bims-mitdis Biomed News
on Mitochondrial Disorders
Issue of 2021‒07‒11
fifty-three papers selected by
Catalina Vasilescu
University of Helsinki


  1. BMJ Neurol Open. 2021 ;3(1): e000180
      Introduction: Mitochondrial diseases exhibit wide phenotypic heterogeneity, and can present as progressive myoclonic epilepsy.Summary: We report a case of adult-onset drug-resistant epilepsy, cortical myoclonus and bilateral optic neuropathies due to m.14487T>C, a rare mitochondrial gene mutation identified on whole-genome sequencing. This mutation, which affects the NADH dehydrogenase 6 (ND6) subunit of the mitochondrial respiratory chain, is most commonly implicated in cases of infantile-onset Leigh syndrome, although a broader phenotypic spectrum including migraine with aura and progressive myoclonic epilepsy have been described. Serial MRI scans over a 2-year period demonstrated the interval development of bihemispheric stroke-like lesions. Giant somatosensory evoked potentials and short-duration myoclonic jerks with craniocaudal spread on surface electromyography were consistent with cortical myoclonus. Optical coherence tomography showed bilateral symmetric thinning of the nerve fibre layer in the papillomacular bundles.
    Conclusion: Whole-genome sequencing can help to provide a definitive diagnosis for mitochondrial disease and should be considered in situations where clinical suspicion remains high despite normal genetic panels or muscle histopathology. Mitochondrial disease can present as adult-onset progressive myoclonic epilepsy, and bilateral optic neuropathies can be a striking feature of ND6 mitochondrial gene mutations. In our case, severe cortical myoclonus affecting speech and swallowing remained highly drug-resistant, however, symptomatic benefit was derived from targeted onabotulinum toxin A injections.
    Keywords:  botulinum toxin; epilepsy; mitochondrial disorders; neurogenetics
    DOI:  https://doi.org/10.1136/bmjno-2021-000180
  2. Front Cell Dev Biol. 2021 ;9 653522
      The retina is among the most metabolically active tissues with high-energy demands. The peculiar distribution of mitochondria in cells of retinal layers is necessary to assure the appropriate energy supply for the transmission of the light signal. Photoreceptor cells (PRs), retinal pigment epithelium (RPE), and retinal ganglion cells (RGCs) present a great concentration of mitochondria, which makes them particularly sensitive to mitochondrial dysfunction. To date, visual loss has been extensively correlated to defective mitochondrial functions. Many mitochondrial diseases (MDs) show indeed neuro-ophthalmic manifestations, including retinal and optic nerve phenotypes. Moreover, abnormal mitochondrial functions are frequently found in the most common retinal pathologies, i.e., glaucoma, age-related macular degeneration (AMD), and diabetic retinopathy (DR), that share clinical similarities with the hereditary primary MDs. MicroRNAs (miRNAs) are established as key regulators of several developmental, physiological, and pathological processes. Dysregulated miRNA expression profiles in retinal degeneration models and in patients underline the potentiality of miRNA modulation as a possible gene/mutation-independent strategy in retinal diseases and highlight their promising role as disease predictive or prognostic biomarkers. In this review, we will summarize the current knowledge about the participation of miRNAs in both rare and common mitochondria-mediated eye diseases. Definitely, given the involvement of miRNAs in retina pathologies and therapy as well as their use as molecular biomarkers, they represent a determining target for clinical applications.
    Keywords:  AMD; MitomiR; diabetic retinopathy; glaucoma; microRNA; mitochondria; mitochondrial diseases; retina
    DOI:  https://doi.org/10.3389/fcell.2021.653522
  3. FASEB J. 2021 Aug;35(8): e21757
      Pyroptosis and intrinsic apoptosis are two forms of regulated cell death driven by active caspases where plasma membrane permeabilization is induced by gasdermin pores. Caspase-1 induces gasdermin D pore formation during pyroptosis, whereas caspase-3 promotes gasdermin E pore formation during apoptosis. These two types of cell death are accompanied by mitochondrial outer membrane permeabilization due to BAK/BAX pore formation in the external membrane of mitochondria, and to some extent, this complex also affects the inner mitochondrial membrane facilitating mitochondrial DNA relocalization from the matrix to the cytosol. However, the detailed mechanism responsible for this process has not been investigated. Herein, we reported that gasdermin processing is required to induce mitochondrial DNA release from cells during pyroptosis and apoptosis. Gasdermin targeted at the plasma membrane promotes a fast mitochondrial collapse along with the initial accumulation of mitochondrial DNA in the cytosol and then facilitates the DNA's release from the cell when the plasma membrane ruptures. These findings demonstrate that gasdermin action has a critical effect on the plasma membrane and facilitates the release of mitochondrial DNA as a damage-associated molecular pattern.
    Keywords:  GSDMD; GSDME; macrophages; mitochondrial DNA; pyroptosis
    DOI:  https://doi.org/10.1096/fj.202100085R
  4. Front Genet. 2021 ;12 692087
      SATB2-associated syndrome (SAS) is an autosomal dominant neurogenetic multisystemic disorder. We describe two individuals with global developmental delay and hypotonia who underwent an extensive evaluation to rule out an underlying mitochondrial disorder before their eventual diagnosis of SAS. Although the strict application of the clinical mitochondrial disease score only led to the designation of "possible" mitochondrial disorder for these two individuals, other documented abnormalities included nonspecific neuroimaging findings on magnetic resonance imaging and magnetic resonance spectroscopy, decreased complex I activity on muscle biopsy for patient 2, and variation in the size and relative proportion of types of muscle fibers in the muscle biopsies that were aligned with mitochondrial diseases. SAS should be in the differential diagnoses of mitochondrial disorders, and broad-spectrum diagnostic tests such as exome sequencing need to be considered early in the evaluation process of undiagnosed neurodevelopmental disorders.
    Keywords:  SATB2; SATB2-Associated syndrome; glass syndrome; mitochondrial disease; muscle biopsy
    DOI:  https://doi.org/10.3389/fgene.2021.692087
  5. Neurologia (Engl Ed). 2021 Jul-Aug;36(6):pii: S2173-5808(21)00052-3. [Epub ahead of print]36(6): 472-473
      
    DOI:  https://doi.org/10.1016/j.nrleng.2020.07.020
  6. Acta Neuropathol Commun. 2021 Jul 07. 9(1): 124
      The cellular and molecular mechanisms that drive neurodegeneration remain poorly defined. Recent clinical trial failures, difficult diagnosis, uncertain etiology, and lack of curative therapies prompted us to re-examine other hypotheses of neurodegenerative pathogenesis. Recent reports establish that mitochondrial and calcium dysregulation occur early in many neurodegenerative diseases (NDDs), including Alzheimer's disease, Parkinson's disease, Huntington's disease, and others. However, causal molecular evidence of mitochondrial and metabolic contributions to pathogenesis remains insufficient. Here we summarize the data supporting the hypothesis that mitochondrial and metabolic dysfunction result from diverse etiologies of neuropathology. We provide a current and comprehensive review of the literature and interpret that defective mitochondrial metabolism is upstream and primary to protein aggregation and other dogmatic hypotheses of NDDs. Finally, we identify gaps in knowledge and propose therapeutic modulation of mCa2+ exchange and mitochondrial function to alleviate metabolic impairments and treat NDDs.
    Keywords:  Alzheimer’s disease; Calcium; Huntington's disease; Metabolism; Mitochondria; Neurodegeneration; Parkinson's disease
    DOI:  https://doi.org/10.1186/s40478-021-01224-4
  7. J Vis Exp. 2021 Jun 21.
      Mitochondrial diseases represent the largest class of inborn errors of metabolism and are currently incurable. These diseases cause neurodevelopmental defects whose underlying mechanisms remain to be elucidated. A major roadblock is the lack of effective models recapitulating the early-onset neuronal impairment seen in the patients. Advances in the technology of induced pluripotent stem cells (iPSCs) enable the generation of three-dimensional (3D) brain organoids that can be used to investigate the impact of diseases on the development and organization of the nervous system. Researchers, including these authors, have recently introduced human brain organoids to model mitochondrial disorders. This paper reports a detailed protocol for the robust generation of human iPSC-derived brain organoids and their use in mitochondrial bioenergetic profiling and imaging analyses. These experiments will allow the use of brain organoids to investigate metabolic and developmental dysfunctions and may provide crucial information to dissect the neuronal pathology of mitochondrial diseases.
