bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2023–04–30
sixty-one papers selected by
Catalina Vasilescu, Helmholz Munich
  1. Methodologies in Mitochondrial Testing: Diagnosing a Primary Mitochondrial Respiratory Chain Disorder.
  2. Why Don't More Mitochondrial Diseases Exhibit Cardiomyopathy?
  3. Opportunities for mitochondrial disease gene therapy.
  4. POLG genotype influences degree of mitochondrial dysfunction in iPSC derived neural progenitors, but not the parent iPSC or derived glia.
  5. Bendless is essential for PINK1-Park mediated Mitofusin degradation under mitochondrial stress caused by loss of LRPPRC.
  6. Mitochondrial carriers set the epigenetic age.
  7. MTSviewer: A database to visualize mitochondrial targeting sequences, cleavage sites, and mutations on protein structures.
  8. FBXL4 ubiquitin ligase deficiency promotes mitophagy by elevating NIX levels.
  9. The MitoLuc Assay System for Accurate Real-Time Monitoring of Mitochondrial Protein Import within Mammalian Cells.
  10. SARM1 deletion delays cerebellar but not spinal cord degeneration in an enhanced mouse model of SPG7 deficiency.
  11. Pleiotropic effects of mitochondria in aging.
  12. Mitochondrial complex III deficiency drives c-MYC overexpression and illicit cell cycle entry leading to senescence and segmental progeria.
  13. A novel protein encoded by circRsrc1 regulates mitochondrial ribosome assembly and translation during spermatogenesis.
  14. MICU1 regulates mitochondrial cristae structure and function independently of the mitochondrial Ca2+ uniporter channel.
  15. iPSC-derived retinal pigmented epithelial cells from patients with macular telangiectasia show decreased mitochondrial function.
  16. Ischemic optic neuropathy as first presentation in patient with m.3243 A > G MELAS classic mutation.
  17. Healthy aging and muscle function are positively associated with NAD+ abundance in humans.
  18. Mitochondrial dynamics define muscle fiber type by modulating cellular metabolic pathways.
  19. Not4-dependent targeting of MMF1 mRNA to mitochondria limits its expression via ribosome pausing, Egd1 ubiquitination, Caf130, no-go-decay and autophagy.
  20. The Translocase of the Outer Mitochondrial Membrane (TOM40) is required for mitochondrial dynamics and neuronal integrity in Dorsal Root Ganglion Neurons.
  21. Mitochondrial Function and Signaling to Regulate Cellular Life.
  22. Multifaceted mitochondria: moving mitochondrial science beyond function and dysfunction.
  23. The Role of PGC-1α-Mediated Mitochondrial Biogenesis in Neurons.
  24. The Potential Use of Mitochondrial Extracellular Vesicles as Biomarkers or Therapeutical Tools.
  25. Multi-omic profiling reveals an RNA processing rheostat that predisposes to prostate cancer.
  26. Chromatin remodeling due to degradation of citrate carrier impairs osteogenesis of aged mesenchymal stem cells.
  27. Dysregulated cellular redox status during hyperammonemia causes mitochondrial dysfunction and senescence by inhibiting sirtuin-mediated deacetylation.
  28. New-Onset Refractory Status Epilepticus Due to a Novel MT-TF Variant: Time for Acute Genetic Testing Before Treatment?
  29. Passive heat stress induces mitochondrial adaptations in skeletal muscle.
  30. Suppression of intestinal dysfunction in a Drosophila model of Parkinson's disease is neuroprotective.
  31. Mitochondrial Bioenergy in Neurodegenerative Disease: Huntington and Parkinson.
  32. Visualizing Cardiolipin In Situ with HKCL-1M, a Highly Selective and Sensitive Fluorescent Probe.
  33. Fluorescence microscopic platforms imaging mitochondrial abnormalities in neurodegenerative diseases.
  34. eyeVarP: a computational framework for the identification of pathogenic variants specific to eye disease.
  35. Recent Advances in Mitochondrial Fission/Fusion-Targeted Therapy in Doxorubicin-Induced Cardiotoxicity.
  36. Apoptotic cell death in disease-Current understanding of the NCCD 2023.
  37. The Expanding Phenotypical Spectrum of WARS2-Related Disorder: Four Novel Cases with a Common Recurrent Variant.
  38. Clinical and genetic characteristics of children with COX20-associated mitochondrial disorder: case report and literature review.
  39. Structure of the human respiratory complex II.
  40. The Emerging Role of Mitochondrial Dysfunction in the Pathogenesis of Idiopathic Inflammatory Myopathies.
  41. The Warburg effect: a signature of mitochondrial overload.
  42. Clinical Validation of Tagmentation-Based Genome Sequencing for Germline Disorders.
  43. Gut mitochondrial defects drive neurodegeneration.
  44. Skeletal muscle mitochondrial interactome remodeling is linked to functional decline in aged female mice.
  45. Targeting Mitochondrial Oxidative Stress as a Strategy to Treat Aging and Age-Related Diseases.
  46. Targeting Mitochondrial Metabolism to Save the Failing Heart.
  47. Fish Models for Exploring Mitochondrial Dysfunction Affecting Neurodegenerative Disorders.
  48. Endogenous neural stem cells characterization using omics approaches: Current knowledge in health and disease.
  49. Branched-chain amino acid catabolism in muscle affects systemic BCAA levels but not insulin resistance.
  50. An Experimental Approach to Address the Functional Relationship between Antioxidant Enzymes and Mitochondrial Respiratory Complexes.
  51. Mitochondrial Dysfunction: A Cellular and Molecular Hub in Pathology of Metabolic Diseases and Infection.
  52. The Key Role of Mitochondrial Function in Health and Disease.
  53. Leveraging base-pair mammalian constraint to understand genetic variation and human disease.
  54. NAD supplementation in Parkinson's disease.
  55. Editorial: Muscle plasticity: Regulation of adaptive changes in muscles and mitochondrial dynamics.
  56. ATAD3A-related pontocerebellar hypoplasia: new patients and insights into phenotypic variability.
  57. Identifying spatial cellular structures with SPACE-GM.
  58. Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data.
  59. Humanin and Its Pathophysiological Roles in Aging: A Systematic Review.
  60. New tools for the investigation of muscle fiber-type spatial distributions across histological sections.
  61. The omics era: a nexus of untapped potential for Mendelian chromatinopathies.
  1. Clin Chem. 2023 Apr 26. pii: hvad037. [Epub ahead of print]
    Methodologies in Mitochondrial Testing: Diagnosing a Primary Mitochondrial Respiratory Chain Disorder.
    Emily L Gill, Jing Wang, Angela N Viaene, Stephen R Master, Rebecca D Ganetzky.
       BACKGROUND: Mitochondria are cytosolic organelles within most eukaryotic cells. Mitochondria generate the majority of cellular energy in the form of adenosine triphosphate (ATP) through oxidative phosphorylation (OxPhos). Pathogenic variants in mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) lead to defects in OxPhos and physiological malfunctions (Nat Rev Dis Primer 2016;2:16080.). Patients with primary mitochondrial disorders (PMD) experience heterogeneous symptoms, typically in multiple organ systems, depending on the tissues affected by mitochondrial dysfunction. Because of this heterogeneity, clinical diagnosis is challenging (Annu Rev Genomics Hum Genet 2017;18:257-75.). Laboratory diagnosis of mitochondrial disease depends on a multipronged analysis that can include biochemical, histopathologic, and genetic testing. Each of these modalities has complementary strengths and limitations in diagnostic utility.
    CONTENT: The primary focus of this review is on diagnosis and testing strategies for primary mitochondrial diseases. We review tissue samples utilized for testing, metabolic signatures, histologic findings, and molecular testing approaches. We conclude with future perspectives on mitochondrial testing.
    SUMMARY: This review offers an overview of the current biochemical, histologic, and genetic approaches available for mitochondrial testing. For each we review their diagnostic utility including complementary strengths and weaknesses. We identify gaps in current testing and possible future avenues for test development.
    DOI:  https://doi.org/10.1093/clinchem/hvad037
  2. J Cardiovasc Dev Dis. 2023 Apr 01. pii: 154. [Epub ahead of print]10(4):
    Why Don't More Mitochondrial Diseases Exhibit Cardiomyopathy?
    Nina Singh, Mindong Ren, Colin K L Phoon.
       BACKGROUND: Although the heart requires abundant energy, only 20-40% of children with mitochondrial diseases have cardiomyopathies.
    METHODS: We looked for differences in genes underlying mitochondrial diseases that do versus do not cause cardiomyopathy using the comprehensive Mitochondrial Disease Genes Compendium. Mining additional online resources, we further investigated possible energy deficits caused by non-oxidative phosphorylation (OXPHOS) genes associated with cardiomyopathy, probed the number of amino acids and protein interactors as surrogates for OXPHOS protein cardiac "importance", and identified mouse models for mitochondrial genes.
    RESULTS: A total of 107/241 (44%) mitochondrial genes was associated with cardiomyopathy; the highest proportion were OXPHOS genes (46%). OXPHOS (p = 0.001) and fatty acid oxidation (p = 0.009) defects were significantly associated with cardiomyopathy. Notably, 39/58 (67%) non-OXPHOS genes associated with cardiomyopathy were linked to defects in aerobic respiration. Larger OXPHOS proteins were associated with cardiomyopathy (p < 0.05). Mouse models exhibiting cardiomyopathy were found for 52/241 mitochondrial genes, shedding additional insights into biological mechanisms.
    CONCLUSIONS: While energy generation is strongly associated with cardiomyopathy in mitochondrial diseases, many energy generation defects are not linked to cardiomyopathy. The inconsistent link between mitochondrial disease and cardiomyopathy is likely to be multifactorial and includes tissue-specific expression, incomplete clinical data, and genetic background differences.
    Keywords:  cardiomyopathy; mitochondrial disease; mouse models; oxidative phosphorylation
    DOI:  https://doi.org/10.3390/jcdd10040154
  3. Nat Rev Drug Discov. 2023 Apr 27.
    Opportunities for mitochondrial disease gene therapy.
    Carlo Viscomi, Jelle van den Ameele, Kathrin C Meyer, Patrick F Chinnery.
      
    DOI:  https://doi.org/10.1038/d41573-023-00067-z
  4. Exp Neurol. 2023 Apr 25. pii: S0014-4886(23)00114-0. [Epub ahead of print] 114429
    POLG genotype influences degree of mitochondrial dysfunction in iPSC derived neural progenitors, but not the parent iPSC or derived glia.
    Yu Hong, Cecilie Katrin Kristiansen, Anbin Chen, Gonzalo Sanchez Nido, Lena Elise Høyland, Mathias Ziegler, Gareth John Sullivan, Laurence A Bindoff, Kristina Xiao Liang.
      Diseases caused by POLG mutations are the most common form of mitochondrial disease and associated with phenotypes of varying severity. Clinical studies have shown that patients with compound heterozygous POLG mutations have a lower survival rate than patients with homozygous mutations, but the molecular mechanisms behind this remain unexplored. Using an induced pluripotent stem cell (iPSC) model, we investigate differences between homozygous and compound heterozygous genotypes in different cell types, including patient-specific fibroblasts, iPSCs, and iPSC-derived neural stem cells (NSCs) and astrocytes. We found that compound heterozygous lines exhibited greater impairment of mitochondrial function in NSCs than homozygous NSCs, but not in fibroblasts, iPSCs, or astrocytes. Compared with homozygous NSCs, compound heterozygous NSCs exhibited more severe functional defects, including reduced ATP production, loss of mitochondrial DNA (mtDNA) copy number and complex I expression, disturbance of NAD+ metabolism, and higher ROS levels, which further led to cellular senescence and activation of mitophagy. RNA sequencing analysis revealed greater downregulation of mitochondrial and metabolic pathways, including the citric acid cycle and oxidative phosphorylation, in compound heterozygous NSCs. Our iPSC-based disease model can be widely used to understand the genotype-phenotype relationship of affected brain cells in mitochondrial diseases, and further drug discovery applications.
    Keywords:  Genotype; Mitochondrial function; Neural stem cells; Neuron; POLG
    DOI:  https://doi.org/10.1016/j.expneurol.2023.114429
  5. PLoS Genet. 2023 Apr 25. 19(4): e1010493
    Bendless is essential for PINK1-Park mediated Mitofusin degradation under mitochondrial stress caused by loss of LRPPRC.
    Rajit Narayanan Cheramangalam, Tarana Anand, Priyanka Pandey, Deepa Balasubramanian, Reshmi Varghese, Neha Singhal, Sonal Nagarkar Jaiswal, Manish Jaiswal.
