bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2022‒08‒28
twenty-one papers selected by
Catalina Vasilescu
University of Helsinki
  1. Modulating Mitochondrial DNA Heteroplasmy with Mitochondrially Targeted Endonucleases.
  2. Varied Responses to a High m.3243A>G Mutation Load and Respiratory Chain Dysfunction in Patient-Derived Cardiomyocytes.
  3. Aberrant RNA processing contributes to the pathogenesis of mitochondrial diseases in trans-mitochondrial mouse model carrying mitochondrial tRNALeu(UUR) with a pathogenic A2748G mutation.
  4. The mitochondrial protein OPA1 regulates the quiescent state of adult muscle stem cells.
  5. Common methods in mitochondrial research (Review).
  6. Mitochondrial dynamics maintain muscle stem cell regenerative competence throughout adult life by regulating metabolism and mitophagy.
  7. Glycerol-3-phosphate shuttle is a backup system securing metabolic flexibility in neurons.
  8. Deletion of ATAD3A inhibits osteogenesis by impairing mitochondria structure and function in pre-osteoblast.
  9. Mitochondrial behavior when things go wrong in the axon.
  10. High-content analysis of neuronal morphology in human iPSC-derived neurons.
  11. Impaired disassembly of the axon initial segment restricts mitochondrial entry into damaged axons.
  12. Standardization and validation of novel ex-vivo method for mitochondrial bioenergetics using mitochondrial modulators.
  13. Epigenomic Approaches for the Diagnosis of Rare Diseases.
  14. A nanopore interface for higher bandwidth DNA computing.
  15. Towards Personalized Allele-Specific Antisense Oligonucleotide Therapies for Toxic Gain-of-Function Neurodegenerative Diseases.
  16. NAD+ metabolism drives astrocyte proinflammatory reprogramming in central nervous system autoimmunity.
  17. Dominantly acting KIF5B variants with pleiotropic cellular consequences cause variable clinical phenotypes.
  18. Mitochondria-lysosome crosstalk in GBA1-associated Parkinson's disease.
  19. Role of Mitochondrial Mutations in Ocular Aggregopathy.
  20. A genome sequencing system for universal newborn screening, diagnosis, and precision medicine for severe genetic diseases.
  21. Central FGF21 production regulates memory but not peripheral metabolism.
  1. Ann Biomed Eng. 2022 Aug 24.
    Modulating Mitochondrial DNA Heteroplasmy with Mitochondrially Targeted Endonucleases.
    Nikita Mikhailov, Riikka H Hämäläinen.
      Mitochondria, mainly known as energy factories of eukaryotic cells, also exert several additional signaling and metabolic functions and are today recognized as major cellular biosynthetic and signaling hubs. Mitochondria possess their own genome (mitochondrial DNA-mtDNA), that encodes proteins essential for oxidative phosphorylation, and mutations in it are an important contributor to human disease. The mtDNA mutations often exist in heteroplasmic conditions, with both healthy and mutant versions of the mtDNA residing in patients' cells and the level of mutant mtDNA may vary between different tissues and organs and affect the clinical outcome of the disease. Thus, shifting the ratio between healthy and mutant mtDNA in patients' cells provides an intriguing therapeutic option for mtDNA diseases. In this review we describe current strategies for modulating mitochondrial heteroplasmy levels with engineered endonucleases including mitochondrially targeted TALENs and Zinc finger nucleases (ZFNs) and discuss their therapeutic potential. These gene therapy tools could in the future provide therapeutic help both for patients with mitochondrial disease as well as in preventing the transfer of pathogenic mtDNA mutations from a mother to her offspring.
    Keywords:  Gene therapy; Genetic engineering; Oxidative phosphorylation; Restriction endonuclease; Zinc finger nuclease; mitoTALEN
    DOI:  https://doi.org/10.1007/s10439-022-03051-7
  2. Cells. 2022 Aug 19. pii: 2593. [Epub ahead of print]11(16):
    Varied Responses to a High m.3243A>G Mutation Load and Respiratory Chain Dysfunction in Patient-Derived Cardiomyocytes.
    Sanna Ryytty, Shalem R Modi, Nikolay Naumenko, Anastasia Shakirzyanova, Muhammad Obaidur Rahman, Miia Vaara, Anu Suomalainen, Pasi Tavi, Riikka H Hämäläinen.
      The m.3243A>G mutation in mitochondrial tRNA-Leu(UUR) is one of the most common pathogenic mitochondrial DNA mutations in humans. The clinical manifestations are highly heterogenous and the causes for the drastic clinical variability are unknown. Approximately one third of patients suffer from cardiac disease, which often increases mortality. Why only some patients develop cardiomyopathy is unknown. Here, we studied the molecular effects of a high m.3243A>G mutation load on cardiomyocyte functionality, using cells derived from induced pluripotent stem cells (iPSC-CM) of two different m.3243A>G patients, only one of them suffering from severe cardiomyopathy. While high mutation load impaired mitochondrial respiration in both patients' iPSC-CMs, the downstream consequences varied. mtDNA mutant cells from a patient with no clinical heart disease showed increased glucose metabolism and retained cellular ATP levels, whereas cells from the cardiac disease patient showed reduced ATP levels. In this patient, the mutations also affected intracellular calcium signaling, while this was not true in the other patient's cells. Our results reflect the clinical variability in mitochondrial disease patients and show that iPSC-CMs retain tissue specific features seen in patients.