    DOI:  https://doi.org/10.3791/62756
  8. Cell Mol Life Sci. 2021 Jul 06.
      Mitochondrial fidelity is a key determinant of longevity and was found to be perturbed in a multitude of disease contexts ranging from neurodegeneration to heart failure. Tight homeostatic control of the mitochondrial proteome is a crucial aspect of mitochondrial function, which is severely complicated by the evolutionary origin and resulting peculiarities of the organelle. This is, on one hand, reflected by a range of basal quality control factors such as mitochondria-resident chaperones and proteases, that assist in import and folding of precursors as well as removal of aggregated proteins. On the other hand, stress causes the activation of several additional mechanisms that counteract any damage that may threaten mitochondrial function. Countermeasures depend on the location and intensity of the stress and on a range of factors that are equipped to sense and signal the nature of the encountered perturbation. Defective mitochondrial import activates mechanisms that combat the accumulation of precursors in the cytosol and the import pore. To resolve proteotoxic stress in the organelle interior, mitochondria depend on nuclear transcriptional programs, such as the mitochondrial unfolded protein response and the integrated stress response. If organelle damage is too severe, mitochondria signal for their own destruction in a process termed mitophagy, thereby preventing further harm to the mitochondrial network and allowing the cell to salvage their biological building blocks. Here, we provide an overview of how different types and intensities of stress activate distinct pathways aimed at preserving mitochondrial fidelity.
    Keywords:  DELE1; Integrated stress response (ISR); Mitochondria; Mitochondrial unfolded protein response (UPRmt); Mitophagy; Protein import
    DOI:  https://doi.org/10.1007/s00018-021-03887-7
  9. Biochemistry (Mosc). 2021 Jun;86(6): 667-679
      Alzheimer's disease is the most common age-related neurodegenerative disease. Understanding of its etiology and pathogenesis is constantly expanding. Thus, the increasing attention of researchers is directed to the study of the role of mitochondrial disorders. In addition, in recent years, the concept of Alzheimer's disease as a stress-induced disease has begun to form more and more actively. The stress-induced damage to the neuronal system can trigger a vicious circle of pathological processes, among which mitochondrial dysfunctions have a significant place, since mitochondria represent a substantial component in the anti-stress activity of the cell. The study of mitochondrial disorders in Alzheimer's disease is relevant for at least two reasons: first, as important pathogenetic component in this disease; second, due to vital role of mitochondria in formation of the body resistance to various conditions, including stressful ones, throughout the life. This literature review analyzes the results of a number of recent studies assessing potential significance of the mitochondrial disorders in Alzheimer's disease. The probable mechanisms of mitochondrial disorders associated with the development of this disease are considered: bioenergetic dysfunctions, changes in mitochondrial DNA (including assessment of the significance of its haplogroup features), disorders in the dynamics of these organelles, oxidative damage to calcium channels, damage to MAM complexes (membranes associated with mitochondria; mitochondria-associated membranes), disruptions of the mitochondrial quality control system, mitochondrial permeability, etc. The issues of the "primary" or "secondary" mitochondrial damage in Alzheimer's disease are discussed. Potentials for the development of new methods for diagnosis and therapy of mitochondrial disorders in Alzheimer's disease are considered.
    Keywords:  Alzheimer’s disease; mitochondria; mitochondrial disorders; stress-induced diseases
    DOI:  https://doi.org/10.1134/S0006297921060055
  10. Cell Death Dis. 2021 Jul 03. 12(7): 671
      The balanced functionality of cellular proteostatic modules is central to both proteome stability and mitochondrial physiology; thus, the age-related decline of proteostasis also triggers mitochondrial dysfunction, which marks multiple degenerative disorders. Non-functional mitochondria are removed by mitophagy, including Parkin/Pink1-mediated mitophagy. A common feature of neuronal or muscle degenerative diseases, is the accumulation of damaged mitochondria due to disrupted mitophagy rates. Here, we exploit Drosophila as a model organism to investigate the functional role of Parkin/Pink1 in regulating mitophagy and proteostatic responses, as well as in suppressing degenerative phenotypes at the whole organism level. We found that Parkin or Pink1 knock down in young flies modulated proteostatic components in a tissue-dependent manner, increased cell oxidative load, and suppressed mitophagy in neuronal and muscle tissues, causing mitochondrial aggregation and neuromuscular degeneration. Concomitant to Parkin or Pink1 knock down cncC/Nrf2 overexpression, induced the proteostasis network, suppressed oxidative stress, restored mitochondrial function, and elevated mitophagy rates in flies' tissues; it also, largely rescued Parkin or Pink1 knock down-mediated neuromuscular degenerative phenotypes. Our in vivo findings highlight the critical role of the Parkin/Pink1 pathway in mitophagy, and support the therapeutic potency of Nrf2 (a druggable pathway) activation in age-related degenerative diseases.
    DOI:  https://doi.org/10.1038/s41419-021-03952-w
  11. Front Pharmacol. 2021 ;12 671929
      Silent information regulator 2-related enzyme 1 (SIRT1) is an NAD+-dependent class III deacetylase and a key component of the cellular metabolic sensing pathway. The requirement of NAD+ for SIRT1 activity led us to assume that NQO1, an NADH oxidoreductase producing NAD+, regulates SIRT1 activity. We show here that SIRT1 is capable of increasing NQO1 (NAD(P)H Dehydrogenase Quinone 1) transcription and protein levels. NQO1 physically interacts with SIRT1 but not with an enzymatically dead SIRT1 H363Y mutant. The interaction of NQO1 with SIRT1 is markedly increased under mitochondrial inhibition. Interestingly, under this condition the nuclear pool of NQO1 is elevated. Depletion of NQO1 compromises the role of SIRT1 in inducing transcription of several target genes and eliminates the protective role of SIRT1 following mitochondrial inhibition. Our results suggest that SIRT1 and NQO1 form a regulatory loop where SIRT1 regulates NQO1 expression and NQO1 binds and mediates the protective role of SIRT1 during mitochondrial stress. The interplay between an NADH oxidoreductase enzyme and an NAD+ dependent deacetylase may act as a rheostat in sensing mitochondrial stress.
    Keywords:  NADH/NAD ratio; PGC1 alpha; SIRT1 activity; mitochondria stress; quinone oxidoreductase 1
    DOI:  https://doi.org/10.3389/fphar.2021.671929
  12. Methods Cell Biol. 2021 ;pii: S0091-679X(20)30212-0. [Epub ahead of print]164 113-118
      Mitophagy is an evolutionally conserved cellular process that eliminates dysfunctional and excess mitochondria, thereby facilitating mitochondrial quality control and metabolic recycling. In addition, mitophagy is essential for cellular homeostasis and tissue development, and mitophagic dysfunction is related to various pathologies including neurodegenerative diseases and cancer. Thus, accurate quantitative measurement of mitophagy is one of the hot topics in the field of mitochondrial research. Fluorescence microscopical technology, one of the most widely used technologies at present, can well explain the occurrence and activity of mitophagy. Here, we introduce in detail an experimental method for the immunofluorescence-based quantitativ determination of mitophagy, which not only servers the in-depth study of mitochondrial homeostasis regulation, but also allows for the analyzing mitochondrial autophagy pathologies such as aging, neurodegenerative diseases and cancer.