      Cells under mitochondrial stress often co-opt mechanisms to maintain energy homeostasis, mitochondrial quality control and cell survival. A mechanistic understanding of such responses is crucial for further insight into mitochondrial biology and diseases. Through an unbiased genetic screen in Drosophila, we identify that mutations in lrpprc2, a homolog of the human LRPPRC gene that is linked to the French-Canadian Leigh syndrome, result in PINK1-Park activation. While the PINK1-Park pathway is well known to induce mitophagy, we show that PINK1-Park regulates mitochondrial dynamics by inducing the degradation of the mitochondrial fusion protein Mitofusin/Marf in lrpprc2 mutants. In our genetic screen, we also discover that Bendless, a K63-linked E2 conjugase, is a regulator of Marf, as loss of bendless results in increased Marf levels. We show that Bendless is required for PINK1 stability, and subsequently for PINK1-Park mediated Marf degradation under physiological conditions, and in response to mitochondrial stress as seen in lrpprc2. Additionally, we show that loss of bendless in lrpprc2 mutant eyes results in photoreceptor degeneration, indicating a neuroprotective role for Bendless-PINK1-Park mediated Marf degradation. Based on our observations, we propose that certain forms of mitochondrial stress activate Bendless-PINK1-Park to limit mitochondrial fusion, which is a cell-protective response.
    DOI:  https://doi.org/10.1371/journal.pgen.1010493
  6. Nat Aging. 2021 Sep;1(9): 755-756
    Mitochondrial carriers set the epigenetic age.
    Carina Groh, Johannes M Herrmann.
      
    DOI:  https://doi.org/10.1038/s43587-021-00111-w
  7. PLoS One. 2023 ;18(4): e0284541
    MTSviewer: A database to visualize mitochondrial targeting sequences, cleavage sites, and mutations on protein structures.
    Andrew N Bayne, Jing Dong, Saeid Amiri, Sali M K Farhan, Jean-François Trempe.
      Mitochondrial dysfunction is implicated in a wide array of human diseases ranging from neurodegenerative disorders to cardiovascular defects. The coordinated localization and import of proteins into mitochondria are essential processes that ensure mitochondrial homeostasis. The localization and import of most mitochondrial proteins are driven by N-terminal mitochondrial targeting sequences (MTS's), which interact with import machinery and are removed by the mitochondrial processing peptidase (MPP). The recent discovery of internal MTS's-those which are distributed throughout a protein and act as import regulators or secondary MPP cleavage sites-has expanded the role of both MTS's and MPP beyond conventional N-terminal regulatory pathways. Still, the global mutational landscape of MTS's remains poorly characterized, both from genetic and structural perspectives. To this end, we have integrated a variety of tools into one harmonized R/Shiny database called MTSviewer (https://neurobioinfo.github.io/MTSvieweR/), which combines MTS predictions, cleavage sites, genetic variants, pathogenicity predictions, and N-terminomics data with structural visualization using AlphaFold models of human and yeast mitochondrial proteomes. Using MTSviewer, we profiled all MTS-containing proteins across human and yeast mitochondrial proteomes and provide multiple case studies to highlight the utility of this database.
    DOI:  https://doi.org/10.1371/journal.pone.0284541
  8. EMBO J. 2023 Apr 27. e112799
    FBXL4 ubiquitin ligase deficiency promotes mitophagy by elevating NIX levels.
    Hannah Elcocks, Ailbhe J Brazel, Katy R McCarron, Manuel Kaulich, Koraljka Husnjak, Heather Mortiboys, Michael J Clague, Sylvie Urbé.
      Selective autophagy of mitochondria, mitophagy, is linked to mitochondrial quality control and as such is critical to a healthy organism. We have used a CRISPR/Cas9 approach to screen human E3 ubiquitin ligases for influence on mitophagy under both basal cell culture conditions and upon acute mitochondrial depolarization. We identify two cullin-RING ligase substrate receptors, VHL and FBXL4, as the most profound negative regulators of basal mitophagy. We show that these converge, albeit via different mechanisms, on control of the mitophagy adaptors BNIP3 and BNIP3L/NIX. FBXL4 restricts NIX and BNIP3 levels via direct interaction and protein destabilization, while VHL acts through suppression of HIF1α-mediated transcription of BNIP3 and NIX. Depletion of NIX but not BNIP3 is sufficient to restore mitophagy levels. Our study contributes to an understanding of the aetiology of early-onset mitochondrial encephalomyopathy that is supported by analysis of a disease-associated mutation. We further show that the compound MLN4924, which globally interferes with cullin-RING ligase activity, is a strong inducer of mitophagy, thus providing a research tool in this context and a candidate therapeutic agent for conditions linked to mitochondrial dysfunction.
    Keywords:  BNIP3; FBXL4; NIX; VHL; mitophagy
    DOI:  https://doi.org/10.15252/embj.2022112799
  9. J Mol Biol. 2023 Apr 25. pii: S0022-2836(23)00199-7. [Epub ahead of print] 168129
    The MitoLuc Assay System for Accurate Real-Time Monitoring of Mitochondrial Protein Import within Mammalian Cells.
    Hope I Needs, James S Lorriman, Gonçalo C Pereira, Jeremy M Henley, Ian Collinson.
      Mitochondrial protein import is critical for organelle biogenesis, bioenergetic function and health. The mechanism of which is poorly understood, particularly of the mammalian system. To address this problem we have established an assay to quantitatively monitor mitochondrial import inside mammalian cells. The reporting is based on a split luciferase, whereby the large fragment is segregated in the mitochondrial matrix and the small complementary fragment is fused to the C-terminus of a purified recombinant precursor protein destined for import. Following import the complementary fragments combine to form an active luciferase-providing a sensitive, accurate and continuous measure of protein import. This advance allows detailed mechanistic examination of the transport process in live cells, including the analysis of import breakdown associated with disease, and high-throughput drug screening. Furthermore, the set-up has the potential to be adapted for the analysis of alternative transport systems within different cell types, and multicellular model organisms.
    Keywords:  in-cell assay; kinetic analysis; mitochondria; protein import; split luciferase
    DOI:  https://doi.org/10.1016/j.jmb.2023.168129
  10. Brain. 2023 Apr 22. pii: awad136. [Epub ahead of print]
    SARM1 deletion delays cerebellar but not spinal cord degeneration in an enhanced mouse model of SPG7 deficiency.
    Carolina Montoro-Gámez, Hendrik Nolte, Thibaut Molinié, Giovanna Evangelista, Simon Tröder, Esther Barth, Milica Popovic, Aleksandra Trifunovic, Branko Zevnik, Thomas Langer, Elena I Rugarli.
      Hereditary spastic paraplegia is a neurological condition characterized by predominant axonal degeneration in long spinal tracts, leading to weakness and spasticity in the lower limbs. The NAD + -consuming enzyme SARM1 has emerged as a key executioner of axonal degeneration upon nerve transection and in some neuropathies. An increase in the nicotinamide mononucleotide/NAD+ ratio activates SARM1, causing catastrophic NAD+ depletion and axonal degeneration. However, the role of SARM1 in the pathogenesis of hereditary spastic paraplegia has not been investigated. Here, we report an enhanced mouse model for hereditary spastic paraplegia caused by mutations in SPG7. eSpg7 knock-out mice carry a deletion in both Spg7 and Afg3l1, a redundant homologue expressed in mice but not in humans. eSpg7 knock-out mice recapitulate the phenotypic features of human patients, showing progressive symptoms of spastic-ataxia and degeneration of axons in the spinal cord as well as the cerebellum. We show that the lack of SPG7 rewires the mitochondrial proteome in both tissues, leading to an early onset decrease in mitoribosomal subunits and a remodelling of mitochondrial solute carriers and transporters. To interrogate mechanisms leading to axonal degeneration in this mouse model, we explored the involvement of SARM1. Deletion of SARM1 delays the appearance of ataxic signs, rescues mitochondrial swelling and axonal degeneration of cerebellar granule cells and dampens neuroinflammation in the cerebellum. The loss of SARM1 also prevents endoplasmic reticulum abnormalities in long spinal cord axons, but does not halt the degeneration of these axons. Our data thus reveal a neuron-specific interplay between SARM1 and mitochondrial dysfunction caused by lack of SPG7 in hereditary spastic paraplegia.
    Keywords:  axonal degeneration; cerebellum; mitochondria; paraplegin; spinal cord
    DOI:  https://doi.org/10.1093/brain/awad136
  11. Nat Aging. 2022 Mar;2(3): 199-213
    Pleiotropic effects of mitochondria in aging.
    Tanes Lima, Terytty Yang Li, Adrienne Mottis, Johan Auwerx.
      Aging is typified by a progressive decline in mitochondrial activity and stress resilience. Here, we review how mitochondrial stress pathways have pleiotropic effects on cellular and systemic homeostasis, which can comprise protective or detrimental responses during aging. We describe recent evidence arguing that defects in these conserved adaptive pathways contribute to aging and age-related diseases. Signaling pathways regulating the mitochondrial unfolded protein response, mitochondrial membrane dynamics, and mitophagy are discussed, emphasizing how their failure contributes to heteroplasmy and de-regulation of key metabolites. Our current understanding of how these processes are controlled and interconnected explains how mitochondria can widely impact fundamental aspects of aging.
    DOI:  https://doi.org/10.1038/s43587-022-00191-2
  12. Nat Commun. 2023 Apr 24. 14(1): 2356
    Mitochondrial complex III deficiency drives c-MYC overexpression and illicit cell cycle entry leading to senescence and segmental progeria.
    Janne Purhonen, Rishi Banerjee, Vilma Wanne, Nina Sipari, Matthias Mörgelin, Vineta Fellman, Jukka Kallijärvi.
      Accumulating evidence suggests mitochondria as key modulators of normal and premature aging, yet whether primary oxidative phosphorylation (OXPHOS) deficiency can cause progeroid disease remains unclear. Here, we show that mice with severe isolated respiratory complex III (CIII) deficiency display nuclear DNA damage, cell cycle arrest, aberrant mitoses, and cellular senescence in the affected organs such as liver and kidney, and a systemic phenotype resembling juvenile-onset progeroid syndromes. Mechanistically, CIII deficiency triggers presymptomatic cancer-like c-MYC upregulation followed by excessive anabolic metabolism and illicit cell proliferation against lack of energy and biosynthetic precursors. Transgenic alternative oxidase dampens mitochondrial integrated stress response and the c-MYC induction, suppresses the illicit proliferation, and prevents juvenile lethality despite that canonical OXPHOS-linked functions remain uncorrected. Inhibition of c-MYC with the dominant-negative Omomyc protein relieves the DNA damage in CIII-deficient hepatocytes in vivo. Our results connect primary OXPHOS deficiency to genomic instability and progeroid pathogenesis and suggest that targeting c-MYC and aberrant cell proliferation may be therapeutic in mitochondrial diseases.
    DOI:  https://doi.org/10.1038/s41467-023-38027-1
  13. BMC Biol. 2023 04 24. 21(1): 94
    A novel protein encoded by circRsrc1 regulates mitochondrial ribosome assembly and translation during spermatogenesis.
    Shu Zhang, Chang Wang, Yue Wang, Hao Zhang, Chen Xu, Yiwei Cheng, Yan Yuan, Jiahao Sha, Xuejiang Guo, Yiqiang Cui.
       BACKGROUND: Circular RNAs (circRNAs) are a large class of mammalian RNAs. Several protein products translated by circRNAs have been reported to be involved in the development of various tissues and systems; however, their physiological functions in male reproduction have yet not been explored.
    RESULTS: Here, we report an endogenous circRNA (circRsrc1) that encodes a novel 161-amino-acid protein which we named Rsrc1-161aa through circRNA sequencing coupled with mass spectrometry analysis on mouse testicular tissues. Deletion of Rsrc1-161aa in mice impaired male fertility with a significant decrease in sperm count and motility due to dysfunctions of mitochondrial energy metabolism. A series of in vitro rescue experiments revealed that circRsrc1 regulates mitochondrial functions via its encoded protein Rsrc1-161aa. Mechanistically, Rsrc1-161aa directly interacts with mitochondrial protein C1qbp and enhances its binding activity to mitochondrial mRNAs, thereby regulating the assembly of mitochondrial ribosomes and affecting the translation of oxidative phosphorylation (OXPHOS) proteins and mitochondrial energy metabolism.
    CONCLUSIONS: Our studies reveal that Rsrc1-161aa protein encoded by circRsrc1 regulates mitochondrial ribosome assembly and translation during spermatogenesis, thereby affecting male fertility.
    Keywords:  C1qbp; Mitochondrial ribosome; Spermatogenesis; Translation; circRsrc1
    DOI:  https://doi.org/10.1186/s12915-023-01597-z
  14. Sci Signal. 2023 04 25. 16(782): eabi8948
    MICU1 regulates mitochondrial cristae structure and function independently of the mitochondrial Ca2+ uniporter channel.
