastically reduce NQO1 protein levels when homozygous or compound heterozygous. This hampers idebenone reduction. In its oxidized form, idebenone inhibits complex I, decreasing respiratory function in cells. By retrospectively analyzing a large cohort of idebenone-treated LHON patients, classified by their response to therapy, we show that patients with homozygous or compound heterozygous NQO1 variants have the poorest therapy response, particularly if carrying the m.3460G>A/MT-ND1 LHON mutation. These results suggest consideration of patient NQO1 genotype and mitochondrial DNA mutation in the context of idebenone therapy.
    Keywords:  LHON; Leber hereditary optic neuropathy; NQO1; complex I; cybrids; fibroblasts; idebenone; mtDNA; retinal ganglion cells
    DOI:  https://doi.org/10.1016/j.xcrm.2023.101383
  5. F1000Res. 2021 ;10 606
    Characterization of a novel variant in the HR1 domain of MFN2 in a patient with ataxia, optic atrophy and sensorineural hearing loss.
    Govinda Sharma, Mashiat Zaman, Rasha Sabouny, Matthew Joel, Kristina Martens, Davide Martino, A P Jason de Koning, Gerald Pfeffer, Timothy E Shutt.
      Background: Pathogenic variants in MFN2 cause Charcot-Marie-Tooth disease (CMT) type 2A (CMT2A) and are the leading cause of the axonal subtypes of CMT. CMT2A is characterized by predominantly distal motor weakness and muscle atrophy, with highly variable severity and onset age. Notably, some MFN2 variants can also lead to other phenotypes such as optic atrophy, hearing loss and lipodystrophy. Despite the clear link between MFN2 and CMT2A, our mechanistic understanding of how dysfunction of the MFN2 protein causes human disease pathologies remains incomplete. This lack of understanding is due in part to the multiple cellular roles of MFN2. Though initially characterized for its role in mediating mitochondrial fusion, MFN2 also plays important roles in mediating interactions between mitochondria and other organelles, such as the endoplasmic reticulum and lipid droplets. Additionally, MFN2 is also important for mitochondrial transport, mitochondrial autophagy, and has even been implicated in lipid transfer. Though over 100 pathogenic MFN2 variants have been described to date, only a few have been characterized functionally, and even then, often only for one or two functions. Method: Several MFN2-mediated functions were characterized in fibroblast cells from a patient presenting with cerebellar ataxia, deafness, blindness, and diffuse cerebral and cerebellar atrophy, who harbours a novel homozygous MFN2 variant, D414V, which is found in a region of the HR1 domain of MFN2 where few pathogenic variants occur. Results: We found evidence for impairment of several MFN2-mediated functions. Consistent with reduced mitochondrial fusion, patient fibroblasts exhibited more fragmented mitochondrial networks and had reduced mtDNA copy number. Additionally, patient fibroblasts had reduced oxygen consumption, fewer mitochondrial-ER contacts, and altered lipid droplets that displayed an unusual perinuclear distribution. Conclusion: Overall, this work characterizes D414V as a novel variant in MFN2 and expands the phenotypic presentation of MFN2 variants to include cerebellar ataxia.
    Keywords:  Ataxia; MFN2; Mitochondria; Mitochondrial Fusion
    DOI:  https://doi.org/10.12688/f1000research.53230.2
  6. Neurotherapeutics. 2024 Jan 19. pii: S1878-7479(23)02027-5. [Epub ahead of print]21(1): e00311
    Challenges and opportunities to bridge translational to clinical research for personalized mitochondrial medicine.
    Andrea L Gropman, Martine N Uittenbogaard, Anne E Chiaramello.
      Mitochondrial disorders are a group of rare and heterogeneous genetic diseases characterized by dysfunctional mitochondria leading to deficient adenosine triphosphate synthesis and chronic energy deficit in patients. The majority of these patients exhibit a wide range of phenotypic manifestations targeting several organ systems, making their clinical diagnosis and management challenging. Bridging translational to clinical research is crucial for improving the early diagnosis and prognosis of these intractable mitochondrial disorders and for discovering novel therapeutic drug candidates and modalities. This review provides the current state of clinical testing in mitochondrial disorders, discusses the challenges and opportunities for converting basic discoveries into clinical settings, explores the most suited patient-centric approaches to harness the extraordinary heterogeneity among patients affected by the same primary mitochondrial disorder, and describes the current outlook of clinical trials.
    Keywords:  Clinical trial; Energy metabolism; Mitochondrial medicine; Next generation therapeutics; Patient-centric approach
    DOI:  https://doi.org/10.1016/j.neurot.2023.e00311
  7. Mitochondrion. 2024 Jan 20. pii: S1567-7249(24)00006-0. [Epub ahead of print]75 101848
    Decoding the nature and complexity of extracellular mtDNA: Types and implications for health and disease.
    Andrés Caicedo, Abigail Benavides-Almeida, Alissen Haro-Vinueza, José Peña-Cisneros, Álvaro A Pérez-Meza, Jeremy Michelson, Sebastian Peñaherrera, Martin Picard.
      The mitochondrial DNA (mtDNA) is replicated and canonically functions within intracellular mitochondria, but recent discoveries reveal that the mtDNA has another exciting extracellular life. mtDNA fragments and mitochondria-containing vesicular structures are detected at high concentrations in cell-free forms, in different biofluids. Commonly referred to as cell-free mtDNA (cf-mtDNA), the field is currently without a comprehensive classification system that acknowledges the various biological forms of mtDNA and whole mitochondria existing outside the cell. This absence of classification hampers the creation of precise and consistent quantification methods across different laboratories, which is crucial for unraveling the molecular and biological characteristics of mtDNA. In this article, we integrate recent findings to propose a classification for different types of Extracellular mtDNA [ex-mtDNA]. The major biologically distinct types include: Naked mtDNA [N-mtDNA], mtDNA within non-mitochondrial Membranes [M-mtDNA], Extracellular mitochondria [exM-mtDNA], and mtDNA within Mitochondria enclosed in a Membrane [MM-mtDNA]. We outline the challenges associated with accurately quantifying these ex-mtDNA types, suggest potential physiological roles for each ex-mtDNA type, and explore how this classification could establish a foundation for future research endeavors and further analysis and definitions for ex-mtDNA. By proposing this classification of circulating mtDNA forms, we draw a parallel with the clinically recognized forms of cholesterol, such as HDL and LDL, to illustrate potential future significance in a similar manner. While not directly analogous, these mtDNA forms may one day be as biologically relevant in clinical interpretation as cholesterol fractions are currently. We also discuss how advancing methodologies to reliably quantify distinct ex-mtDNA forms could significantly enhance their utility as health or disease biomarkers, and how their application may offer innovative therapeutic approaches.
    Keywords:  Aging; Biomarker; Classification; Extracellular mitochondria (ex-mito); Extracellular mitochondrial DNA (ex-mtDNA); Health; Identification methods; Stress; Therapeutic agent
    DOI:  https://doi.org/10.1016/j.mito.2024.101848
  8. bioRxiv. 2024 Jan 13. pii: 2024.01.12.575075. [Epub ahead of print]
    Mitochondrial membrane potential regulates nuclear DNA methylation and gene expression through phospholipid remodeling.
    Mateus Prates Mori, Oswaldo Lozoya, Ashley M Brooks, Dagoberto Grenet, Cristina A Nadalutti, Birgitta Ryback, Kai Ting Huang, Prottoy Hasan, Gyӧrgy Hajnóczky, Janine H Santos.
      Maintenance of the mitochondrial inner membrane potential (ΔΨM) is critical for many aspects of mitochondrial function, including mitochondrial protein import and ion homeostasis. While ΔΨM loss and its consequences are well studied, little is known about the effects of increased ΔΨM. In this study, we used cells deleted of ATPIF1 , a natural inhibitor of the hydrolytic activity of the ATP synthase, as a genetic model of mitochondrial hyperpolarization. Our data show that chronic ΔΨM increase leads to nuclear DNA hypermethylation, regulating transcription of mitochondria, carbohydrate and lipid metabolism genes. Surprisingly, remodeling of phospholipids, but not metabolites or redox changes, mechanistically links the ΔΨM to the epigenome. These changes were also observed upon chemical exposures and reversed by decreasing the ΔΨM, highlighting them as hallmark adaptations to chronic mitochondrial hyperpolarization. Our results reveal the ΔΨM as the upstream signal conveying the mitochondrial status to the epigenome to regulate cellular biology, providing a new framework for how mitochondria can influence health outcomes in the absence of canonical dysfunction.Highlights: Mitochondria hyperpolarization leads to nuclear DNA hypermethylationDNA methylation regulates expression of mitochondrial and lipid metabolism genesPhospholipid remodeling mediates the epigenetic effects of mitochondrial hyperpolarization.
    DOI:  https://doi.org/10.1101/2024.01.12.575075
  9. Mol Neurodegener. 2024 Jan 25. 19(1): 12
    Mitochondrial CISD1/Cisd accumulation blocks mitophagy and genetic or pharmacological inhibition rescues neurodegenerative phenotypes in Pink1/parkin models.
    Aitor Martinez, Alvaro Sanchez-Martinez, Jake T Pickering, Madeleine J Twyning, Ana Terriente-Felix, Po-Lin Chen, Chun-Hong Chen, Alexander J Whitworth.
      BACKGROUND: Mitochondrial dysfunction and toxic protein aggregates have been shown to be key features in the pathogenesis of neurodegenerative diseases, such as Parkinson's disease (PD). Functional analysis of genes linked to PD have revealed that the E3 ligase Parkin and the mitochondrial kinase PINK1 are important factors for mitochondrial quality control. PINK1 phosphorylates and activates Parkin, which in turn ubiquitinates mitochondrial proteins priming them and the mitochondrion itself for degradation. However, it is unclear whether dysregulated mitochondrial degradation or the toxic build-up of certain Parkin ubiquitin substrates is the driving pathophysiological mechanism leading to PD. The iron-sulphur cluster containing proteins CISD1 and CISD2 have been identified as major targets of Parkin in various proteomic studies.METHODS: We employed in vivo Drosophila and human cell culture models to study the role of CISD proteins in cell and tissue viability as well as aged-related neurodegeneration, specifically analysing aspects of mitophagy and autophagy using orthogonal assays.
    RESULTS: We show that the Drosophila homolog Cisd accumulates in Pink1 and parkin mutant flies, as well as during ageing. We observed that build-up of Cisd is particularly toxic in neurons, resulting in mitochondrial defects and Ser65-phospho-Ubiquitin accumulation. Age-related increase of Cisd blocks mitophagy and impairs autophagy flux. Importantly, reduction of Cisd levels upregulates mitophagy in vitro and in vivo, and ameliorates pathological phenotypes in locomotion, lifespan and neurodegeneration in Pink1/parkin mutant flies. In addition, we show that pharmacological inhibition of CISD1/2 by rosiglitazone and NL-1 induces mitophagy in human cells and ameliorates the defective phenotypes of Pink1/parkin mutants.
    CONCLUSION: Altogether, our studies indicate that Cisd accumulation during ageing and in Pink1/parkin mutants is a key driver of pathology by blocking mitophagy, and genetically and pharmacologically inhibiting CISD proteins may offer a potential target for therapeutic intervention.
    Keywords:  Ageing; Autophagy; CISD1; CISD2; Cisd; Mitochondria; Mitophagy; Neurodegeneration; PINK1; Parkin; Parkinson’s disease
    DOI:  https://doi.org/10.1186/s13024-024-00701-3
  10. Int J Biol Sci. 2024 ;20(3): 831-847
    The SIRT3-ATAD3A axis regulates MAM dynamics and mitochondrial calcium homeostasis in cardiac hypertrophy.
    Zeyu Li, Ou Hu, Suowen Xu, Chenjia Lin, Wenjing Yu, Dinghu Ma, Jing Lu, Peiqing Liu.
      Mitochondria are energy-producing organelles that are mobile and harbor dynamic network structures. Although mitochondria and endoplasmic reticulum (ER) play distinct cellular roles, they are physically connected to maintain functional homeostasis. Abnormal changes in this interaction have been linked to pathological states, including cardiac hypertrophy. However, the exact regulatory molecules and mechanisms are yet to be elucidated. Here, we report that ATPase family AAA-domain containing protein 3A (ATAD3A) is an essential regulator of ER-mitochondria interplay within the mitochondria-associated membrane (MAM). ATAD3A prevents isoproterenol (ISO)-induced mitochondrial calcium accumulation, improving mitochondrial dysfunction and ER stress, which preserves cardiac function and attenuates cardiac hypertrophy. We also find that ATAD3A is a new substrate of NAD+-dependent deacetylase Sirtuin 3 (SIRT3). Notably, the heart mitochondria of SIRT3 knockout mice exhibited excessive formation of MAMs. Mechanistically, ATAD3A specifically undergoes acetylation, which reduces self-oligomerization and promotes cardiac hypertrophy. ATAD3A oligomerization is disrupted by acetylation at K134 site, and ATAD3A monomer closely interacts with the IP3R1-GRP75-VDAC1 complex, which leads to mitochondrial calcium overload and dysfunction. In summary, ATAD3A localizes to the MAMs, where it protects the homeostasis of ER-mitochondria contacts, quenching mitochondrial calcium overload and keeping mitochondrial bioenergetics unresponsive to ER stress. The SIRT3-ATAD3A axis represents a potential therapeutic target for cardiac hypertrophy.
    Keywords:  Cardiac hypertrophy; ER stress; IP3R1-GRP75-VDAC1 complex; Mitochondria; Mitochondria-associated membranes; acetylation
    DOI:  https://doi.org/10.7150/ijbs.89253
  11. Int J Mol Sci. 2024 Jan 18. pii: 1175. [Epub ahead of print]25(2):
    The Research Progress of Mitochondrial Transplantation in the Treatment of Mitochondrial Defective Diseases.
    Cuilan Hu, Zheng Shi, Xiongxiong Liu, Chao Sun.
      Mitochondria are double-membrane organelles that are involved in energy production, apoptosis, and signaling in eukaryotic cells. Several studies conducted over the past decades have correlated mitochondrial dysfunction with various diseases, including cerebral ischemia, myocardial ischemia-reperfusion, and cancer. Mitochondrial transplantation entails importing intact mitochondria from healthy tissues into diseased tissues with damaged mitochondria to rescue the injured cells. In this review, the different mitochondrial transplantation techniques and their clinical applications have been discussed. In addition, the challenges and future directions pertaining to mitochondrial transplantation and its potential in the treatment of diseases with defective mitochondria have been summarized.
    Keywords:  cancer; cerebral ischemia; mitochondrial defective diseases; mitochondrial transplantation; myocardial ischemia-reperfusion
    DOI:  https://doi.org/10.3390/ijms25021175
  12. STAR Protoc. 2024 Jan 18. pii: S2666-1667(24)00007-8. [Epub ahead of print]5(1): 102842
    Protocol for measuring mitochondrial size in mouse and human liver tissues.
    Balamurugan Ramatchandirin, Miho Iijima, Arisa Ikeda, Alexia Pearah, Sally Radovick, Fredric E Wondisford, Hiromi Sesaki, Ling He.
      Mitochondrial dynamic process is important for cell viability, metabolic activity, and mitochondria health. Here, we present a protocol for measuring mitochondrial size through immunofluorescence staining, confocal imaging, and analysis in ImageJ. We describe the steps for tissue processing, antigen retrieval, mitochondrial staining using an integrating immunofluorescence assay, and computerized image analysis to measure each mitochondrial size in mouse and human liver tissues. This protocol reduces tissue sample volume and processing time for the preparation of primary cells. For complete details on the use and execution of this protocol, please refer to Pearah et al.1.
    Keywords:  Cell Biology; Health Sciences; Metabolism
    DOI:  https://doi.org/10.1016/j.xpro.2024.102842
  13. Am J Ophthalmol. 2024 Jan 24. pii: S0002-9394(24)00014-X. [Epub ahead of print]
    AFG3L2 and ACO2-linked Dominant Optic Atrophy: genotype-phenotype characterization compared to OPA1 patients.
    Giulia Amore, Martina Romagnoli, Michele Carbonelli, Maria Lucia Cascavilla, Anna Maria De Negri, Arturo Carta, Vincenzo Parisi, Antonio Di Renzo, Costantino Schiavi, Chiara Lenzetti, Corrado Zenesini, Danara Ormanbekova, Flavia Palombo, Claudio Fiorini, Leonardo Caporali, Valerio Carelli, Piero Barboni, Chiara La Morgia.
      PURPOSE: Heterozygous mutations in AFG3L2 gene (encoding a mitochondrial protease indirectly reflecting on OPA1 cleavage) and ACO2 gene (encoding the mitochondrial enzyme aconitase) are associated to isolated forms of Dominant Optic Atrophy (DOA). We aimed at describing their neuro-ophthalmological phenotype as compared with classic OPA1-related DOA.DESIGN: Cross-sectional study.
    METHODS: The following neuro-ophthalmological parameters were collected: Log MAR visual acuity (VA), color vision, mean deviation and foveal threshold at visual fields, average and sectorial retinal nerve fiber layer (RNFL) and ganglion cell layer (GCL) thickness at optic coherence tomography. ACO2 and AFG3L2 patients were compared with an age- and gender-matched group of OPA1 patients with 1:2 ratio. All eyes were analysed using Clustered Wilcoxon rank sum test using Rosner-Glynn-Lee method.
    RESULTS: 44 eyes from 23 ACO2 and 26 eyes from 13 AFG3L2 patients were compared with 143 eyes from 72 OPA1 patients. All cases presented with bilateral temporal-predominant optic atrophy with various degree of visual impairment. Comparison between AFG3L2 and OPA1 failed to reveal any significant difference. ACO2 patients compared to both AFG3L2 and OPA1 presented overall higher values of nasal RNFL thickness (p=0.029, p=0.023), average (p=0.012, p=0.0007) and sectorial GCL thickness. These results were confirmed also comparing separately affected and subclinical patients.