    Keywords:  Detection; Fluorescence microscope; Method; MitoTracker; Mitophagy
    DOI:  https://doi.org/10.1016/bs.mcb.2020.12.006
  13. FEBS J. 2021 Jul 06.
      Mitochondria possess their own genome which can be replicated independently of nuclear DNA. Mitochondria being the powerhouse of the cell, produce reactive oxygen species, due to which the mitochondrial genome is frequently exposed to oxidative damage. Previous studies have demonstrated association of mitochondrial deletions to aging and human disorders. Many of these deletions were present adjacent to non-B DNA structures. Thus, we investigate noncanonical structures associated with instability in mitochondrial genome. In silico studies revealed the presence of >100 G-quadruplex motifs (of which 5 have the potential to form 3 plate G4 DNA), 23 inverted repeats, and 3 mirror repeats in the mitochondrial DNA (mtDNA). Further analysis revealed that among the deletion breakpoints from patients with mitochondrial disorders, majority are located at G4 DNA motifs. Interestingly, ~50% of the deletions were at base-pair positions 8271-8281, ~35% were due to deletion at 12362-12384 and ~12% due to deletion at 15516-15545. Formation of 3 plate G-quadruplex DNA structures at mitochondrial fragile regions was characterized using electromobility shift assay, circular dichroism (CD) and Taq polymerase stop assay. All 5 regions could fold into both intramolecular and intermolecular G-quadruplex structures in a KCl dependent manner. G4 DNA formation was in parallel orientation, which was abolished in presence of LiCl. The formation of G4 DNA affected both replication and transcription. Finally, immunolocalization of BG4 with MitoTracker confirmed the formation of G-quadruplex in mitochondrial genome. Thus, we characterize formation of 5 different G-quadruplex structures in human mitochondrial region, which may contribute towards formation of mitochondrial deletions.
    Keywords:  G4 DNA; Mitochondrial deletion; Mitochondrial fragility; Tetraplexes; non-B DNA structure
    DOI:  https://doi.org/10.1111/febs.16113
  14. STAR Protoc. 2021 Sep 17. 2(3): 100628
      Defects in protein quality control are the underlying cause of age-related diseases. The western blot analysis of detergent-soluble and insoluble protein fractions has proven useful in identifying interventions that regulate proteostasis. Here, we describe the protocol for such analyses in Drosophila tissues, mouse skeletal muscle, human organoids, and HEK293 cells. We describe key adaptations of this protocol and provide key information that will help modify this protocol for future studies in other tissues and disease models. For complete details on the use and execution of this protocol, please refer to Rai et al. (2021) and Hunt el al. (2021).
    Keywords:  Cell Biology; Developmental biology; Model Organisms; Molecular Biology; Organoids; Protein Biochemistry
    DOI:  https://doi.org/10.1016/j.xpro.2021.100628
  15. Front Mol Biosci. 2021 ;8 697913
      Alzheimer's Disease (AD) is the most common form of dementia, characterised by intra- and extracellular protein aggregation. In AD, the cellular protein quality control (PQC) system is derailed and fails to prevent the formation of these aggregates. Especially the mitochondrial paralogue of the conserved Hsp90 chaperone class, tumour necrosis factor receptor-associated protein 1 (TRAP1), is strongly downregulated in AD, more than other major PQC factors. Here, we review molecular mechanism and cellular function of TRAP1 and subsequently discuss possible links to AD. TRAP1 is an interesting paradigm for the Hsp90 family, as it chaperones proteins with vital cellular function, despite not being regulated by any of the co-chaperones that drive its cytosolic paralogues. TRAP1 encloses late folding intermediates in a non-active state. Thereby, it is involved in the assembly of the electron transport chain, and it favours the switch from oxidative phosphorylation to glycolysis. Another key function is that it ensures mitochondrial integrity by regulating the mitochondrial pore opening through Cyclophilin D. While it is still unclear whether TRAP1 itself is a driver or a passenger in AD, it might be a guide to identify key factors initiating neurodegeneration.
    Keywords:  mitochondria; molecular chaperones; neurodegeneration; protein aggregation; protein folding; protein quality control; proteostasis
    DOI:  https://doi.org/10.3389/fmolb.2021.697913
  16. Nature. 2021 Jul 07.
      Peptide-chain elongation during protein synthesis entails sequential aminoacyl-tRNA selection and translocation reactions that proceed rapidly (2-20 per second) and with a low error rate (around 10-3 to 10-5 at each step) over thousands of cycles1. The cadence and fidelity of ribosome transit through mRNA templates in discrete codon increments is a paradigm for movement in biological systems that must hold for diverse mRNA and tRNA substrates across domains of life. Here we use single-molecule fluorescence methods to guide the capture of structures of early translocation events on the bacterial ribosome. Our findings reveal that the bacterial GTPase elongation factor G specifically engages spontaneously achieved ribosome conformations while in an active, GTP-bound conformation to unlock and initiate peptidyl-tRNA translocation. These findings suggest that processes intrinsic to the pre-translocation ribosome complex can regulate the rate of protein synthesis, and that energy expenditure is used later in the translocation mechanism than previously proposed.
    DOI:  https://doi.org/10.1038/s41586-021-03713-x
  17. Transl Vis Sci Technol. 2021 Jul 01. 10(8): 4
      Translational Relevance: Mitochondria are viable therapeutic targets for a broad spectrum of ocular diseases.
    DOI:  https://doi.org/10.1167/tvst.10.8.4
  18. iScience. 2021 Jul 23. 24(7): 102712
      Skeletal muscle insulin resistance is a central defect in the pathogenesis of type 2 diabetes (T2D). Here, we analyzed skeletal muscle proteome in 148 vastus lateralis muscle biopsies obtained from men covering all glucose tolerance phenotypes: normal, impaired fasting glucose (IFG), impaired glucose tolerance (IGT) and T2D. Skeletal muscle proteome was analyzed by a sequential window acquisition of all theoretical mass spectra (SWATH-MS) proteomics technique. Our data indicate a downregulation in several proteins involved in mitochondrial electron transport or respiratory chain complex assembly already in IFG and IGT muscles, with most profound decreases observed in T2D. Additional phosphoproteomic analysis reveals altered phosphorylation in several signaling pathways in IFG, IGT, and T2D muscles, including those regulating glucose metabolic processes, and the structure of muscle cells. These data reveal several alterations present in skeletal muscle already in prediabetes and highlight impaired mitochondrial energy metabolism in the trajectory from prediabetes into T2D.
    Keywords:  Diabetology; Molecular biology; Proteomics
    DOI:  https://doi.org/10.1016/j.isci.2021.102712
  19. Arch Biochem Biophys. 2021 Jul 03. pii: S0003-9861(21)00232-0. [Epub ahead of print] 108983
      Lon is an ATP-dependent protease belonging to the "ATPase associated with diverse cellular activities" (AAA+) protein family. In humans, Lon is translated as a precursor and imported into the mitochondria matrix through deletion of the first 114 amino acid residues. In mice, embryonic knockout of lon is lethal. In humans, some dysfunctional lon mutations are tolerated but they cause a developmental disorder known as the CODAS syndrome. To gain a better understanding on the enzymology of human mitochondrial Lon, this study compares the structure-function relationship of the WT versus one of the CODAS mutants R721G to identify the mechanistic features in Lon catalysis that are affected. To this end, steady-state kinetics were used to quantify the difference in ATPase and ATP-dependent peptidase activities between WT and R721G. The Km values for the intrinsic as well as protein-stimulated ATPase were increased whereas the kcat value for ATP-dependent peptidase activity was decreased in the R721G mutant. The mutant protease also displayed substrate inhibition kinetics. In vitro studies revealed that R721G did not degrade the endogenous mitochondrial Lon substrate pyruvate dehydrogenase kinase isoform 4 (PDK4) effectively like WT hLon. Furthermore, the pyruvate dehydrogenase complex (PDH) protected PDK4 from hLon degradation. Using hydrogen deuterium exchange/mass spectrometry and negative stain electron microscopy, structural perturbations associated with the R721G mutation were identified. To validate the in vitro findings under a physiologically relevant condition, the intrinsic stability as well as proteolytic activity of WT versus R721G mutant towards PDK 4 were compared in cell lysates prepared from immortalized B lymphocytes expressing the respective protease. The lifetime of PDK4 is longer in the mutant cells, but the lifetime of Lon protein is longer in the WT cells, which corroborate the in vitro structure-functional relationship findings.