    Dhanendra Tomar, Manfred Thomas, Joanne F Garbincius, Devin W Kolmetzky, Oniel Salik, Pooja Jadiya, Suresh K Joseph, April C Carpenter, György Hajnóczky, John W Elrod.
      MICU1 is a calcium (Ca2+)-binding protein that regulates the mitochondrial Ca2+ uniporter channel complex (mtCU) and mitochondrial Ca2+ uptake. MICU1 knockout mice display disorganized mitochondrial architecture, a phenotype that is distinct from that of mice with deficiencies in other mtCU subunits and, thus, is likely not explained by changes in mitochondrial matrix Ca2+ content. Using proteomic and cellular imaging techniques, we found that MICU1 localized to the mitochondrial contact site and cristae organizing system (MICOS) and directly interacted with the MICOS components MIC60 and CHCHD2 independently of the mtCU. We demonstrated that MICU1 was essential for MICOS complex formation and that MICU1 ablation resulted in altered cristae organization, mitochondrial ultrastructure, mitochondrial membrane dynamics, and cell death signaling. Together, our results suggest that MICU1 is an intermembrane space Ca2+ sensor that modulates mitochondrial membrane dynamics independently of matrix Ca2+ uptake. This system enables distinct Ca2+ signaling in the mitochondrial matrix and at the intermembrane space to modulate cellular energetics and cell death in a concerted manner.
    DOI:  https://doi.org/10.1126/scisignal.abi8948
  15. J Clin Invest. 2023 May 01. pii: e163771. [Epub ahead of print]133(9):
    iPSC-derived retinal pigmented epithelial cells from patients with macular telangiectasia show decreased mitochondrial function.
    Kevin T Eade, Brendan Robert E Ansell, Sarah Giles, Regis Fallon, Sarah Harkins-Perry, Takayuki Nagasaki, Simone Tzaridis, Martina Wallace, Elizabeth A Mills, Samaneh Farashi, Alec Johnson, Lydia Sauer, Barbara Hart, Elena D Rubio, Melanie Bahlo, Christian Metallo, Rando Allikmets, Marin L Gantner, Paul S Bernstein, Martin Friedlander.
      Patient-derived induced pluripotent stem cells (iPSCs) provide a powerful tool for identifying cellular and molecular mechanisms of disease. Macular telangiectasia type 2 (MacTel) is a rare, late-onset degenerative retinal disease with an extremely heterogeneous genetic architecture, lending itself to the use of iPSCs. Whole-exome sequencing screens and pedigree analyses have identified rare causative mutations that account for less than 5% of cases. Metabolomic surveys of patient populations and GWAS have linked MacTel to decreased circulating levels of serine and elevated levels of neurotoxic 1-deoxysphingolipids (1-dSLs). However, retina-specific, disease-contributing factors have yet to be identified. Here, we used iPSC-differentiated retinal pigmented epithelial (iRPE) cells derived from donors with or without MacTel to screen for novel cell-intrinsic pathological mechanisms. We show that MacTel iRPE cells mimicked the low serine levels observed in serum from patients with MacTel. Through RNA-Seq and gene set enrichment pathway analysis, we determined that MacTel iRPE cells are enriched in cellular stress pathways and dysregulation of central carbon metabolism. Using respirometry and mitochondrial stress testing, we functionally validated that MacTel iRPE cells had a reduction in mitochondrial function that was independent of defects in serine biosynthesis and 1-dSL accumulation. Thus, we identified phenotypes that may constitute alternative disease mechanisms beyond the known serine/sphingolipid pathway.
    Keywords:  Mitochondria; Ophthalmology; Retinopathy; Stem cells; iPS cells
    DOI:  https://doi.org/10.1172/JCI163771
  16. BMC Neurol. 2023 Apr 24. 23(1): 165
    Ischemic optic neuropathy as first presentation in patient with m.3243 A > G MELAS classic mutation.
    Simone Scarcella, Laura Dell'Arti, Delia Gagliardi, Francesca Magri, Alessandra Govoni, Daniele Velardo, Claudia Mainetti, Valeria Minorini, Dario Ronchi, Daniela Piga, Giacomo Pietro Comi, Stefania Corti, Megi Meneri.
       BACKGROUND: Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome is a systemic disorder in which multi-organ dysfunction may occur from mitochondrial metabolism failure. Maternally inherited mutations in the MT-TL1 gene are the most frequent causes for this disorder. Clinical manifestations may include stroke-like episodes, epilepsy, dementia, headache and myopathy. Among these, acute visual failure, usually in association with cortical blindness, can occur because of stroke-like episodes affecting the occipital cortex or the visual pathways. Vision loss due to optic neuropathy is otherwise considered a typical manifestation of other mitochondrial diseases such as Leber hereditary optic neuropathy (LHON).
    CASE PRESENTATION: Here we describe a 55-year-old woman, sister of a previously described patient with MELAS harbouring the m.3243A > G (p.0, MT-TL1) mutation, with otherwise unremarkable medical history, that presented with subacute, painful visual impairment of one eye, accompanied by proximal muscular pain and headache. Over the next weeks, she developed severe and progressive vision loss limited to one eye. Ocular examination confirmed unilateral swelling of the optic nerve head; fluorescein angiography showed segmental perfusion delay in the optic disc and papillary leakage. Neuroimaging, blood and CSF examination and temporal artery biopsy ruled out neuroinflammatory disorders and giant cell arteritis (GCA). Mitochondrial sequencing analysis confirmed the m.3243A > G transition, and excluded the three most common LHON mutations, as well as the m.3376G > A LHON/MELAS overlap syndrome mutation. Based on the constellation of clinical symptoms and signs presented in our patient, including the muscular involvement, and the results of the investigations, the diagnosis of optic neuropathy as a stroke-like event affecting the optic disc was performed. L-arginine and ubidecarenone therapies were started with the aim to improve stroke-like episode symptoms and prevention. The visual defect remained stable with no further progression or outbreak of new symptoms.
    CONCLUSIONS: Atypical clinical presentations must be always considered in mitochondrial disorders, even in well-described phenotypes and when mutational load in peripheral tissue is low. Mitotic segregation of mitochondrial DNA (mtDNA) does not allow to know the exact degree of heteroplasmy existent within different tissue, such as retina and optic nerve. Important therapeutic implications arise from a correct diagnosis of atypical presentation of mitochondrial disorders.
    Keywords:  MELAS; Mitochondrial disease; NAION; Optic neuropathy; Stroke-like episodes
    DOI:  https://doi.org/10.1186/s12883-023-03198-3
  17. Nat Aging. 2022 Mar;2(3): 254-263
    Healthy aging and muscle function are positively associated with NAD+ abundance in humans.
    Georges E Janssens, Lotte Grevendonk, Ruben Zapata Perez, Bauke V Schomakers, Johan de Vogel-van den Bosch, Jan M W Geurts, Michel van Weeghel, Patrick Schrauwen, Riekelt H Houtkooper, Joris Hoeks.
      Skeletal muscle is greatly affected by aging, resulting in a loss of metabolic and physical function. However, the underlying molecular processes and how (lack of) physical activity is involved in age-related metabolic decline in muscle function in humans is largely unknown. Here, we compared, in a cross-sectional study, the muscle metabolome from young to older adults, whereby the older adults were exercise trained, had normal physical activity levels or were physically impaired. Nicotinamide adenine dinucleotide (NAD+) was one of the most prominent metabolites that was lower in older adults, in line with preclinical models. This lower level was even more pronounced in impaired older individuals, and conversely, exercise-trained older individuals had NAD+ levels that were more similar to those found in younger individuals. NAD+ abundance positively correlated with average number of steps per day and mitochondrial and muscle functioning. Our work suggests that a clear association exists between NAD+ and health status in human aging.
    DOI:  https://doi.org/10.1038/s43587-022-00174-3
  18. Cell Rep. 2023 Apr 24. pii: S2211-1247(23)00445-X. [Epub ahead of print]42(5): 112434
    Mitochondrial dynamics define muscle fiber type by modulating cellular metabolic pathways.
    Tatsuki Yasuda, Takaya Ishihara, Ayaka Ichimura, Naotada Ishihara.
      Skeletal muscle is highly developed after birth, consisting of glycolytic fast-twitch and oxidative slow-twitch fibers; however, the mechanisms of fiber-type-specific differentiation are poorly understood. Here, we found an unexpected role of mitochondrial fission in the differentiation of fast-twitch oxidative fibers. Depletion of the mitochondrial fission factor dynamin-related protein 1 (Drp1) in mouse skeletal muscle and cultured myotubes results in specific reduction of fast-twitch muscle fibers independent of respiratory function. Altered mitochondrial fission causes activation of the Akt/mammalian target of rapamycin (mTOR) pathway via mitochondrial accumulation of mTOR complex 2 (mTORC2), and rapamycin administration rescues the reduction of fast-twitch fibers in vivo and in vitro. Under Akt/mTOR activation, the mitochondria-related cytokine growth differentiation factor 15 is upregulated, which represses fast-twitch fiber differentiation. Our findings reveal a crucial role of mitochondrial dynamics in the activation of mTORC2 on mitochondria, resulting in the differentiation of muscle fibers.
    Keywords:  Akt; CP: Metabolism; Drp1; GDF-15; mTOR; mitochondria; mitochondrial dynamics; muscle atrophy; muscle differentiation
    DOI:  https://doi.org/10.1016/j.celrep.2023.112434
  19. Nucleic Acids Res. 2023 Apr 24. pii: gkad299. [Epub ahead of print]
    Not4-dependent targeting of MMF1 mRNA to mitochondria limits its expression via ribosome pausing, Egd1 ubiquitination, Caf130, no-go-decay and autophagy.
    Siyu Chen, George Allen, Olesya O Panasenko, Martine A Collart.
      The Ccr4-Not complex is a conserved multi protein complex with diverse roles in the mRNA life cycle. Recently we determined that the Not1 and Not4 subunits of Ccr4-Not inversely regulate mRNA solubility and thereby impact dynamics of co-translation events. One mRNA whose solubility is limited by Not4 is MMF1 encoding a mitochondrial matrix protein. In this work we uncover a mechanism that limits MMF1 overexpression and depends upon its co-translational targeting to the mitochondria. We have named this mechanism Mito-ENCay. This mechanism relies on Not4 promoting ribosome pausing during MMF1 translation, and hence the co-translational docking of the MMF1 mRNA to mitochondria via the mitochondrial targeting sequence of the Mmf1 nascent chain, the Egd1 chaperone, the Om14 mitochondrial outer membrane protein and the co-translational import machinery. Besides co-translational Mitochondrial targeting, Mito-ENCay depends upon Egd1 ubiquitination by Not4, the Caf130 subunit of the Ccr4-Not complex, the mitochondrial outer membrane protein Cis1, autophagy and no-go-decay.
    DOI:  https://doi.org/10.1093/nar/gkad299
  20. Mol Cell Neurosci. 2023 Apr 24. pii: S1044-7431(23)00047-7. [Epub ahead of print] 103853
    The Translocase of the Outer Mitochondrial Membrane (TOM40) is required for mitochondrial dynamics and neuronal integrity in Dorsal Root Ganglion Neurons.
    Caitlin Overmeyer, Kylie Jorgensen, Bhupinder P S Vohra.
      Polymorphisms and altered expression of the Translocase of the Outer Mitochondrial Membrane - 40 kD (Tom40) are observed in neurodegenerative disease subjects. We utilized in vitro cultured dorsal root ganglion (DRG) neurons to investigate the association of TOM40 depletion to neurodegeneration, and to unravel the mechanism of neurodegeneration induced by decreased levels of TOM40 protein. We provide evidence that severity of neurodegeneration induced in the TOM40 depleted neurons increases with the increase in the depletion of TOM40 and is exacerbated by an increase in the duration of TOM40 depletion. We also demonstrate that TOM40 depletion causes a surge in neuronal calcium levels, decreases mitochondrial motility, increases mitochondrial fission, and decreases neuronal ATP levels. We observed that alterations in the neuronal calcium homeostasis and mitochondrial dynamics precede BCL-xl and NMNAT1 dependent neurodegenerative pathways in the TOM40 depleted neurons. This data also suggests that manipulation of BCL-xl and NMNAT1 may be of therapeutic value in TOM40 associated neurodegenerative disorders.
    Keywords:  Axon degeneration; Bcl-xl; Mitochondrial dynamics; Nmnat1; Tom40
    DOI:  https://doi.org/10.1016/j.mcn.2023.103853
  21. Life (Basel). 2023 Apr 09. pii: 975. [Epub ahead of print]13(4):
    Mitochondrial Function and Signaling to Regulate Cellular Life.
    Rafael A Casuso.
      Mitochondria are essential organelles found in nearly all eukaryotic cells, responsible for producing the energy that drives cellular processes [...].
    DOI:  https://doi.org/10.3390/life13040975
  22. Nat Metab. 2023 Apr;5(4): 546-562
    Multifaceted mitochondria: moving mitochondrial science beyond function and dysfunction.
