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Crane AB, Jetti SK, Littleton JT. A stochastic RNA editing process targets a limited number of sites in individual Drosophila glutamatergic motoneurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594696. [PMID: 38798345 PMCID: PMC11118563 DOI: 10.1101/2024.05.17.594696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
RNA editing is a post-transcriptional source of protein diversity and occurs across the animal kingdom. Given the complete profile of mRNA targets and their editing rate in individual cells is unclear, we analyzed single cell RNA transcriptomes from Drosophila larval tonic and phasic glutamatergic motoneuron subtypes to determine the most highly edited targets and identify cell-type specific editing. From ∼15,000 genes encoded in the genome, 316 high confidence A-to-I canonical RNA edit sites were identified, with 102 causing missense amino acid changes in proteins regulating membrane excitability, synaptic transmission, and cellular function. Some sites showed 100% editing in single neurons as observed with mRNAs encoding mammalian AMPA receptors. However, most sites were edited at lower levels and generated variable expression of edited and unedited mRNAs within individual neurons. Together, these data provide insights into how the RNA editing landscape alters protein function to modulate the properties of two well-characterized neuronal populations in Drosophila .
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Achzet LM, Jackson DA. Sex-Dependent Differences in the Ischemia/Reperfusion-Induced Expression of AMPA Receptors. Int J Mol Sci 2024; 25:2231. [PMID: 38396906 PMCID: PMC10889403 DOI: 10.3390/ijms25042231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/02/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Following ischemia/reperfusion, AMPA receptors (AMPARs) mediate pathologic delayed neuronal death through sustained expression of calcium-permeable AMPARs, leading to excitotoxicity. Preventing the surface removal of GluA2-containing AMPARs may yield new therapeutic targets for the treatment of ischemia/reperfusion. This study utilized acute organotypic hippocampal slices from aged male and female Sprague Dawley rats and subjected them to oxygen-glucose deprivation/reperfusion (OGD/R) to examine the mechanisms underlying the internalization and degradation of GluA2-containing AMPARs. We determined the effect of OGD/R on AMPAR subunits at the protein and mRNA transcript levels utilizing Western blot and RT-qPCR, respectively. Hippocampal slices from male and female rats responded to OGD/R in a paradoxical manner with respect to AMPARs. GluA1 and GluA2 AMPAR subunits were degraded following OGD/R in male rats but were increased in female rats. There was a rapid decrease in GRIA1 (GluA1) and GRIA2 (GluA2) mRNA levels in the male hippocampus following ischemic insult, but this was not observed in females. These data indicate a sex-dependent difference in how AMPARs in the hippocampus respond to ischemic insult, and may help explain, in part, why premenopausal women have a lower incidence/severity of ischemic stroke compared with men of the same age.
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Affiliation(s)
| | - Darrell A. Jackson
- Department of Pharmaceutical Sciences and Molecular Medicine, Washington State University—Health Sciences, Spokane, WA 99201, USA;
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Zhang F, Ignatova VV, Ming GL, Song H. Advances in brain epitranscriptomics research and translational opportunities. Mol Psychiatry 2024; 29:449-463. [PMID: 38123727 PMCID: PMC11116067 DOI: 10.1038/s41380-023-02339-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Various chemical modifications of all RNA transcripts, or epitranscriptomics, have emerged as crucial regulators of RNA metabolism, attracting significant interest from both basic and clinical researchers due to their diverse functions in biological processes and immense clinical potential as highlighted by the recent profound success of RNA modifications in improving COVID-19 mRNA vaccines. Rapid accumulation of evidence underscores the critical involvement of various RNA modifications in governing normal neural development and brain functions as well as pathogenesis of brain disorders. Here we provide an overview of RNA modifications and recent advancements in epitranscriptomic studies utilizing animal models to elucidate important roles of RNA modifications in regulating mammalian neurogenesis, gliogenesis, synaptic formation, and brain function. Moreover, we emphasize the pivotal involvement of RNA modifications and their regulators in the pathogenesis of various human brain disorders, encompassing neurodevelopmental disorders, brain tumors, psychiatric and neurodegenerative disorders. Furthermore, we discuss potential translational opportunities afforded by RNA modifications in combatting brain disorders, including their use as biomarkers, in the development of drugs or gene therapies targeting epitranscriptomic pathways, and in applications for mRNA-based vaccines and therapies. We also address current limitations and challenges hindering the widespread clinical application of epitranscriptomic research, along with the improvements necessary for future progress.