    CONCLUSIONS: Clinically, DOA remains a fairly homogeneous entity despite the growing genetic heterogeneity. ACO2 seems associated to an overall better preservation of retinal ganglion cells, probably depending on the different pathogenic mechanism involving mtDNA maintenance, as opposed to AFG3L2, which is involved in OPA1 processing and resulted virtually indistinguishable from classic OPA1-DOA.
    Keywords:  Clinical Genetics; Dominant Optic Atrophy; Genotype-phenotype; Mitochondrial Optic Neuropathies; Neuro-ophthalmology; Optic Coherence Tomography
    DOI:  https://doi.org/10.1016/j.ajo.2024.01.011
  14. Life Sci Alliance. 2024 Apr;pii: e202302177. [Epub ahead of print]7(4):
    Drosophila MIC10b can polymerize into cristae-shaping filaments.
    Till Stephan, Stefan Stoldt, Mariam Barbot, Travis D Carney, Felix Lange, Mark Bates, Peter Bou Dib, Kaushik Inamdar, Halyna R Shcherbata, Michael Meinecke, Dietmar Riedel, Sven Dennerlein, Peter Rehling, Stefan Jakobs.
      Cristae are invaginations of the mitochondrial inner membrane that are crucial for cellular energy metabolism. The formation of cristae requires the presence of a protein complex known as MICOS, which is conserved across eukaryotic species. One of the subunits of this complex, MIC10, is a transmembrane protein that supports cristae formation by oligomerization. In Drosophila melanogaster, three MIC10-like proteins with different tissue-specific expression patterns exist. We demonstrate that CG41128/MINOS1b/DmMIC10b is the major MIC10 orthologue in flies. Its loss destabilizes MICOS, disturbs cristae architecture, and reduces the life span and fertility of flies. We show that DmMIC10b has a unique ability to polymerize into bundles of filaments, which can remodel mitochondrial crista membranes. The formation of these filaments relies on conserved glycine and cysteine residues, and can be suppressed by the co-expression of other Drosophila MICOS proteins. These findings provide new insights into the regulation of MICOS in flies, and suggest potential mechanisms for the maintenance of mitochondrial ultrastructure.
    DOI:  https://doi.org/10.26508/lsa.202302177
  15. J Cell Biol. 2024 Mar 04. pii: e202305087. [Epub ahead of print]223(3):
    CLPB disaggregase dysfunction impacts the functional integrity of the proteolytic SPY complex.
    Megan J Baker, Kai Uwe Blau, Alexander J Anderson, Catherine S Palmer, Laura F Fielden, Jordan J Crameri, Dusanka Milenkovic, David R Thorburn, Ann E Frazier, Thomas Langer, Diana Stojanovski.
      CLPB is a mitochondrial intermembrane space AAA+ domain-containing disaggregase. CLPB mutations are associated with 3-methylglutaconic aciduria and neutropenia; however, the molecular mechanism underscoring disease and the contribution of CLPB substrates to disease pathology remains unknown. Interactions between CLPB and mitochondrial quality control (QC) factors, including PARL and OPA1, have been reported, hinting at dysregulation of organelle QC in disease. Utilizing proteomic and biochemical approaches, we show a stress-specific aggregation phenotype in a CLPB-null environment and define the CLPB substrate profile. We illustrate an interplay between intermembrane space proteins including CLPB, HAX1, HTRA2, and the inner membrane quality control proteins (STOML2, PARL, YME1L1; SPY complex), with CLPB deficiency impeding SPY complex function by virtue of protein aggregation in the intermembrane space. We conclude that there is an interdependency of mitochondrial QC components at the intermembrane space/inner membrane interface, and perturbations to this network may underscore CLPB disease pathology.
    DOI:  https://doi.org/10.1083/jcb.202305087
  16. Stem Cell Rev Rep. 2024 Jan 24.
    Mitochondria in Mesenchymal Stem Cells: Key to Fate Determination and Therapeutic Potential.
    Yang Liu, Lingjuan Wang, Jihui Ai, Kezhen Li.
      Mesenchymal stem cells (MSCs) have become popular tool cells in the field of transformation and regenerative medicine due to their function of cell rescue and cell replacement. The dynamically changing mitochondria serve as an energy metabolism factory and signal transduction platform, adapting to different cell states and maintaining normal cell activities. Therefore, a clear understanding of the regulatory mechanism of mitochondria in MSCs is profit for more efficient clinical transformation of stem cells. This review highlights the cutting-edge knowledge regarding mitochondrial biology from the following aspects: mitochondrial morphological dynamics, energy metabolism and signal transduction. The manuscript mainly focuses on mitochondrial mechanistic insights in the whole life course of MSCs, as well as the potential roles played by mitochondria in MSCs treatment of transplantation, for seeking pivotal targets of stem cell fate regulation and stem cell therapy.
    Keywords:  Mesenchymal stem cells; Mitochondria; Mitochondrial morphology; Mitochondrial transfer; Regenerative therapy; Signal transduction
    DOI:  https://doi.org/10.1007/s12015-024-10681-y
  17. Front Physiol. 2023 ;14 1279548
    Mitochondrial-related microRNAs and their roles in cellular senescence.
    Ling Luo, Xingna An, Yinghui Xiao, Xiguang Sun, Sijie Li, Yingzhao Wang, Weixia Sun, Dehai Yu.
      Aging is a natural aspect of mammalian life. Although cellular mortality is inevitable, various diseases can hasten the aging process, resulting in abnormal or premature senescence. As cells age, they experience distinctive morphological and biochemical shifts, compromising their functions. Research has illuminated that cellular senescence coincides with significant alterations in the microRNA (miRNA) expression profile. Notably, a subset of aging-associated miRNAs, originally encoded by nuclear DNA, relocate to mitochondria, manifesting a mitochondria-specific presence. Additionally, mitochondria themselves house miRNAs encoded by mitochondrial DNA (mtDNA). These mitochondria-residing miRNAs, collectively referred to as mitochondrial miRNAs (mitomiRs), have been shown to influence mtDNA transcription and protein synthesis, thereby impacting mitochondrial functionality and cellular behavior. Recent studies suggest that mitomiRs serve as critical sensors for cellular senescence, exerting control over mitochondrial homeostasis and influencing metabolic reprogramming, redox equilibrium, apoptosis, mitophagy, and calcium homeostasis-all processes intimately connected to senescence. This review synthesizes current findings on mitomiRs, their mitochondrial targets, and functions, while also exploring their involvement in cellular aging. Our goal is to shed light on the potential molecular mechanisms by which mitomiRs contribute to the aging process.
    Keywords:  cellular senescence; epigenetics; mitochondria; mitomiRs; noncoding RNA
    DOI:  https://doi.org/10.3389/fphys.2023.1279548
  18. Eur J Neurol. 2024 Jan 21. e16216
    A diagnostic framework to identify vestibular involvement in multi-sensory neurological disease.
    Amanda J Male, Sarah L Holmes, Nehzat Koohi, Magdalena Dudziec, Michael G Hanna, Gita M Ramdharry, Chiara Pizzamiglio, Robert D S Pitceathly, Diego Kaski.
      BACKGROUND AND PURPOSE: Identifying vestibular causes of dizziness and unsteadiness in multi-sensory neurological disease can be challenging, with problems typically attributed to central or peripheral nerve involvement. Acknowledging vestibular dysfunction as part of the presentation provides an opportunity to access targeted vestibular rehabilitation, for which extensive evidence exists. A diagnostic framework was developed and validated to detect vestibular dysfunction, benign paroxysmal positional vertigo or vestibular migraine. The specificity and sensitivity of the diagnostic framework was tested in patients with primary mitochondrial disease.METHODS: Adults with a confirmed diagnosis of primary mitochondrial disease were consented, between September 2020 and February 2022. Participants with and without dizziness or unsteadiness underwent remote physiotherapy assessment and had in-person detailed neuro-otological assessment. The six framework question responses were compared against objective neuro-otological assessment or medical notes. The output was binary, with sensitivity and specificity calculated.
    RESULTS: Seventy-four adults completed the study: age range 20-81 years (mean 48 years, ±SD 15.05 years); ratio 2:1 female to male. The framework identified a vestibular diagnosis in 35 participants, with seven having two diagnoses. The framework was able to identify vestibular diagnoses in adults with primary mitochondrial disease, with a moderate (40-59) to very high (90-100) sensitivity and positive predictive value, and moderate to high (60-74) to very high (90-100) specificity and negative predictive value.
    CONCLUSIONS: Overall, the clinical framework identified common vestibular diagnoses with a moderate to very high specificity and sensitivity. This presents an opportunity for patients to access effective treatment in a timely manner, to reduce falls and improve quality of life.
    Keywords:  diagnosis; dizziness; neurotology; vertigo
    DOI:  https://doi.org/10.1111/ene.16216
  19. Front Psychiatry. 2023 ;14 1301272
    Multilevel evidence of MECP2-associated mitochondrial dysfunction and its therapeutic implications.
    Peter Balicza, Andras Gezsi, Mariann Fedor, Judit C Sagi, Aniko Gal, Noemi Agnes Varga, Maria Judit Molnar.
      We present a male patient carrying a pathogenic MECP2 p. Arg179Trp variant with predominant negative psychiatric features and multilevel evidence of mitochondrial dysfunction who responded to the cariprazine treatment. He had delayed speech development and later experienced severe social anxiety, learning disabilities, cognitive slowing, and predominant negative psychiatric symptoms associated with rigidity. Clinical examinations showed multisystemic involvement. Together with elevated ergometric lactate levels, the clinical picture suggested mitochondrial disease, which was also supported by muscle histopathology. Exploratory transcriptome analysis also revealed the involvement of metabolic and oxidative phosphorylation pathways. Whole-exome sequencing identified a pathogenic MECP2 variant, which can explain both the dopamine imbalance and mitochondrial dysfunction in this patient. Mitochondrial dysfunction was previously suggested in classical Rett syndrome, and we detected related phenotype evidence on multiple consistent levels for the first time in a MECP2 variant carrier male. This study further supports the importance of the MECP2 gene in the mitochondrial pathways, which can open the gate for more personalized therapeutic interventions. Good cariprazine response highlights the role of dopamine dysfunction in the complex psychiatric symptoms of Rett syndrome. This can help identify the optimal treatment strategy from a transdiagnostic perspective instead of a classical diagnostic category.
    Keywords:  MECP2 mutation; RNA sequencing; Rett syndrome; anxiety; cariprazine; learning disability; mitochondrial dysfunction; negative symptoms
    DOI:  https://doi.org/10.3389/fpsyt.2023.1301272
  20. J Neurochem. 2024 Jan 26.
    Acetylated tau exacerbates apoptosis by disturbing mitochondrial dynamics in HEK293 cells.
    Jun-Fei Zhang, Zhi-Ting Fang, Jun-Ning Zhao, Gong-Ping Liu, Xin Shen, Gao-Feng Jiang, Qian Liu.
      An increase in tau acetylation at K274 and K281 and abnormal mitochondrial dynamics have been observed in the brains of Alzheimer's disease (AD) patients. Here, we constructed three types of tau plasmids, TauKQ (acetylated tau mutant, by mutating its K274/K281 into glutamine to mimic disease-associated lysine acetylation), TauKR (non-acetylated tau mutant, by mutating its K274/K281 into arginine), and TauWT (wild-type human full-length tau). By transfecting these tau plasmids in HEK293 cells, we found that TauWT and TauKR induced mitochondrial fusion by increasing the level of mitochondrial fusion proteins. Conversely, TauKQ induced mitochondrial fission by reducing mitochondrial fusion proteins, exacerbating mitochondrial dysfunction and apoptosis. BGP-15 ameliorated TauKQ-induced mitochondrial dysfunction and apoptosis by improving mitochondrial dynamics. Our findings suggest that acetylation of K274/281 represents an important post-translational modification site regulating mitochondrial dynamics, and that BGP-15 holds potential as a therapeutic agent for mitochondria-associated diseases such as AD.
    Keywords:  Alzheimer's disease; acetylation; apoptosis; mitochondrial dynamics; tau
    DOI:  https://doi.org/10.1111/jnc.16053
  21. Bioengineering (Basel). 2024 Jan 03. pii: 52. [Epub ahead of print]11(1):
    Hereditary Optic Neuropathies: A Systematic Review on the Interplay between Biomaterials and Induced Pluripotent Stem Cells.
    Miguel Ladero, Jose Alberto Reche-Sainz, M Esther Gallardo.
      Hereditary optic neuropathies (HONs) such as dominant optic atrophy (DOA) and Leber Hereditary Optic Neuropathy (LHON) are mitochondrial diseases characterized by a degenerative loss of retinal ganglion cells (RGCs) and are a cause of blindness worldwide. To date, there are only limited disease-modifying treatments for these disorders. The discovery of induced pluripotent stem cell (iPSC) technology has opened several promising opportunities in the field of HON research and the search for therapeutic approaches. This systematic review is focused on the two most frequent HONs (LHON and DOA) and on the recent studies related to the application of human iPSC technology in combination with biomaterials technology for their potential use in the development of RGC replacement therapies with the final aim of the improvement or even the restoration of the vision of HON patients. To this purpose, the combination of natural and synthetic biomaterials modified with peptides, neurotrophic factors, and other low- to medium-molecular weight compounds, mimicking the ocular extracellular matrices, with human iPSC or iPSC-derived cell retinal progenitors holds enormous potential to be exploited in the near future for the generation of transplantable RGC populations.
    Keywords:  DOA; LHON; RGCs; biomaterial; decellularized extracellular matrix; differentiation; hydrogel; iPSCs; optic neuropathies; synthetic polymer; transplantation
    DOI:  https://doi.org/10.3390/bioengineering11010052
  22. Front Cell Dev Biol. 2023 ;11 1356278
    Editorial: Mitochondria at the nexus of metabolism, aging, and disease.
    Karthik Babu Mallilankaraman, Brian K Kennedy, Vincenzo Sorrentino, Alessandro Luciani.
      
    Keywords:  ageing; dietary intervention; drug discovery; metabolic disease; metabolic signaling; metabolism; mitochondrial dysfuncion; mitophagy
    DOI:  https://doi.org/10.3389/fcell.2023.1356278
  23. Int J Mol Sci. 2024 Jan 09. pii: 834. [Epub ahead of print]25(2):
    From Beach to the Bedside: Harnessing Mitochondrial Function in Human Diseases Using New Marine-Derived Strategies.
    Serena Mirra, Gemma Marfany.
      Mitochondria are double-membrane organelles within eukaryotic cells that act as cellular power houses owing to their ability to efficiently generate the ATP required to sustain normal cell function. Also, they represent a "hub" for the regulation of a plethora of processes, including cellular homeostasis, metabolism, the defense against oxidative stress, and cell death. Mitochondrial dysfunctions are associated with a wide range of human diseases with complex pathologies, including metabolic diseases, neurodegenerative disorders, and cancer. Therefore, regulating dysfunctional mitochondria represents a pivotal therapeutic opportunity in biomedicine. Marine ecosystems are biologically very diversified and harbor a broad range of organisms, providing both novel bioactive substances and molecules with meaningful biomedical and pharmacological applications. Recently, many mitochondria-targeting marine-derived molecules have been described to regulate mitochondrial biology, thus exerting therapeutic effects by inhibiting mitochondrial abnormalities, both in vitro and in vivo, through different mechanisms of action. Here, we review different strategies that are derived from marine organisms which modulate specific mitochondrial processes or mitochondrial molecular pathways and ultimately aim to find key molecules to treat a wide range of human diseases characterized by impaired mitochondrial function.
    Keywords:  disease; marine natural products; marine organisms; mitochondria; therapy
    DOI:  https://doi.org/10.3390/ijms25020834
  24. Neuron. 2024 Jan 17. pii: S0896-6273(23)00978-9. [Epub ahead of print]
    Direct neuronal reprogramming of NDUFS4 patient cells identifies the unfolded protein response as a novel general reprogramming hurdle.
    Giovanna Sonsalla, Ana Belen Malpartida, Therese Riedemann, Mirjana Gusic, Ejona Rusha, Giorgia Bulli, Sonia Najas, Aleks Janjic, Bob A Hersbach, Pawel Smialowski, Micha Drukker, Wolfgang Enard, Jochen H M Prehn, Holger Prokisch, Magdalena Götz, Giacomo Masserdotti.
      Mitochondria account for essential cellular pathways, from ATP production to nucleotide metabolism, and their deficits lead to neurological disorders and contribute to the onset of age-related diseases. Direct neuronal reprogramming aims at replacing neurons lost in such conditions, but very little is known about the impact of mitochondrial dysfunction on the direct reprogramming of human cells. Here, we explore the effects of mitochondrial dysfunction on the neuronal reprogramming of induced pluripotent stem cell (iPSC)-derived astrocytes carrying mutations in the NDUFS4 gene, important for Complex I and associated with Leigh syndrome. This led to the identification of the unfolded protein response as a major hurdle in the direct neuronal conversion of not only astrocytes and fibroblasts from patients but also control human astrocytes and fibroblasts. Its transient inhibition potently improves reprogramming by influencing the mitochondria-endoplasmic-reticulum-stress-mediated pathways. Taken together, disease modeling using patient cells unraveled novel general hurdles and ways to overcome these in human astrocyte-to-neuron reprogramming.