    Anna S Monzel, José Antonio Enríquez, Martin Picard.
      Mitochondria have cell-type specific phenotypes, perform dozens of interconnected functions and undergo dynamic and often reversible physiological recalibrations. Given their multifunctional and malleable nature, the frequently used terms 'mitochondrial function' and 'mitochondrial dysfunction' are misleading misnomers that fail to capture the complexity of mitochondrial biology. To increase the conceptual and experimental specificity in mitochondrial science, we propose a terminology system that distinguishes between (1) cell-dependent properties, (2) molecular features, (3) activities, (4) functions and (5) behaviours. A hierarchical terminology system that accurately captures the multifaceted nature of mitochondria will achieve three important outcomes. It will convey a more holistic picture of mitochondria as we teach the next generations of mitochondrial biologists, maximize progress in the rapidly expanding field of mitochondrial science, and also facilitate synergy with other disciplines. Improving specificity in the language around mitochondrial science is a step towards refining our understanding of the mechanisms by which this unique family of organelles contributes to cellular and organismal health.
    DOI:  https://doi.org/10.1038/s42255-023-00783-1
  23. Neurochem Res. 2023 Apr 25.
    The Role of PGC-1α-Mediated Mitochondrial Biogenesis in Neurons.
    Mengjie Chen, Ruyu Yan, Jiansheng Luo, Jiaqi Ning, Ruiling Zhou, Lingling Ding.
      Neurons are highly dependent on mitochondrial ATP production and Ca2+ buffering. Neurons have unique compartmentalized anatomy and energy requirements, and each compartment requires continuously renewed mitochondria to maintain neuronal survival and activity. Peroxisome proliferator-activated receptor-gamma coactivator-1α (PGC-1α) is a key factor in the regulation of mitochondrial biogenesis. It is widely accepted that mitochondria are synthesized in the cell body and transported via axons to the distal end. However, axonal mitochondrial biogenesis is necessary to maintain axonal bioenergy supply and mitochondrial density due to limitations in mitochondrial axonal transport rate and mitochondrial protein lifespan. In addition, impaired mitochondrial biogenesis leading to inadequate energy supply and neuronal damage has been observed in neurological disorders. In this review, we focus on the sites where mitochondrial biogenesis occurs in neurons and the mechanisms by which it maintains axonal mitochondrial density. Finally, we summarize several neurological disorders in which mitochondrial biogenesis is affected.
    Keywords:  Axons; Cell body; Mitochondrial biogenesis; Neurological disorders; Neurons; PGC-1α
    DOI:  https://doi.org/10.1007/s11064-023-03934-8
  24. Int J Mol Sci. 2023 Apr 10. pii: 7005. [Epub ahead of print]24(8):
    The Potential Use of Mitochondrial Extracellular Vesicles as Biomarkers or Therapeutical Tools.
    Jorge Sanz-Ros, Cristina Mas-Bargues, Nekane Romero-García, Javier Huete-Acevedo, Mar Dromant, Consuelo Borrás.
      The mitochondria play a crucial role in cellular metabolism, reactive oxygen species (ROS) production, and apoptosis. Aberrant mitochondria can cause severe damage to the cells, which have established a tight quality control for the mitochondria. This process avoids the accumulation of damaged mitochondria and can lead to the release of mitochondrial constituents to the extracellular milieu through mitochondrial extracellular vesicles (MitoEVs). These MitoEVs carry mtDNA, rRNA, tRNA, and protein complexes of the respiratory chain, and the largest MitoEVs can even transport whole mitochondria. Macrophages ultimately engulf these MitoEVs to undergo outsourced mitophagy. Recently, it has been reported that MitoEVs can also contain healthy mitochondria, whose function seems to be the rescue of stressed cells by restoring the loss of mitochondrial function. This mitochondrial transfer has opened the field of their use as potential disease biomarkers and therapeutic tools. This review describes this new EVs-mediated transfer of the mitochondria and the current application of MitoEVs in the clinical environment.
    Keywords:  MitoEVs; biomarker; extracellular vesicles; mitochondria; therapy
    DOI:  https://doi.org/10.3390/ijms24087005
  25. EMBO Mol Med. 2023 Apr 24. e17463
    Multi-omic profiling reveals an RNA processing rheostat that predisposes to prostate cancer.
    Maike Stentenbach, Judith A Ermer, Danielle L Rudler, Kara L Perks, Samuel A Raven, Richard G Lee, Tim McCubbin, Esteban Marcellin, Stefan J Siira, Oliver Rackham, Aleksandra Filipovska.
      Prostate cancer is the most commonly diagnosed malignancy and the third leading cause of cancer deaths. GWAS have identified variants associated with prostate cancer susceptibility; however, mechanistic and functional validation of these mutations is lacking. We used CRISPR-Cas9 genome editing to introduce a missense variant identified in the ELAC2 gene, which encodes a dually localised nuclear and mitochondrial RNA processing enzyme, into the mouse Elac2 gene as well as to generate a prostate-specific knockout of Elac2. These mutations caused enlargement and inflammation of the prostate and nodule formation. The Elac2 variant or knockout mice on the background of the transgenic adenocarcinoma of the mouse prostate (TRAMP) model show that Elac2 mutation with a secondary genetic insult exacerbated the onset and progression of prostate cancer. Multiomic profiling revealed defects in energy metabolism that activated proinflammatory and tumorigenic pathways as a consequence of impaired noncoding RNA processing and reduced protein synthesis. Our physiologically relevant models show that the ELAC2 variant is a predisposing factor for prostate cancer and identify changes that underlie the pathogenesis of this cancer.
    Keywords:  RNA processing; gene expression; mitochondria; prostate cancer susceptibility
    DOI:  https://doi.org/10.15252/emmm.202317463
  26. Nat Aging. 2021 Sep;1(9): 810-825
    Chromatin remodeling due to degradation of citrate carrier impairs osteogenesis of aged mesenchymal stem cells.
    Andromachi Pouikli, Swati Parekh, Monika Maleszewska, Chrysa Nikopoulou, Maarouf Baghdadi, Ignacio Tripodi, Kat Folz-Donahue, Yvonne Hinze, Andrea Mesaros, David Hoey, Patrick Giavalisco, Robin Dowell, Linda Partridge, Peter Tessarz.
      Aging is accompanied by a general decline in the function of many cellular pathways. However, whether these are causally or functionally interconnected remains elusive. Here, we study the effect of mitochondrial-nuclear communication on stem cell aging. We show that aged mesenchymal stem cells exhibit reduced chromatin accessibility and lower histone acetylation, particularly on promoters and enhancers of osteogenic genes. The reduced histone acetylation is due to impaired export of mitochondrial acetyl-CoA, owing to the lower levels of citrate carrier (CiC). We demonstrate that aged cells showed enhanced lysosomal degradation of CiC, which is mediated via mitochondrial-derived vesicles. Strikingly, restoring cytosolic acetyl-CoA levels either by exogenous CiC expression or via acetate supplementation, remodels the chromatin landscape and rescues the osteogenesis defects of aged mesenchymal stem cells. Collectively, our results establish a tight, age-dependent connection between mitochondrial quality control, chromatin and stem cell fate, which are linked together by CiC.
    DOI:  https://doi.org/10.1038/s43587-021-00105-8
  27. Aging Cell. 2023 Apr 26. e13852
    Dysregulated cellular redox status during hyperammonemia causes mitochondrial dysfunction and senescence by inhibiting sirtuin-mediated deacetylation.
    Saurabh Mishra, Nicole Welch, Manikandan Karthikeyan, Annette Bellar, Ryan Musich, Shashi Shekhar Singh, Dongmei Zhang, Jinendiran Sekar, Amy H Attaway, Aruna Chelluboyina, Shuhui Wang Lorkowski, Sanjoy Roychowdhary, Ling Li, Belinda Willard, Jonathan D Smith, Charles L Hoppel, Vidula Vachharajani, Avinash Kumar, Srinivasan Dasarathy.
      Perturbed metabolism of ammonia, an endogenous cytotoxin, causes mitochondrial dysfunction, reduced NAD+ /NADH (redox) ratio, and postmitotic senescence. Sirtuins are NAD+ -dependent deacetylases that delay senescence. In multiomics analyses, NAD metabolism and sirtuin pathways are enriched during hyperammonemia. Consistently, NAD+ -dependent Sirtuin3 (Sirt3) expression and deacetylase activity were decreased, and protein acetylation was increased in human and murine skeletal muscle/myotubes. Global acetylomics and subcellular fractions from myotubes showed hyperammonemia-induced hyperacetylation of cellular signaling and mitochondrial proteins. We dissected the mechanisms and consequences of hyperammonemia-induced NAD metabolism by complementary genetic and chemical approaches. Hyperammonemia inhibited electron transport chain components, specifically complex I that oxidizes NADH to NAD+ , that resulted in lower redox ratio. Ammonia also caused mitochondrial oxidative dysfunction, lower mitochondrial NAD+ -sensor Sirt3, protein hyperacetylation, and postmitotic senescence. Mitochondrial-targeted Lactobacillus brevis NADH oxidase (MitoLbNOX), but not NAD+ precursor nicotinamide riboside, reversed ammonia-induced oxidative dysfunction, electron transport chain supercomplex disassembly, lower ATP and NAD+ content, protein hyperacetylation, Sirt3 dysfunction and postmitotic senescence in myotubes. Even though Sirt3 overexpression reversed ammonia-induced hyperacetylation, lower redox status or mitochondrial oxidative dysfunction were not reversed. These data show that acetylation is a consequence of, but is not the mechanism of, lower redox status or oxidative dysfunction during hyperammonemia. Targeting NADH oxidation is a potential approach to reverse and potentially prevent ammonia-induced postmitotic senescence in skeletal muscle. Since dysregulated ammonia metabolism occurs with aging, and NAD+ biosynthesis is reduced in sarcopenia, our studies provide a biochemical basis for cellular senescence and have relevance in multiple tissues.
    Keywords:  acetylation; human inducible pluripotent stem cells; mitochondria; multiomics; redox; sirtuin; skeletal muscle; systems biology
    DOI:  https://doi.org/10.1111/acel.13852
  28. Neurol Genet. 2023 Apr;9(2): e200063
    New-Onset Refractory Status Epilepticus Due to a Novel MT-TF Variant: Time for Acute Genetic Testing Before Treatment?
    Elisabetta Indelicato, Johannes Pfeilstetter, Michael Zech, Iris Unterberger, Julia Wanschitz, Steffen Berweck, Sylvia Boesch.
       Objective: The gene MT-TF encodes the mitochondrial tRNA of phenylalanine (tRNAphe). Its variations have been described as extremely rare etiologies of a variety of mitochondrial phenotypes.
    Methods: By means of whole-exome sequencing (WES), we detected a novel likely causative MT-TF variant (m.610T>C) in a family presenting with a combined movement disorder and epilepsy phenotype. The variant was present at 97% heteroplasmy in the peripheral blood and in a homoplasmic state in skin fibroblast-derived DNA.
    Results: The inaugural manifestation in the index patient was new-onset refractory myoclonic status epilepticus (NORSE) at the age of 29 years. Her son presented later with developmental regression and myoclonic epilepsy. On the beginning of valproate because of ongoing myoclonic seizures, the index patient developed a generalized brain edema requiring bilateral craniotomy. In the course of the disease, epileptic manifestations abated, and both patients developed a severe movement disorder phenotype with prominent spastic-dystonic features. Both patients did not display any further sign of mitochondrial disease.
    Discussion: Our report expands the clinicogenetic background of tRNAphe disease spectrum and highlights pitfalls in the diagnostics and management of mitochondrial epilepsy. The present findings advocate the introduction of rapid genetic testing in the diagnostic flow chart of NORSE in adults.
    DOI:  https://doi.org/10.1212/NXG.0000000000200063
  29. Int J Hyperthermia. 2023 ;40(1): 2205066
    Passive heat stress induces mitochondrial adaptations in skeletal muscle.
    Erik D Marchant, W Bradley Nelson, Robert D Hyldahl, Jayson R Gifford, Chad R Hancock.
      The mitochondria are central to skeletal muscle metabolic health. Impaired mitochondrial function is associated with various muscle pathologies, including insulin resistance and muscle atrophy. As a result, continuous efforts are made to find ways to improve mitochondrial health in the context of disuse and disease. While exercise is known to cause robust improvements in mitochondrial health, not all individuals are able to exercise. This creates a need for alternate interventions which elicit some of the same benefits as exercise. Passive heating (i.e., application of heat in the absence of muscle contractions) is one potential intervention which has been shown to increase mitochondrial enzyme content and activity, and to improve mitochondrial respiration. Associated with increases in mitochondrial content and/or function, passive heating can also improve insulin sensitivity in the context of type II diabetes and preserve muscle mass in the face of limb disuse. This area of research remains in its infancy, with many questions yet to be answered about how to maximize the benefits of passive heating and elucidate the mechanisms by which heat stress affects muscle mitochondria.