    Keywords:  cardiomyocyte; cardiomyopathy; iPS-cell; mitochondria; mtDNA; respiratory chain dysfunction
    DOI:  https://doi.org/10.3390/cells11162593
  3. Nucleic Acids Res. 2022 Aug 24. pii: gkac699. [Epub ahead of print]
    Aberrant RNA processing contributes to the pathogenesis of mitochondrial diseases in trans-mitochondrial mouse model carrying mitochondrial tRNALeu(UUR) with a pathogenic A2748G mutation.
    Haruna Tani, Kaori Ishikawa, Hiroaki Tamashiro, Emi Ogasawara, Takehiro Yasukawa, Shigeru Matsuda, Akinori Shimizu, Dongchon Kang, Jun-Ichi Hayashi, Fan-Yan Wei, Kazuto Nakada.
      Mitochondrial tRNAs are indispensable for the intra-mitochondrial translation of genes related to respiratory subunits, and mutations in mitochondrial tRNA genes have been identified in various disease patients. However, the molecular mechanism underlying pathogenesis remains unclear due to the lack of animal models. Here, we established a mouse model, designated 'mito-mice tRNALeu(UUR)2748', that carries a pathogenic A2748G mutation in the tRNALeu(UUR) gene of mitochondrial DNA (mtDNA). The A2748G mutation is orthologous to the human A3302G mutation found in patients with mitochondrial diseases and diabetes. A2748G mtDNA was maternally inherited, equally distributed among tissues in individual mice, and its abundance did not change with age. At the molecular level, A2748G mutation is associated with aberrant processing of precursor mRNA containing tRNALeu(UUR) and mt-ND1, leading to a marked decrease in the steady-levels of ND1 protein and Complex I activity in tissues. Mito-mice tRNALeu(UUR)2748 with ≥50% A2748G mtDNA exhibited age-dependent metabolic defects including hyperglycemia, insulin insensitivity, and hepatic steatosis, resembling symptoms of patients carrying the A3302G mutation. This work demonstrates a valuable mouse model with an inheritable pathological A2748G mutation in mt-tRNALeu(UUR) that shows metabolic syndrome-like phenotypes at high heteroplasmy level. Furthermore, our findings provide molecular basis for understanding A3302G mutation-mediated mitochondrial disorders.
    DOI:  https://doi.org/10.1093/nar/gkac699
  4. Cell Stem Cell. 2022 Aug 19. pii: S1934-5909(22)00333-2. [Epub ahead of print]
    The mitochondrial protein OPA1 regulates the quiescent state of adult muscle stem cells.
    Nicole Baker, Steven Wade, Matthew Triolo, John Girgis, Damian Chwastek, Sarah Larrigan, Peter Feige, Ryo Fujita, Colin Crist, Michael A Rudnicki, Yan Burelle, Mireille Khacho.
      Quiescence regulation is essential for adult stem cell maintenance and sustained regeneration. Our studies uncovered that physiological changes in mitochondrial shape regulate the quiescent state of adult muscle stem cells (MuSCs). We show that MuSC mitochondria rapidly fragment upon an activation stimulus, via systemic HGF/mTOR, to drive the exit from deep quiescence. Deletion of the mitochondrial fusion protein OPA1 and mitochondrial fragmentation transitions MuSCs into G-alert quiescence, causing premature activation and depletion upon a stimulus. OPA1 loss activates a glutathione (GSH)-redox signaling pathway promoting cell-cycle progression, myogenic gene expression, and commitment. MuSCs with chronic OPA1 loss, leading to mitochondrial dysfunction, continue to reside in G-alert but acquire severe cell-cycle defects. Additionally, we provide evidence that OPA1 decline and impaired mitochondrial dynamics contribute to age-related MuSC dysfunction. These findings reveal a fundamental role for OPA1 and mitochondrial dynamics in establishing the quiescent state and activation potential of adult stem cells.
    Keywords:  G-alert; GSH; OPA1; ROS; adult muscle stem cells; aging; glutathione; mTOR; mitochondrial dynamics; quiescence; reactive oxygen species; stem cell activation; stem cell maintenance; systemic factors
    DOI:  https://doi.org/10.1016/j.stem.2022.07.010
  5. Int J Mol Med. 2022 Oct;pii: 126. [Epub ahead of print]50(4):
    Common methods in mitochondrial research (Review).
    Yiyuan Yin, Haitao Shen.
      Mitochondrial abnormalities are primarily seen in morphology, structure and function. They can cause damage to organs, including the heart, brain and muscle, by various mechanisms, such as oxidative stress, abnormal energy metabolism, or genetic mutations. Identifying and detecting pathophysiological alterations in mitochondria is the principal means of studying mitochondrial abnormalities. The present study reviewed methods in mitochondrial research and focused on three aspects: Mitochondrial extraction and purification, morphology and structure and function. In addition to classical methods, such as electron microscopy and mitochondrial membrane potential monitoring, newly developed methods, such as mitochondrial ultrastructural determination, mtDNA mutation assays, metabolomics and analyses of regulatory mechanisms, have also been utilized in recent years. These approaches enable the accurate detection of mitochondrial abnormalities and provide guidance for the diagnosis and treatment of related diseases.