    Keywords:  Leigh syndrome; astrocytes; direct neuronal reprogramming; mitochondria; unfolded protein response
    DOI:  https://doi.org/10.1016/j.neuron.2023.12.020
  25. Genet Med. 2024 Jan 18. pii: S1098-3600(24)00008-X. [Epub ahead of print] 101075
    Diagnostic utility and reporting recommendations for clinical DNA methylation episignature testing in genetically undiagnosed rare diseases.
    Jennifer Kerkhof, Cassandra Rastin, Michael A Levy, Raissa Relator, Haley McConkey, Leigh Demain, Elena Dominguez-Garrido, Laura Donker Kaat, Sofia Douzgou Houge, Barbara R DuPont, Timothy Fee, Robin S Fletcher, David Gokhale, Bjørn Ivar Haukanes, Peter Henneman, Sarah Hilton, Benjamin A Hilton, Sarah Jenkinson, Jennifer A Lee, Raymond J Louie, M Mahdi Motazacker, Jessica Rzasa, Roger E Stevenson, Astrid Plomp, Liselot van der Laan, Jasper van der Smagt, Kellie K Walden, Siddharth Banka, Marcel Mannens, Steven A Skinner, Michael J Friez, Christopher Campbell, Matthew L Tedder, Marielle Alders, Bekim Sadikovic.
      PURPOSE: This study aims to assess the diagnostic utility and provide reporting recommendations for clinical DNA methylation episignature testing based on the cohort of patients tested through the EpiSignTM Clinical Testing Network (ECTN).METHODS: The EpiSignTM assay utilized unsupervised clustering techniques and a support vector machine-based classification algorithm to compare each patient's genome-wide DNA methylation profile with the EpiSignTM Knowledge Database, yielding the result which was reported. An international working group, representing distinct ECTN health jurisdictions, collaborated to establish recommendations for interpretation and reporting of episignature testing.
    RESULTS: Among 2399 cases analyzed, 1667 cases underwent a comprehensive screen of validated episignatures, imprinting, and promoter regions, resulting in 18.7% (312/1667) positive reports. The remaining 732 referrals underwent targeted episignature analysis for assessment of sequence or copy number variants of uncertain significance, or for assessment of clinical diagnoses without confirmed molecular findings and 32.4% (237/732) were positive. Cases with detailed clinical information were highlighted to describe various utility scenarios for episignature testing.
    CONCLUSION: Clinical DNA methylation testing including episignatures, imprinting and promoter analysis provided by an integrated network of clinical laboratories enables test standardization and demonstrates significant diagnostic yield and clinical utility beyond DNA sequence analysis in rare diseases.
    Keywords:  DNA methylation; DNA methylation interpretation; DNA methylation test standardization; EpiSign; Epigenetics; Neurodevelopmental disorders; VUS classification; episignature; molecular diagnostics; rare disease diagnostics
    DOI:  https://doi.org/10.1016/j.gim.2024.101075
  26. EMBO J. 2024 Jan 24.
    Shared structural features of Miro binding control mitochondrial homeostasis.
    Christian Covill-Cooke, Brian Kwizera, Guillermo López-Doménech, Caleb Od Thompson, Ngaam J Cheung, Ema Cerezo, Martin Peterka, Josef T Kittler, Benoît Kornmann.
      Miro proteins are universally conserved mitochondrial calcium-binding GTPases that regulate a multitude of mitochondrial processes, including transport, clearance, and lipid trafficking. The exact role of Miro in these functions is unclear but involves binding to a variety of client proteins. How this binding is operated at the molecular level and whether and how it is important for mitochondrial health, however, remains unknown. Here, we show that known Miro interactors-namely, CENPF, Trak, and MYO19-all use a similar short motif to bind the same structural element: a highly conserved hydrophobic pocket in the first calcium-binding domain of Miro. Using these Miro-binding motifs, we identified direct interactors de novo, including MTFR1/2/1L, the lipid transporters Mdm34 and VPS13D, and the ubiquitin E3-ligase Parkin. Given the shared binding mechanism of these functionally diverse clients and its conservation across eukaryotes, we propose that Miro is a universal mitochondrial adaptor coordinating mitochondrial health.
    Keywords:  AlphaFold; ERMES; Lipid Transport; Mitophagy; Organelle Transport
    DOI:  https://doi.org/10.1038/s44318-024-00028-1
  27. Cell Death Discov. 2024 Jan 26. 10(1): 54
    Caspase-dependent apoptosis in Ribloflavin transporter deficiency iPSCs and derived motor neurons.
    Chiara Marioli, Maurizio Muzzi, Fiorella Colasuonno, Cristian Fiorucci, Nicolò Cicolani, Stefania Petrini, Enrico Bertini, Marco Tartaglia, Claudia Compagnucci, Sandra Moreno.
      Riboflavin Transporter Deficiency (RTD) is a rare genetic, childhood-onset disease. This pathology has a relevant neurological involvement, being characterized by motor symptoms, ponto-bulbar paralysis and sensorineural deafness. Such clinical presentation is associated with muscle weakness and motor neuron (MN) degeneration, so that RTD is considered part of the MN disease spectrum. Based on previous findings demonstrating energy dysmetabolism and mitochondrial impairment in RTD induced Pluripotent Stem cells (iPSCs) and iPSC-derived MNs, here we address the involvement of intrinsic apoptotic pathways in disease pathogenesis using these patient-specific in vitro models by combined ultrastructural and confocal analyses. We show impaired neuronal survival of RTD iPSCs and MNs. Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) documents severe alterations in patients' cells, including deranged mitochondrial ultrastructure, and altered plasma membrane and nuclear organization. Occurrence of aberrantly activated apoptosis is confirmed by immunofluorescence and TUNEL assays. Overall, our work provides evidence of a role played by mitochondrial dysfunction in RTD, and identifies neuronal apoptosis as a contributing event in disease pathogenesis, indicating intrinsic apoptosis pathways as possible relevant targets for more effective therapeutical approaches.
    DOI:  https://doi.org/10.1038/s41420-024-01812-y
  28. Brief Bioinform. 2024 Jan 22. pii: bbad508. [Epub ahead of print]25(2):
    Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges.
    Yury A Barbitoff, Mikhail O Ushakov, Tatyana E Lazareva, Yulia A Nasykhova, Andrey S Glotov, Alexander V Predeus.
      Next-generation sequencing (NGS) has revolutionized the field of rare disease diagnostics. Whole exome and whole genome sequencing are now routinely used for diagnostic purposes; however, the overall diagnosis rate remains lower than expected. In this work, we review current approaches used for calling and interpretation of germline genetic variants in the human genome, and discuss the most important challenges that persist in the bioinformatic analysis of NGS data in medical genetics. We describe and attempt to quantitatively assess the remaining problems, such as the quality of the reference genome sequence, reproducible coverage biases, or variant calling accuracy in complex regions of the genome. We also discuss the prospects of switching to the complete human genome assembly or the human pan-genome and important caveats associated with such a switch. We touch on arguably the hardest problem of NGS data analysis for medical genomics, namely, the annotation of genetic variants and their subsequent interpretation. We highlight the most challenging aspects of annotation and prioritization of both coding and non-coding variants. Finally, we demonstrate the persistent prevalence of pathogenic variants in the coding genome, and outline research directions that may enhance the efficiency of NGS-based disease diagnostics.
    Keywords:  NGS; WES; reference genome; variant annotation; variant calling
    DOI:  https://doi.org/10.1093/bib/bbad508
  29. Genes (Basel). 2024 Jan 22. pii: 136. [Epub ahead of print]15(1):
    Lessons Learned from Translating Genome Sequencing to Clinical Routine: Understanding the Accuracy of a Diagnostic Pipeline.
    Joohyun Park, Marc Sturm, Olga Seibel-Kelemen, Stephan Ossowski, Tobias B Haack.
      The potential of genome sequencing (GS), which allows detection of almost all types of genetic variation across nearly the entire genome of an individual, greatly expands the possibility for diagnosing genetic disorders. The opportunities provided with this single test are enticing to researchers and clinicians worldwide for human genetic research as well as clinical application. Multiple studies have highlighted the advantages of GS for genetic variant discovery, emphasizing its added value for routine clinical use. We have implemented GS as first-line genetic testing for patients with rare diseases. Here, we report on our experiences in establishing GS as a reliable diagnostic method for almost all types of genetic disorders, from validating diagnostic accuracy of sequencing pipelines to clinical implementation in routine practice.
    Keywords:  genetic diagnostics; genome sequencing; molecular diagnostics
    DOI:  https://doi.org/10.3390/genes15010136
  30. Neurotherapeutics. 2024 Jan 19. pii: S1878-7479(24)00009-6. [Epub ahead of print]21(1): e00323
    Applications of near-infrared spectroscopy in epilepsy, with a focus on mitochondrial disorders.
    Kosar Khaksari, Wei-Liang Chen, Mongkol Chanvanichtrakool, Alexa Taylor, Rohan Kotla, Andrea L Gropman.
      Mitochondrial diseases are inherited disorders that impede the mitochondria's ability to produce sufficient energy for the cells. They can affect different parts of the body, notably the brain. Neurological symptoms and epilepsy are prevalent in patients with mitochondrial disorders. The epileptogenicity of mitochondrial disorder is a complex process involving the intricate interplay between abnormal energy metabolism and neuronal activity. Several modalities have been used to detect seizures in different disorders including mitochondrial disorders. EEG serve as the gold standard for diagnosis and localization, commonly complemented by additional imaging modalities to enhance source localization. In the current work, we propose the use of functional near-infrared spectroscopy (fNIRS) to identify the occurrence of epilepsy and seizure in patients with mitochondrial disorders. fNIRS proves an advantageous imaging technique due to its portability and insensitivity to motion especially for imaging infants and children. It has added a valuable factor to our understanding of energy metabolism and neuronal activity. Its real-time monitoring with high spatial resolution supplements traditional diagnostic tools such as EEG and provides a comprehensive understanding of seizure and epileptogenesis. The utility of fNIRS extends to its ability to detect changes in Cytochrome c oxidase (CcO) which is a crucial enzyme in cellular respiration. This facet enhances our insight into the metabolic dimension of epilepsy related to mitochondrial dysfunction. By providing valuable insights into both energy metabolism and neuronal activity, fNIRS emerges as a promising imaging technique for unveiling the complexities of mitochondrial disorders and their neurological manifestations.
    Keywords:  Brain biomarkers; Epilepsy; Mitochondrial disease; Near-infrared spectroscopy; Neuromonitoring; Seizure
    DOI:  https://doi.org/10.1016/j.neurot.2024.e00323
  31. Ann Clin Transl Neurol. 2024 Jan 23.
    Neurological outcome in long-chain hydroxy fatty acid oxidation disorders.
    Ulrike Mütze, Alina Ottenberger, Florian Gleich, Esther M Maier, Martin Lindner, Ralf A Husain, Katja Palm, Skadi Beblo, Peter Freisinger, René Santer, Eva Thimm, Stephan Vom Dahl, Natalie Weinhold, Karina Grohmann-Held, Claudia Haase, Julia B Hennermann, Alexandra Hörbe-Blindt, Clemens Kamrath, Iris Marquardt, Thorsten Marquardt, Robert Behne, Dorothea Haas, Ute Spiekerkoetter, Georg F Hoffmann, Sven F Garbade, Sarah C Grünert, Stefan Kölker.
      OBJECTIVE: This study aims to elucidate the long-term benefit of newborn screening (NBS) for individuals with long-chain 3-hydroxy-acyl-CoA dehydrogenase (LCHAD) and mitochondrial trifunctional protein (MTP) deficiency, inherited metabolic diseases included in NBS programs worldwide.METHODS: German national multicenter study of individuals with confirmed LCHAD/MTP deficiency identified by NBS between 1999 and 2020 or selective metabolic screening. Analyses focused on NBS results, confirmatory diagnostics, and long-term clinical outcomes.
    RESULTS: Sixty-seven individuals with LCHAD/MTP deficiency were included in the study, thereof 54 identified by NBS. All screened individuals with LCHAD deficiency survived, but four with MTP deficiency (14.8%) died during the study period. Despite NBS and early treatment neonatal decompensations (28%), symptomatic disease course (94%), later metabolic decompensations (80%), cardiomyopathy (28%), myopathy (82%), hepatopathy (32%), retinopathy (17%), and/or neuropathy (22%) occurred. Hospitalization rates were high (up to a mean of 2.4 times/year). Disease courses in screened individuals with LCHAD and MTP deficiency were similar except for neuropathy, occurring earlier in individuals with MTP deficiency (median 3.9 vs. 11.4 years; p = 0.0447). Achievement of dietary goals decreased with age, from 75% in the first year of life to 12% at age 10, and consensus group recommendations on dietary management were often not achieved.
    INTERPRETATION: While NBS and early treatment result in improved (neonatal) survival, they cannot reliably prevent long-term morbidity in screened individuals with LCHAD/MTP deficiency, highlighting the urgent need of better therapeutic strategies and the development of disease course-altering treatment.
    DOI:  https://doi.org/10.1002/acn3.52002
  32. Free Radic Biol Med. 2024 Jan 22. pii: S0891-5849(24)00042-X. [Epub ahead of print]
    Cardiomyocyte maturation alters molecular stress response capacities and determines cell survival upon mitochondrial dysfunction.
    Nina Schraps, Michaela Tirre, Simon Pyschny, Anna Reis, Hannah Schlierbach, Matthias Seidl, Hans-Gerd Kehl, Anne Schänzer, Jacqueline Heger, Christian Jux, Jörg-Detlef Drenckhahn.
      Cardiomyocyte maturation during pre- and postnatal development requires multiple intertwined processes, including a switch in energy generation from glucose utilization in the embryonic heart towards fatty acid oxidation after birth. This is accompanied by a boost in mitochondrial mass to increase capacities for oxidative phosphorylation and ATP generation required for efficient contraction. Whether cardiomyocyte differentiation is paralleled by augmented capacities to deal with reactive oxygen species (ROS), physiological byproducts of the mitochondrial electron transport chain (ETC), is less clear. Here we show that expression of genes and proteins involved in redox homeostasis and protein quality control within mitochondria increases after birth in the mouse and human heart. Using primary embryonic, neonatal and adult mouse cardiomyocytes in vitro we investigated how excessive ROS production induced by mitochondrial dysfunction affects cell survival and stress response at different stages of maturation. Embryonic and neonatal cardiomyocytes largely tolerate inhibition of ETC complex III by antimycin A (AMA) as well as ATP synthase (complex V) by oligomycin but are susceptible to complex I inhibition by rotenone. All three inhibitors alter the intracellular distribution and ultrastructure of mitochondria in neonatal cardiomyocytes. In contrast, adult cardiomyocytes treated with AMA undergo rapid morphological changes and cellular disintegration. At the molecular level embryonic cardiomyocytes activate antioxidative defense mechanisms, the integrated stress response (ISR) and ER stress but not the mitochondrial unfolded protein response upon complex III inhibition. In contrast, adult cardiomyocytes fail to activate the ISR and antioxidative proteins following AMA treatment. In conclusion, our results identified fundamental differences in cell survival and stress response in differentiated compared to immature cardiomyocytes subjected to mitochondrial dysfunction. The high stress tolerance of immature cardiomyocytes might allow outlasting unfavorable intrauterine conditions thereby preventing fetal or perinatal heart disease and may contribute to the regenerative capacity of the embryonic and neonatal mammalian heart.
    Keywords:  Cardiomyocyte differentiation; Cardiomyocyte survival; Cellular stress response; Mitochondrial dysfunction; Oxidative stress
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2024.01.034
  33. EMBO Rep. 2024 Jan 23.
    Mitochondrial translocation of TFEB regulates complex I and inflammation.
    Chiara Calabrese, Hendrik Nolte, Melissa R Pitman, Raja Ganesan, Philipp Lampe, Raymond Laboy, Roberto Ripa, Julia Fischer, Ruhi Polara, Sameer Kumar Panda, Sandhya Chipurupalli, Saray Gutierrez, Daniel Thomas, Stuart M Pitson, Adam Antebi, Nirmal Robinson.
      TFEB is a master regulator of autophagy, lysosome biogenesis, mitochondrial metabolism, and immunity that works primarily through transcription controlled by cytosol-to-nuclear translocation. Emerging data indicate additional regulatory interactions at the surface of organelles such as lysosomes. Here we show that TFEB has a non-transcriptional role in mitochondria, regulating the electron transport chain complex I to down-modulate inflammation. Proteomics analysis reveals extensive TFEB co-immunoprecipitation with several mitochondrial proteins, whose interactions are disrupted upon infection with S. Typhimurium. High resolution confocal microscopy and biochemistry confirms TFEB localization in the mitochondrial matrix. TFEB translocation depends on a conserved N-terminal TOMM20-binding motif and is enhanced by mTOR inhibition. Within the mitochondria, TFEB and protease LONP1 antagonistically co-regulate complex I, reactive oxygen species and the inflammatory response. Consequently, during infection, lack of TFEB specifically in the mitochondria exacerbates the expression of pro-inflammatory cytokines, contributing to innate immune pathogenesis.
    Keywords:  LONP1; Metabolism; Mitochondria; Salmonella; TFEB
    DOI:  https://doi.org/10.1038/s44319-024-00058-0
  34. Int J Biol Macromol. 2024 Jan 20. pii: S0141-8130(24)00410-0. [Epub ahead of print]260(Pt 2): 129607
    A comprehensive review on signaling attributes of serine and serine metabolism in health and disease.
    Di Wu, Kejia Zhang, Faheem Ahmed Khan, Nuruliarizki Shinta Pandupuspitasari, Kaifeng Guan, Fei Sun, Chunjie Huang.