    Keywords:  HSP; Heat; atrophy; chaperones; heat shock response (i.e.; hypoxia; metabolism; microenvironment; mitochondria; pH; perfusion effects; physiological effects of hyperthermia (i.e.,; redox); skeletal muscle; thermal; thermotolerance)
    DOI:  https://doi.org/10.1080/02656736.2023.2205066
  30. Nat Aging. 2022 Apr;2(4): 317-331
    Suppression of intestinal dysfunction in a Drosophila model of Parkinson's disease is neuroprotective.
    Giorgio Fedele, Samantha H Y Loh, Ivana Celardo, Nuno Santos Leal, Susann Lehmann, Ana C Costa, L Miguel Martins.
      The innate immune response mounts a defense against foreign invaders and declines with age. An inappropriate induction of this response can cause diseases. Previous studies showed that mitochondria can be repurposed to promote inflammatory signaling. Damaged mitochondria can also trigger inflammation and promote diseases. Mutations in pink1, a gene required for mitochondrial health, cause Parkinson's disease, and Drosophila melanogaster pink1 mutants accumulate damaged mitochondria. Here, we show that defective mitochondria in pink1 mutants activate Relish targets and demonstrate that inflammatory signaling causes age-dependent intestinal dysfunction in pink1-mutant flies. These effects result in the death of intestinal cells, metabolic reprogramming and neurotoxicity. We found that Relish signaling is activated downstream of a pathway stimulated by cytosolic DNA. Suppression of Relish in the intestinal midgut of pink1-mutant flies restores mitochondrial function and is neuroprotective. We thus conclude that gut-brain communication modulates neurotoxicity in a fly model of Parkinson's disease through a mechanism involving mitochondrial dysfunction.
    DOI:  https://doi.org/10.1038/s43587-022-00194-z
  31. Int J Mol Sci. 2023 Apr 13. pii: 7221. [Epub ahead of print]24(8):
    Mitochondrial Bioenergy in Neurodegenerative Disease: Huntington and Parkinson.
    Annalisa Tassone, Maria Meringolo, Giulia Ponterio, Paola Bonsi, Tommaso Schirinzi, Giuseppina Martella.
      Strong evidence suggests a correlation between degeneration and mitochondrial deficiency. Typical cases of degeneration can be observed in physiological phenomena (i.e., ageing) as well as in neurological neurodegenerative diseases and cancer. All these pathologies have the dyshomeostasis of mitochondrial bioenergy as a common denominator. Neurodegenerative diseases show bioenergetic imbalances in their pathogenesis or progression. Huntington's chorea and Parkinson's disease are both neurodegenerative diseases, but while Huntington's disease is genetic and progressive with early manifestation and severe penetrance, Parkinson's disease is a pathology with multifactorial aspects. Indeed, there are different types of Parkinson/Parkinsonism. Many forms are early-onset diseases linked to gene mutations, while others could be idiopathic, appear in young adults, or be post-injury senescence conditions. Although Huntington's is defined as a hyperkinetic disorder, Parkinson's is a hypokinetic disorder. However, they both share a lot of similarities, such as neuronal excitability, the loss of striatal function, psychiatric comorbidity, etc. In this review, we will describe the start and development of both diseases in relation to mitochondrial dysfunction. These dysfunctions act on energy metabolism and reduce the vitality of neurons in many different brain areas.
    Keywords:  Huntington’s disease; Parkinson’s disease; basal ganglia; calcium; energy metabolism; mitochondria; movement disorders; synaptic plasticity
    DOI:  https://doi.org/10.3390/ijms24087221
  32. J Am Chem Soc. 2023 Apr 27.
    Visualizing Cardiolipin In Situ with HKCL-1M, a Highly Selective and Sensitive Fluorescent Probe.
    Wei Wang, Nai-Kei Wong, Siu-Lun Bok, You Xu, Yang Guo, Lu Xu, Meiling Zuo, Claudette M St Croix, Gaowei Mao, Alexandr Kapralov, Hülya Bayir, Valerian E Kagan, Dan Yang.
      Reliable probing of cardiolipin (CL) content in dynamic cellular milieux presents significant challenges and great opportunities for understanding mitochondria-related diseases, including cancer, neurodegeneration, and diabetes mellitus. In intact respiring cells, selectivity and sensitivity for CL detection are technically demanding due to structural similarities among phospholipids and compartmental secludedness of the inner mitochondrial membrane. Here, we report a novel "turn-on" fluorescent probe HKCL-1M for detecting CL in situ. HKCL-1M displays outstanding sensitivity and selectivity toward CL through specific noncovalent interactions. In live-cell imaging, its hydrolyzed product HKCL-1 efficiently retained itself in intact cells independent of mitochondrial membrane potential (Δψm). The probe robustly co-localizes with mitochondria and outperforms 10-N-nonyl acridine orange (NAO) and Δψm-dependent dyes with superior photostability and negligible phototoxicity. Our work thus opens up new opportunities for studying mitochondrial biology through efficient and reliable visualization of CL in situ.
    DOI:  https://doi.org/10.1021/jacs.3c00243
  33. Adv Drug Deliv Rev. 2023 Apr 21. pii: S0169-409X(23)00156-4. [Epub ahead of print] 114841
    Fluorescence microscopic platforms imaging mitochondrial abnormalities in neurodegenerative diseases.
    Yicheng Wang, Pengwei Wang, Cong Li.
      Neurodegenerative diseases (NDs) are progressive disorders that cause the degeneration of neurons. Mitochondrial dysfunction is a common symptom in NDs and plays a crucial role in neuronal loss. Mitochondrial abnormalities can be observed in the early stages of NDs and evolve throughout disease progression. Visualizing mitochondrial abnormalities can help understand ND progression and develop new therapeutic strategies. Fluorescence microscopy is a powerful tool for dynamically imaging mitochondria due to its high sensitivity and spatiotemporal resolution. This review discusses the relationship between mitochondrial dysfunction and ND progression, potential biomarkers for imaging dysfunctional mitochondria, advances in fluorescence microscopy for detecting organelles, the performance of fluorescence probes in visualizing ND-associated mitochondria, and the challenges and opportunities for developing new generations of fluorescence imaging platforms for monitoring mitochondria in NDs.
    Keywords:  Fluorescence microscopic imaging; Fluorescence probes; Mitochondria dysfunction; Neurodegenerative diseases
    DOI:  https://doi.org/10.1016/j.addr.2023.114841
  34. Genet Med. 2023 Apr 20. pii: S1098-3600(23)00875-4. [Epub ahead of print] 100862
    eyeVarP: a computational framework for the identification of pathogenic variants specific to eye disease.
    Manojkumar Kumaran, Bharanidharan Devarajan.
       PURPOSE: Disease-specific pathogenic variants prediction tools that predict pathogenic variants from benign have been improved through disease specificity recently. However, they have not been evaluated on disease-specific pathogenic variants compared to other diseases, which would help to prioritize disease-specific variants from several genes or novel genes. Thus, we hypothesize that features of pathogenic variants alone would provide a better model.
    METHODS: We developed eyeVarP, an eye disease-specific variant prioritization tool, which applied the Random Forest (RF) algorithm to the dataset of pathogenic variants of eye diseases and other diseases. We also developed the VarP tool and generalized pipeline to filter missense and InDels and predict their pathogenicity from Exome or genome sequencing data, which provides a complete computational procedure.
    RESULTS: eyeVarP outperformed pan-disease-specific tools in identifying eye disease-specific pathogenic variants under the top ten. VarP outperformed twelve pathogenicity prediction tools with an accuracy of 95% in correctly identifying the pathogenicity of missense and InDels. The complete pipeline would help to develop disease-specific tools for other genetic disorders.
    CONCLUSION: eyeVarP performs better in identifying eye disease-specific pathogenic variants using pathogenic variant features and gene features. Implementing such complete computational procedures would significantly improve the clinical variant interpretation for specific diseases.
    Keywords:  Eye disease; Machine Learning; Pathogenic Variants; Variant Filtering; Variant Prioritization
    DOI:  https://doi.org/10.1016/j.gim.2023.100862
  35. Pharmaceutics. 2023 Apr 07. pii: 1182. [Epub ahead of print]15(4):
    Recent Advances in Mitochondrial Fission/Fusion-Targeted Therapy in Doxorubicin-Induced Cardiotoxicity.
    Chayodom Maneechote, Siriporn C Chattipakorn, Nipon Chattipakorn.
      Doxorubicin (DOX) has been recognized as one of the most effective chemotherapies and extensively used in the clinical settings of human cancer. However, DOX-mediated cardiotoxicity is known to compromise the clinical effectiveness of chemotherapy, resulting in cardiomyopathy and heart failure. Recently, accumulation of dysfunctional mitochondria via alteration of the mitochondrial fission/fusion dynamic processes has been identified as a potential mechanism underlying DOX cardiotoxicity. DOX-induced excessive fission in conjunction with impaired fusion could severely promote mitochondrial fragmentation and cardiomyocyte death, while modulation of mitochondrial dynamic proteins using either fission inhibitors (e.g., Mdivi-1) or fusion promoters (e.g., M1) can provide cardioprotection against DOX-induced cardiotoxicity. In this review, we focus particularly on the roles of mitochondrial dynamic pathways and the current advanced therapies in mitochondrial dynamics-targeted anti-cardiotoxicity of DOX. This review summarizes all the novel insights into the development of anti-cardiotoxic effects of DOX via the targeting of mitochondrial dynamic pathways, thereby encouraging and guiding future clinical investigations to focus on the potential application of mitochondrial dynamic modulators in the setting of DOX-induced cardiotoxicity.
    Keywords:  cardiotoxicity; doxorubicin; mitochondrial dynamics; mitochondrial fission; mitochondrial fusion
    DOI:  https://doi.org/10.3390/pharmaceutics15041182
  36. Cell Death Differ. 2023 Apr 26.
    Apoptotic cell death in disease-Current understanding of the NCCD 2023.