    Keywords:  mitochondria; mitochondrial DNA; mitochondrial diseases; mitochondrial dysfunction; mitochondrial morphology
    DOI:  https://doi.org/10.3892/ijmm.2022.5182
  6. Cell Stem Cell. 2022 Aug 19. pii: S1934-5909(22)00304-6. [Epub ahead of print]
    Mitochondrial dynamics maintain muscle stem cell regenerative competence throughout adult life by regulating metabolism and mitophagy.
    Xiaotong Hong, Joan Isern, Silvia Campanario, Eusebio Perdiguero, Ignacio Ramírez-Pardo, Jessica Segalés, Pablo Hernansanz-Agustín, Andrea Curtabbi, Oleg Deryagin, Angela Pollán, José A González-Reyes, José M Villalba, Marco Sandri, Antonio L Serrano, José A Enríquez, Pura Muñoz-Cánoves.
      Skeletal muscle regeneration depends on the correct expansion of resident quiescent stem cells (satellite cells), a process that becomes less efficient with aging. Here, we show that mitochondrial dynamics are essential for the successful regenerative capacity of satellite cells. The loss of mitochondrial fission in satellite cells-due to aging or genetic impairment-deregulates the mitochondrial electron transport chain (ETC), leading to inefficient oxidative phosphorylation (OXPHOS) metabolism and mitophagy and increased oxidative stress. This state results in muscle regenerative failure, which is caused by the reduced proliferation and functional loss of satellite cells. Regenerative functions can be restored in fission-impaired or aged satellite cells by the re-establishment of mitochondrial dynamics (by activating fission or preventing fusion), OXPHOS, or mitophagy. Thus, mitochondrial shape and physical networking controls stem cell regenerative functions by regulating metabolism and proteostasis. As mitochondrial fission occurs less frequently in the satellite cells in older humans, our findings have implications for regeneration therapies in sarcopenia.
    Keywords:  Drp1; OXPHOS; aging; metabolism; mitochondria; mitochondrial dynamics; mitophagy; muscle regeneration; muscle stem cells; satellite cells
    DOI:  https://doi.org/10.1016/j.stem.2022.07.009
  7. J Neurosci. 2022 Aug 19. pii: JN-RM-0193-22. [Epub ahead of print]
    Glycerol-3-phosphate shuttle is a backup system securing metabolic flexibility in neurons.
    Ankit Dhoundiyal, Vanessa Goeschl, Stefan Boehm, Helmut Kubista, Matej Hotka.
      Electrical activity in neurons is highly energy demanding and accompanied by rises in cytosolic Ca2+ Cytosolic Ca2+, in turn, secures energy supply by pushing mitochondrial metabolism either through augmented NADH transfer into mitochondria via the malate aspartate shuttle (MAS) or via direct activation of dehydrogenases of the TCA cycle after passing into the matrix through the mitochondrial Ca2+ uniporter (MCU). Another Ca2+-sensitive booster of mitochondrial ATP synthesis is the glycerol-3-phosphate shuttle (G3PS) whose role in neuronal energy supply has remained elusive. Essential components of G3PS are expressed in hippocampal neurons. Single neuron metabolic measurements in primary hippocampal cultures derived from rat pups of either sex reveal only moderate, if any, constitutive activity of G3PS. However, during electrical activity neurons fully rely on G3PS when MAS and MCU are unavailable. Under these conditions, G3PS is required for appropriate action potential firing. Accordingly, G3PS safeguards metabolic flexibility of neurons to cope with energy demands of electrical signaling.SIGNIFICANCE STATEMENT:Ca2+ ions are known to provide a link between the energy-demanding electrical activity and an adequate ATP supply in neurons. To do so, Ca2+ acts both, from outside and inside of the mitochondrial inner membrane. Neuronal function critically depend on this regulation and its defects are often found in various neurological disorders. Although interest in neuronal metabolism increases, many aspects thereof have remained unresolved. In particular, a Ca2+-sensitive NADH shuttling system, the glycerol-3-phosphate shuttle, has been largely ignored with respect to its function in neurons. Our results demonstrate that this shuttle is functional in hippocampal neurons and safeguards ATP supply and appropriate action potential firing when malate aspartate shuttle and mitochondrial Ca2+ uniporter are unavailable, thereby ensuring neuronal metabolic flexibility.
    DOI:  https://doi.org/10.1523/JNEUROSCI.0193-22.2022
  8. Dev Dyn. 2022 Aug 24.
    Deletion of ATAD3A inhibits osteogenesis by impairing mitochondria structure and function in pre-osteoblast.
    Hyeri Lee, Dae-Won Kim.