      Serine is a metabolite with ever-expanding metabolic and non-metabolic signaling attributes. By providing one‑carbon units for macromolecule biosynthesis and functional modifications, serine and serine metabolism largely impinge on cellular survival and function. Cancer cells frequently have a preference for serine metabolic reprogramming to create a conducive metabolic state for survival and aggressiveness, making intervention of cancer-associated rewiring of serine metabolism a promising therapeutic strategy for cancer treatment. Beyond providing methyl donors for methylation in modulation of innate immunity, serine metabolism generates formyl donors for mitochondrial tRNA formylation which is required for mitochondrial function. Interestingly, fully developed neurons lack the machinery for serine biosynthesis and rely heavily on astrocytic l-serine for production of d-serine to shape synaptic plasticity. Here, we recapitulate recent discoveries that address the medical significance of serine and serine metabolism in malignancies, mitochondrial-associated disorders, and neurodegenerative pathologies. Metabolic control and epigenetic- and posttranslational regulation of serine metabolism are also discussed. Given the metabolic similarities between cancer cells, neurons and germ cells, we further propose the relevance of serine metabolism in testicular homeostasis. Our work provides valuable hints for future investigations that will lead to a deeper understanding of serine and serine metabolism in cellular physiology and pathology.
    Keywords:  Cancer therapeutics; Mitochondrial-associated disorders; Neurodegenerative pathologies; Serine; Serine metabolic reprogramming
    DOI:  https://doi.org/10.1016/j.ijbiomac.2024.129607
  35. Comp Biochem Physiol B Biochem Mol Biol. 2024 Jan 24. pii: S1096-4959(24)00014-9. [Epub ahead of print] 110947
    Mitochondrial techniques for physiologists.
    Soren Z Coulson, Brynne M Duffy, James F Staples.
      Mitochondria serve several important roles in maintaining cellular homeostasis, including adenosine triphosphate (ATP) synthesis, apoptotic signalling, and regulation of both reactive oxygen species (ROS) and calcium. Therefore, mitochondrial studies may reveal insights into metabolism at higher levels of physiological organization. The apparent complexity of mitochondrial function may be daunting to researchers new to mitochondrial physiology. This review is aimed, therefore, at such researchers to provide a brief, yet approachable overview of common techniques used to assess mitochondrial function. Here we discuss the use of high-resolution respirometry in mitochondrial experiments and common analytical platforms used for this technique. Next, we compare the use of common mitochondrial preparation techniques, including adherent cells, tissue homogenate, permeabilized fibers and isolated mitochondria. Finally, we outline additional techniques that can be used in tandem with high-resolution respirometry to assess additional aspects of mitochondrial metabolism, including ATP synthesis, calcium uptake, membrane potential and reactive oxygen species emission. We also include limitations to each of these techniques and outline recommendations for experimental design and interpretation. With a general understanding of methodologies commonly used to study mitochondrial physiology, experimenters may begin contributing to our understanding of this organelle, and how it affects other physiological phenotypes.
    Keywords:  Beginner; Bioenergetics; Methodology; Mitochondria; Physiology
    DOI:  https://doi.org/10.1016/j.cbpb.2024.110947
  36. Hum Genome Var. 2024 Jan 25. 11(1): 6
    Epigenetic regulation of the nuclear genome associated with mitochondrial dysfunction in Leber's hereditary optic neuropathy (LHON).
    Aswathy P Nair, Ambika Selvakumar, Janani Gopalarethinam, B Abishek Kumar, Balachandar Vellingiri, Mohana Devi Subramaniam.
      Leber's hereditary optic neuropathy (LHON) is a mitochondrial hereditary disease in which visual loss affects complex 1 activity of the electron transport chain of mitochondria. It first manifests as painless dulling or blurry in one or even both eyes, and as it develops, sharpness and color perception are lost. In addition to primary mitochondrial DNA (mtDNA) mutations, there are also other environmental and epigenetic factors involved in the pathogenesis of LHON. One of the most common locations for deadly pathogenic mutations in humans is the human complex I accessory NDUFS4 subunit gene. The iron-sulfur clusters of the electron input domain were distorted in the absence of NDUFS4, which reduced complex I function and elevated the production of reactive oxygen species. Therefore, here, we studied the epigenetic alterations of NDUFS4 by focusing on histone activation and repressive markers. We isolated peripheral blood mononuclear cells (PBMCs) from LHON patients and healthy individuals and examined epigenetic modifications in ND4 mutant cells and control cells. Chromatin immunoprecipitation-qRT PCR (ChIP-qRT PCR) assays were performed to investigate the modifications of histones. In comparison to their controls, both LHON patients and ND4 mutant cells exhibited a significant enrichment in activation and repressive markers. This finding indicates that these modifications might mitigate the impact of LHON mutations on complex 1 and aid in elucidating the mechanism underlying the progression of LHON disease.
    DOI:  https://doi.org/10.1038/s41439-023-00258-5
  37. EMBO Rep. 2024 Jan 23.
    ChemRAP uncovers specific mRNA translation regulation via RNA 5' phospho-methylation.
    Hélène Ipas, Ellen B Gouws, Nathan S Abell, Po-Chin Chiou, Sravan K Devanathan, Solène Hervé, Sidae Lee, Marvin Mercado, Calder Reinsborough, Levon Halabelian, Cheryl H Arrowsmith, Blerta Xhemalçe.
      5'-end modifications play key roles in determining RNA fates. Phospho-methylation is a noncanonical cap occurring on either 5'-PPP or 5'-P ends. We used ChemRAP, in which affinity purification of cellular proteins with chemically synthesized modified RNAs is coupled to quantitative proteomics, to identify 5'-Pme "readers". We show that 5'-Pme is directly recognized by EPRS, the central subunit of the multisynthetase complex (MSC), through its linker domain, which has previously been involved in key noncanonical EPRS and MSC functions. We further determine that the 5'-Pme writer BCDIN3D regulates the binding of EPRS to specific mRNAs, either at coding regions rich in MSC codons, or around start codons. In the case of LRPPRC (leucine-rich pentatricopeptide repeat containing), a nuclear-encoded mitochondrial protein associated with the French Canadian Leigh syndrome, BCDIN3D deficiency abolishes binding of EPRS around its mRNA start codon, increases its translation but ultimately results in LRPPRC mislocalization. Overall, our results suggest that BCDIN3D may regulate the translation of specific mRNA via RNA-5'-Pme.
    Keywords:  BCDIN3D; LRPPRC; Local Translation; RNA Modification Reader; RNA Phospho-methylation
    DOI:  https://doi.org/10.1038/s44319-024-00059-z
  38. Front Public Health. 2023 ;11 1330131
    A mito-centric view on muscle aging and function.
    Johannes Burtscher, Barbara Strasser, Martin Burtscher.
      
    Keywords:  aging; diet; exercise; hypoxia; mitochondria; physical function; sarcopenia
    DOI:  https://doi.org/10.3389/fpubh.2023.1330131
  39. bioRxiv. 2024 Jan 02. pii: 2024.01.02.573913. [Epub ahead of print]
    Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures.
    Seulki Kwon, Jordan Safer, Duyen T Nguyen, David Hoksza, Patrick May, Jeremy A Arbesfeld, Alan F Rubin, Arthur J Campbell, Alex Burgin, Sumaiya Iqbal.
      Recent advances in AI-based methods have revolutionized the field of structural biology. Concomitantly, high-throughput sequencing and functional genomics technologies have enabled the detection and generation of variants at an unprecedented scale. However, efficient tools and resources are needed to link these two disparate data types - to "map" variants onto protein structures, to better understand how the variation causes disease and thereby design therapeutics. Here we present the Genomics 2 Proteins Portal (G2P; g2p.broadinstitute.org/): a human proteome-wide resource that maps 19,996,443 genetic variants onto 42,413 protein sequences and 77,923 structures, with a comprehensive set of structural and functional features. Additionally, the G2P portal generalizes the capability of linking genomics to proteins beyond databases by allowing users to interactively upload protein residue-wise annotations (variants, scores, etc.) as well as the protein structure to establish the connection. The portal serves as an easy-to-use discovery tool for researchers and scientists to hypothesize the structure-function relationship between natural or synthetic variations and their molecular phenotype.
    DOI:  https://doi.org/10.1101/2024.01.02.573913
  40. Res Sq. 2024 Jan 04. pii: rs.3.rs-3740259. [Epub ahead of print]
    Deep generative modeling of the human proteome reveals over a hundred novel genes involved in rare genetic disorders.
    Debora Marks, Rose Orenbuch, Aaron Kollasch, Hansen Spinner, Courtney Shearer, Thomas Hopf, Dinko Franceschi, Mafalda Dias, Jonathan Frazer.
      Identifying causal mutations accelerates genetic disease diagnosis, and therapeutic development. Missense variants present a bottleneck in genetic diagnoses as their effects are less straightforward than truncations or nonsense mutations. While computational prediction methods are increasingly successful at prediction for variants in known disease genes, they do not generalize well to other genes as the scores are not calibrated across the proteome 1-6 . To address this, we developed a deep generative model, popEVE, that combines evolutionary information with population sequence data 7 and achieves state-of-the-art performance at ranking variants by severity to distinguish patients with severe developmental disorders 8 from potentially healthy individuals 9 . popEVE identifies 442 genes in patients this developmental disorder cohort, including evidence of 123 novel genetic disorders, many without the need for gene-level enrichment and without overestimating the prevalence of pathogenic variants in the population. A majority of these variants are close to interacting partners in 3D complexes. Preliminary analyses on child exomes indicate that popEVE can identify candidate variants without the need for inheritance labels. By placing variants on a unified scale, our model offers a comprehensive perspective on the distribution of fitness effects across the entire proteome and the broader human population. popEVE provides compelling evidence for genetic diagnoses even in exceptionally rare single-patient disorders where conventional techniques relying on repeated observations may not be applicable.
    DOI:  https://doi.org/10.21203/rs.3.rs-3740259/v1
  41. ACS Chem Biol. 2024 Jan 25.
    Forward Genetic Screens Identify Mechanisms of Resistance to Small-Molecule Lactate Dehydrogenase Inhibitors.
    Anderson R Frank, Florentina Vandiver, David G McFadden.
      Altered metabolism is a hallmark of cancer; however, it has been difficult to specifically target metabolism in cancer for therapeutic benefit. Cancers with genetically defined defects in metabolic enzymes constitute a subset of cancers where targeting metabolism is potentially accessible. Hürthle cell carcinoma of the thyroid (HTC) tumors frequently harbor deleterious mitochondrial DNA (mtDNA) mutations in subunits of complex I of the mitochondrial electron transport chain (ETC). Previous work has shown that HTC models with deleterious mtDNA mutations exhibit mitochondrial ETC defects that expose lactate dehydrogenase (LDH) as a therapeutic vulnerability. Here, we performed forward genetic screens to identify mechanisms of resistance to small-molecule LDH inhibitors. We identified two distinct mechanisms of resistance: upregulation of an LDH isoform and a compound-specific resistance mutation. Using these tools, we demonstrate that the anticancer activity of LDH inhibitors in cell line and xenograft models of complex I mutant HTC is through on-target LDH inhibition.
    DOI:  https://doi.org/10.1021/acschembio.3c00663
  42. Front Pharmacol. 2023 ;14 1332567
    The potential influence of melatonin on mitochondrial quality control: a review.
    Xudan Lei, Zhenni Xu, Lingxiao Huang, Yujun Huang, Siyu Tu, Lu Xu, Dengqun Liu.
      Mitochondria are critical for cellular energetic metabolism, intracellular signaling orchestration and programmed death regulation. Therefore, mitochondrial dysfunction is associated with various pathogeneses. The maintenance of mitochondrial homeostasis and functional recovery after injury are coordinated by mitochondrial biogenesis, dynamics and autophagy, which are collectively referred to as mitochondrial quality control. There is increasing evidence that mitochondria are important targets for melatonin to exert protective effects under pathological conditions. Melatonin, an evolutionarily conserved tryptophan metabolite, can be synthesized, transported and metabolized in mitochondria. In this review, we summarize the important role of melatonin in the damaged mitochondria elimination and mitochondrial energy supply recovery by regulating mitochondrial quality control, which may provide new strategies for clinical treatment of mitochondria-related diseases.
    Keywords:  autophagy; melatonin; mitochondria-related diseases; mitochondrial dynamics; oxidative phosphorylation
    DOI:  https://doi.org/10.3389/fphar.2023.1332567
  43. Methods Mol Biol. 2024 ;2766 199-206
    Evaluation of Mitochondrial Respiratory Function in Murine Splenocytes.
    Mochitsuki Marii, Shuang Liu.
      Accumulated evidence has demonstrated a key role of mitochondria in the onset and progression of autoimmune disease. Understanding and modulation of mitochondrial dysfunction could provide new molecular targets for both preventive and therapeutic intervention in disease management. The ability to assess mitochondrial function has enabled rheumatologists to advance the understanding of the contribution of cellular metabolism in cellular physiology and disease pathology and etiology. Direct measurement of oxygen consumption rate using an Agilent Seahorse XF measurement system has been widely used as the gold-standard assay for evaluating mitochondrial function in cells. Using this assay system, measurement of parameters of basal respiration, ATP production, proton leak, maximal respiration, spare respiratory capacity, and nonmitochondrial respiration can be achieved. An optimized method which works well in mouse splenocytes and a Jurkat cell line is presented in this chapter.
    Keywords:  Agilent Seahorse XF Mito stress test; Mitochondrial function; Mouse; Oxygen consumption rate; Splenocyte
    DOI:  https://doi.org/10.1007/978-1-0716-3682-4_22
  44. Biomolecules. 2023 Dec 21. pii: 12. [Epub ahead of print]14(1):
    Mitochondria in Multi-Directional Differentiation of Dental-Derived Mesenchymal Stem Cells.
    Haotian Liu, Ke Xu, Yifan He, Fang Huang.
      The pursuit of tissue regeneration has fueled decades of research in regenerative medicine. Among the numerous types of mesenchymal stem cells (MSCs), dental-derived mesenchymal stem cells (DMSCs) have recently emerged as a particularly promising candidate for tissue repair and regeneration. In recent years, evidence has highlighted the pivotal role of mitochondria in directing and orchestrating the differentiation processes of DMSCs. Beyond mitochondrial energy metabolism, the multifaceted functions of mitochondria are governed by the mitochondrial quality control (MQC) system, encompassing biogenesis, autophagy, and dynamics. Notably, mitochondrial energy metabolism not only governs the decision to differentiate but also exerts a substantial influence on the determination of differentiation directions. Furthermore, the MQC system exerts a nuanced impact on the differentiation of DMSCs by finely regulating the quality and mass of mitochondria. The review aims to provide a comprehensive overview of the regulatory mechanisms governing the multi-directional differentiation of DMSCs, mediated by both mitochondrial energy metabolism and the MQC system. We also focus on a new idea based on the analysis of data from many research groups never considered before, namely, DMSC-based regenerative medicine applications.
    Keywords:  dental-derived mesenchymal stem cells; mitochondrial biogenesis; mitochondrial dynamics; mitochondrial energy metabolism; mitophagy; multi-directional differentiation
    DOI:  https://doi.org/10.3390/biom14010012
  45. Heliyon. 2024 Jan 15. 10(1): e24029
    Advances in crosstalk among innate immune pathways activated by mitochondrial DNA.
    Guangwei Tao, Wenyan Liao, Jiafeng Hou, Xinmiao Jiang, Xin Deng, Guodong Chen, Chengming Ding.
      Mitochondria are not only the power plant for intracellular oxidative phosphorylation and ATP synthesis, but also involved in cell proliferation, differentiation, signaling and apoptosis. Recent studies have shown that mitochondria play an important role in other pathophysiological functions in addition to cellular energy metabolism. Mitochondria release mitochondrial DNA (mtDNA) as a damage-associated molecular pattern (DAMP) to activate Toll-like receptor 9 (TLR9), NOD-, LRR-, and pyrin domain-containing 3 (NLRP3) inflammasome and cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) innate immune signaling pathways against foreign pathogenic microorganisms. The innate immune response not only promotes antimicrobial immune defense and regulates antiviral signaling, but their overactivation also induces the onset and progression of inflammatory diseases. In this paper, we review the role of mtDNA in the activation of innate immune signaling pathways and the crosstalk among innate immune signaling pathways activated by mtDNA, providing clues for the study of inflammatory diseases caused by mtDNA cytoplasmic translocation.
    Keywords:  NLRP3 inflammasome; TLR9; cGAS-STING signaling pathway; mtDNA
    DOI:  https://doi.org/10.1016/j.heliyon.2024.e24029
  46. Front Mol Neurosci. 2023 ;16 1329554
    Post-translational modification and mitochondrial function in Parkinson's disease.
    Shishi Luo, Danling Wang, Zhuohua Zhang.
      Parkinson's disease (PD) is the second most common neurodegenerative disease with currently no cure. Most PD cases are sporadic, and about 5-10% of PD cases present a monogenic inheritance pattern. Mutations in more than 20 genes are associated with genetic forms of PD. Mitochondrial dysfunction is considered a prominent player in PD pathogenesis. Post-translational modifications (PTMs) allow rapid switching of protein functions and therefore impact various cellular functions including those related to mitochondria. Among the PD-associated genes, Parkin, PINK1, and LRRK2 encode enzymes that directly involved in catalyzing PTM modifications of target proteins, while others like α-synuclein, FBXO7, HTRA2, VPS35, CHCHD2, and DJ-1, undergo substantial PTM modification, subsequently altering mitochondrial functions. Here, we summarize recent findings on major PTMs associated with PD-related proteins, as enzymes or substrates, that are shown to regulate important mitochondrial functions and discuss their involvement in PD pathogenesis. We will further highlight the significance of PTM-regulated mitochondrial functions in understanding PD etiology. Furthermore, we emphasize the potential for developing important biomarkers for PD through extensive research into PTMs.