    Ilio Vitale, Federico Pietrocola, Emma Guilbaud, Stuart A Aaronson, John M Abrams, Dieter Adam, Massimiliano Agostini, Patrizia Agostinis, Emad S Alnemri, Lucia Altucci, Ivano Amelio, David W Andrews, Rami I Aqeilan, Eli Arama, Eric H Baehrecke, Siddharth Balachandran, Daniele Bano, Nickolai A Barlev, Jiri Bartek, Nicolas G Bazan, Christoph Becker, Francesca Bernassola, Mathieu J M Bertrand, Marco E Bianchi, Mikhail V Blagosklonny, J Magarian Blander, Giovanni Blandino, Klas Blomgren, Christoph Borner, Carl D Bortner, Pierluigi Bove, Patricia Boya, Catherine Brenner, Petr Broz, Thomas Brunner, Rune Busk Damgaard, George A Calin, Michelangelo Campanella, Eleonora Candi, Michele Carbone, Didac Carmona-Gutierrez, Francesco Cecconi, Francis K-M Chan, Guo-Qiang Chen, Quan Chen, Youhai H Chen, Emily H Cheng, Jerry E Chipuk, John A Cidlowski, Aaron Ciechanover, Gennaro Ciliberto, Marcus Conrad, Juan R Cubillos-Ruiz, Peter E Czabotar, Vincenzo D'Angiolella, Mads Daugaard, Ted M Dawson, Valina L Dawson, Ruggero De Maria, Bart De Strooper, Klaus-Michael Debatin, Ralph J Deberardinis, Alexei Degterev, Giannino Del Sal, Mohanish Deshmukh, Francesco Di Virgilio, Marc Diederich, Scott J Dixon, Brian D Dynlacht, Wafik S El-Deiry, John W Elrod, Kurt Engeland, Gian Maria Fimia, Claudia Galassi, Carlo Ganini, Ana J Garcia-Saez, Abhishek D Garg, Carmen Garrido, Evripidis Gavathiotis, Motti Gerlic, Sourav Ghosh, Douglas R Green, Lloyd A Greene, Hinrich Gronemeyer, Georg Häcker, György Hajnóczky, J Marie Hardwick, Ygal Haupt, Sudan He, David M Heery, Michael O Hengartner, Claudio Hetz, David A Hildeman, Hidenori Ichijo, Satoshi Inoue, Marja Jäättelä, Ana Janic, Bertrand Joseph, Philipp J Jost, Thirumala-Devi Kanneganti, Michael Karin, Hamid Kashkar, Thomas Kaufmann, Gemma L Kelly, Oliver Kepp, Adi Kimchi, Richard N Kitsis, Daniel J Klionsky, Ruth Kluck, Dmitri V Krysko, Dagmar Kulms, Sharad Kumar, Sergio Lavandero, Inna N Lavrik, John J Lemasters, Gianmaria Liccardi, Andreas Linkermann, Stuart A Lipton, Richard A Lockshin, Carlos López-Otín, Tom Luedde, Marion MacFarlane, Frank Madeo, Walter Malorni, Gwenola Manic, Roberto Mantovani, Saverio Marchi, Jean-Christophe Marine, Seamus J Martin, Jean-Claude Martinou, Pier G Mastroberardino, Jan Paul Medema, Patrick Mehlen, Pascal Meier, Gerry Melino, Sonia Melino, Edward A Miao, Ute M Moll, Cristina Muñoz-Pinedo, Daniel J Murphy, Maria Victoria Niklison-Chirou, Flavia Novelli, Gabriel Núñez, Andrew Oberst, Dimitry Ofengeim, Joseph T Opferman, Moshe Oren, Michele Pagano, Theocharis Panaretakis, Manolis Pasparakis, Josef M Penninger, Francesca Pentimalli, David M Pereira, Shazib Pervaiz, Marcus E Peter, Paolo Pinton, Giovanni Porta, Jochen H M Prehn, Hamsa Puthalakath, Gabriel A Rabinovich, Krishnaraj Rajalingam, Kodi S Ravichandran, Markus Rehm, Jean-Ehrland Ricci, Rosario Rizzuto, Nirmal Robinson, Cecilia M P Rodrigues, Barak Rotblat, Carla V Rothlin, David C Rubinsztein, Thomas Rudel, Alessandro Rufini, Kevin M Ryan, Kristopher A Sarosiek, Akira Sawa, Emre Sayan, Kate Schroder, Luca Scorrano, Federico Sesti, Feng Shao, Yufang Shi, Giuseppe S Sica, John Silke, Hans-Uwe Simon, Antonella Sistigu, Anastasis Stephanou, Brent R Stockwell, Flavie Strapazzon, Andreas Strasser, Liming Sun, Erwei Sun, Qiang Sun, Gyorgy Szabadkai, Stephen W G Tait, Daolin Tang, Nektarios Tavernarakis, Carol M Troy, Boris Turk, Nicoletta Urbano, Peter Vandenabeele, Tom Vanden Berghe, Matthew G Vander Heiden, Jacqueline L Vanderluit, Alexei Verkhratsky, Andreas Villunger, Silvia von Karstedt, Anne K Voss, Karen H Vousden, Domagoj Vucic, Daniela Vuri, Erwin F Wagner, Henning Walczak, David Wallach, Ruoning Wang, Ying Wang, Achim Weber, Will Wood, Takahiro Yamazaki, Huang-Tian Yang, Zahra Zakeri, Joanna E Zawacka-Pankau, Lin Zhang, Haibing Zhang, Boris Zhivotovsky, Wenzhao Zhou, Mauro Piacentini, Guido Kroemer, Lorenzo Galluzzi.
      Apoptosis is a form of regulated cell death (RCD) that involves proteases of the caspase family. Pharmacological and genetic strategies that experimentally inhibit or delay apoptosis in mammalian systems have elucidated the key contribution of this process not only to (post-)embryonic development and adult tissue homeostasis, but also to the etiology of multiple human disorders. Consistent with this notion, while defects in the molecular machinery for apoptotic cell death impair organismal development and promote oncogenesis, the unwarranted activation of apoptosis promotes cell loss and tissue damage in the context of various neurological, cardiovascular, renal, hepatic, infectious, neoplastic and inflammatory conditions. Here, the Nomenclature Committee on Cell Death (NCCD) gathered to critically summarize an abundant pre-clinical literature mechanistically linking the core apoptotic apparatus to organismal homeostasis in the context of disease.
    DOI:  https://doi.org/10.1038/s41418-023-01153-w
  37. Genes (Basel). 2023 Mar 29. pii: 822. [Epub ahead of print]14(4):
    The Expanding Phenotypical Spectrum of WARS2-Related Disorder: Four Novel Cases with a Common Recurrent Variant.
    Martje G Pauly, G Christoph Korenke, Sokhna Haissatou Diaw, Anne Grözinger, Ana Cazurro-Gutiérrez, Belén Pérez-Dueñas, Victoria González, Alfons Macaya, Ana Teresa Serrano Antón, Borut Peterlin, Ivana Babić Božović, Aleš Maver, Alexander Münchau, Katja Lohmann.
      Biallelic variants in the mitochondrial form of the tryptophanyl-tRNA synthetases (WARS2) can cause a neurodevelopmental disorder with movement disorders including early-onset tremor-parkinsonism syndrome. Here, we describe four new patients, who all presented at a young age with a tremor-parkinsonism syndrome and responded well to levodopa. All patients carry the same recurrent, hypomorphic missense variant (NM_015836.4: c.37T>G; p.Trp13Gly) either together with a previously described truncating variant (NM_015836.4: c.797Cdel; p.Pro266ArgfsTer10), a novel truncating variant (NM_015836.4: c.346C>T; p.Gln116Ter), a novel canonical splice site variant (NM_015836.4: c.349-1G>A), or a novel missense variant (NM_015836.4: c.475A>C, p.Thr159Pro). We investigated the mitochondrial function in patients and found increased levels of mitochondrially encoded cytochrome C Oxidase II as part of the mitochondrial respiratory chain as well as decreased mitochondrial integrity and branching. Finally, we conducted a literature review and here summarize the broad phenotypical spectrum of reported WARS2-related disorders. In conclusion, WARS2-related disorders are diagnostically challenging diseases due to the broad phenotypic spectrum and the disease relevance of a relatively common missense change that is often filtered out in a diagnostic setting since it occurs in ~0.5% of the general European population.
    Keywords:  WARS2; levodopa; parkinsonism; tremor
    DOI:  https://doi.org/10.3390/genes14040822
  38. BMC Med Genomics. 2023 Apr 24. 16(1): 86
    Clinical and genetic characteristics of children with COX20-associated mitochondrial disorder: case report and literature review.
    Liqing Chen, Yan Liu.
       BACKGROUND: The deficiency of cytochrome c oxidase 20 is a rare autosomal recessive mitochondrial disorder characterized by ataxia, dysarthria, dystonia and sensory neuropathy.
    CASE PRESENTATION: In this study, we describe a patient from a non-consanguineous family exhibiting developmental delay, ataxia, hypotonia, dysarthria, strabismus, visual impairment and areflexia. An examination of nerve conduction showed a normal result at first but revealed axonal sensory neuropathy later. This situation has not been reported in any literatures. The whole-exome sequencing analysis revealed that the patient harbored compound heterozygous mutations (c.41 A > G and c.259G > T) of the COX20 gene. By literature review, 5 patients carried the same compound heterozygous mutations.
    CONCLUSION: COX20 might be considered as a potential gene for the early-onset ataxia and the axonal sensory neuropathy. Our patient exhibited strabismus and visual impairment, which expands the clinical presentation of COX20 related mitochondrial disorders caused by the compound heterozygous variants (c.41 A > G and c.259G > T). However, a clear genotype/phenotype correlation has not yet been established. Additional researches and cases are needed to further confirm the correlation.
    Keywords:  COX20; Case report; Sensory neuropathy; Visual impairment; ataxia
    DOI:  https://doi.org/10.1186/s12920-023-01513-y
  39. Proc Natl Acad Sci U S A. 2023 May 02. 120(18): e2216713120
    Structure of the human respiratory complex II.
    Zhanqiang Du, Xiaoting Zhou, Yuezheng Lai, Jinxu Xu, Yuying Zhang, Shan Zhou, Ziyan Feng, Long Yu, Yanting Tang, Weiwei Wang, Lu Yu, Changlin Tian, Ting Ran, Hongming Chen, Luke W Guddat, Fengjiang Liu, Yan Gao, Zihe Rao, Hongri Gong.
      Human complex II is a key protein complex that links two essential energy-producing processes: the tricarboxylic acid cycle and oxidative phosphorylation. Deficiencies due to mutagenesis have been shown to cause mitochondrial disease and some types of cancers. However, the structure of this complex is yet to be resolved, hindering a comprehensive understanding of the functional aspects of this molecular machine. Here, we have determined the structure of human complex II in the presence of ubiquinone at 2.86 Å resolution by cryoelectron microscopy, showing it comprises two water-soluble subunits, SDHA and SDHB, and two membrane-spanning subunits, SDHC and SDHD. This structure allows us to propose a route for electron transfer. In addition, clinically relevant mutations are mapped onto the structure. This mapping provides a molecular understanding to explain why these variants have the potential to produce disease.
    Keywords:  cryoelectron microscopy; electron transport chain; human complex II
    DOI:  https://doi.org/10.1073/pnas.2216713120
  40. Rambam Maimonides Med J. 2023 Apr 30. 14(2):
    The Emerging Role of Mitochondrial Dysfunction in the Pathogenesis of Idiopathic Inflammatory Myopathies.
    Alexandra Balbir-Gurman, Jorge Armando Gonzalez-Chapa, Marina Barguil Macêdo, Christian Lood.
      Increasing evidence points towards mitochondria as crucial players in the initiation and progression of auto-immune and degenerative disorders, to which impaired cell metabolism is but a facet of the subjacent etiopathogenesis. This review aims to introduce the reader to essential concepts of mitochondrial abnormalities in idiopathic inflammatory myopathy (IIM), underscoring inclusion-body myositis and dermatomyositis. Far surpassing the initial simplistic view of being responsible for energy generation, mitochondria have gathered attention regarding their role in inflammatory processes, being able to fuel autoimmunity, as shown by the presence of anti-mitochondrial antibodies (AMAs) in up to 10% of IIM patients. As cellular respiration takes place, mitochondrial metabolites might help to shape the pro-inflammatory milieu in affected muscle, beyond generating reactive oxygen species, which are well-recognized inducers of damage-associated molecular patterns. A series of mitochondrial components might facilitate the sterile activation of pro-inflammatory cells and the production of several cytokines responsible for enhancing auto-immune responses. Marked variation in the mitochondrial genome has also been reported in IIM patients. As such, we summarize key historical and recent advances linking aberrations and instabilities of mitochondrial DNA to impaired muscle function. Besides discussing mitochondrial dysfunction as an essential part of IIM development, we also highlight possible associations between presence of AMAs and a particular phenotype of IIM, with its own characteristic clinical and radiological pattern. Finally, we present promising treatment approaches targeting mitochondria, while briefly discussing experimental models for gaining deeper insight into the disease process, and ultimately leading to novel drug development.
    DOI:  https://doi.org/10.5041/RMMJ.10493
  41. Trends Cell Biol. 2023 Apr 26. pii: S0962-8924(23)00070-3. [Epub ahead of print]
    The Warburg effect: a signature of mitochondrial overload.
    Yahui Wang, Gary J Patti.
      A long-standing question in cancer biology has been why oxygenated tumors ferment the majority of glucose they consume to lactate rather than oxidizing it in their mitochondria, a phenomenon known as the 'Warburg effect.' An abundance of evidence shows not only that most cancer cells have fully functional mitochondria but also that mitochondrial activity is important to proliferation. It is therefore difficult to rationalize the metabolic benefit of cancer cells switching from respiration to fermentation. An emerging perspective is that rather than mitochondrial metabolism being suppressed in tumors, as is often suggested, mitochondrial activity increases to the level of saturation. As such, the Warburg effect becomes a signature of excess glucose being released as lactate due to mitochondrial overload.
    Keywords:  Warburg effect; aerobic fermentation; aerobic glycolysis; cancer metabolism; mitochondrial metabolism
    DOI:  https://doi.org/10.1016/j.tcb.2023.03.013
  42. J Mol Diagn. 2023 Apr 21. pii: S1525-1578(23)00077-6. [Epub ahead of print]
    Clinical Validation of Tagmentation-Based Genome Sequencing for Germline Disorders.
    Wei Shen, Heidi L Sellers, Lauren A Choate, Mariam I Stein, Pratyush P Tandale, Jiayu Tan, Rohit Setlem, Yuta Sakai, Numrah Fadra, Carlos Sosa, Shawn P McClelland, Sarah S Barnett, Kristen J Rasmussen, Cassandra K Runke, Stephanie A Smoley, Lori S Tillmans, Cherisse A Marcou, Ross A Rowsey, Erik C Thorland, Nicole J Boczek, Hutton M Kearney.