      BACKGROUND: ATAD3A (ATPase family AAA-domain containing protein 3A) is a nuclear encoded mitochondrial membrane protein that spans inner and outer membrane, and it has been shown to regulate mitochondrial dynamics and cholesterol metabolism. Since the mitochondrial functions have been implicated for osteogenic differentiation, a role of ATAD3A in skeletal development has been investigated.RESULTS: Mesenchyme-specific ATAD3 knockout mice displayed severe defects in skeletal development. Additionally, osteoblast-specific deletion of ATAD3 in mice caused significant reduction in bone mass, while cartilage-specific ATAD3 knockout mice did not show any significant phenotypes. Consistent with these in vivo findings, ATAD3A knockdown impaired mitochondrial morphology and function in calvarial pre-osteoblast cultures, which, in turn, suppressed osteogenic differentiation in vitro.
    CONCLUSIONS: The current findings suggest that ATAD3A plays a crucial role in mitochondria homeostasis, which is required for osteogenic differentiation during skeletal development. This article is protected by copyright. All rights reserved.
    Keywords:  ATAD3A; lipid droplet; mitochondria; osteogenesis; skeletal development
    DOI:  https://doi.org/10.1002/dvdy.528
  9. Front Cell Neurosci. 2022 ;16 959598
    Mitochondrial behavior when things go wrong in the axon.
    Victorio M Pozo Devoto, Isaac G Onyango, Gorazd B Stokin.
      Axonal homeostasis is maintained by processes that include cytoskeletal regulation, cargo transport, synaptic activity, ionic balance, and energy supply. Several of these processes involve mitochondria to varying degrees. As a transportable powerplant, the mitochondria deliver ATP and Ca2+-buffering capabilities and require fusion/fission to maintain proper functioning. Taking into consideration the long distances that need to be covered by mitochondria in the axons, their transport, distribution, fusion/fission, and health are of cardinal importance. However, axonal homeostasis is disrupted in several disorders of the nervous system, or by traumatic brain injury (TBI), where the external insult is translated into physical forces that damage nervous tissue including axons. The degree of damage varies and can disconnect the axon into two segments and/or generate axonal swellings in addition to cytoskeletal changes, membrane leakage, and changes in ionic composition. Cytoskeletal changes and increased intra-axonal Ca2+ levels are the main factors that challenge mitochondrial homeostasis. On the other hand, a proper function and distribution of mitochondria can determine the recovery or regeneration of the axonal physiological state. Here, we discuss the current knowledge regarding mitochondrial transport, fusion/fission, and Ca2+ regulation under axonal physiological or pathological conditions.
    Keywords:  axonal degeneration; calcium homeostasis; mitochondria; mitochondrial dynamics; mitochondrial transport; traumatic brain injury
    DOI:  https://doi.org/10.3389/fncel.2022.959598
  10. STAR Protoc. 2022 Sep 16. 3(3): 101567
    High-content analysis of neuronal morphology in human iPSC-derived neurons.
    Selene Lickfett, Carmen Menacho, Annika Zink, Narasimha Swamy Telugu, Mathias Beller, Sebastian Diecke, Sidney Cambridge, Alessandro Prigione.
      We present a high-content analysis (HCA) protocol for monitoring the outgrowth capacity of human neurons derived from induced pluripotent stem cells (iPSCs). We describe steps to perform HCA imaging, followed by quantifying the morphology of dendrites and axons within a high-throughput system to evaluate neurons obtained through various differentiation approaches. This protocol can be used to screen for modulators of neuronal morphogenesis or neurotoxicity. The approach can be applied to patient-derived iPSCs to identify patient-specific defects and possible therapeutic strategies. For complete details on the use and execution of this protocol, please refer to Zink et al. (2020) and Inak et al. (2021). The protocol can be used in combination with Zink et al. (2022).
    Keywords:  Cell Differentiation; High Throughput Screening; Microscopy; Neuroscience; Stem Cells
    DOI:  https://doi.org/10.1016/j.xpro.2022.101567
  11. EMBO J. 2022 Aug 25. e110486
    Impaired disassembly of the axon initial segment restricts mitochondrial entry into damaged axons.
    Sumiko Kiryu-Seo, Reika Matsushita, Yoshitaka Tashiro, Takeshi Yoshimura, Yohei Iguchi, Masahisa Katsuno, Ryosuke Takahashi, Hiroshi Kiyama.
      The proteasome is essential for cellular responses to various physiological stressors. However, how proteasome function impacts the stress resilience of regenerative damaged motor neurons remains unclear. Here, we develop a unique mouse model using a regulatory element of the activating transcription factor (Atf3) gene to label mitochondria in a damage-induced manner while simultaneously genetically disrupting the proteasome. Using this model, we observed that in injury-induced proteasome-deficient mouse motor neurons, the increase of mitochondrial influx from soma into axons is inhibited because neurons fail to disassemble ankyrin G, an organizer of the axon initial segment (AIS), in a proteasome-dependent manner. Further, these motor neurons exhibit amyotrophic lateral sclerosis (ALS)-like degeneration despite having regenerative potential. Selectively vulnerable motor neurons in SOD1G93A ALS mice, which induce ATF3 in response to pathological damage, also fail to disrupt the AIS, limiting the number of axonal mitochondria at a pre-symptomatic stage. Thus, damage-induced proteasome-sensitive AIS disassembly could be a critical post-translational response for damaged motor neurons to temporarily transit to an immature state and meet energy demands for axon regeneration or preservation.