    Keywords:  Parkinson’s disease; SUMOylation; acetylation; mitochondrial function; phosphorylation; post-translational modification (PTM); s-nitrosylation; ubiquitination
    DOI:  https://doi.org/10.3389/fnmol.2023.1329554
  47. Lancet Neurol. 2024 Feb;pii: S1474-4422(23)00404-0. [Epub ahead of print]23(2): 191-204
    A biological classification of Parkinson's disease: the SynNeurGe research diagnostic criteria.
    Günter U Höglinger, Charles H Adler, Daniela Berg, Christine Klein, Tiago F Outeiro, Werner Poewe, Ronald Postuma, A Jon Stoessl, Anthony E Lang.
      With the hope that disease-modifying treatments could target the molecular basis of Parkinson's disease, even before the onset of symptoms, we propose a biologically based classification. Our classification acknowledges the complexity and heterogeneity of the disease by use of a three-component system (SynNeurGe): presence or absence of pathological α-synuclein (S) in tissues or CSF; evidence of underlying neurodegeneration (N) defined by neuroimaging procedures; and documentation of pathogenic gene variants (G) that cause or strongly predispose to Parkinson's disease. These three components are linked to a clinical component (C), defined either by a single high-specificity clinical feature or by multiple lower-specificity clinical features. The use of a biological classification will enable advances in both basic and clinical research, and move the field closer to the precision medicine required to develop disease-modifying therapies. We emphasise the initial application of these criteria exclusively for research. We acknowledge its ethical implications, its limitations, and the need for prospective validation in future studies.
    DOI:  https://doi.org/10.1016/S1474-4422(23)00404-0
  48. Sci Rep. 2024 01 24. 14(1): 2083
    Nuclear and mitochondrial genetic variants associated with mitochondrial DNA copy number.
    Adriana Koller, Michele Filosi, Hansi Weissensteiner, Federica Fazzini, Mathias Gorski, Cristian Pattaro, Sebastian Schönherr, Lukas Forer, Janina M Herold, Klaus J Stark, Patricia Döttelmayer, Andrew A Hicks, Peter P Pramstaller, Reinhard Würzner, Kai-Uwe Eckardt, Iris M Heid, Christian Fuchsberger, Claudia Lamina, Florian Kronenberg.
      Mitochondrial DNA copy number (mtDNA-CN) is a biomarker for mitochondrial dysfunction associated with several diseases. Previous genome-wide association studies (GWAS) have been performed to unravel underlying mechanisms of mtDNA-CN regulation. However, the identified gene regions explain only a small fraction of mtDNA-CN variability. Most of this data has been estimated from microarrays based on various pipelines. In the present study we aimed to (1) identify genetic loci for qPCR-measured mtDNA-CN from three studies (16,130 participants) using GWAS, (2) identify potential systematic differences between our qPCR derived mtDNA-CN measurements compared to the published microarray intensity-based estimates, and (3) disentangle the nuclear from mitochondrial regulation of the mtDNA-CN phenotype. We identified two genome-wide significant autosomal loci associated with qPCR-measured mtDNA-CN: at HBS1L (rs4895440, p = 3.39 × 10-13) and GSDMA (rs56030650, p = 4.85 × 10-08) genes. Moreover, 113/115 of the previously published SNPs identified by microarray-based analyses were significantly equivalent with our findings. In our study, the mitochondrial genome itself contributed only marginally to mtDNA-CN regulation as we only detected a single rare mitochondrial variant associated with mtDNA-CN. Furthermore, we incorporated mitochondrial haplogroups into our analyses to explore their potential impact on mtDNA-CN. However, our findings indicate that they do not exert any significant influence on our results.
    DOI:  https://doi.org/10.1038/s41598-024-52373-0
  49. Nature. 2024 Jan 24.
    Motion of VAPB molecules reveals ER-mitochondria contact site subdomains.
    Christopher J Obara, Jonathon Nixon-Abell, Andrew S Moore, Federica Riccio, David P Hoffman, Gleb Shtengel, C Shan Xu, Kathy Schaefer, H Amalia Pasolli, Jean-Baptiste Masson, Harald F Hess, Christopher P Calderon, Craig Blackstone, Jennifer Lippincott-Schwartz.
      To coordinate cellular physiology, eukaryotic cells rely on the rapid exchange of molecules at specialized organelle-organelle contact sites1,2. Endoplasmic reticulum-mitochondrial contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signalling molecules, lipids and metabolites3,4. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle5,6. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation7,8, a clear understanding of their nanoscale organization and regulation is still lacking. Here we combine three-dimensional electron microscopy with high-speed molecular tracking of a model organelle tether, Vesicle-associated membrane protein (VAMP)-associated protein B (VAPB), to map the structure and diffusion landscape of ERMCSs. We uncovered dynamic subdomains within VAPB contact sites that correlate with ER membrane curvature and undergo rapid remodelling. We show that VAPB molecules enter and leave ERMCSs within seconds, despite the contact site itself remaining stable over much longer time scales. This metastability allows ERMCSs to remodel with changes in the physiological environment to accommodate metabolic needs of the cell. An amyotrophic lateral sclerosis-associated mutation in VAPB perturbs these subdomains, likely impairing their remodelling capacity and resulting in impaired interorganelle communication. These results establish high-speed single-molecule imaging as a new tool for mapping the structure of contact site interfaces and reveal that the diffusion landscape of VAPB at contact sites is a crucial component of ERMCS homeostasis.
    DOI:  https://doi.org/10.1038/s41586-023-06956-y
  50. Nature. 2024 Jan 22.
    Deciphering cell states and genealogies of human hematopoiesis.
    Chen Weng, Fulong Yu, Dian Yang, Michael Poeschla, L Alexander Liggett, Matthew G Jones, Xiaojie Qiu, Lara Wahlster, Alexis Caulier, Jeffrey A Hussmann, Alexandra Schnell, Kathryn E Yost, Luke Koblan, Jorge D Martin-Rufino, Joseph Min, Alessandro Hammond, Daniel Ssozi, Raphael Bueno, Hari Mallidi, Antonia Kreso, Javier Escabi, William M Rideout, Tyler Jacks, Sahand Hormoz, Peter van Galen, Jonathan S Weissman, Vijay G Sankaran.
      The human blood system is maintained through the differentiation and massive amplification of a limited number of long-lived hematopoietic stem cells (HSCs)1. Perturbations to this process underlie diverse diseases, but the clonal contributions to human hematopoiesis and how this changes with age remain incompletely understood. While recent insights have emerged from barcoding studies in model systems4,5,16,17, simultaneous detection of cell states and phylogenies from natural barcodes in humans has been challenging. Here, we introduce an improved single-cell lineage tracing system based on deep detection of naturally-occurring mitochondrial DNA (mtDNA) mutations with simultaneous readout of transcriptional states and chromatin accessibility. We use this system to define the clonal architecture of HSCs and map the physiological state and output of clones. We uncover functional heterogeneity in HSC clones, which is stable over months and manifests as differences in total HSC output as well as biases toward the production of different mature cell types. We also find that the diversity of HSC clones decreases dramatically with age leading to an oligoclonal structure with multiple distinct clonal expansions. Our study thus provides the first clonally-resolved and cell-state aware atlas of human hematopoiesis at single-cell resolution revealing an unappreciated functional diversity of human HSC clones and more broadly paves the way for refined studies of clonal dynamics across a range of tissues in human health and disease.
    DOI:  https://doi.org/10.1038/s41586-024-07066-z
  51. medRxiv. 2024 Jan 11. pii: 2024.01.10.24301111. [Epub ahead of print]
    Complex trait associations in rare diseases and impacts on Mendelian variant interpretation.
    Genomic Answers for Kids Consortium
      Emerging evidence implicates common genetic variation - aggregated into polygenic scores (PGS) - impacting the onset and phenotypic presentation of rare diseases. In this study, we quantified individual polygenic liability for 1,151 previously published PGS in a cohort of 2,374 probands enrolled in the Genomic Answers for Kids (GA4K) rare disease study, revealing widespread associations between rare disease phenotypes and PGSs for common complex diseases and traits, blood protein levels, and brain and other organ morphological measurements. We observed increased polygenic burden in probands with variants of unknown significance (VUS) compared to unaffected carrier parents. We further observed an enrichment in overlap between diagnostic and candidate rare disease genes and large-effect PGS genes. Overall, our study supports and expands on previous findings of complex trait associations in rare disease phenotypes and provides a framework for identifying novel candidate rare disease genes and in understanding variable penetrance of candidate Mendelian disease variants.
    DOI:  https://doi.org/10.1101/2024.01.10.24301111
  52. Ageing Res Rev. 2024 Jan 23. pii: S1568-1637(24)00022-9. [Epub ahead of print] 102204
    Epigenetic Reprogramming as a Key to Reverse Ageing and Increase Longevity.
    Beatriz Pereira, Francisca P Correia, Inês A Alves, Margarida Costa, Mariana Gameiro, Ana P Martins, Jorge A Saraiva.
      The pursuit for the fountain of youth has long been a fascination amongst scientists and humanity. Ageing is broadly characterized by a cellular decline with increased susceptibility to age-related diseases, being intimately associated with epigenetic modifications. Recently, reprogramming-induced rejuvenation strategies have begun to greatly alter longevity research not only to tackle age-related defects but also to possibly reverse the cellular ageing process. Hence, in this review, we highlight the major epigenetic changes during ageing and the state-of-art of the current emerging epigenetic reprogramming strategies leveraging on transcription factors. Notably, partial reprogramming enables the resetting of the ageing clock without erasing cellular identity. Promising chemical-based rejuvenation strategies harnessing small molecules, including DNA methyltransferase and histone deacetylase inhibitors are also discussed. Moreover, in parallel to longevity interventions, the foundations of epigenetic clocks for accurate ageing assessment and evaluation of reprogramming approaches are briefly presented. Going further, with such scientific breakthroughs, we are witnessing a rise in the longevity biotech industry aiming to extend the health span and ideally achieve human rejuvenation one day. In this context, we overview the main scenarios proposed for the future of the socio-economic and ethical challenges associated with such an emerging field. Ultimately, this review aims to inspire future research on interventions that promote healthy ageing for all.
    Keywords:  DNA methylation; epigenetic clock; epigenetic reprogramming; histones; longevity; small molecules
    DOI:  https://doi.org/10.1016/j.arr.2024.102204
  53. medRxiv. 2024 Jan 12. pii: 2024.01.11.24301165. [Epub ahead of print]
    Impact of genome build on RNA-seq interpretation and diagnostics.
    Undiagnosed Diseases Network
      Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To identify the extent genome build also impacts transcriptomics analyses, we studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples from both the Undiagnosed Diseases Network (UDN) and Genomics Research to Elucidate the Genetics of Rare Disease (GREGoR) Consortium. We identified 2,800 genes with build-dependent quantification across six routinely-collected biospecimens, including 1,391 protein-coding genes and 341 known rare disease genes. We further observed multiple genes that only have detectable expression in a subset of genome builds. Finally, we characterized how genome build impacts the detection of outlier transcriptomic events. Combined, we provide a database of genes impacted by build choice, and recommend that transcriptomics-guided analyses and diagnoses are cross-referenced with these data for robustness.
    DOI:  https://doi.org/10.1101/2024.01.11.24301165
  54. bioRxiv. 2024 Jan 09. pii: 2024.01.09.574893. [Epub ahead of print]
    ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism.
    Edrees H Rashan, Abigail K Bartlett, Daven B Khana, Jingying Zhang, Raghav Jain, Andrew J Smith, Zakery N Baker, Taylor Cook, Alana Caldwell, Autumn R Chevalier, Brian F Pfleger, Peng Yuan, Daniel Amador-Noguez, Judith A Simcox, David J Pagliarini.
      Fatty acid β-oxidation (FAO) is a central catabolic pathway with broad implications for organismal health. However, various fatty acids are largely incompatible with standard FAO machinery until they are modified by other enzymes. Included among these are the 4-hydroxy acids (4-HAs)-fatty acids hydroxylated at the 4 (γ) position-which can be provided from dietary intake, lipid peroxidation, and certain drugs of abuse. Here, we reveal that two atypical and poorly characterized acyl-CoA dehydrogenases (ACADs), ACAD10 and ACAD11, drive 4-HA catabolism in mice. Unlike other ACADs, ACAD10 and ACAD11 feature kinase domains N-terminal to their ACAD domains that phosphorylate the 4-OH position as a requisite step in the conversion of 4-hydroxyacyl-CoAs into 2-enoyl-CoAs-conventional FAO intermediates. Our ACAD11 cryo-EM structure and molecular modeling reveal a unique binding pocket capable of accommodating this phosphorylated intermediate. We further show that ACAD10 is mitochondrial and necessary for catabolizing shorter-chain 4-HAs, whereas ACAD11 is peroxisomal and enables longer-chain 4-HA catabolism. Mice lacking ACAD11 accumulate 4-HAs in their plasma while comparable 3- and 5-hydroxy acids remain unchanged. Collectively, this work defines ACAD10 and ACAD11 as the primary gatekeepers of mammalian 4-HA catabolism and sets the stage for broader investigations into the ramifications of aberrant 4-HA metabolism in human health and disease.
    DOI:  https://doi.org/10.1101/2024.01.09.574893
  55. Biomedicines. 2024 Jan 22. pii: 240. [Epub ahead of print]12(1):
    The Role of Chorein Deficiency in Late Spermatogenesis.
    Kaoru Arai, Yoshiaki Nishizawa, Omi Nagata, Hitoshi Sakimoto, Natsuki Sasaki, Akira Sano, Masayuki Nakamura.
      VPS13A, also known as chorein, whose loss of function causes chorea-acanthocytosis (ChAc), is characterized by Huntington's-disease-like neurodegeneration and neuropsychiatric symptoms in addition to acanthocytosis in red blood cells. We previously reported that ChAc-model mice with a loss of chorein function exhibited male infertility, with asthenozoospermia and mitochondrial dysmorphology in the spermatozoa. Here, we report a novel aspect of chorein dysfunction in male fertility, particularly its role in spermatogenesis and mitochondrial integrity. An increase in anti-malondialdehyde antibody immunoreaction within the testes, predominantly observed at the advanced stages of sperm formation in chorein-deficient mice, suggests oxidative stress as a contributing factor to mitochondrial dysfunction and impaired sperm maturation. The chorein immunoreactivity in spermatids of wild-type mice accentuates its significance in sperm development. ChAc-model mice exhibit mitochondrial ultrastructural abnormalities, specifically during the late stages of sperm maturation, suggesting a critical timeframe for chorein's action in spermiogenesis. We observed an increase in TOM20 protein levels, indicative of disrupted mitochondrial import mechanisms. The concurrent decrease in metabolic enzymes such as IDH3A, LDHC, PGK2, and ACAT1 suggests a complex chorein-mediated metabolic network that is essential for sperm vitality. Additionally, heightened separation of cytoplasmic droplets from sperm highlights the potential membrane instability in chorein-deficient spermatozoa. Metabolomic profiling further suggests a compensatory metabolic shift, with elevated glycolytic and TCA-cycle substrates. Our findings suggest that chorein is involved in anti-ferroptosis and the maturation of mitochondrial morphology in the late stages of spermatogenesis, and its deficiency leads to asthenozoospermia characterized by membrane instability, abnormal cytosolic glycolysis, abnormal mitochondrial function, and a disrupted TCA cycle. Further analyses are required to unravel the molecular mechanisms that directly link these findings and to elucidate the role of chorein in spermatogenesis as well as its broader implications.
    Keywords:  IDH3A; TOM20; VPS13A; asthenozoospermia; chorea-acanthocytosis; chorein; ferroptosis; mitochondria
    DOI:  https://doi.org/10.3390/biomedicines12010240
  56. iScience. 2024 Jan 19. 27(1): 108681
    HDAC1/2 inhibitor therapy improves multiple organ systems in aged mice.
    Alessandra Tammaro, Eileen G Daniels, Iman M Hu, Kelly C 't Hart, Kim Reid, Rio P Juni, Loes M Butter, Goutham Vasam, Rashmi Kamble, Aldo Jongejan, Richard I Aviv, Joris J T H Roelofs, Eleonora Aronica, Reinier A Boon, Keir J Menzies, Riekelt H Houtkooper, Georges E Janssens.
      Aging increases the risk of age-related diseases, imposing substantial healthcare and personal costs. Targeting fundamental aging mechanisms pharmacologically can promote healthy aging and reduce this disease susceptibility. In this work, we employed transcriptome-based drug screening to identify compounds emulating transcriptional signatures of long-lived genetic interventions. We discovered compound 60 (Cmpd60), a selective histone deacetylase 1 and 2 (HDAC1/2) inhibitor, mimicking diverse longevity interventions. In extensive molecular, phenotypic, and bioinformatic assessments using various cell and aged mouse models, we found Cmpd60 treatment to improve age-related phenotypes in multiple organs. Cmpd60 reduces renal epithelial-mesenchymal transition and fibrosis in kidney, diminishes dementia-related gene expression in brain, and enhances cardiac contractility and relaxation for the heart. In sum, our two-week HDAC1/2 inhibitor treatment in aged mice establishes a multi-tissue, healthy aging intervention in mammals, holding promise for therapeutic translation to promote healthy aging in humans.
    Keywords:  Drugs; Epigenetics; Molecular biology; Omics; Transcriptomics
    DOI:  https://doi.org/10.1016/j.isci.2023.108681
  57. Int J Biol Sci. 2024 ;20(3): 987-1003
    Glutamine Metabolism Promotes Renal Fibrosis through Regulation of Mitochondrial Energy Generation and Mitochondrial Fission.