    Keywords:  CODAS; Hydrogen-deuterium exchange; Lon protease; Nucleotide induced conformational changes; Steady-state kinetics
    DOI:  https://doi.org/10.1016/j.abb.2021.108983
  20. NPJ Parkinsons Dis. 2021 Jul 07. 7(1): 56
      The translocase of outer mitochondrial membrane 40 (TOMM40) '523' polymorphism has previously been associated with age of Alzheimer's disease onset and cognitive functioning in non-pathological ageing, but has not been explored as a candidate risk marker for cognitive decline in Parkinson's disease (PD). Therefore, this longitudinal study investigated the role of the '523' variant in cognitive decline in a patient cohort from the Parkinson's Progression Markers Initiative. As such, a group of 368 people with PD were assessed annually for cognitive performance using multiple neuropsychological protocols, and were genotyped for the TOMM40 '523' variant using whole-genome sequencing data. Covariate-adjusted generalised linear mixed models were utilised to examine the relationship between TOMM40 '523' allele lengths and cognitive scores, while taking into account the APOE ε genotype. Cognitive scores declined over the 5-year study period and were lower in males than in females. When accounting for APOE ε4, the TOMM40 '523' variant was not robustly associated with overall cognitive performance. However, in APOE ε3/ε3 carriers, who accounted for ~60% of the whole cohort, carriage of shorter '523' alleles was associated with more severe cognitive decline in both sexes, while carriage of the longer alleles in females were associated with better preservation of global cognition and a number of cognitive sub-domains, and with a delay in progression to dementia. The findings indicate that when taken in conjunction with the APOE genotype, TOMM40 '523' allele length is a significant independent determinant and marker for the trajectory of cognitive decline and risk of dementia in PD.
    DOI:  https://doi.org/10.1038/s41531-021-00200-y
  21. Food Funct. 2021 Jul 05.
      Pathological myocardial hypertrophy, which lacks effective prevention and treatment strategies, makes the elderly susceptible to various cardiovascular diseases. Based on the beneficial attributes of lactoferrin in aging-related diseases, we aimed to investigate whether lactoferrin could exert protection against aging-related cardiac hypertrophy and further explore the underlying mechanisms. Here, we assessed the effects of lactoferrin on myocardial pathology, apoptotic proteins, mitochondrial morphology, kinetics, autophagy, and aging-related markers, including lipofuscin deposition, overloaded iron, and oxidative stress, which are known to destabilize the mitochondrial-lysosomal axis in aged mice. Upon the administration of lactoferrin, aged hearts showed amelioration of pathological cardiac hypertrophy, which was associated with decreased apoptosis, improved morphology, rearrangement of mitochondrial dynamics, increased lysosome-dependent autophagy, and inhibition of factors detrimental to the mitochondrial-lysosomal axis. In conclusion, lactoferrin ameliorated pathological cardiac hypertrophy, potentially by improving the mitochondrial quality related to mitochondrial dynamics and the mitochondrial-lysosomal axis, thus reducing mitochondria-dependent apoptosis, which is the pivotal factor for cardiac hypertrophy in aged mice.
    DOI:  https://doi.org/10.1039/d0fo03346d
  22. Eur J Clin Invest. 2021 Jul 05. e13648
      Receptor interacting protein kinase 3 (RIPK3) is a key player of regulated necrosis or necroptosis, an inflammatory form of cell death possibly governing outcomes in chronic liver diseases, such as non-alcoholic fatty liver disease and non-alcoholic steatohepatitis. RIPK3 activation depends on post-transcriptional modifications, including phosphorylation, hence coordinating the assembly of macromolecular death complex named "necrosome", which may also involve diverse mitochondrial components. Curiously, recent studies suggested a potential link between RIPK3 and mitochondrial bioenergetics. RIPK3 can modulate mitochondrial function and quality through the regulation of mitochondrial reactive oxygen species production, sequestration of metabolic enzymes and resident mitochondrial proteins, activity of mitochondrial respiratory chain complexes, mitochondrial biogenesis and fatty acid oxidation. Since mitochondrial dysfunction and RIPK3-mediated necroptosis are intimately involved in chronic liver diseases pathogenesis, understanding the role of RIPK3 in mitochondrial bioenergetics and its potential translational application are of great interest.
    Keywords:  Mitochondria; NAFLD; NASH; RIPK3; necroptosis
    DOI:  https://doi.org/10.1111/eci.13648
  23. Neuropathol Appl Neurobiol. 2021 Jul 08.
      AIMS: Mitochondrial dysfunction and inflammation are at the core of axonal degeneration in several multifactorial neurodegenerative diseases, including multiple sclerosis, Alzheimer's and Parkinson's disease. The transcriptional coregulator RIP140/NRIP1 (receptor-interacting protein 140) modulates these functions in liver and adipose tissue, but its role in the nervous system remains unexplored. Here, we investigated the impact of RIP140 in the Abcd1- mouse model of X-linked adrenoleukodystrophy (X-ALD), a genetic model of chronic axonopathy involving the convergence of redox imbalance, bioenergetic failure and chronic inflammation.METHODS AND RESULTS: We provide evidence that RIP140 is modulated through a redox-dependent mechanism driven by very long-chain fatty acids (VLCFAs), the levels of which are increased in X-ALD. Genetic inactivation of RIP140 prevented mitochondrial depletion and dysfunction, bioenergetic failure, inflammatory dysregulation, axonal degeneration and associated locomotor disabilities in vivo in X-ALD mouse models.
    CONCLUSIONS: Together, these findings show that aberrant overactivation of RIP140 promotes neurodegeneration in X-ALD, underscoring its potential as a therapeutic target for X-ALD and other neurodegenerative disorders that present with metabolic and inflammatory dyshomeostasis.
    Keywords:  RIP140; adrenoleukodystrophy; mitochondria; neuroinflammation; oxidative stress
    DOI:  https://doi.org/10.1111/nan.12747
  24. RNA Biol. 2021 Jul 09.
      The eukaryotic tRNA guanine transglycosylase (TGT) is an RNA modifying enzyme incorporating queuine, a hypermodified guanine derivative, into the tRNAsAsp,Asn,His,Tyr. While both subunits of the functional heterodimer have been crystallized individually, much of our understanding of its dimer interface or recognition of a target RNA have been inferred from its more thoroughly studied bacterial homolog. However, since bacterial TGT, by incorporating queuine precursor preQ1, deviates not only in function, but, as a homodimer, also in its subunit architecture, any inferences regarding the subunit association of the eukaryotic heterodimer or the significance of its unique catalytically inactive subunit are based on unstable footing. Here, we report the crystal structure of human TGT in its heterodimeric form and in complex with a 25-mer stem loop RNA, enabling detailed analysis of its dimer interface and interaction with a minimal substrate RNA. Based on a model of bound tRNA we addressed a potential functional role of the catalytically inactive subunit QTRT2 by UV-crosslinking and mutagenesis experiments, identifying the two-stranded βEβF-sheet of the QTRT2 subunit as an additional RNA-binding motif.
    Keywords:  RNA-binding protein; X-ray crystallography; eukaryotic; heterodimer; queuine; structural biology; tRNA modification; transglycosylase
    DOI:  https://doi.org/10.1080/15476286.2021.1950980
  25. Cell Death Discov. 2021 Jun 28. 7(1): 151
      L-3,4-Dihydroxyphenylalanin (L-DOPA or levodopa) is currently the most used drug to treat symptoms of Parkinson's disease (PD). After crossing the blood-brain barrier, it is enzymatically converted to dopamine by neuronal cells and restores depleted endogenous neurotransmitter levels. L-DOPA is prone to auto-oxidation and reactive intermediates of its degradation including reactive oxygen species (ROS) have been implicated in cellular damage. In this study, we investigated how oxygen tension effects L-DOPA stability. We applied oxygen tensions comparable to those in the mammalian brain and demonstrated that 2% oxygen almost completely stopped its auto-oxidation. L-DOPA even exerted a ROS scavenging function. Further mechanistic analysis indicated that L-DOPA reprogrammed mitochondrial metabolism and reduced oxidative phosphorylation, depolarized the mitochondrial membrane, induced reductive glutamine metabolism, and depleted the NADH pool. These results shed new light on the cellular effects of L-DOPA and its neuro-toxicity under physiological oxygen levels that are very distinct to normoxic in vitro conditions.