    Keywords:  axonal transport; nerve injury; neurodegenerative disease; organelle; stress response
    DOI:  https://doi.org/10.15252/embj.2021110486
  12. J Pharmacol Toxicol Methods. 2022 Aug 22. pii: S1056-8719(22)00056-9. [Epub ahead of print] 107209
    Standardization and validation of novel ex-vivo method for mitochondrial bioenergetics using mitochondrial modulators.
    Prabha Rajput, Sairam Krishnamurthy.
      Mitochondria is an essential organelle; it produces 95% of the adenine triphosphate (ATP) of cells, their dysfunction is related to the pathogenesis of multiple diseases, such as diabetes mellitus, cardiovascular and neurological disorders. Various pharmacologic agents are known to target mitochondrial function. Moreover, the toxic side effects of multiple drugs used to treat diseases are related to the impairment of mitochondrial function. Thus, there is a need to develop a method to evaluate the effect of pharmacologic agents for their potential and side effects to identify effective mitochondrial-modulating agents. Therefore, the objective of this study was to develop and validate an ex-vivo method for studying the effect of pharmacologic agents on mitochondrial function and rescue of dysfunction. Dimethyl sulfoxide (DMSO) concentrations that drugs were soluble in and maintained mitochondrial function were determined. Metformin (MET) is a known mitochondrial complex-1 inhibitor tested for its ability to compromise mitochondrion function. Coenzyme Q10 (Q10) and Resveratrol (RSV), which are known to enhance mitochondrial function, were added alone and dose-dependent, tested for the ability to rescue metformin-induced mitochondrial dysfunction. Ex-vivo liver and brain mitochondrial function was assessed using an oxytherm Clark-type oxygen electrode. DMSO was found to be toxic above 10% and drugs insoluble below 5%. The addition of 0.5 mg/ml MET decreased liver and brain mitochondrial respiratory control rate (RCR). At the same time, Q10 improved RCR in normal mitochondria and a concentration-dependent manner in MET-induced dysfunctional mitochondria. RSV was added in the last step of the experiment to confirm that compromised function is due to MET. Hence this method can be used to screen pharmacological agents for their potential therapeutics or toxic effect on mitochondria.
    Keywords:  Complex enzyme activity; Electron transport chain; Mitochondrial bioenergetics; Mitochondrial toxicity; Oxidative phosphorylation; Respiratory control rate
    DOI:  https://doi.org/10.1016/j.vascn.2022.107209
  13. Epigenomes. 2022 Jul 27. pii: 21. [Epub ahead of print]6(3):
    Epigenomic Approaches for the Diagnosis of Rare Diseases.
    Beatriz Martinez-Delgado, Maria J Barrero.
      Rare diseases affect more than 300 million people worldwide. Diagnosing rare diseases is a major challenge as they have different causes and etiologies. Careful assessment of clinical symptoms often leads to the testing of the most common genetic alterations that could explain the disease. Patients with negative results for these tests frequently undergo whole exome or genome sequencing, leading to the identification of the molecular cause of the disease in 50% of patients at best. Therefore, a significant proportion of patients remain undiagnosed after sequencing their genome. Recently, approaches based on functional aspects of the genome, including transcriptomics and epigenomics, are beginning to emerge. Here, we will review these approaches, including studies that have successfully provided diagnoses for complex undiagnosed cases.
    Keywords:  epigenetics; molecular diagnosis; rare diseases; transcriptomics
    DOI:  https://doi.org/10.3390/epigenomes6030021
  14. Nat Commun. 2022 Aug 20. 13(1): 4904
    A nanopore interface for higher bandwidth DNA computing.
    Karen Zhang, Yuan-Jyue Chen, Delaney Wilde, Kathryn Doroschak, Karin Strauss, Luis Ceze, Georg Seelig, Jeff Nivala.
      DNA has emerged as a powerful substrate for programming information processing machines at the nanoscale. Among the DNA computing primitives used today, DNA strand displacement (DSD) is arguably the most popular, with DSD-based circuit applications ranging from disease diagnostics to molecular artificial neural networks. The outputs of DSD circuits are generally read using fluorescence spectroscopy. However, due to the spectral overlap of typical small-molecule fluorescent reporters, the number of unique outputs that can be detected in parallel is limited, requiring complex optical setups or spatial isolation of reactions to make output bandwidths scalable. Here, we present a multiplexable sequencing-free readout method that enables real-time, kinetic measurement of DSD circuit activity through highly parallel, direct detection of barcoded output strands using nanopore sensor array technology (Oxford Nanopore Technologies' MinION device). These results increase DSD output bandwidth by an order of magnitude over what is currently feasible with fluorescence spectroscopy.
    DOI:  https://doi.org/10.1038/s41467-022-32526-3
  15. Pharmaceutics. 2022 Aug 16. pii: 1708. [Epub ahead of print]14(8):
    Towards Personalized Allele-Specific Antisense Oligonucleotide Therapies for Toxic Gain-of-Function Neurodegenerative Diseases.