    Yang Cai, Beichen Tian, Yuanjun Deng, Lele Liu, Chunjiang Zhang, Wei Peng, Qian Li, Tianjing Zhang, Min Han, Gang Xu.
      Fibroblast activation and proliferation is an essential phase in the progression of renal fibrosis. Despite the recognized significance of glutamine metabolism in cellular growth and proliferation, its precise pathophysiological relevance in renal fibrosis remains uncertain. Therefore, this study aims to investigate the involvement of glutamine metabolism in fibroblast activation and its possible mechanism. Our findings highlight the importance of glutamine metabolism in fibroblast activation and reveal that patients with severe fibrosis exhibit elevated serum glutamine levels and increased expression of kidney glutamine synthetase. Furthermore, the deprivation of glutamine metabolism in vitro and in vivo could inhibit fibroblast activation, thereby ameliorating renal fibrosis. It was also detected that glutamine metabolism is crucial for maintaining mitochondrial function and morphology. These effects may partially depend on the metabolic intermediate α-ketoglutaric acid. Moreover, glutamine deprivation led to upregulated mitochondrial fission in fibroblasts and the activation of the mammalian target of rapamycin / mitochondrial fission process 1 / dynamin-related protein 1 pathway. Thus, these results provide compelling evidence that the modulation of glutamine metabolism initiates the regulation of mitochondrial function, thereby facilitating the progression of renal fibrosis. Consequently, targeting glutamine metabolism emerges as a novel and promising avenue for therapeutic intervention and prevention of renal fibrosis.
    Keywords:  Fibroblasts; Glutamine; Mitochondria; Mitochondrial fission; Renal fibrosis; α-ketoglutaric acid
    DOI:  https://doi.org/10.7150/ijbs.89960
  58. Sci Data. 2024 Jan 23. 11(1): 112
    Mass spectrometry-based proteomics data from thousands of HeLa control samples.
    Henry Webel, Yasset Perez-Riverol, Annelaura Bach Nielsen, Simon Rasmussen.
      Here we provide a curated, large scale, label free mass spectrometry-based proteomics data set derived from HeLa cell lines for general purpose machine learning and analysis. Data access and filtering is a tedious task, which takes up considerable amounts of time for researchers. Therefore we provide machine based metadata for easy selection and overview along the 7,444 raw files and MaxQuant search output. For convenience, we provide three filtered and aggregated development datasets on the protein groups, peptides and precursors level. Next to providing easy to access training data, we provide a SDRF file annotating each raw file with instrument settings allowing automated reprocessing. We encourage others to enlarge this data set by instrument runs of further HeLa samples from different machine types by providing our workflows and analysis scripts.
    DOI:  https://doi.org/10.1038/s41597-024-02922-z
  59. J Allergy Clin Immunol Pract. 2024 Jan 19. pii: S2213-2198(24)00071-0. [Epub ahead of print]
    What a Clinician Needs to Know about Genome Editing: Status and Opportunities for Inborn Errors of Immunity.
    Anne Ca Mudde, Caroline Y Kuo, Donald B Kohn, Claire Booth.
      During the past twenty years, gene editing has emerged as a novel form of gene therapy. Since the publication of the first potentially therapeutic gene editing platform for genetic disorders, increasingly sophisticated editing technologies have been developed. As with viral vector mediated gene addition, inborn errors of immunity (IEIs) are excellent candidate diseases for a corrective autologous haematopoietic stem cell gene editing strategy. Research on gene editing for IEIs is still entirely preclinical, with no trials yet underway. However, with editing techniques maturing, scientists are investigating this novel form of gene therapy in context of an increasing number of IEIs. Here, we present an overview of these studies and the recent progress moving these technologies closer to clinical benefit.
    Keywords:  CRISPR/Cas; base editing; gene editing; inborn errors of immunity; prime editing
    DOI:  https://doi.org/10.1016/j.jaip.2024.01.019
  60. Oxf Med Case Reports. 2023 Nov;2023(11): omad119
    Variants in the SARS2 gene cause HUPRA syndrome with atypical features: two case reports and review of the literature.
    Elias Edward Lahham, Juhina Jamal Hasassneh, Dua Osamah Adawi, Mohamad Khaled Ismail.
      Hyperuricemia, pulmonary hypertension, renal failure in infancy, and alkalosis (HUPRA syndrome) is a rare autosomal recessive mitochondrial disease with a prevalence of <1:1 000 000, due to variations in the seryl-tRNA synthetase (SARS2) gene encoding SARS on chromosome 19 (19q13.2). This study investigated two Palestinian girls from the same village who presented with progressive renal failure during infancy, with atypical clinical manifestations of HUPRA syndrome including leukopenia, anemia, salt wasting, renal failure, marked hyperuricemia, hypercholesterolemia, hyperlactatemia, and hypertriglyceridemia but without pulmonary hypertension or alkalosis. Instead, they showed acidosis on routine follow-up, distinguishing them from previous cases. Using single whole exome sequencing, we identified two homozygous pathogenic variants in the SARS2 gene (c.1175A>G (p.D392G)) and (c.1169A>G (p.D390G)). These cases with their unique phenotypes, expand the SARS2 pathogenic variant spectrum and describe clinical differences between homozygous and compound heterozygous variants.
    Keywords:  HUPRA syndromeSARS2 geneseryl-tRNA synthetaseprogressive renal failure in infancymitochondrial diseases
    DOI:  https://doi.org/10.1093/omcr/omad119
  61. Int J Mol Sci. 2024 Jan 12. pii: 963. [Epub ahead of print]25(2):
    Mitochondrial and Cellular Function in Fibroblasts, Induced Neurons, and Astrocytes Derived from Case Study Patients: Insights into Major Depression as a Mitochondria-Associated Disease.
    Iseline Cardon, Sonja Grobecker, Selin Kücükoktay, Stefanie Bader, Tatjana Jahner, Caroline Nothdurfter, Kevin Koschitzki, Mark Berneburg, Bernhard H F Weber, Heidi Stöhr, Marcus Höring, Gerhard Liebisch, Frank Braun, Tanja Rothammer-Hampl, Markus J Riemenschneider, Rainer Rupprecht, Vladimir M Milenkovic, Christian H Wetzel.
      The link between mitochondria and major depressive disorder (MDD) is increasingly evident, underscored both by mitochondria's involvement in many mechanisms identified in depression and the high prevalence of MDD in individuals with mitochondrial disorders. Mitochondrial functions and energy metabolism are increasingly considered to be involved in MDD's pathogenesis. This study focused on cellular and mitochondrial (dys)function in two atypical cases: an antidepressant non-responding MDD patient ("Non-R") and another with an unexplained mitochondrial disorder ("Mito"). Skin biopsies from these patients and controls were used to generate various cell types, including astrocytes and neurons, and cellular and mitochondrial functions were analyzed. Similarities were observed between the Mito patient and a broader MDD cohort, including decreased respiration and mitochondrial function. Conversely, the Non-R patient exhibited increased respiratory rates, mitochondrial calcium, and resting membrane potential. In conclusion, the Non-R patient's data offered a new perspective on MDD, suggesting a detrimental imbalance in mitochondrial and cellular processes, rather than simply reduced functions. Meanwhile, the Mito patient's data revealed the extensive effects of mitochondrial dysfunctions on cellular functions, potentially highlighting new MDD-associated impairments. Together, these case studies enhance our comprehension of MDD.
    Keywords:  iPS-astrocytes; iPS-neurons; major depressive disorder; mitochondrial functions; mitochondriopathy; treatment-resistant depression
    DOI:  https://doi.org/10.3390/ijms25020963
  62. Front Genet. 2023 ;14 1304520
    Lessons learned from rapid exome sequencing for 575 critically ill patients across the broad spectrum of rare disease.
    Abderrahim Marouane, Kornelia Neveling, A Chantal Deden, Simone van den Heuvel, Dimitra Zafeiropoulou, Steven Castelein, Frank van de Veerdonk, David A Koolen, Annet Simons, Richard Rodenburg, Dineke Westra, Arjen R Mensenkamp, Nicole de Leeuw, Marjolijn Ligtenberg, Rene Matthijsse, Rolph Pfundt, Erik Jan Kamsteeg, Han G Brunner, Christian Gilissen, Ilse Feenstra, Willem P de Boode, Helger G Yntema, Wendy A G van Zelst-Stams, Marcel Nelen, Lisenka E L M Vissers.
      Introduction: Rapid exome sequencing (rES) has become the first-choice genetic test for critically ill patients, mostly neonates, young infants, or fetuses in prenatal care, in time-sensitive situations and when it is expected that the genetic test result may guide clinical decision making. The implementation of rES has revolutionized medicine by enabling timely identification of genetic causes for various rare diseases. The utilization of rES has increasingly been recognized as an essential diagnostic tool for the identification of complex and undiagnosed genetic disorders. Methods: We conducted a retrospective evaluation of our experiences with rES performed on 575 critically ill patients from various age groups (prenatal to adulthood), over a four-year period (2016-2019). These patients presented with a wide spectrum of rare diseases, including but not limited to neurological disorders, severe combined immune deficiency, and cancer. Results: During the study period, there was a significant increase in rES referrals, with a rise from a total of two referrals in Q1-2016 to 10 referrals per week in Q4-2019. The median turnaround time (TAT) decreased from 17 to 11 days in the period 2016-2019, with an overall median TAT of 11 days (IQR 8-15 days). The overall diagnostic yield for this cohort was 30.4%, and did not significantly differ between the different age groups (e.g. adults 22.2% vs children 31.0%; p-value 0.35). However, variability in yield was observed between clinical entities: craniofacial anomalies yielded 58.3%, while for three clinical entities (severe combined immune deficiency, aneurysm, and hypogonadotropic hypogonadism) no diagnoses were obtained. Discussion: Importantly, whereas clinical significance is often only attributed to a conclusive diagnosis, we also observed impact on clinical decision-making for individuals in whom no genetic diagnosis was established. Hence, our experience shows that rES has an important role for patients of all ages and across the broad spectrum of rare diseases to impact clinical outcomes.
    Keywords:  clinical outcome; diagnostic workflow; diagnostic yield; rapid exome sequencing; turnaround time
    DOI:  https://doi.org/10.3389/fgene.2023.1304520
  63. Genet Med. 2024 Jan 23. pii: S1098-3600(24)00010-8. [Epub ahead of print] 101077
    Gene selection for genomic newborn screening: moving towards consensus?
    Lilian Downie, Sophie E Bouffler, David J Amor, John Christodoulou, Alison Yeung, Ari E Horton, Ivan Macciocca, Alison D Archibald, Meghan Wall, Jade Caruana, Sebastian Lunke, Zornitza Stark.
      BACKGROUND: Gene selection for genomic newborn screening (gNBS) underpins the validity, acceptability, and ethical application of this technology. Existing gNBS gene lists are highly variable despite being based on shared principles of gene-disease validity, treatability, and age of onset.AIM: To curate a gNBS gene list that builds upon existing efforts and provide a core consensus list of gene-disease pairs assessed by multiple expert groups worldwide.
    METHODS: Our multidisciplinary expert team curated a gene list using an open platform and multiple existing curated resources. We included severe treatable disorders with age of disease onset <5years with established gene-disease associations and reliable variant detection. We compared the final list with published lists from five other gNBS projects to determine consensus genes and to identify areas of discrepancy.
    RESULTS: We reviewed 1279 genes and 604 met our inclusion criteria. Metabolic conditions comprised the largest group (25%), followed by immunodeficiencies (21%) and endocrine disorders (15%). We identified 55 consensus genes included by all six gNBS research projects. Common reasons for discrepancy included variable definitions of treatability and strength of gene-disease association.
    CONCLUSION: We have identified a consensus gene list for gNBS that can be used as a basis for systematic harmonization efforts internationally.
    Keywords:  actionability; clinical validity; gene selection; gene-disease association; genomic newborn screening
    DOI:  https://doi.org/10.1016/j.gim.2024.101077
  64. Biosensors (Basel). 2024 Jan 15. pii: 46. [Epub ahead of print]14(1):
    Recent Advances in Electrochemical Detection of Cell Energy Metabolism.
    Kyeong-Mo Koo, Chang-Dae Kim, Tae-Hyung Kim.
      Cell energy metabolism is a complex and multifaceted process by which some of the most important nutrients, particularly glucose and other sugars, are transformed into energy. This complexity is a result of dynamic interactions between multiple components, including ions, metabolic intermediates, and products that arise from biochemical reactions, such as glycolysis and mitochondrial oxidative phosphorylation (OXPHOS), the two main metabolic pathways that provide adenosine triphosphate (ATP), the main source of chemical energy driving various physiological activities. Impaired cell energy metabolism and perturbations or dysfunctions in associated metabolites are frequently implicated in numerous diseases, such as diabetes, cancer, and neurodegenerative and cardiovascular disorders. As a result, altered metabolites hold value as potential disease biomarkers. Electrochemical biosensors are attractive devices for the early diagnosis of many diseases and disorders based on biomarkers due to their advantages of efficiency, simplicity, low cost, high sensitivity, and high selectivity in the detection of anomalies in cellular energy metabolism, including key metabolites involved in glycolysis and mitochondrial processes, such as glucose, lactate, nicotinamide adenine dinucleotide (NADH), reactive oxygen species (ROS), glutamate, and ATP, both in vivo and in vitro. This paper offers a detailed examination of electrochemical biosensors for the detection of glycolytic and mitochondrial metabolites, along with their many applications in cell chips and wearable sensors.
    Keywords:  cell chip; electrochemical biosensor; glycolytic metabolites; mitochondrial metabolites; wearable sensor
    DOI:  https://doi.org/10.3390/bios14010046
  65. Res Sq. 2024 Jan 05. pii: rs.3.rs-3641411. [Epub ahead of print]
    Yeast EndoG prevents genome instability by degrading cytoplasmic DNA.
    Grzegorz Ira, Yang Yu, Xin Wang, Jordan Fox, Ruofan Yu, Brenna McCauley, Nic Nikoloutsos, Qian Li, Philip Hastings, Weiwei Dang, Kaifu Chen, Pilendra Thakre.
      In metazoans release of mitochondrial DNA or retrotransposon cDNA to cytoplasm can cause sterile inflammation and disease 1. Cytoplasmic nucleases degrade these DNA species to limit inflammation 2,3. It remains unknown whether degradation these DNA also prevents nuclear genome instability. To address this question, we decided to identify the nuclease regulating transfer of these cytoplasmic DNA species to the nucleus. We used an amplicon sequencing-based method in yeast enabling analysis of millions of DSB repair products. Nuclear mtDNA (NUMTs) and retrotransposon cDNA insertions increase dramatically in nondividing stationary phase cells. Yeast EndoG (Nuc1) nuclease limits insertions of cDNA and transfer of very long mtDNA (>10 kb) that forms unstable circles or rarely insert in the genome, but it promotes formation of short NUMTs (~45-200 bp). Nuc1 also regulates transfer of cytoplasmic DNA to nucleus in aging or during meiosis. We propose that Nuc1 preserves genome stability by degrading retrotransposon cDNA and long mtDNA, while short NUMTs can originate from incompletely degraded mtDNA. This work suggests that nucleases eliminating cytoplasmic DNA play a role in preserving genome stability.
    DOI:  https://doi.org/10.21203/rs.3.rs-3641411/v1
  66. Front Endocrinol (Lausanne). 2023 ;14 1281213
    Sirtuins mediate mitochondrial quality control mechanisms: a novel therapeutic target for osteoporosis.
    Tianchi Zhang, Lining Wang, Xiping Duan, Yuanyuan Niu, Muzhe Li, Li Yun, Haitao Sun, Yong Ma, Yang Guo.
      Mitochondria plays a role in cell differentiation and apoptosis processes. Maintaining mitochondrial function is critical, and this involves various aspects of mitochondrial quality control such as protein homeostasis, biogenesis, dynamics, and mitophagy. Osteoporosis, a metabolic bone disorder, primarily arises from two factors: the dysregulation between lipogenic and osteogenic differentiation of aging bone marrow mesenchymal stem cells, and the imbalance between osteoblast-mediated bone formation and osteoclast-mediated bone resorption. Mitochondrial quality control has the potential to mitigate or even reverse the effects. Among the Sirtuin family, consisting of seven Sirtuins (SIRT1-7), SIRT1-SIRT6 play a crucial role in maintaining mitochondrial quality control. Additionally, SIRT1, SIRT3, SIRT6, and SIRT7 are directly involved in normal bone development and homeostasis by modulating bone cells. However, the precise mechanism by which these Sirtuins exert their effects remains unclear. This article reviews the impact of various aspects of mitochondrial quality control on osteoporosis, focusing on how SIRT1, SIRT3, and SIRT6 can improve osteoporosis by regulating mitochondrial protein homeostasis, biogenesis, and mitophagy. Furthermore, we provide an overview of the current state of clinical and preclinical drugs that can activate Sirtuins to improve osteoporosis. Specific Sirtuin-activating compounds are effective, but further studies are needed. The findings of this study may offer valuable insights for future research on osteoporosis and the development of clinical prevention and therapeutic target strategies.
    Keywords:  bone; mitochondrial dysfunction; mitochondrial quality control; osteoporosis; sirtuins
    DOI:  https://doi.org/10.3389/fendo.2023.1281213
  67. Cells. 2024 Jan 21. pii: 198. [Epub ahead of print]13(2):
    AIBP: A New Safeguard against Glaucomatous Neuroinflammation.
    Seunghwan Choi, Soo-Ho Choi, Tonking Bastola, Younggun Park, Jonghyun Oh, Keun-Young Kim, Sinwoo Hwang, Yury I Miller, Won-Kyu Ju.