    DOI:  https://doi.org/10.1038/s41420-021-00547-4
  26. Orphanet J Rare Dis. 2021 Jul 03. 16(1): 295
      BACKGROUND: No curative therapy for mitochondrial disease (MD) exists, prioritizing supportive treatment for symptom relief. In animal and cell models ketones decrease oxidative stress, increase antioxidants and scavenge free radicals, putting ketogenic diets (KDs) on the list of management options for MD. Furthermore, KDs are well-known, safe and effective treatments for epilepsy, a frequent symptom of MD. This systematic review evaluates efficacy and safety of KD for MD.METHODS: We searched Pubmed, Cochrane, Embase and Cinahl (November 2020) with search terms linked to MD and KD. From the identified records, we excluded studies on Pyruvate Dehydrogenase Complex deficiency. From these eligible reports, cases without a genetically confirmed diagnosis and cases without sufficient data on KD and clinical course were excluded. The remaining studies were included in the qualitative analysis.
    RESULTS: Only 20 cases (14 pediatric) from the 694 papers identified met the inclusion criteria (one controlled trial (n = 5), 15 case reports). KD led to seizure control in 7 out of 8 cases and improved muscular symptoms in 3 of 10 individuals. In 4 of 20 cases KD reversed the clinical phenotype (e.g. cardiomyopathy, movement disorder). In 5 adults with mitochondrial DNA deletion(s) related myopathy rhabdomyolysis led to cessation of KD. Three individuals with POLG mutations died while being on KD, however, their survival was not different compared to individuals with POLG mutations without KD.
    CONCLUSION: Data on efficacy and safety of KD for MD is too scarce for general recommendations. KD should be considered in individuals with MD and therapy refractory epilepsy, while KD is contraindicated in mitochondrial DNA deletion(s) related myopathy. When considering KD for MD the high rate of adverse effects should be taken into account, but also spectacular improvements in individual cases. KD is a highly individual management option in this fragile patient group and requires an experienced team. To increase knowledge on this-individually-promising management option more (prospective) studies using adequate outcome measures are crucial.
    Keywords:  Adverse event; Complex I; Epilepsy; High fat diet; Management; Mitochondrial DNA deletion; Mitochondrial myopathy; Modified Atkins diet; OXPHOS; Treatment
    DOI:  https://doi.org/10.1186/s13023-021-01927-w
  27. Methods Mol Biol. 2021 ;2312 277-285
      There are increasing evidence and growing interest in the relationship between protein aggregates/phase separation and various human diseases, especially neurodegenerative diseases. However, we do not entirely comprehend how aggregates generate or the clearance network of chaperones, proteasomes, ubiquitin ligases, and other factors interact with aggregates. Here, we describe chemically controllable systems compose with a genetically engineered cell and a small drug that enables us to rapidly induce protein aggregates' formation by withdrawing the small molecule. This trigger does not activate global stress responses induced by stimuli, such as proteasome inhibitors or heat shock. This method can produce aggregates in a specific compartment and diverse experimental systems, including live animals.
    Keywords:  Chaperones; Chemical biology; Destabilizing domain; Phase separation; Proteasome; Protein aggregates
    DOI:  https://doi.org/10.1007/978-1-0716-1441-9_16
  28. Elife. 2021 Jul 05. pii: e57376. [Epub ahead of print]10
      Understanding cellular stress response pathways is challenging because of the complexity of regulatory mechanisms and response dynamics, which can vary with both time and the type of stress. We developed a reverse genetic method called ReporterSeq to comprehensively identify genes regulating a stress-induced transcription factor under multiple conditions in a time-resolved manner. ReporterSeq links RNA-encoded barcode levels to pathway-specific output under genetic perturbations, allowing pooled pathway activity measurements via DNA sequencing alone and without cell enrichment or single-cell isolation. We used ReporterSeq to identify regulators of the heat shock response (HSR), a conserved, poorly understood transcriptional program that protects cells from proteotoxicity and is misregulated in disease. Genome-wide HSR regulation in budding yeast was assessed across 15 stress conditions, uncovering novel stress-specific, time-specific, and constitutive regulators. ReporterSeq can assess the genetic regulators of any transcriptional pathway with the scale of pooled genetic screens and the precision of pathway-specific readouts.
    Keywords:  CRISPR; HSF1; S. cerevisiae; cell biology; chaperones; genetic screens; genetics; genomics; heat shock response; protein quality control
    DOI:  https://doi.org/10.7554/eLife.57376
  29. Clin Neurol Neurosurg. 2021 Jun 25. pii: S0303-8467(21)00302-4. [Epub ahead of print]207 106773
      We present a case of Huntington's Disease (HD) with two reduced penetrance alleles and show that age of onset and motor symptoms are comparable to heterozygous patients with the same number of CAG triplet repeats. We performed a review of the literature on clinical presentation of homozygous HD cases and highlight that, so far, evidence exists that HD is a truly dominant disorder. This has important implications for pathophysiology concepts of the disease.
    Keywords:  Homozygote; Huntington’s disease; Reduced penetrance
    DOI:  https://doi.org/10.1016/j.clineuro.2021.106773
  30. FEMS Microbiol Rev. 2021 Jul 05. pii: fuab037. [Epub ahead of print]
      Nicotinamide adenine dinucleotide (NAD+) is a major cofactor in redox reactions in all lifeforms. A stable level of NAD+ is vital to ensure cellular homeostasis. Some pathogens can modulate NAD+ metabolism to their advantage and even utilize or cleave NAD+ from the host using specialized effectors known as ADP-ribosyltransferase toxins and NADases, leading to energy store depletion, immune evasion, or even cell death. This review explores recent advances in the field of bacterial NAD+-targeting toxins, highlighting the relevance of NAD+ modulation as an emerging pathogenesis strategy. In addition, we discuss the role of specific NAD+-targeting toxins in niche colonization and bacterial lifestyle as components of Toxin/Antitoxin systems and key players in inter-bacterial competition. Understanding the mechanisms of toxicity, regulation, and secretion of these toxins will provide interesting leads in the search for new antimicrobial treatments in the fight against infectious diseases.
    Keywords:  ADP-ribosylation; NAD+; NADase; bacterial virulence factor; immune response evasion; secretion pathway
    DOI:  https://doi.org/10.1093/femsre/fuab037
  31. Methods Mol Biol. 2021 ;2361 229-248
      Protein-protein interaction networks have a crucial role in biological processes. Proteins perform multiple functions in forming physical and functional interactions in cellular systems. Information concerning an enormous number of protein interactions in a wide range of species has accumulated and has been integrated into various resources for molecular biology and systems biology. This chapter provides a review of the representative databases and the major computational methods used for protein-protein interactions.
    Keywords:  Computational methods; Molecular interactions; Protein interaction networks; Protein structures; Protein–protein interactions
    DOI:  https://doi.org/10.1007/978-1-0716-1641-3_14
  32. Biol Chem. 2021 Jul 05.
      Using results from genome-wide association studies for understanding complex traits is a current challenge. Here we review how genotype data can be used with different machine learning (ML) methods to predict phenotype occurrence and severity from genotype data. We discuss common feature encoding schemes and how studies handle the often small number of samples compared to the huge number of variants. We compare which ML methods are being applied, including recent results using deep neural networks. Further, we review the application of methods for feature explanation and interpretation.
    Keywords:  deep neural networks; disease prediction; machine learning
    DOI:  https://doi.org/10.1515/hsz-2021-0109
  33. Methods Mol Biol. 2021 ;2314 323-342
      With increasing prevalence of antimicrobial resistance, a fundamental goal of antibiotic discovery is to uncover new small molecules that prevent growth of pathogenic bacteria through diverse mechanisms of action. This goal is particularly pertinent for tuberculosis, caused by Mycobacterium tuberculosis. In this chapter, we describe the application of a chemical-genetic method, PROSPECT (primary screening of strains to prioritize expanded chemistry and targets), for sensitively detecting small molecule bioactivity using a pooled panel of hypomorphs (strains depleted in a particular essential gene) of M. tuberculosis. We describe statistical and heuristic approaches to assign small molecule mechanism of action from the resulting chemical-genetic interaction profiles.