    Jacob Helm, Ludger Schöls, Stefan Hauser.
      Antisense oligonucleotides (ASOs) are single-stranded nucleic acid strings that can be used to selectively modify protein synthesis by binding complementary (pre-)mRNA sequences. By specific arrangements of DNA and RNA into a chain of nucleic acids and additional modifications of the backbone, sugar, and base, the specificity and functionality of the designed ASOs can be adjusted. Thereby cellular uptake, toxicity, and nuclease resistance, as well as binding affinity and specificity to its target (pre-)mRNA, can be modified. Several neurodegenerative diseases are caused by autosomal dominant toxic gain-of-function mutations, which lead to toxic protein products driving disease progression. ASOs targeting such mutations-or even more comprehensively, associated variants, such as single nucleotide polymorphisms (SNPs)-promise a selective degradation of the mutant (pre-)mRNA while sparing the wild type allele. By this approach, protein expression from the wild type strand is preserved, and side effects from an unselective knockdown of both alleles can be prevented. This makes allele-specific targeting strategies a focus for future personalized therapies. Here, we provide an overview of current strategies to develop personalized, allele-specific ASO therapies for the treatment of neurodegenerative diseases, such Huntington's disease (HD) and spinocerebellar ataxia type 3 (SCA3/MJD).
    Keywords:  ASO; SNP; allele-specific targeting; antisense oligonucleotide; neurodegenerative diseases; toxic gain-of-function
    DOI:  https://doi.org/10.3390/pharmaceutics14081708
  16. Proc Natl Acad Sci U S A. 2022 Aug 30. 119(35): e2211310119
    NAD+ metabolism drives astrocyte proinflammatory reprogramming in central nervous system autoimmunity.
    Tom Meyer, Dor Shimon, Sawsan Youssef, Gal Yankovitz, Adi Tessler, Tom Chernobylsky, Anat Gaoni-Yogev, Rita Perelroizen, Noga Budick-Harmelin, Lawrence Steinman, Lior Mayo.
      Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS). Astrocytes are the most abundant glial cells in the CNS, and their dysfunction contributes to the pathogenesis of MS and its animal model, experimental autoimmune encephalomyelitis (EAE). Recent advances highlight the pivotal role of cellular metabolism in programming immune responses. However, the underlying immunometabolic mechanisms that drive astrocyte pathogenicity remain elusive. Nicotinamide adenine dinucleotide (NAD+) is a vital coenzyme involved in cellular redox reactions and a substrate for NAD+-dependent enzymes. Cellular NAD+ levels are dynamically controlled by synthesis and degradation, and dysregulation of this balance has been associated with inflammation and disease. Here, we demonstrate that cell-autonomous generation of NAD+ via the salvage pathway regulates astrocyte immune function. Inhibition of nicotinamide phosphoribosyltransferase (NAMPT), a key enzyme in the salvage pathway, results in depletion of NAD+, inhibits oxidative phosphorylation, and limits astrocyte inflammatory potential. We identified CD38 as the main NADase up-regulated in reactive mouse and human astrocytes in models of neuroinflammation and MS. Genetic or pharmacological blockade of astrocyte CD38 activity augmented NAD+ levels, suppressed proinflammatory transcriptional reprogramming, impaired chemotactic potential to inflammatory monocytes, and ameliorated EAE. We found that CD38 activity is mediated via calcineurin/NFAT signaling in mouse and human reactive astrocytes. Thus, NAMPT-NAD+-CD38 circuitry in astrocytes controls their ability to meet their energy demands and drives the expression of proinflammatory transcriptional modules, contributing to CNS pathology in EAE and, potentially, MS. Our results identify candidate therapeutic targets in MS.
    Keywords:  Nicotinamide adenine dinucleotide; astrocyte; multiple sclerosis; neuroinflammation; tryptophan catabolism
    DOI:  https://doi.org/10.1073/pnas.2211310119
  17. Hum Mol Genet. 2022 Aug 26. pii: ddac213. [Epub ahead of print]
    Dominantly acting KIF5B variants with pleiotropic cellular consequences cause variable clinical phenotypes.
    Elisabetta Flex, Shahad Albadri, Francesca Clementina Radio, Serena Cecchetti, Antonella Lauri, Manuela Priolo, Marta Kissopoulos, Giovanna Carpentieri, Giulia Fasano, Martina Venditti, Valentina Magliocca, Emanuele Bellacchio, Carrie L Welch, Paolo C Colombo, Stephanie M Kochav, Richard Chang, Rebekah Barrick, Marina Trivisano, Alessia Micalizzi, Rossella Borghi, Elena Messina, Cecilia Mancini, Simone Pizzi, Flavia De Santis, Marion Rosello, Nicola Specchio, Claudia Compagnucci, Kirsty McWalter, Wendy K Chung, Filippo Del Bene, Marco Tartaglia.