      Glaucoma is a group of ocular diseases that cause irreversible blindness. It is characterized by multifactorial degeneration of the optic nerve axons and retinal ganglion cells (RGCs), resulting in the loss of vision. Major components of glaucoma pathogenesis include glia-driven neuroinflammation and impairment of mitochondrial dynamics and bioenergetics, leading to retinal neurodegeneration. In this review article, we summarize current evidence for the emerging role of apolipoprotein A-I binding protein (AIBP) as an important anti-inflammatory and neuroprotective factor in the retina. Due to its association with toll-like receptor 4 (TLR4), extracellular AIBP selectively removes excess cholesterol from the plasma membrane of inflammatory and activated cells. This results in the reduced expression of TLR4-associated, cholesterol-rich lipid rafts and the inhibition of downstream inflammatory signaling. Intracellular AIBP is localized to mitochondria and modulates mitophagy through the ubiquitination of mitofusins 1 and 2. Importantly, elevated intraocular pressure induces AIBP deficiency in mouse models and in human glaucomatous retina. AIBP deficiency leads to the activation of TLR4 in Müller glia, triggering mitochondrial dysfunction in both RGCs and Müller glia, and compromising visual function in a mouse model. Conversely, restoring AIBP expression in the retina reduces neuroinflammation, prevents RGCs death, and protects visual function. These results provide new insight into the mechanism of AIBP function in the retina and suggest a therapeutic potential for restoring retinal AIBP expression in the treatment of glaucoma.
    Keywords:  AAV; AIBP; TLR4; cholesterol; gene therapy; glaucoma; lipid rafts; mitochondria; neuroinflammation
    DOI:  https://doi.org/10.3390/cells13020198
  68. Cell Biochem Funct. 2024 Jan;42(1): e3926
    One carbon metabolism and its implication in health and immune functions.
    Shreya Dang, Arushi Jain, Garima Dhanda, Neetu Bhattacharya, Amit Bhattacharya, Sabyasachi Senapati.
      One carbon (1C) metabolism is critical for cellular viability and physiological homeostasis. Starting from its crucial involvement in purine biosynthesis to posttranslational modification of proteins, 1C metabolism contributes significantly to the development and cellular differentiation through methionine and folate cycles that are pivotal for cellular function. Genetic polymorphisms of several genes of these pathways are implicated in disease pathogenesis and drug metabolism. Metabolic products of 1C metabolism have significant roles in epigenetic modifications through DNA and histone protein methylation. Homocysteine is a product that has clinical significance in the diagnosis and prognosis of several critical illnesses, including chronic immune diseases and cancers. Regulation of the function and differentiation of immune cells, including T-cells, B-cells, macrophages, and so forth, are directly influenced by 1C metabolism and thus have direct implications in several immune disease biology. Recent research on therapeutic approaches is targeting nuclear, cytoplasmic, and mitochondrial 1C metabolism to manage and treat metabolic (i.e., type 2 diabetes), neurodegenerative (i.e., Alzheimer's disease), or immune (i.e., rheumatoid arthritis) diseases. 1C metabolism is being explored for therapeutic intervention as a common determinant for a spectrum of immune and metabolic diseases. Identifying the association or correlation between essential metabolic products of this pathway and disease onset or prognosis would further facilitate the clinical monitoring of diseases.
    Keywords:  chronic disease; folic acid metabolism; immune function; metabolic diseases; one carbon metabolism; purine biosynthesis
    DOI:  https://doi.org/10.1002/cbf.3926
  69. Nature. 2024 Jan;625(7996): 844-848
    Seven technologies to watch in 2024.
    Michael Eisenstein.
      
    Keywords:  Biological techniques; Gene therapy; Machine learning; Microscopy; Structural biology
    DOI:  https://doi.org/10.1038/d41586-024-00173-x
  70. Front Cell Dev Biol. 2023 ;11 1328522
    Metabolic control of induced pluripotency.
    Sergey A Sinenko, Alexey N Tomilin.
      Pluripotent stem cells of the mammalian epiblast and their cultured counterparts-embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs)-have the capacity to differentiate in all cell types of adult organisms. An artificial process of reactivation of the pluripotency program in terminally differentiated cells was established in 2006, which allowed for the generation of induced pluripotent stem cells (iPSCs). This iPSC technology has become an invaluable tool in investigating the molecular mechanisms of human diseases and therapeutic drug development, and it also holds tremendous promise for iPSC applications in regenerative medicine. Since the process of induced reprogramming of differentiated cells to a pluripotent state was discovered, many questions about the molecular mechanisms involved in this process have been clarified. Studies conducted over the past 2 decades have established that metabolic pathways and retrograde mitochondrial signals are involved in the regulation of various aspects of stem cell biology, including differentiation, pluripotency acquisition, and maintenance. During the reprogramming process, cells undergo major transformations, progressing through three distinct stages that are regulated by different signaling pathways, transcription factor networks, and inputs from metabolic pathways. Among the main metabolic features of this process, representing a switch from the dominance of oxidative phosphorylation to aerobic glycolysis and anabolic processes, are many critical stage-specific metabolic signals that control the path of differentiated cells toward a pluripotent state. In this review, we discuss the achievements in the current understanding of the molecular mechanisms of processes controlled by metabolic pathways, and vice versa, during the reprogramming process.
    Keywords:  cellular reprogramming; embryonic stem cells (ESCs); glycolysis; induced pluripotent stem cells (iPSCs); mitochondria; oxidative phosphorylation (OxPhos); pluripotency; reactive oxygen species (ROS)
    DOI:  https://doi.org/10.3389/fcell.2023.1328522
  71. Antioxidants (Basel). 2023 Dec 21. pii: 19. [Epub ahead of print]13(1):
    High Sucrose Diet-Induced Subunit I Tyrosine 304 Phosphorylation of Cytochrome c Oxidase Leads to Liver Mitochondrial Respiratory Dysfunction in the Cohen Diabetic Rat Model.
    Tasnim Arroum, Lucynda Pham, Taryn E Raisanen, Paul T Morse, Junmei Wan, Jamie Bell, Rachel Lax, Ann Saada, Maik Hüttemann, Sarah Weksler-Zangen.
      The mitochondrial oxidative phosphorylation process generates most of the cellular energy and free radicals in mammalian tissues. Both factors play a critical role in numerous human diseases that could be affected by reversible phosphorylation events that regulate the function and activity of the oxidative phosphorylation complexes. In this study, we analyzed liver mitochondria of Cohen diabetes-sensitive (CDs) and Cohen diabetes-resistant (CDr) rats, using blue native gel electrophoresis (BN-PAGE) in combination with mitochondrial activity measurements and a site-specific tyrosine phosphorylation implicated in inflammation, a known driver of diabetes pathology. We uncovered the presence of a specific inhibitory phosphorylation on tyrosine 304 of catalytic subunit I of dimeric cytochrome c oxidase (CcO, complex IV). Driven by a high sucrose diet in both CDr and CDs rats, Y304 phosphorylation, which occurs close to the catalytic oxygen binding site, correlates with a decrease in CcO activity and respiratory dysfunction in rat liver tissue under hyperglycemic conditions. We propose that this phosphorylation, specifically seen in dimeric CcO and induced by high sucrose diet-mediated inflammatory signaling, triggers enzymatic activity decline of complex IV dimers and the assembly of supercomplexes in liver tissue as a molecular mechanism underlying a (pre-)diabetic phenotype.
    Keywords:  Cohen diabetic rat; blue native gel; cytochrome c oxidase; dimeric complex IV; high sucrose diet; inflammation; inhibitory phosphorylation; liver mitochondria; mitochondria; mitochondrial dysfunction; respiratory dysfunction; type 2 diabetes; tyrosine 304 CcO subunit I; tyrosine phosphorylation
    DOI:  https://doi.org/10.3390/antiox13010019
  72. Int J Mol Sci. 2024 Jan 21. pii: 1314. [Epub ahead of print]25(2):
    Mitochondrial Glutathione in Cellular Redox Homeostasis and Disease Manifestation.
    Tsung-Hsien Chen, Hsiang-Chen Wang, Chia-Jung Chang, Shih-Yu Lee.
      Mitochondria are critical for providing energy to maintain cell viability. Oxidative phosphorylation involves the transfer of electrons from energy substrates to oxygen to produce adenosine triphosphate. Mitochondria also regulate cell proliferation, metastasis, and deterioration. The flow of electrons in the mitochondrial respiratory chain generates reactive oxygen species (ROS), which are harmful to cells at high levels. Oxidative stress caused by ROS accumulation has been associated with an increased risk of cancer, and cardiovascular and liver diseases. Glutathione (GSH) is an abundant cellular antioxidant that is primarily synthesized in the cytoplasm and delivered to the mitochondria. Mitochondrial glutathione (mGSH) metabolizes hydrogen peroxide within the mitochondria. A long-term imbalance in the ratio of mitochondrial ROS to mGSH can cause cell dysfunction, apoptosis, necroptosis, and ferroptosis, which may lead to disease. This study aimed to review the physiological functions, anabolism, variations in organ tissue accumulation, and delivery of GSH to the mitochondria and the relationships between mGSH levels, the GSH/GSH disulfide (GSSG) ratio, programmed cell death, and ferroptosis. We also discuss diseases caused by mGSH deficiency and related therapeutics.
    Keywords:  GSH deficiency; GSH/GSSG; glutathione; mitochondria; oxidative phosphorylation; programmed cell death; reactive oxygen species (ROS)
    DOI:  https://doi.org/10.3390/ijms25021314
  73. Endocr Metab Immune Disord Drug Targets. 2024 Jan 12.
    Uniparental Disomy as a Mechanism for Combined Oxidative Phosphorylation Deficiency Associated with MRPS34 Gene.
    Marta P Soares, André M Travessa, Sónia Custódio, Carla Pereira, Patrícia Pinto, Ana Berta Sousa.
      INTRODUCTION: Mitochondrial oxidative phosphorylation (OXPHOS) is a cellular process that generates most of the cellular energy required by the body. Disorders affecting OXPHOS are multisystem diseases caused by pathogenic variants in more than 50 genes. In 2017, biallelic variants in the MRPS34 gene were shown to cause combined oxidative phosphorylation deficiency type 32 (COPD32) (OMIM#617664); however, only 7 patients have been reported in the literature up to this moment. COPD32 is characterized mainly by a severe Leigh-like syndrome.METHODS: Whole-exome sequencing identified a homozygous pathogenic variant in the MRPS34 gene, c.322-10G>A. Only the mother was heterozygous for this variant. SNP-array analysis was performed, which revealed a region of absence of heterozygosity in variant 16q with 9.8Mb, compatible with maternal uniparental disomy.
    RESULTS/CASE REPORT: We report the case of an 18-year-old female with unremarkable family history. The pregnancy was complicated by oligohydramnios, and the neonatal period was unremarkable. She evolved with low weight, mild-moderate developmental delay/intellectual disability, and hypogonadotropic hypogonadism. On examination, she had slender habitus, joint laxity, and kyphoscoliosis. The cardiac evaluation was normal, and the head MRI showed bilateral olivary nucleus degeneration that was not confirmed subsequently. Extensive metabolic studies documented only mild lactate and pyruvate elevation, and the chromosomal microarray was normal.
    CONCLUSION: We have reported the case of the first patient with COPD32 due to partial maternal uniparental disomy of chromosome 16, being first in Portugal and seventh in the literature. Contrarily to previous patients, who died in the first months of life or survived with severe DD/ID, and had a Leigh-like syndrome, this case is significantly milder, contributing to a better characterization of the phenotypic spectrum. Recurrence risk is unexpectedly low in this instance. This case illustrates the importance of segregation analysis in patients with homozygous recessive mutations.
    Keywords:  Leigh-like syndrome; MRPS34 gene; Mitochondrial oxidative phosphorylation; combined oxidative phosphorylation deficiency type 32; oxidative phosphorylation deficiency type 32; uniparental disouniparental disomy
    DOI:  https://doi.org/10.2174/0118715303283767231120113921
  74. Am J Med Genet A. 2024 Jan 23.
    Whole genome sequencing as a first-tier diagnostic test for infants in neonatal intensive care units: A pilot study in Brazil.
    Michele P Migliavacca, Joselito Sobreira, Diana Bermeo, Mireille Gomes, Dayse Alencar, Luciane Sussuchi, Camila Alves Souza, Juliana Santos Silva, José Eduardo Kroll, Matheus Burger, Rodrigo Guarischi-Sousa, Darine Villela, Guilherme L Yamamoto, Fernanda Milanezi, Nelson Horigoshi, Regina Grigolli Cesar, Werther Brunow de Carvalho, Rachel Sayuri Honjo, Debora Romeo Bertola, Chong Ae Kim, Lucian de Souza, Renato S Procianoy, Rita C Silveria, Carla Rosenberg, Roberto Giugliani, Gustavo Aguiar Campana, Cristovam Scapulatempo-Neto, Nara Sobreira.
      In this pilot study, we aimed to evaluate the feasibility of whole genome sequencing (WGS) as a first-tier diagnostic test for infants hospitalized in neonatal intensive care units in the Brazilian healthcare system. The cohort presented here results from a joint collaboration between private and public hospitals in Brazil considering the initiative of a clinical laboratory to provide timely diagnosis for critically ill infants. We performed trio (proband and parents) WGS in 21 infants suspected of a genetic disease with an urgent need for diagnosis to guide medical care. Overall, the primary indication for genetic testing was dysmorphic syndromes (n = 14, 67%) followed by inborn errors of metabolism (n = 6, 29%) and skeletal dysplasias (n = 1, 5%). The diagnostic yield in our cohort was 57% (12/21) based on cases that received a definitive or likely definitive diagnostic result from WGS analysis. A total of 16 pathogenic/likely pathogenic variants and 10 variants of unknown significance were detected, and in most cases inherited from an unaffected parent. In addition, the reported variants were of different types, but mainly missense (58%) and associated with autosomal diseases (19/26); only three were associated with X-linked diseases, detected in hemizygosity in the proband an inherited from an unaffected mother. Notably, we identified 10 novel variants, absent from public genomic databases, in our cohort. Considering the entire diagnostic process, the average turnaround time from enrollment to medical report in our study was 53 days. Our findings demonstrate the remarkable utility of WGS as a diagnostic tool, elevating the potential of transformative impact since it outperforms conventional genetic tests. Here, we address the main challenges associated with implementing WGS in the medical care system in Brazil, as well as discuss the potential benefits and limitations of WGS as a diagnostic tool in the neonatal care setting.
    Keywords:  clinical pediatrics; diagnostic yield; genetic diseases; next-generation sequencing (NGS); trio testing; whole genome sequencing
    DOI:  https://doi.org/10.1002/ajmg.a.63544
  75. Life (Basel). 2024 Jan 15. pii: 124. [Epub ahead of print]14(1):
    Protein-Protein Interactions of Seryl-tRNA Synthetases with Emphasis on Human Counterparts and Their Connection to Health and Disease.
    Morana Dulic, Vlatka Godinic-Mikulcic, Mario Kekez, Valentina Evic, Jasmina Rokov-Plavec.
      Seryl-tRNA synthetases (SerRSs), members of the aminoacyl-tRNA synthetase family, interact with diverse proteins, enabling SerRSs to enhance their role in the translation of the genetic message or to perform alternative functions in cellular processes beyond translation. Atypical archaeal SerRS interacts with arginyl-tRNA synthetase and proteins of the ribosomal P-stalk to optimize translation through tRNA channeling. The complex between yeast SerRS and peroxin Pex21p provides a connection between translation and peroxisome function. The partnership between Arabidopsis SerRS and BEN1 indicates a link between translation and brassinosteroid metabolism and may be relevant in plant stress response mechanisms. In Drosophila, the unusual heterodimeric mitochondrial SerRS coordinates mitochondrial translation and replication via interaction with LON protease. Evolutionarily conserved interactions of yeast and human SerRSs with m3C32 tRNA methyltransferases indicate coordination between tRNA modification and aminoacylation in the cytosol and mitochondria. Human cytosolic SerRS is a cellular hub protein connecting translation to vascular development, angiogenesis, lipogenesis, and telomere maintenance. When translocated to the nucleus, SerRS acts as a master negative regulator of VEGFA gene expression. SerRS alone or in complex with YY1 and SIRT2 competes with activating transcription factors NFκB1 and c-Myc, resulting in balanced VEGFA expression important for proper vascular development and angiogenesis. In hypoxia, SerRS phosphorylation diminishes its binding to the VEGFA promoter, while the lack of nutrients triggers SerRS glycosylation, reducing its nuclear localization. Additionally, SerRS binds telomeric DNA and cooperates with the shelterin protein POT1 to regulate telomere length and cellular senescence. As an antitumor and antiangiogenic factor, human cytosolic SerRS appears to be a promising drug target and therapeutic agent for treating cancer, cardiovascular diseases, and possibly obesity and aging.
    Keywords:  SARS1; VEGFA; aminoacyl-tRNA synthetase; angiogenesis; protein–protein interaction; senescence; seryl-tRNA synthetase; tRNA channeling; telomere; translation
    DOI:  https://doi.org/10.3390/life14010124
  76. Adv Healthc Mater. 2024 Jan 25. e2303041
    Precision Medicine in Parkinson's Disease using Induced Pluripotent Stem Cells.
    Min Seong Kim, Hyesoo Kim, Gabsang Lee.