    Keywords:  Chemical biology; Chemical genetics; Genetics; Mechanism of action; Mycobacterium tuberculosis; Next generation sequencing
    DOI:  https://doi.org/10.1007/978-1-0716-1460-0_15
  34. Methods Mol Biol. 2021 ;2312 225-233
      The CRISPR-Cas9 system offers targeted genome manipulation with simplicity. Combining the CRISPR-Cas9 with optogenetics technology, we have engineered photoactivatable Cas9 to precisely control the genome sequence in a spatiotemporal manner. Here we provide a detailed protocol for optogenetic genome editing experiments using photoactivatable Cas9, including that for the generation of guide RNA vectors, light-mediated Cas9 activation, and quantification of genome editing efficiency in mammalian cells.
    Keywords:  CRISPR-Cas9; Genome editing; Genomic PCR; Guide RNA; HDR; NHEJ; Optogenetics; T7E1 assay
    DOI:  https://doi.org/10.1007/978-1-0716-1441-9_13
  35. Neurol Res Pract. 2021 Jul 08. 3(1): 40
      A 53-year old male with a history of progressive visual impairment, hearing loss, peripheral neuropathy, poorly controlled diabetes mellitus, cardiomyopathy, and weight loss was referred to the rare disease center due to the suspicion of mitochondrial cytopathy. In line with mitochondrial dysfunction, lactate in CSF was increased. Genetic testing by whole-exome sequencing and mitochondrial DNA did not reveal a likely cause. The case remained unsolved until he developed pain in his right hip, where he had received total hip arthroplasty 12 years earlier. An orthopedic evaluation revealed substantial shrinkage of the head of the hip prosthesis. Due to metal-on-metal wear, debris chromium and cobalt levels in serum were massively increased and significantly improved with multisystemic impairment after exchanging the defective implant.
    Keywords:  Chromium; Cobalt; Intoxication; Mitochondriopathy
    DOI:  https://doi.org/10.1186/s42466-021-00141-0
  36. Pain. 2021 Jul 02.
      ABSTRACT: Painful diabetic neuropathy (PDN) is an intractable complication affecting 25% of diabetic patients. PDN is characterized by neuropathic pain accompanied by dorsal root ganglion (DRG) nociceptor hyperexcitability, resulting in calcium overload, axonal degeneration, and loss of cutaneous innervation. The molecular pathways underlying these effects are unknown. Using high-throughput and deep-proteome profiling, we found that mitochondrial fission proteins were elevated in DRG neurons from mice with PDN induced by a high-fat diet (HFD). In vivo calcium imaging revealed increased calcium signaling in DRG nociceptors from mice with PDN. Furthermore, using electron microscopy, we showed that mitochondria in DRG nociceptors had fragmented morphology as early as two weeks after starting HFD, preceding the onset of mechanical allodynia and small-fiber degeneration. Moreover, preventing calcium entry into the mitochondria, by selectively deleting the mitochondrial calcium uniporter (MCU) from these neurons restored normal mitochondrial morphology, prevented axonal degeneration, and reversed mechanical allodynia in the HFD mouse model of PDN. These studies suggest a molecular cascade linking neuropathic pain to axonal degeneration in PDN. In particular, nociceptor hyperexcitability and the associated increased intracellular calcium concentrations could lead to excessive calcium entry into mitochondria mediated by the MCU, resulting in increased calcium-dependent mitochondrial fission and ultimately contributing to small-fiber degeneration and neuropathic pain in PDN. Hence, we propose that targeting calcium entry into nociceptor mitochondria may represent a promising effective and disease-modifying therapeutic approach for this currently intractable and widespread affliction. Moreover, these results are likely to inform studies of other neurodegenerative disease involving similar underlying events.
    DOI:  https://doi.org/10.1097/j.pain.0000000000002391
  37. Cell Death Dis. 2021 Jul 03. 12(7): 673
      The STING pathway and its induction of autophagy initiate a potent immune defense response upon the recognition of pathogenic DNA. However, this protective response is minimal, as STING activation worsens organ damage, and abnormal autophagy is observed during progressive sepsis. Whether and how the STING pathway affects autophagic flux during sepsis-induced acute lung injury (sALI) are currently unknown. Here, we demonstrate that the level of circulating mtDNA and degree of STING activation are increased in sALI patients. Furthermore, STING activation was found to play a pivotal role in mtDNA-mediated lung injury by evoking an inflammatory storm and disturbing autophagy. Mechanistically, STING activation interferes with lysosomal acidification in an interferon (IFN)-dependent manner without affecting autophagosome biogenesis or fusion, aggravating sepsis. Induction of autophagy or STING deficiency alleviated lung injury. These findings provide new insights into the role of STING in the regulatory mechanisms behind extrapulmonary sALI.
    DOI:  https://doi.org/10.1038/s41419-021-03961-9
  38. Hepatology. 2021 Jul 07.
      BACKGROUND & AIMS: Non-alcoholic fatty liver disease (NAFLD) is the most common hepatic pathology in western countries and no treatment is currently available. NAFLD is characterized by the aberrant hepatocellular accumulation of fatty acids in the form of lipid droplets (LD). Recently, it was shown that liver LD degradation occurs via a process termed lipophagy; a novel form of autophagy. However, the molecular mechanisms governing liver lipophagy are elusive. Here, we aimed to ascertain the key molecular players that regulate hepatic lipophagy and their importance in NAFLD.APPROACH & RESULTS: We analyzed the formation and degradation of LD in vitro (fibroblasts and primary mouse hepatocytes), in vivo and ex vivo (mouse and human liver slices) and focused on the role of the autophagy master regulator mammalian Target Of Rapamycin Complex 1 (mTORC1) and the LD coating protein Plin3 in these processes. We show that the autophagy machinery is recruited to the LD upon hepatic overload of oleic acid in all experimental settings. This led to activation of lipophagy, a process that was abolished by Plin3 knockdown using RNA interference. Furthermore, Plin3 directly interacted with the autophagy proteins Fip200 and Atg16L, suggesting that Plin3 functions as a docking protein or is involved in autophagosome formation to activate lipophagy. Finally, we show that mTORC1 phosphorylated Plin3 to promote LD degradation.
    CONCLUSIONS: These results reveal that mTORC1 regulates liver lipophagy through a mechanism dependent on Plin3 phosphorylation. We propose that stimulating this pathway can enhance lipophagy in hepatocytes to help protect the liver from lipid-mediated toxicity, thus offering a new therapeutic strategy in NAFLD.
    Keywords:  autophagy; fatty liver disease; hepatocytes; lipid droplets; perilipin
    DOI:  https://doi.org/10.1002/hep.32048
  39. Nat Methods. 2021 Jul;18(7): 779-787
      Chimeric MS/MS spectra contain fragments from multiple precursor ions and therefore hinder compound identification in metabolomics. Historically, deconvolution of these chimeric spectra has been challenging and relied on specific experimental methods that introduce variation in the ratios of precursor ions between multiple tandem mass spectrometry (MS/MS) scans. DecoID provides a complementary, method-independent approach where database spectra are computationally mixed to match an experimentally acquired spectrum by using LASSO regression. We validated that DecoID increases the number of identified metabolites in MS/MS datasets from both data-independent and data-dependent acquisition without increasing the false discovery rate. We applied DecoID to publicly available data from the MetaboLights repository and to data from human plasma, where DecoID increased the number of identified metabolites from data-dependent acquisition data by over 30% compared to direct spectral matching. DecoID is compatible with any user-defined MS/MS database and provides automated searching for some of the largest MS/MS databases currently available.