      Genome sequencing (GS) is a powerful clinical tool used for the comprehensive diagnosis of germline disorders. GS library preparation typically involves mechanical DNA fragmentation, end repair, and bead-based library size selection followed by adapter ligation, which can require a large amount of input genomic DNA. Tagmentation using bead-linked transposomes can simplify the library preparation process and reduce the DNA input requirement. Here we describe the clinical validation of tagmentation-based PCR-free genome sequencing (GS) as a clinical test for rare germline disorders. When compared to the Genome in a Bottle Consortium (GIAB) benchmark variant sets, GS had a recall above 99.7% and a precision of 99.8% for single nucleotide variants (SNVs) and small insertion-deletions (indels). GS also showed a 100% sensitivity for clinically reported sequence variants and copy number variants (CNVs) examined. Furthermore, GS detected mitochondrial sequence variants above 5% heteroplasmy, and showed reliable detection of disease-relevant repeat expansions and SMN1 homozygous loss. Our results demonstrate that while lowering DNA input requirement and reducing library preparation time, GS enables uniform coverage across the genome and robust detection of various types of genetic alterations. With the advantage of comprehensive profiling of multiple types of genetic alterations, GS is positioned as an ideal first-tier diagnostic test for germline disorders.
    DOI:  https://doi.org/10.1016/j.jmoldx.2023.04.001
  43. Nat Aging. 2022 Apr;2(4): 277-279
    Gut mitochondrial defects drive neurodegeneration.
    Ricardo Aparicio, Edward T Schmid, David W Walker.
      
    DOI:  https://doi.org/10.1038/s43587-022-00206-y
  44. Nat Aging. 2023 Mar;3(3): 313-326
    Skeletal muscle mitochondrial interactome remodeling is linked to functional decline in aged female mice.
    Anna A Bakhtina, Gavin A Pharaoh, Matthew D Campbell, Andrew Keller, Rudolph S Stuppard, David J Marcinek, James E Bruce.
      Genomic, transcriptomic and proteomic approaches have been used to gain insight into molecular underpinnings of aging in laboratory animals and in humans. However, protein function in biological systems is under complex regulation and includes factors besides abundance levels, such as modifications, localization, conformation and protein-protein interactions. By making use of quantitative chemical cross-linking technologies, we show that changes in the muscle mitochondrial interactome contribute to mitochondrial functional decline in aging in female mice. Specifically, we identify age-related changes in protein cross-links relating to assembly of electron transport system complexes I and IV, activity of glutamate dehydrogenase, and coenzyme-A binding in fatty acid β-oxidation and tricarboxylic acid cycle enzymes. These changes show a remarkable correlation with complex I respiration differences within the same young-old animal pairs. Each observed cross-link can serve as a protein conformational or protein-protein interaction probe in future studies, which will provide further molecular insights into commonly observed age-related phenotypic differences. Therefore, this data set could become a valuable resource for additional in-depth molecular studies that are needed to better understand complex age-related molecular changes.
    DOI:  https://doi.org/10.1038/s43587-023-00366-5
  45. Antioxidants (Basel). 2023 Apr 15. pii: 934. [Epub ahead of print]12(4):
    Targeting Mitochondrial Oxidative Stress as a Strategy to Treat Aging and Age-Related Diseases.
    Yun Haeng Lee, Myeong Uk Kuk, Moon Kyoung So, Eun Seon Song, Haneur Lee, Soon Kil Ahn, Hyung Wook Kwon, Joon Tae Park, Sang Chul Park.
      Mitochondria are one of the organelles undergoing rapid alteration during the senescence process. Senescent cells show an increase in mitochondrial size, which is attributed to the accumulation of defective mitochondria, which causes mitochondrial oxidative stress. Defective mitochondria are also targets of mitochondrial oxidative stress, and the vicious cycle between defective mitochondria and mitochondrial oxidative stress contributes to the onset and development of aging and age-related diseases. Based on the findings, strategies to reduce mitochondrial oxidative stress have been suggested for the effective treatment of aging and age-related diseases. In this article, we discuss mitochondrial alterations and the consequent increase in mitochondrial oxidative stress. Then, the causal role of mitochondrial oxidative stress on aging is investigated by examining how aging and age-related diseases are exacerbated by induced stress. Furthermore, we assess the importance of targeting mitochondrial oxidative stress for the regulation of aging and suggest different therapeutic strategies to reduce mitochondrial oxidative stress. Therefore, this review will not only shed light on a new perspective on the role of mitochondrial oxidative stress in aging but also provide effective therapeutic strategies for the treatment of aging and age-related diseases through the regulation of mitochondrial oxidative stress.
    Keywords:  ROS; aging control; mitochondria; mitochondrial oxidative stress
    DOI:  https://doi.org/10.3390/antiox12040934
  46. Life (Basel). 2023 Apr 16. pii: 1027. [Epub ahead of print]13(4):
    Targeting Mitochondrial Metabolism to Save the Failing Heart.
    Christina Schenkl, Estelle Heyne, Torsten Doenst, Paul Christian Schulze, Tien Dung Nguyen.
      Despite considerable progress in treating cardiac disorders, the prevalence of heart failure (HF) keeps growing, making it a global medical and economic burden. HF is characterized by profound metabolic remodeling, which mostly occurs in the mitochondria. Although it is well established that the failing heart is energy-deficient, the role of mitochondria in the pathophysiology of HF extends beyond the energetic aspects. Changes in substrate oxidation, tricarboxylic acid cycle and the respiratory chain have emerged as key players in regulating myocardial energy homeostasis, Ca2+ handling, oxidative stress and inflammation. This work aims to highlight metabolic alterations in the mitochondria and their far-reaching effects on the pathophysiology of HF. Based on this knowledge, we will also discuss potential metabolic approaches to improve cardiac function.
    Keywords:  heart failure; heart failure treatment; metabolism; mitochondria
    DOI:  https://doi.org/10.3390/life13041027
  47. Int J Mol Sci. 2023 Apr 11. pii: 7079. [Epub ahead of print]24(8):
    Fish Models for Exploring Mitochondrial Dysfunction Affecting Neurodegenerative Disorders.
    Takayoshi Otsuka, Hideaki Matsui.
      Neurodegenerative disorders are characterized by the progressive loss of neuronal structure or function, resulting in memory loss and movement disorders. Although the detailed pathogenic mechanism has not been elucidated, it is thought to be related to the loss of mitochondrial function in the process of aging. Animal models that mimic the pathology of a disease are essential for understanding human diseases. In recent years, small fish have become ideal vertebrate models for human disease due to their high genetic and histological homology to humans, ease of in vivo imaging, and ease of genetic manipulation. In this review, we first outline the impact of mitochondrial dysfunction on the progression of neurodegenerative diseases. Then, we highlight the advantages of small fish as model organisms, and present examples of previous studies regarding mitochondria-related neuronal disorders. Lastly, we discuss the applicability of the turquoise killifish, a unique model for aging research, as a model for neurodegenerative diseases. Small fish models are expected to advance our understanding of the mitochondrial function in vivo, the pathogenesis of neurodegenerative diseases, and be important tools for developing therapies to treat diseases.
    Keywords:  medaka; mitochondria; neurodegenerative disorders; turquoise killifish; zebrafish
    DOI:  https://doi.org/10.3390/ijms24087079
  48. Front Cell Neurosci. 2023 ;17 1125785
    Endogenous neural stem cells characterization using omics approaches: Current knowledge in health and disease.
    Valentina Murtaj, Erica Butti, Gianvito Martino, Paola Panina-Bordignon.
      Neural stem cells (NSCs), an invaluable source of neuronal and glial progeny, have been widely interrogated in the last twenty years, mainly to understand their therapeutic potential. Most of the studies were performed with cells derived from pluripotent stem cells of either rodents or humans, and have mainly focused on their potential in regenerative medicine. High-throughput omics technologies, such as transcriptomics, epigenetics, proteomics, and metabolomics, which exploded in the past decade, represent a powerful tool to investigate the molecular mechanisms characterizing the heterogeneity of endogenous NSCs. The transition from bulk studies to single cell approaches brought significant insights by revealing complex system phenotypes, from the molecular to the organism level. Here, we will discuss the current literature that has been greatly enriched in the "omics era", successfully exploring the nature and function of endogenous NSCs and the process of neurogenesis. Overall, the information obtained from omics studies of endogenous NSCs provides a sharper picture of NSCs function during neurodevelopment in healthy and in perturbed environments.
    Keywords:  SVZ (subventricular zone); neural stem cells; neurodegeneration; omics; transciptome analysis
    DOI:  https://doi.org/10.3389/fncel.2023.1125785
  49. Nat Metab. 2023 Apr;5(4): 589-606
    Branched-chain amino acid catabolism in muscle affects systemic BCAA levels but not insulin resistance.
    Megan C Blair, Michael D Neinast, Cholsoon Jang, Qingwei Chu, Jae Woo Jung, Jessie Axsom, Marc R Bornstein, Chelsea Thorsheim, Kristina Li, Atsushi Hoshino, Steven Yang, Rachel J Roth Flach, Bei B Zhang, Joshua D Rabinowitz, Zoltan Arany.
      Elevated levels of plasma branched-chain amino acids (BCAAs) have been associated with insulin resistance and type 2 diabetes since the 1960s. Pharmacological activation of branched-chain α-ketoacid dehydrogenase (BCKDH), the rate-limiting enzyme of BCAA oxidation, lowers plasma BCAAs and improves insulin sensitivity. Here we show that modulation of BCKDH in skeletal muscle, but not liver, affects fasting plasma BCAAs in male mice. However, despite lowering BCAAs, increased BCAA oxidation in skeletal muscle does not improve insulin sensitivity. Our data indicate that skeletal muscle controls plasma BCAAs, that lowering fasting plasma BCAAs is insufficient to improve insulin sensitivity and that neither skeletal muscle nor liver account for the improved insulin sensitivity seen with pharmacological activation of BCKDH. These findings suggest potential concerted contributions of multiple tissues in the modulation of BCAA metabolism to alter insulin sensitivity.
    DOI:  https://doi.org/10.1038/s42255-023-00794-y
  50. Methods Protoc. 2023 Mar 24. pii: 32. [Epub ahead of print]6(2):
    An Experimental Approach to Address the Functional Relationship between Antioxidant Enzymes and Mitochondrial Respiratory Complexes.
    Daniela Mendes, Ana Maria Silva, Maria Manuel Oliveira, Paula B Andrade, Romeu A Videira.
      Mitochondrial dysfunction and cytosolic oxidative stress are pathological biomarkers interlinked in several chronic diseases and cellular toxicity promoted by high-energy radiation or xenobiotics. Thus, assessing the activities of the mitochondrial redox chain complexes and the cytosolic antioxidant enzymes in the same cell culture system is a valuable approach to addressing the challenge of chronic diseases or unveiling the molecular mechanisms underlying the toxicity of physical and chemical stress agents. The present article gathers the experimental procedures to obtain, from isolated cells, a mitochondria-free cytosolic fraction and a mitochondria-rich fraction. Furthermore, we describe the methodologies to evaluate the activity of the main antioxidant enzymes in the mitochondria-free cytosolic fraction (superoxide dismutase, catalase, glutathione reductase and glutathione peroxidase), and the activity of the individual mitochondrial complexes I, II and IV, as well as the conjugated activity of complexes I-III and complexes II-III in the mitochondria-rich fraction. The protocol to test the citrate synthase activity was also considered and used to normalize complexes. The procedures were optimized within an experimental setup to allow that each condition to be tested only requires sampling of one T-25 flask of cells 2D cultured, as the typical results presented and discussed here.
    Keywords:  antioxidant enzymes activity assays; cytosolic redox state; mitochondria; respiratory complex activity assays
    DOI:  https://doi.org/10.3390/mps6020032
  51. J Clin Med. 2023 Apr 14. pii: 2882. [Epub ahead of print]12(8):
    Mitochondrial Dysfunction: A Cellular and Molecular Hub in Pathology of Metabolic Diseases and Infection.
    Tapan Behl, Rashita Makkar, Md Khalid Anwer, Rym Hassani, Gulrana Khuwaja, Asaad Khalid, Syam Mohan, Hassan A Alhazmi, Monika Sachdeva, Mahesh Rachamalla.
      Mitochondria are semiautonomous doubly membraned intracellular components of cells. The organelle comprises of an external membrane, followed by coiled structures within the membrane called cristae, which are further surrounded by the matrix spaces followed by the space between the external and internal membrane of the organelle. A typical eukaryotic cell contains thousands of mitochondria within it, which make up 25% of the cytoplasm present in the cell. The organelle acts as a common point for the metabolism of glucose, lipids, and glutamine. Mitochondria chiefly regulate oxidative phosphorylation-mediated aerobic respiration and the TCA cycle and generate energy in the form of ATP to fulfil the cellular energy needs. The organelle possesses a unique supercoiled doubly stranded mitochondrial DNA (mtDNA) which encodes several proteins, including rRNA and tRNA crucial for the transport of electrons, oxidative phosphorylation, and initiating genetic repair processors. Defects in the components of mitochondria act as the principal factor for several chronic cellular diseases. The dysfunction of mitochondria can cause a malfunction in the TCA cycle and cause the leakage of the electron respiratory chain, leading to an increase in reactive oxygen species and the signaling of aberrant oncogenic and tumor suppressor proteins, which further alter the pathways involved in metabolism, disrupt redox balance, and induce endurance towards apoptosis and several treatments which play a major role in developing several chronic metabolic conditions. The current review presents the knowledge on the aspects of mitochondrial dysfunction and its role in cancer, diabetes mellitus, infections, and obesity.