      Kinesins are motor proteins involved in microtubule-mediated intracellular transport. They contribute to key cellular processes, including intracellular trafficking, organelle dynamics and cell division. Pathogenic variants in kinesin-encoding genes underlie several human diseases characterized by an extremely variable clinical phenotype, ranging from isolated neurodevelopmental/neurodegenerative disorders to syndromic phenotypes belonging to a family of conditions collectively termed as 'ciliopathies'. Among kinesins, kinesin-1 is the most abundant microtubule motor for transport of cargoes towards the plus end of microtubules. Three kinesin-1 heavy chain isoforms exist in mammals. Different from KIF5A and KIF5C, which are specifically expressed in neurons and established to cause neurological diseases when mutated, KIF5B is an ubiquitous protein. Three de novo missense KIF5B variants were recently described in four subjects with a syndromic skeletal disorder characterized by kyphomelic dysplasia, hypotonia and DD/ID. Here, we report three dominantly acting KIF5B variants (p.Asn255del, p.Leu498Pro and p.Leu537Pro) resulting in a clinically wide phenotypic spectrum, ranging from dilated cardiomyopathy with adult-onset ophthalmoplegia and progressive skeletal myopathy to a neurodevelopmental condition characterized by severe hypotonia with or without seizures. In vitro and in vivo analyses provide evidence that the identified disease-associated KIF5B variants disrupt lysosomal, autophagosome and mitochondrial organization, and impact cilium biogenesis. All variants, and one of the previously reported missense changes, were shown to affect multiple developmental processes in zebrafish. These findings document pleiotropic consequences of aberrant KIF5B function on development and cell homeostasis, and expand the phenotypic spectrum resulting from altered kinesin-mediated processes.
    DOI:  https://doi.org/10.1093/hmg/ddac213
  18. 3 Biotech. 2022 Sep;12(9): 230
    Mitochondria-lysosome crosstalk in GBA1-associated Parkinson's disease.
    M Sahyadri, Abhishek P R Nadiga, Seema Mehdi, K Mruthunjaya, Pawan G Nayak, Vipan K Parihar, S N Manjula.
      Organelle crosstalk is significant in regulating their respective functions and subsequent cell fate. Mitochondria and lysosomes are amongst the essential organelles in maintaining cellular homeostasis. Mitochondria-lysosome connections, which may develop dynamically in the human neurons, have been identified as sites of bidirectional communication. Aberrancies are often associated with neurodegenerative disorders like Parkinson's disease (PD), suggesting the physical and functional link between these two organelles. PD is often linked with genetic mutations of several mutations discovered in the familial forms of the disease; some are considered risk factors. Many of these genes are either associated with mitochondrial function or belong to endo-lysosomal pathways. The recent investigations have indicated that neurons with mutant glucosylceramidase beta (GBA1) exhibit extended mitochondria-lysosome connections in individuals with PD. This may be due to impaired control of the untethering protein, which aids in the hydrolysis of Rab7 GTP required for contact untethering. A GCase modulator may be used to augment the reduced GBA1 lysosomal enzyme activity in the neurons of PD patients. This review focuses on how GBA1 mutation in PD is interlinked with mitochondria-lysosome (ML) crosstalk, exploring the pathways governing these interactions and mechanistically comprehending the mitochondrial and lysosomal miscommunication in the pathophysiology of PD. This review is based on the limited literature available on the topic and hence may be subject to bias in its views. Our estimates may be conservative and limited due to the lack of studies under the said discipline due to its inherent complex nature. The current association of GBA1 to PD pathogenesis is based on the limited scope of study and further research is necessary to explore the risk factors further and identify the relationship with more detail.
    Keywords:  Glucosylceramidase Beta (GBA); Lysosome; ML crosstalk; Mitochondria; Neuronal dysfunction; Parkinson's disease
    DOI:  https://doi.org/10.1007/s13205-022-03261-9
  19. Cureus. 2022 Jul;14(7): e27129
    Role of Mitochondrial Mutations in Ocular Aggregopathy.
    Munmun Chakraborty, Aparna Rao, Kuldeep Mohanty.
      Background Mitochondria are essential cellular organelles that are responsible for oxidative stress-induced damage in age-dependent neurodegenerations such as glaucoma. Previous studies have linked mitochondrial DNA (mtDNA) mutations to cellular energy shortages that result in eye degeneration. Methodology To look for nucleotide variations in mtDNA in exfoliation syndrome/glaucoma (XFS/XFG), we performed a polymerase chain reaction (PCR) to amplify the entire coding region of the mitochondrial genome from peripheral blood of XFS/XFG (n = 25) patients and controls (n = 25). Results This study identified a total of 65 variations in XFS/XFG patients, of which 25 (38%) variations were non-synonymous single-nucleotide polymorphism (nsSNPs). Out of 25 nsSNPs, seven (five nsSNP in MT-ND4 and two in MT-ATP6 gene) were predicted as pathogenic using four different software, namely, SIFT, Polyphene2, mutation taster, and MutPred2. The pathogenic nsSNPs were then subjected to structural change analysis using online tools. Conclusions The pathogenic nsSNPs were found in both proteins' transmembrane domains and were expected to be conserved, but with lower protein stability (ΔΔG <- 0.5), indicating a possibly harmful effect in exfoliation. However, three-dimensional protein analysis indicated that the predicted mutations in MT-ND4 and MT-ATP6 were unlikely to alter the protein function.