    DOI:  https://doi.org/10.1038/s41592-021-01195-3
  40. Public Health Genomics. 2021 Jul 08. 1-11
      BACKGROUND: In the context of medical genetics, gene hunting is the process of identifying and functionally characterizing genes or genetic variations that contribute to disease phenotypes. In this review, we would like to summarize gene hunting process in terms of historical aspects from Darwin to now. For this purpose, different approaches and recent developments will be detailed.SUMMARY: Linkage analysis and association studies are the most common methods in use for explaining the genetic background of hereditary diseases and disorders. Although linkage analysis is a relatively old approach, it is still a powerful method to detect disease-causing rare variants using family-based data, particularly for consanguineous marriages. As is known that, consanguineous marriages or endogamy poses a social problem in developing countries, however, this same condition also provides a unique opportunity for scientists to identify and characterize pathogenic variants. The rapid advancements in sequencing technologies and their parallel implementation together with linkage analyses now allow us to identify the candidate variants related to diseases in a relatively short time. Furthermore, we can now go one step further and functionally characterize the causative variant through in vitro and in vivo studies and unveil the variant-phenotype relationships on a molecular level more robustly. Key Messages: Herein, we suggest that the combined analysis of linkage and exome analysis is a powerful and precise tool to diagnose clinically rare and recessively inherited conditions.
    Keywords:  Consanguineous marriages; Gene hunting; Linkage analysis; Mendelian diseases; Whole-exome sequencing
    DOI:  https://doi.org/10.1159/000517102
  41. Exp Eye Res. 2021 Jul 01. pii: S0014-4835(21)00253-0. [Epub ahead of print]209 108687
      Age-related macular degeneration (AMD) is a severe retinal eye disease where dysfunctional mitochondria and damaged mitochondrial DNA in retinal pigment epithelium (RPE) have been demonstrated to underlie the pathogenesis of this devastating disease. In the present study, we aimed to examine whether damaged mitochondria induce inflammasome activation in human RPE cells. Therefore, ARPE-19 cells were primed with IL-1α and exposed to the mitochondrial electron transport chain complex III inhibitor, antimycin A. We found that antimycin A-induced mitochondrial dysfunction caused caspase-1-dependent inflammasome activation and subsequent production of mature IL-1β and IL-18 in human RPE cells. AIM2 and NLRP3 appeared to be the responsible inflammasome receptors upon antimycin A-induced mitochondrial damage. We aimed at verifying our findings using hESC-RPE cells but antimycin A was absorbed by melanin. Therefore, results were repeated on D407 RPE cell cultures. Antimycin A-induced mitochondrial and NADPH oxidase-dependent ROS production occurred upstream of inflammasome activation, whereas K+ efflux was not required for inflammasome activation in antimycin A-treated human RPE cells. Collectively, our data emphasize that dysfunctional mitochondria regulate the assembly of inflammasome multiprotein complexes in the human RPE cells. The present study associates AIM2 with the pathogenesis of AMD.
    Keywords:  AIM2; Age-related macular degeneration; Inflammasome; Interleukin-1beta; Mitochondrial damage; NLRP3; Retinal pigment epithelium
    DOI:  https://doi.org/10.1016/j.exer.2021.108687
  42. Nat Commun. 2021 07 05. 12(1): 4110
      We hypothesized that the highly controlled pattern of gene expression that is essential for liver regeneration is encoded by an epigenetic code set in quiescent hepatocytes. Here we report that epigenetic and transcriptomic profiling of quiescent and regenerating mouse livers define chromatin states that dictate gene expression and transposon repression. We integrate ATACseq and DNA methylation profiling with ChIPseq for the histone marks H3K4me3, H3K27me3 and H3K9me3 and the histone variant H2AZ to identify 6 chromatin states with distinct functional characteristics. We show that genes involved in proliferation reside in active states, but are marked with H3K27me3 and silenced in quiescent livers. We find that during regeneration, H3K27me3 is depleted from their promoters, facilitating their dynamic expression. These findings demonstrate that hepatic chromatin states in quiescent livers predict gene expression and that pro-regenerative genes are maintained in active chromatin states, but are restrained by H3K27me3, permitting a rapid and synchronized response during regeneration.
    DOI:  https://doi.org/10.1038/s41467-021-24466-1
  43. Biol Chem. 2021 Jul 05.
      The placenta is a highly vascularized and complex foetal organ that performs various tasks, crucial to a healthy pregnancy. Its dysfunction leads to complications such as stillbirth, preeclampsia, and intrauterine growth restriction. The specific cause of placental dysfunction remains unknown. Recently, the role of mitochondrial function and mitochondrial adaptations in the context of angiogenesis and placental dysfunction is getting more attention. The required energy for placental remodelling, nutrient transport, hormone synthesis, and the reactive oxygen species leads to oxidative stress, stemming from mitochondria. Mitochondria adapt to environmental changes and have been shown to adjust their oxygen and nutrient use to best support placental angiogenesis and foetal development. Angiogenesis is the process by which blood vessels form and is essential for the delivery of nutrients to the body. This process is regulated by different factors, pro-angiogenic factors and anti-angiogenic factors, such as sFlt-1. Increased circulating sFlt-1 levels have been linked to different preeclamptic phenotypes. One of many effects of increased sFlt-1 levels, is the dysregulation of mitochondrial function. This review covers mitochondrial adaptations during placentation, the importance of the anti-angiogenic factor sFlt-1in placental dysfunction and its role in the dysregulation of mitochondrial function.
    Keywords:  computational modelling; endothelial dysfunction; mitochondrial dysfunction; preeclampsia; systems biology; vascular deregulation
    DOI:  https://doi.org/10.1515/hsz-2021-0121
  44. EMBO Mol Med. 2021 Jul 07. e13086
      Ceramide-induced mitochondrial fission drives high-fat diet (HFD)-induced obesity. However, molecules targeting mitochondrial dynamics have shown limited benefits in murine obesity models. Here, we reveal that these compounds are either unable to block ceramide-induced mitochondrial fission or require extended incubation periods to be effective. In contrast, targeting endolysosomal trafficking events important for mitochondrial fission rapidly and robustly prevented ceramide-induced disruptions in mitochondrial form and function. By simultaneously inhibiting ARF6- and PIKfyve-dependent trafficking events, the synthetic sphingolipid SH-BC-893 blocked palmitate- and ceramide-induced mitochondrial fission, preserved mitochondrial function, and prevented ER stress in␣vitro. Similar benefits were observed in the tissues of HFD-fed mice. Within 4 h of oral administration, SH-BC-893 normalized mitochondrial morphology in the livers and brains of HFD-fed mice, improved mitochondrial function in white adipose tissue, and corrected aberrant plasma leptin and adiponectin levels. As an interventional agent, SH-BC-893 restored normal body weight, glucose disposal, and hepatic lipid levels in mice consuming a HFD. In sum, the sphingolipid analog SH-BC-893 robustly and acutely blocks ceramide-induced mitochondrial dysfunction, correcting diet-induced obesity and its metabolic sequelae.
    Keywords:  ceramide; high-fat diet; leptin resistance; mitochondrial fission; obesity
    DOI:  https://doi.org/10.15252/emmm.202013086
  45. Optica. 2021 Apr 20. 8(4): 442-450
      Stimulated emission depletion (STED) microscopy enables the three-dimensional (3D) visualization of dynamic nanoscale structures in living cells, offering unique insights into their organization. However, 3D-STED imaging deep inside biological tissue is obstructed by optical aberrations and light scattering. We present a STED system that overcomes these challenges. Through the combination of two-photon excitation, adaptive optics, red-emitting organic dyes, and a long-working-distance water-immersion objective lens, our system achieves aberration-corrected 3D super-resolution imaging, which we demonstrate 164 µm deep in fixed mouse brain tissue and 76 µm deep in the brain of a living mouse.
    DOI:  https://doi.org/10.1364/OPTICA.416841
  46. J Cell Sci. 2021 Jul 09. pii: jcs.258374. [Epub ahead of print]
      Analysis of histone variants and epigenetic marks is dominated by genome-wide approaches in the form of chromatin immunoprecipitation-sequencing (ChIP-seq) and related methods. While uncontested in their value for single-copy genes, mapping the chromatin of DNA repeats is problematic for biochemical techniques based on averaging cell populations or high number of repeats in a single cell analysis. Extending chromatin and DNA fibers allows us to study the epigenetics of individual repeats in their specific chromosomal context and thus constitutes an important tool for a wholesome understanding of the epigenetic organization of genomes. We present that using an optimized fiber extension protocol is essential to obtain more reproducible data, where the clustering of fibers is minimized. We also demonstrate that applying super-resolution microscopy is important to reliably evaluate the distribution of histone modifications on individual fibers. Furthermore, we introduce a custom script to analyse methylation levels on DNA fibers and apply it to map the methylation of telomeres, ribosomal genes and centromeres.