    Keywords:  cancer; diabetes mellitus; infection; metabolic disorders; mitochondria dysfunction; obesity
    DOI:  https://doi.org/10.3390/jcm12082882
  52. Antioxidants (Basel). 2023 Mar 23. pii: 782. [Epub ahead of print]12(4):
    The Key Role of Mitochondrial Function in Health and Disease.
    Iñigo San-Millán.
      The role of mitochondrial function in health and disease has become increasingly recognized, particularly in the last two decades. Mitochondrial dysfunction as well as disruptions of cellular bioenergetics have been shown to be ubiquitous in some of the most prevalent diseases in our society, such as type 2 diabetes, cardiovascular disease, metabolic syndrome, cancer, and Alzheimer's disease. However, the etiology and pathogenesis of mitochondrial dysfunction in multiple diseases have yet to be elucidated, making it one of the most significant medical challenges in our history. However, the rapid advances in our knowledge of cellular metabolism coupled with the novel understanding at the molecular and genetic levels show tremendous promise to one day elucidate the mysteries of this ancient organelle in order to treat it therapeutically when needed. Mitochondrial DNA mutations, infections, aging, and a lack of physical activity have been identified to be major players in mitochondrial dysfunction in multiple diseases. This review examines the complexities of mitochondrial function, whose ancient incorporation into eukaryotic cells for energy purposes was key for the survival and creation of new species. Among these complexities, the tightly intertwined bioenergetics derived from the combustion of alimentary substrates and oxygen are necessary for cellular homeostasis, including the production of reactive oxygen species. This review discusses different etiological mechanisms by which mitochondria could become dysregulated, determining the fate of multiple tissues and organs and being a protagonist in the pathogenesis of many non-communicable diseases. Finally, physical activity is a canonical evolutionary characteristic of humans that remains embedded in our genes. The normalization of a lack of physical activity in our modern society has led to the perception that exercise is an "intervention". However, physical activity remains the modus vivendi engrained in our genes and being sedentary has been the real intervention and collateral effect of modern societies. It is well known that a lack of physical activity leads to mitochondrial dysfunction and, hence, it probably becomes a major etiological factor of many non-communicable diseases affecting modern societies. Since physical activity remains the only stimulus we know that can improve and maintain mitochondrial function, a significant emphasis on exercise promotion should be imperative in order to prevent multiple diseases. Finally, in populations with chronic diseases where mitochondrial dysfunction is involved, an individualized exercise prescription should be crucial for the "metabolic rehabilitation" of many patients. From lessons learned from elite athletes (the perfect human machines), it is possible to translate and apply multiple concepts to the betterment of populations with chronic diseases.
    Keywords:  Alzheimer’s disease; cancer; cardiovascular disease; cellular bioenergetics; diabetes; exercise; metabolic flexibility; mitochondrial dysfunction
    DOI:  https://doi.org/10.3390/antiox12040782
  53. Science. 2023 Apr 28. 380(6643): eabn2937
    Leveraging base-pair mammalian constraint to understand genetic variation and human disease.
    Zoonomia Consortium§
      Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.
    DOI:  https://doi.org/10.1126/science.abn2937
  54. Nat Aging. 2022 Apr;2(4): 274
    NAD supplementation in Parkinson's disease.
    Anna Kriebs.
      
    DOI:  https://doi.org/10.1038/s43587-022-00217-9
  55. Front Physiol. 2023 ;14 1192759
    Editorial: Muscle plasticity: Regulation of adaptive changes in muscles and mitochondrial dynamics.
    Prasanna Katti, Yuho Kim, N Ravi Sundaresan, Gilles Gouspillou, Antentor Hinton.
      
    Keywords:  HIIT; TCAP-1; mitochondria; muscles; resistant exercise; sarcopenia
    DOI:  https://doi.org/10.3389/fphys.2023.1192759
  56. Orphanet J Rare Dis. 2023 04 24. 18(1): 92
    ATAD3A-related pontocerebellar hypoplasia: new patients and insights into phenotypic variability.
    Martina Skopkova, Hana Stufkova, Vibhuti Rambani, Viktor Stranecky, Katarina Brennerova, Miriam Kolnikova, Michaela Pietrzykova, Miloslav Karhanek, Lenka Noskova, Marketa Tesarova, Hana Hansikova, Daniela Gasperikova.
       BACKGROUND: Pathogenic variants in the ATAD3A gene lead to a heterogenous clinical picture and severity ranging from recessive neonatal-lethal pontocerebellar hypoplasia through milder dominant Harel-Yoon syndrome up to, again, neonatal-lethal but dominant cardiomyopathy. The genetic diagnostics of ATAD3A-related disorders is also challenging due to three paralogous genes in the ATAD3 locus, making it a difficult target for both sequencing and CNV analyses.
    RESULTS: Here we report four individuals from two families with compound heterozygous p.Leu77Val and exon 3-4 deletion in the ATAD3A gene. One of these patients was characterized as having combined OXPHOS deficiency based on decreased complex IV activities, decreased complex IV, I, and V holoenzyme content, as well as decreased levels of COX2 and ATP5A subunits and decreased rate of mitochondrial proteosynthesis. All four reported patients shared a strikingly similar clinical picture to a previously reported patient with the p.Leu77Val variant in combination with a null allele. They presented with a less severe course of the disease and a longer lifespan than in the case of biallelic loss-of-function variants. This consistency of the phenotype in otherwise clinically heterogenous disorder led us to the hypothesis that the severity of the phenotype could depend on the severity of variant impact. To follow this rationale, we reviewed the published cases and sorted the recessive variants according to their impact predicted by their type and the severity of the disease in the patients.
    CONCLUSION: The clinical picture and severity of ATAD3A-related disorders are homogenous in patients sharing the same combinations of variants. This knowledge enables deduction of variant impact severity based on known cases and allows more accurate prognosis estimation, as well as a better understanding of the ATAD3A function.
    Keywords:  ATAD3A; Mitochondria; OXPHOS; Pontocerebellar hypoplasia
    DOI:  https://doi.org/10.1186/s13023-023-02689-3
  57. Nat Rev Cancer. 2023 Apr 28.
    Identifying spatial cellular structures with SPACE-GM.
    Zhenqin Wu.
      
    DOI:  https://doi.org/10.1038/s41568-023-00582-6
  58. Genome Biol. 2023 Apr 24. 24(1): 91
    Transformation of alignment files improves performance of variant callers for long-read RNA sequencing data.
    Vladimir B C de Souza, Ben T Jordan, Elizabeth Tseng, Elizabeth A Nelson, Karen K Hirschi, Gloria Sheynkman, Mark D Robinson.
      Long-read RNA sequencing (lrRNA-seq) produces detailed information about full-length transcripts, including novel and sample-specific isoforms. Furthermore, there is an opportunity to call variants directly from lrRNA-seq data. However, most state-of-the-art variant callers have been developed for genomic DNA. Here, there are two objectives: first, we perform a mini-benchmark on GATK, DeepVariant, Clair3, and NanoCaller primarily on PacBio Iso-Seq, data, but also on Nanopore and Illumina RNA-seq data; second, we propose a pipeline to process spliced-alignment files, making them suitable for variant calling with DNA-based callers. With such manipulations, high calling performance can be achieved using DeepVariant on Iso-seq data.
    DOI:  https://doi.org/10.1186/s13059-023-02923-y
  59. Biology (Basel). 2023 Apr 06. pii: 558. [Epub ahead of print]12(4):
    Humanin and Its Pathophysiological Roles in Aging: A Systematic Review.
    Donatella Coradduzza, Antonella Congiargiu, Zhichao Chen, Sara Cruciani, Angelo Zinellu, Ciriaco Carru, Serenella Medici.
       BACKGROUND: Senescence is a cellular aging process in all multicellular organisms. It is characterized by a decline in cellular functions and proliferation, resulting in increased cellular damage and death. These conditions play an essential role in aging and significantly contribute to the development of age-related complications. Humanin is a mitochondrial-derived peptide (MDP), encoded by mitochondrial DNA, playing a cytoprotective role to preserve mitochondrial function and cell viability under stressful and senescence conditions. For these reasons, humanin can be exploited in strategies aiming to counteract several processes involved in aging, including cardiovascular disease, neurodegeneration, and cancer. Relevance of these conditions to aging and disease: Senescence appears to be involved in the decay in organ and tissue function, it has also been related to the development of age-related diseases, such as cardiovascular conditions, cancer, and diabetes. In particular, senescent cells produce inflammatory cytokines and other pro-inflammatory molecules that can participate to the development of such diseases. Humanin, on the other hand, seems to contrast the development of such conditions, and it is also known to play a role in these diseases by promoting the death of damaged or malfunctioning cells and contributing to the inflammation often associated with them. Both senescence and humanin-related mechanisms are complex processes that have not been fully clarified yet. Further research is needed to thoroughly understand the role of such processes in aging and disease and identify potential interventions to target them in order to prevent or treat age-related conditions.
    OBJECTIVES: This systematic review aims to assess the potential mechanisms underlying the link connecting senescence, humanin, aging, and disease.
    Keywords:  aging and diseases; humanin; senescence
    DOI:  https://doi.org/10.3390/biology12040558
  60. Skelet Muscle. 2023 04 22. 13(1): 7
    New tools for the investigation of muscle fiber-type spatial distributions across histological sections.
    Anna K Redmond, Tilman M Davies, Matthew R Schofield, Philip W Sheard.
       BACKGROUND: The functional and metabolic properties of skeletal muscles are partly a function of the spatial arrangement of fibers across the muscle belly. Many muscles feature a non-uniform spatial pattern of fiber types, and alterations to the arrangement can reflect age or disease and correlate with changes in muscle mass and strength. Despite the significance of this event, descriptions of spatial fiber-type distributions across a muscle section are mainly provided qualitatively, by eye. Whilst several quantitative methods have been proposed, difficulties in implementation have meant that robust statistical analysis of fiber type distributions has not yielded new insight into the biological processes that drive the age- or disease-related changes in fiber type distributions.
    METHODS: We review currently available approaches for analysis of data reporting fast/slow fiber type distributions on muscle sections before proposing a new method based on a generalized additive model. We compare current approaches with our new method by analysis of sections of three mouse soleus muscles that exhibit visibly different spatial fiber patterns, and we also apply our model to a dataset representing the fiber type proportions and distributions of the mouse tibialis anterior.
    RESULTS: We highlight how current methods can lead to differing interpretations when applied to the same dataset and demonstrate how our new method is the first to permit location-based estimation of fiber-type probabilities, in turn enabling useful graphical representation.
    CONCLUSIONS: We present an open-access online application that implements current methods as well as our new method and which aids the interpretation of a variety of statistical tools for the spatial analysis of muscle fiber distributions.
    Keywords:  Aging; Clumping; Fiber type; Neuromuscular disease; Pattern; Skeletal muscle; Spatial distribution; Statistical methods
    DOI:  https://doi.org/10.1186/s13395-023-00316-0
  61. Hum Genet. 2023 Apr 28.
    The omics era: a nexus of untapped potential for Mendelian chromatinopathies.
    Aileen A Nava, Valerie A Arboleda.
      The OMICs cascade describes the hierarchical flow of information through biological systems. The epigenome sits at the apex of the cascade, thereby regulating the RNA and protein expression of the human genome and governs cellular identity and function. Genes that regulate the epigenome, termed epigenes, orchestrate complex biological signaling programs that drive human development. The broad expression patterns of epigenes during human development mean that pathogenic germline mutations in epigenes can lead to clinically significant multi-system malformations, developmental delay, intellectual disabilities, and stem cell dysfunction. In this review, we refer to germline developmental disorders caused by epigene mutation as "chromatinopathies". We curated the largest number of human chromatinopathies to date and our expanded approach more than doubled the number of established chromatinopathies to 179 disorders caused by 148 epigenes. Our study revealed that 20.6% (148/720) of epigenes cause at least one chromatinopathy. In this review, we highlight key examples in which OMICs approaches have been applied to chromatinopathy patient biospecimens to identify underlying disease pathogenesis. The rapidly evolving OMICs technologies that couple molecular biology with high-throughput sequencing or proteomics allow us to dissect out the causal mechanisms driving temporal-, cellular-, and tissue-specific expression. Using the full repertoire of data generated by the OMICs cascade to study chromatinopathies will provide invaluable insight into the developmental impact of these epigenes and point toward future precision targets for these rare disorders.
    DOI:  https://doi.org/10.1007/s00439-023-02560-2
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