    Keywords:  aggregopathy; exfoliation glaucoma; exfoliation syndrome; mitochondrial mutation; snps
    DOI:  https://doi.org/10.7759/cureus.27129
  20. Am J Hum Genet. 2022 Aug 18. pii: S0002-9297(22)00355-X. [Epub ahead of print]
    A genome sequencing system for universal newborn screening, diagnosis, and precision medicine for severe genetic diseases.
    Stephen F Kingsmore, Laurie D Smith, Chris M Kunard, Matthew Bainbridge, Sergey Batalov, Wendy Benson, Eric Blincow, Sara Caylor, Christina Chambers, Guillermo Del Angel, David P Dimmock, Yan Ding, Katarzyna Ellsworth, Annette Feigenbaum, Erwin Frise, Robert C Green, Lucia Guidugli, Kevin P Hall, Christian Hansen, Charlotte A Hobbs, Scott D Kahn, Mark Kiel, Lucita Van Der Kraan, Chad Krilow, Yong H Kwon, Lakshminarasimha Madhavrao, Jennie Le, Sebastien Lefebvre, Rebecca Mardach, William R Mowrey, Danny Oh, Mallory J Owen, George Powley, Gunter Scharer, Seth Shelnutt, Mari Tokita, Shyamal S Mehtalia, Albert Oriol, Stavros Papadopoulos, James Perry, Edwin Rosales, Erica Sanford, Steve Schwartz, Duke Tran, Martin G Reese, Meredith Wright, Narayanan Veeraraghavan, Kristen Wigby, Mary J Willis, Aaron R Wolen, Thomas Defay.
      Newborn screening (NBS) dramatically improves outcomes in severe childhood disorders by treatment before symptom onset. In many genetic diseases, however, outcomes remain poor because NBS has lagged behind drug development. Rapid whole-genome sequencing (rWGS) is attractive for comprehensive NBS because it concomitantly examines almost all genetic diseases and is gaining acceptance for genetic disease diagnosis in ill newborns. We describe prototypic methods for scalable, parentally consented, feedback-informed NBS and diagnosis of genetic diseases by rWGS and virtual, acute management guidance (NBS-rWGS). Using established criteria and the Delphi method, we reviewed 457 genetic diseases for NBS-rWGS, retaining 388 (85%) with effective treatments. Simulated NBS-rWGS in 454,707 UK Biobank subjects with 29,865 pathogenic or likely pathogenic variants associated with 388 disorders had a true negative rate (specificity) of 99.7% following root cause analysis. In 2,208 critically ill children with suspected genetic disorders and 2,168 of their parents, simulated NBS-rWGS for 388 disorders identified 104 (87%) of 119 diagnoses previously made by rWGS and 15 findings not previously reported (NBS-rWGS negative predictive value 99.6%, true positive rate [sensitivity] 88.8%). Retrospective NBS-rWGS diagnosed 15 children with disorders that had been undetected by conventional NBS. In 43 of the 104 children, had NBS-rWGS-based interventions been started on day of life 5, the Delphi consensus was that symptoms could have been avoided completely in seven critically ill children, mostly in 21, and partially in 13. We invite groups worldwide to refine these NBS-rWGS conditions and join us to prospectively examine clinical utility and cost effectiveness.
    Keywords:  UK Biobank; clinical decision support; clinical utility; diagnosis; diagnostic odyssey; gene therapy; genetic disease; newborn screening; orphan drug; rapid whole-genome sequencing; sensitivity; specificity; virtual management guidance
    DOI:  https://doi.org/10.1016/j.ajhg.2022.08.003
  21. Cell Rep. 2022 Aug 23. pii: S2211-1247(22)01056-7. [Epub ahead of print]40(8): 111239
    Central FGF21 production regulates memory but not peripheral metabolism.
    Bolu Zhou, Kristin E Claflin, Kyle H Flippo, Andrew I Sullivan, Arvand Asghari, Satya M Tadinada, Sharon O Jensen-Cody, Ted Abel, Matthew J Potthoff.
      Fibroblast growth factor 21 (FGF21) is a liver-derived endocrine hormone that functions to regulate energy homeostasis and macronutrient intake. Recently, FGF21 was reported to be produced and secreted from hypothalamic tanycytes, to regulate peripheral lipid metabolism; however, rigorous investigation of FGF21 expression in the brain has yet to be accomplished. Using a mouse model that drives CRE recombinase in FGF21-expressing cells, we demonstrate that FGF21 is not expressed in the hypothalamus, but instead is produced from the retrosplenial cortex (RSC), an essential brain region for spatial learning and memory. Furthermore, we find that central FGF21 produced in the RSC enhances spatial memory but does not regulate energy homeostasis or sugar intake. Finally, our data demonstrate that administration of FGF21 prolongs the duration of long-term potentiation in the hippocampus and enhances activation of hippocampal neurons. Thus, endogenous and pharmacological FGF21 appear to function in the hippocampus to enhance spatial memory.
    Keywords:  CP: Metabolism; CP: Neuroscience; FGF21; betaklotho; central; hippocampus; hypothalamus; liver; memory; tanycytes
    DOI:  https://doi.org/10.1016/j.celrep.2022.111239
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