      Parkinson's Disease (PD) is one of the most devastating neurological diseases, however there is no effective cure yet. The availability of human induced pluripotent stem cells (iPSCs) provides unprecedented opportunities to understand the pathogenic mechanism and identification of new therapy for PD. In this review, we will introduce new model system of PD, including two-dimensional (2D) human iPSC-derived midbrain dopaminergic (mDA) neurons, 3D iPSC-derived midbrain organoids (MOs) with cellular complexity, and more advanced microphysiological systems (MPS) with three-dimensional (3D) organoids. We believe that successful integrations and applications of iPSC, organoid, and MPS technologies can bring new insight on PD's pathogenesis that will lead to more effective treatments for this debilitating disease. This article is protectd by copyright. All rights reserved.
    Keywords:  Parkinson's disease; induced pluripotent stem cells; microphysiological systems; midbrain organoids
    DOI:  https://doi.org/10.1002/adhm.202303041
  77. J Cachexia Sarcopenia Muscle. 2024 Jan 25.
    RORα-GABP-TFAM axis alleviates myosteatosis with fatty atrophy through reinforcement of mitochondrial capacity.
    Hyeon-Ji Kim, Sang-Heon Lee, Cheolhee Jeong, Yong-Hyun Han, Mi-Ock Lee.
      BACKGROUND: Fat infiltration in muscle, called 'myosteatosis', precedes muscle atrophy, which subsequently results in sarcopenia. Myosteatosis is frequently observed in patients with nonalcoholic fatty liver disease (NAFLD). We have previously reported that retinoic acid receptor-related orphan receptor-α (RORα) regulates mitochondrial dynamics and mitophagy in hepatocytes, resulting in an alleviation of NAFLD. In this study, we aimed to investigate the role of RORα in skeletal muscle and to understand molecular mechanisms by which RORα controls mitochondrial capacity, using an NAFLD-associated myosteatosis mouse model.METHODS: To establish a myosteatosis model, 7-week-old C57BL/6N mice were fed with high-fat diet (HFD). After 15 weeks of diet feeding, an adeno-associated virus vector encoding RORα (AAV-RORα) was injected to gastrocnemius (GA) muscles, or after 7 weeks of HFD feeding, JC1-40, an RORα agonistic ligand, was administered daily at a dose of 5 mg/kg/day by oral gavage for 5 weeks. Histological, biochemical and molecular analyses in various in vivo and in vitro experiments were performed.
    RESULTS: First, the number of oxidative MyHC2a fibres with intensive lipid infiltration increased by 3.8-fold in the red region of the GA of mice with myosteatosis (P < 0.001). RORα was expressed around MyHC2a fibres, and its level increased by 2.7-fold after HFD feeding (P < 0.01). Second, treatment of RORα ligands in C2C12 myoblasts, such as cholesterol sulfate and JC1-40, enhanced the number of oxidative fibres stained for MyHC1 and MyHC2a by two-fold to four-fold (P < 0.01), while it reduced the lipid levels in MyHC2a fibres by 20-50% (P < 0.001) in the presence of palmitic acids. Third, mitochondrial membrane potential (P < 0.01) and total area of mitochondria (P < 0.01) were enhanced by treatment of these ligands. Chromatin immunoprecipitation analysis showed that RORα bound the promoter of GA-binding protein α subunit gene that led to activation of mitochondrial transcription factor A (TFAM) in C2C12 myoblasts (P < 0.05). Finally, intramuscular transduction of AAV-RORα alleviated the HFD-induced myosteatosis with fatty atrophy; lipid contents in MyHC2a fibres decreased by 48% (P < 0.001), whereas the number of MyHC2b fibre increased by 22% (P < 0.001). Also, administration of JC1-40 improved the signs of myosteatosis in that it decreased the level of adipose differentiation-related protein (P < 0.01) but increased mitochondrial proteins such as cytochrome c oxidase 4 and TFAM in GA muscle (P < 0.01).
    CONCLUSIONS: RORα plays a versatile role in regulating the quantity of mitochondria and the oxidative capacity, ultimately leading to an improvement in myosteatosis symptoms.
    Keywords:  NAFLD; RORα; fatty atrophy; mitochondrial biogenesis; myosteatosis
    DOI:  https://doi.org/10.1002/jcsm.13432
  78. Front Neurol. 2023 ;14 1320757
    Case report: Clinical profile, molecular genetics, and neuroimaging findings presenting in a patient with Kearns-Sayre syndrome associated with inherited thrombophilia.
    Anca Elena Gogu, Dragos Catalin Jianu, Florina Parv, Andrei Gheorghe Marius Motoc, Any Axelerad, Alina Zorina Stuparu, Andreea Alexandra Gogu.
      Background: Kearns-Sayre syndrome (KSS) is classified as one of the mitochondrial DNA (mtDNA) deletion syndromes with multisystemic involvement. Additionally, the negative prognosis is associated with inherited thrombophilia, which includes the presence of homozygous Factor V G1691A Leiden mutation, MTHFR gene polymorphisms C677T and A1298C, and PAI-1 675 homozygous genotype 5G/5G.Case presentation: This case report presents a 48-year-old man with chronic progressive external ophthalmoplegia, bilateral ptosis, cerebellar ataxia, cardiovascular signs (syncope, dilated cardiomyopathy, and cardiac arrest) with electrocardiographic abnormalities (first-degree atrioventricular block and major right bundle branch block), endocrine dysfunction (short stature, growth hormone insufficiency, primary gonadal insufficiency, hypothyroidism, and secondary hyperparathyroidism), molecular genetic tests (MT-TL2 gene), and abnormal MRI brain images, thus leading to the diagnosis of KSS. The patient came back 4 weeks after the diagnosis to the emergency department with massive bilateral pulmonary embolism with syncope at onset, acute cardiorespiratory failure, deep left femoral-popliteal vein thrombophlebitis, and altered neurological status. In the intensive care unit, he received mechanical ventilation through intubation. Significant improvement was seen after 2 weeks. The patient tested positive for inherited thrombophilia and was discharged in stable conditions on a new treatment with Rivaroxaban 20 mg/day. At 6 months of follow-up, ECG-Holter monitoring and MRI brain images remained unchanged. However, after 3 months, the patient died suddenly while sleeping at home.
    Conclusion: The genetic tests performed on KSS patients should also include those for inherited thrombophilia. By detecting these mutations, we can prevent major complications such as cerebral venous sinus thrombosis, coronary accidents, or sudden death.
    Keywords:  Kearns-Sayre syndrome (KSS); brain magnetic resonance imaging; genetic tests; heart conduction block; inherited thrombophilia
    DOI:  https://doi.org/10.3389/fneur.2023.1320757
  79. Hum Mol Genet. 2024 Jan 25. pii: ddae009. [Epub ahead of print]
    Challenges and approaches to calibrating patient phenotype as evidence for cancer gene variant classification under ACMG/AMP guidelines.
    Cristina Fortuno, Kyriaki Michailidou, Michael Parsons, Jill S Dolinsky, Tina Pesaran, Amal Yussuf, Jessica L Mester, Kathleen S Hruska, Susan Hiraki, Robert O'Connor, Raymond C Chan, Serra Kim, Sean V Tavtigian, David Goldgar, Paul A James, Amanda B Spurdle.
      Since first publication of the American College of Medical Genetics and Genomics/Association for Medical Pathology (ACMG/AMP) variant classification guidelines, additional recommendations for application of certain criteria have been released (https://clinicalgenome.org/docs/), to improve their application in the diagnostic setting. However, none have addressed use of the PS4 and PP4 criteria, capturing patient presentation as evidence towards pathogenicity. Application of PS4 can be done through traditional case-control studies, or "proband counting" within or across clinical testing cohorts. Review of the existing PS4 and PP4 specifications for Hereditary Cancer Gene Variant Curation Expert Panels revealed substantial differences in the approach to defining specifications. Using BRCA1, BRCA2 and TP53 as exemplar genes, we calibrated different methods proposed for applying the "PS4 proband counting" criterion. For each approach, we considered limitations, non-independence with other ACMG/AMP criteria, broader applicability, and variability in results for different datasets. Our findings highlight inherent overlap of proband-counting methods with ACMG/AMP frequency codes, and the importance of calibration to derive dataset-specific code weights that can account for potential between-dataset differences in ascertainment and other factors. Our work emphasizes the advantages and generalizability of logistic regression analysis over simple proband-counting approaches to empirically determine the relative predictive capacity and weight of various personal clinical features in the context of multigene panel testing, for improved variant interpretation. We also provide a general protocol, including instructions for data formatting and a web-server for analysis of personal history parameters, to facilitate dataset-specific calibration analyses required to use such data for germline variant classification.
    Keywords:  ACMG PS4; cancer gene; germline variant classification; logistic regression; proband counting
    DOI:  https://doi.org/10.1093/hmg/ddae009
  80. medRxiv. 2024 Jan 13. pii: 2024.01.12.24301168. [Epub ahead of print]
    Lethal phenotypes in Mendelian disorders.
    Pilar Cacheiro, Samantha Lawson, Ignatia B Van den Veyver, Gabriel Marengo, David Zocche, Stephen A Murray, Michael Duyzend, Peter N Robinson, Damian Smedley.
      Essential genes are those whose function is required for cell proliferation and/or organism survival. A gene's intolerance to loss-of-function can be allocated within a spectrum, as opposed to being considered a binary feature, since this function might be essential at different stages of development, genetic backgrounds or other contexts. Existing resources that collect and characterise the essentiality status of genes are based on either proliferation assessment in human cell lines, embryonic and postnatal viability evaluation in different model organisms, and gene metrics such as intolerance to variation scores derived from human population sequencing studies. There are also several repositories available that document phenotypic annotations for rare disorders in humans such as the Online Mendelian Inheritance in Man (OMIM) and the Human Phenotype Ontology (HPO) knowledgebases. This raises the prospect of being able to use clinical data, including lethality as the most severe phenotypic manifestation, to further our characterisation of gene essentiality. Here we queried OMIM for terms related to lethality and classified all Mendelian genes into categories, according to the earliest age of death recorded for the associated disorders, from prenatal death to no reports of premature death. To showcase this curated catalogue of human essential genes, we developed the Lethal Phenotypes Portal ( https://lethalphenotypes.research.its.qmul.ac.uk ), where we also explore the relationships between these lethality categories, constraint metrics and viability in cell lines and mouse. Further analysis of the genes in these categories reveals differences in the mode of inheritance of the associated disorders, physiological systems affected and disease class. We highlight how the phenotypic similarity between genes in the same lethality category combined with gene family/group information can be used for novel disease gene discovery. Finally, we explore the overlaps and discrepancies between the lethal phenotypes observed in mouse and human and discuss potential explanations that include differences in transcriptional regulation, functional compensation and molecular disease mechanisms. We anticipate that this resource will aid clinicians in the diagnosis of early lethal conditions and assist researchers in investigating the properties that make these genes essential for human development.
    DOI:  https://doi.org/10.1101/2024.01.12.24301168
  81. Lancet Neurol. 2024 Feb;pii: S1474-4422(23)00512-4. [Epub ahead of print]23(2): 133-134
    Parkinson's disease is a recognisable and useful diagnostic entity.
    Jose A Obeso, Paolo Calabressi.
      
    DOI:  https://doi.org/10.1016/S1474-4422(23)00512-4
  82. bioRxiv. 2024 Jan 09. pii: 2024.01.08.574722. [Epub ahead of print]
    A mouse model to study glutathione limitation in vivo.
    Rebecca C Timson, Artem Khan, Beste Uygur, Marwa Saad, Hsi-Wen Yeh, Nicole DelGaudio, Ross Weber, Hanan Alwaseem, Jing Gao, Chingwen Yang, Kıvanç Birsoy.
      Glutathione (GSH) is a highly abundant tripeptide thiol that performs diverse protective and biosynthetic functions in cells. While changes in GSH availability are linked to many diseases, including cancer and neurodegenerative disorders, determining the function of GSH in physiology and disease has been challenging due to its tight regulation. To address this, we generated cell and mouse models that express a bifunctional glutathione-synthesizing enzyme from Streptococcus Thermophilus (GshF). GshF expression allows efficient production of GSH in the cytosol and mitochondria and prevents cell death in response to GSH depletion, but not ferroptosis, indicating that GSH is not a limiting factor under lipid peroxidation. CRISPR screens using engineered enzymes revealed metabolic liabilities under compartmentalized GSH depletion. Finally, GshF expression in mice is embryonically lethal but sustains postnatal viability when restricted to adulthood. Overall, our work identifies a conditional mouse model to investigate the role of GSH availability in physiology and disease.
    DOI:  https://doi.org/10.1101/2024.01.08.574722
  83. Orphanet J Rare Dis. 2024 Jan 25. 19(1): 25
    Are the European reference networks for rare diseases ready to embrace machine learning? A mixed-methods study.
    Georgi Iskrov, Ralitsa Raycheva, Kostadin Kostadinov, Sandra Gillner, Carl Rudolf Blankart, Edith Sky Gross, Gulcin Gumus, Elena Mitova, Stefan Stefanov, Georgi Stefanov, Rumen Stefanov.
      BACKGROUND: The delay in diagnosis for rare disease (RD) patients is often longer than for patients with common diseases. Machine learning (ML) technologies have the potential to speed up and increase the precision of diagnosis in this population group. We aim to explore the expectations and experiences of the members of the European Reference Networks (ERNs) for RDs with those technologies and their potential for application.METHODS: We used a mixed-methods approach with an online survey followed by a focus group discussion. Our study targeted primarily medical professionals but also other individuals affiliated with any of the 24 ERNs.
    RESULTS: The online survey yielded 423 responses from ERN members. Participants reported a limited degree of knowledge of and experience with ML technologies. They considered improved diagnostic accuracy the most important potential benefit, closely followed by the synthesis of clinical information, and indicated the lack of training in these new technologies, which hinders adoption and implementation in routine care. Most respondents supported the option that ML should be an optional but recommended part of the diagnostic process for RDs. Most ERN members saw the use of ML limited to specialised units only in the next 5 years, where those technologies should be funded by public sources. Focus group discussions concluded that the potential of ML technologies is substantial and confirmed that the technologies will have an important impact on healthcare and RDs in particular. As ML technologies are not the core competency of health care professionals, participants deemed a close collaboration with developers necessary to ensure that results are valid and reliable. However, based on our results, we call for more research to understand other stakeholders' opinions and expectations, including the views of patient organisations.
    CONCLUSIONS: We found enthusiasm to implement and apply ML technologies, especially diagnostic tools in the field of RDs, despite the perceived lack of experience. Early dialogue and collaboration between health care professionals, developers, industry, policymakers, and patient associations seem to be crucial to building trust, improving performance, and ultimately increasing the willingness to accept diagnostics based on ML technologies.
    Keywords:  Artificial intelligence; Diagnosis; Diagnostic delay; European reference networks; Machine learning; Rare diseases
    DOI:  https://doi.org/10.1186/s13023-024-03047-7
  84. J Biol Chem. 2024 Jan 23. pii: S0021-9258(24)00061-9. [Epub ahead of print] 105685
    Discovery and engineering of AiEvo2, a novel Cas12a nuclease for human gene editing applications.
    Allison Sharrar, Luisa Arake de Tacca, Zuriah Meacham, Johanna Staples-Ager, Trevor Collingwood, David Rabuka, Michael Schelle.
      The precision of gene editing technology is critical to creating safe and effective therapies for treating human disease. While the programmability of CRISPR-Cas systems has allowed for rapid innovation of new gene editing techniques, the off-target activity of these enzymes has hampered clinical development for novel therapeutics. Here we report the identification and characterization of a novel CRISPR-Cas12a enzyme from Acinetobacter indicus (AiCas12a). We engineer the nuclease (termed AiEvo2) for increased specificity, PAM recognition, and efficacy on a variety of human clinical targets. AiEvo2 is highly precise and able to efficiently discriminate between normal and disease-causing alleles in Huntington's patient derived cells by taking advantage of a single nucleotide polymorphism on the disease-associated allele. AiEvo2 efficiently edits several liver-associated target genes including PCSK9 and TTR when delivered to primary hepatocytes as mRNA encapsulated in a lipid nanoparticle. The enzyme also engineers an effective CD19 CAR-T therapy from primary human T cells using multiplexed simultaneous editing and CAR insertion. To further ensure precise editing, we engineered an anti-CRISPR protein (ErAcr) to selectively inhibit off-target gene editing while retaining therapeutic on-target editing. The engineered AiEvo2 nuclease coupled with a novel ErAcr protein represents a new way to control the fidelity of editing and improve the safety and efficacy of gene editing therapies.
    Keywords:  CRISPR/Cas; drug discovery; gene therapy; genetic disease; protein engineering
    DOI:  https://doi.org/10.1016/j.jbc.2024.105685
  85. Stud Health Technol Inform. 2024 Jan 25. 310 94-98
    User Centered Rare Disease Clinical Trial Knowledge Graph (RCTKG).
    Jeremy Parker Yang, Devon Leadman, Richard M Ballew, Eric Sid, Yanji Xu, Ewy A Mathé, Qian Zhu.
      Drug development in rare diseases is challenging due to the limited availability of subjects with the diseases and recruiting from a small patient population. The high cost and low success rate of clinical trials motivate deliberate analysis of existing clinical trials to understand status of clinical development of orphan drugs and discover new insight for new trial. In this project, we aim to develop a user centered Rare disease based Clinical Trial Knowledge Graph (RCTKG) to integrate publicly available clinical trial data with rare diseases from the Genetic and Rare Disease (GARD) program in a semantic and standardized form for public use. To better serve and represent the interests of rare disease users, user stories were defined for three types of users, patients, healthcare providers and informaticians, to guide the RCTKG design in supporting the GARD program at NCATS/NIH and the broad clinical/research community in rare diseases.
    Keywords:  Clinical trial; data model; knowledge graph; rare disease; user story
    DOI:  https://doi.org/10.3233/SHTI230934
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