    Keywords:  Chromatin; DNA; Fiber; Methylation; Microscopy
    DOI:  https://doi.org/10.1242/jcs.258374
  47. Prog Biophys Mol Biol. 2021 Jun 30. pii: S0079-6107(21)00073-0. [Epub ahead of print]
      Over the last ten years, developments in whole-brain microscopy now allow for high-resolution imaging of intact brains of small rodents such as mice. These complex images contain a wealth of information, but many neuroscience laboratories do not have all of the computational knowledge and tools needed to process these data. We review recent open source tools for registration of images to atlases, and the segmentation, visualisation and analysis of brain regions and labelled structures such as neurons. Since the field lacks fully integrated analysis pipelines for all types of whole-brain microscopy analysis, we propose a pathway for tool developers to work together to meet this challenge.
    Keywords:  Image registration; Neuroscience; Segmentation; Visualisation; whole Brain microscopy
    DOI:  https://doi.org/10.1016/j.pbiomolbio.2021.06.013
  48. J Cardiovasc Pharmacol. 2021 Jul 01. 78(1): e30-e39
      ABSTRACT: Mitophagy is involved in the development of various cardiovascular diseases, such as atherosclerosis, heart failure, myocardial ischemia/reperfusion injury, and hypertension. Mitophagy is essential for maintaining intracellular homeostasis and physiological function in most cardiovascular origin cells, such as cardiomyocytes, endothelial cells, and vascular smooth muscle cells. Mitophagy is crucial to ensuring energy supply by selectively removing dysfunctional mitochondria, maintaining a balance in the number of mitochondria in cells, ensuring the integrity of mitochondrial structure and function, maintaining homeostasis, and promoting cell survival. Substantial research has indicated a "dual" effect of mitophagy on cardiac function, with inadequate and increased mitochondrial degradation both likely to influence the progression of cardiovascular disease. This review summarizes the main regulatory pathways of mitophagy and emphasizes that an appropriate amount of mitophagy can prevent endothelial cell injury, vascular smooth muscle cell proliferation, macrophage polarization, and cardiomyocyte apoptosis, avoiding further progression of cardiovascular diseases.
    DOI:  https://doi.org/10.1097/FJC.0000000000001046
  49. Mol Neurobiol. 2021 Jul 07.
      Mitochondrial damage has been reported to be a critical factor for secondary brain injury (SBI) induced by intracerebral hemorrhage (ICH). MIC60 is a key element of the mitochondrial contact site and cristae junction organizing system (MICOS), which takes a principal part in maintaining mitochondrial structure and function. The role of MIC60 and its underlying mechanisms in ICH-induced SBI are not clear, which will be investigated in this present study. To establish and emulate ICH model in vivo and in vitro, autologous blood was injected into the right basal ganglia of Sprague-Dawley (SD) rats; and primary-cultured cortical neurons were treated by oxygen hemoglobin (OxyHb). First, after ICH induction, mitochondria were damaged and exhibited mitochondrial crista-structure remodeling, and MIC60 protein levels were reduced. Furthermore, MIC60 overexpression reduced ICH-induced neuronal death both in vivo and in vitro. In addition, MIC60 upregulation reduced ICH-induced cerebral edema, neurobehavioral impairment, and cognitive dysfunction; by contrast, MIC60 knockdown had the opposite effect. Additionally, in primary-cultured neurons, MIC60 overexpression could reverse ICH-induced neuronal cell death and apoptosis, mitochondrial membrane potential collapse, and decrease of mitophagy, indicating that MIC60 overexpression can maintain the integrity of mitochondrial structures. Moreover, loss of MIC60 is after ICH-induced reduction in PINK1 levels and mislocalization of Parkin in primary-cultured neurons. Taken together, our findings suggest that MIC60 plays an important role in ICH-induced SBI and may represent a promising target for ICH therapy.
    Keywords:  Intracerebral hemorrhage; MIC60; Mitochondrial dysfunction; Neuronal death; Secondary brain injury
    DOI:  https://doi.org/10.1007/s12035-021-02468-w
  50. Eur Heart J. 2021 Jul 06. pii: ehab249. [Epub ahead of print]
      AIMS : Lifestyle-related diseases promote atherosclerosis, a chronic inflammatory disease; however, the molecular mechanism remains largely unknown. Endogenous DNA fragments released under over-nutrient condition provoke sterile inflammation through the recognition by DNA sensors. Here, we investigated the role of stimulator of interferon genes (STING), a cytosolic DNA sensor, in atherogenesis.METHODS AND RESULTS : Apolipoprotein E-deficient (Apoe-/-) mice fed a western-type diet (WTD), a hypercholesterolaemic mouse model, showed higher STING expression and markers for DNA damage such as γH2AX, p53, and single-stranded DNA (ssDNA) accumulation in macrophages in the aorta compared with wild-type (WT) mice. The level of cGAMP, a STING agonist, in the aorta was higher in Apoe-/- mice. Genetic deletion of Sting in Apoe-/- mice reduced atherosclerotic lesions in the aortic arch, lipid, and macrophage accumulation in plaques, and inflammatory molecule expression in the aorta compared with the control. Pharmacological blockade of STING using a specific inhibitor, C-176, ameliorated atherogenesis in Apoe-/- mice. In contrast, bone marrow-specific STING expression in Apoe-/- mice stimulated atherogenesis. Expression or deletion of STING did not affect metabolic parameters and blood pressure. In vitro studies revealed that STING activation by cGAMP or mitochondrial DNA accelerated inflammatory molecule expression (e.g. TNF-α or IFN-β) in mouse and human macrophages. Activation of nuclear factor-κB and TANK binding kinase 1 was involved in STING-associated vascular inflammation and macrophage activation. Furthermore, human atherosclerotic lesions in the carotid arteries expressed STING and cGAMP.
    CONCLUSION : Stimulator of interferon genes stimulates pro-inflammatory activation of macrophages, leading to the development of atherosclerosis. Stimulator of interferon genes signalling may serve as a potential therapeutic target for atherosclerosis.
    Keywords:  Atherosclerosis; DNA; Inflammation; Macrophage; STING
    DOI:  https://doi.org/10.1093/eurheartj/ehab249
  51. Nature. 2021 Jul 07.
      The majority of gene transcripts generated by RNA polymerase II in mammalian genomes initiate at CpG island (CGI) promoters1,2, yet our understanding of their regulation remains limited. This is in part due to the incomplete information that we have on transcription factors, their DNA-binding motifs and which genomic binding sites are functional in any given cell type3-5. In addition, there are orphan motifs without known binders, such as the CGCG element, which is associated with highly expressed genes across human tissues and enriched near the transcription start site of a subset of CGI promoters6-8. Here we combine single-molecule footprinting with interaction proteomics to identify BTG3-associated nuclear protein (BANP) as the transcription factor that binds this element in the mouse and human genome. We show that BANP is a strong CGI activator that controls essential metabolic genes in pluripotent stem and terminally differentiated neuronal cells. BANP binding is repelled by DNA methylation of its motif in vitro and in vivo, which epigenetically restricts most binding to CGIs and accounts for differential binding at aberrantly methylated CGI promoters in cancer cells. Upon binding to an unmethylated motif, BANP opens chromatin and phases nucleosomes. These findings establish BANP as a critical activator of a set of essential genes and suggest a model in which the activity of CGI promoters relies on methylation-sensitive transcription factors that are capable of chromatin opening.
    DOI:  https://doi.org/10.1038/s41586-021-03689-8
  52. Cell Metab. 2021 Jul 06. pii: S1550-4131(21)00278-3. [Epub ahead of print]33(7): 1274-1275
      Numerous preclinical studies implicate the decline in NAD+ signaling in developing aging- and obesity-associated metabolic disorders. Yoshino et al. (2021) now provide the clinical evidence that an NAD+ booster increases muscle insulin sensitivity in postmenopausal prediabetic women, validating the therapeutic promises of NAD+ boosters in humans.
    DOI:  https://doi.org/10.1016/j.cmet.2021.06.008