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Affiliation(s)
- Feng Zhang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Valentina V Ignatova
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Milham LT, Morris GP, Konen LM, Rentsch P, Avgan N, Vissel B. Quantification of AMPA receptor subunits and RNA editing-related proteins in the J20 mouse model of Alzheimer's disease by capillary western blotting. Front Mol Neurosci 2024; 16:1338065. [PMID: 38299128 PMCID: PMC10828003 DOI: 10.3389/fnmol.2023.1338065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/29/2023] [Indexed: 02/02/2024] Open
Abstract
Introduction Accurate modelling of molecular changes in Alzheimer's disease (AD) dementia is crucial for understanding the mechanisms driving neuronal pathology and for developing treatments. Synaptic dysfunction has long been implicated as a mechanism underpinning memory dysfunction in AD and may result in part from changes in adenosine deaminase acting on RNA (ADAR) mediated RNA editing of the GluA2 subunit of AMPA receptors and changes in AMPA receptor function at the post synaptic cleft. However, few studies have investigated changes in proteins which influence RNA editing and notably, AD studies that focus on studying changes in protein expression, rather than changes in mRNA, often use traditional western blotting. Methods Here, we demonstrate the value of automated capillary western blotting to investigate the protein expression of AMPA receptor subunits (GluA1-4), the ADAR RNA editing proteins (ADAR1-3), and proteins known to regulate RNA editing (PIN1, WWP2, FXR1P, and CREB1), in the J20 AD mouse model. We describe extensive optimisation and validation of the automated capillary western blotting method, demonstrating the use of total protein to normalise protein load, in addition to characterising the optimal protein/antibody concentrations to ensure accurate protein quantification. Following this, we assessed changes in proteins of interest in the hippocampus of 44-week-old J20 AD mice. Results We observed an increase in the expression of ADAR1 p110 and GluA3 and a decrease in ADAR2 in the hippocampus of 44-week-old J20 mice. These changes signify a shift in the balance of proteins that play a critical role at the synapse. Regression analysis revealed unique J20-specific correlations between changes in AMPA receptor subunits, ADAR enzymes, and proteins that regulate ADAR stability in J20 mice, highlighting potential mechanisms mediating RNA-editing changes found in AD. Discussion Our findings in J20 mice generally reflect changes seen in the human AD brain. This study underlines the importance of novel techniques, like automated capillary western blotting, to assess protein expression in AD. It also provides further evidence to support the hypothesis that a dysregulation in RNA editing-related proteins may play a role in the initiation and/or progression of AD.
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Affiliation(s)
- Luke T. Milham
- Centre for Neuroscience and Regenerative Medicine, St Vincent’s Centre for Applied Medical Research, St Vincent’s Hospital, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Gary P. Morris
- Centre for Neuroscience and Regenerative Medicine, St Vincent’s Centre for Applied Medical Research, St Vincent’s Hospital, Sydney, NSW, Australia
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Lyndsey M. Konen
- Centre for Neuroscience and Regenerative Medicine, St Vincent’s Centre for Applied Medical Research, St Vincent’s Hospital, Sydney, NSW, Australia
| | - Peggy Rentsch
- Centre for Neuroscience and Regenerative Medicine, St Vincent’s Centre for Applied Medical Research, St Vincent’s Hospital, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Nesli Avgan
- Centre for Neuroscience and Regenerative Medicine, St Vincent’s Centre for Applied Medical Research, St Vincent’s Hospital, Sydney, NSW, Australia
| | - Bryce Vissel
- Centre for Neuroscience and Regenerative Medicine, St Vincent’s Centre for Applied Medical Research, St Vincent’s Hospital, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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Gaidin SG, Kosenkov AM. Calcium-permeable AMPA receptors: an underestimated pharmacological target for the therapy of brain pathologies. Neural Regen Res 2023; 18:2669-2670. [PMID: 37449615 DOI: 10.4103/1673-5374.373714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Affiliation(s)
- Sergei G Gaidin
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino, Russia
| | - Artem M Kosenkov
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino, Russia
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Wright AL, Konen LM, Mockett BG, Morris GP, Singh A, Burbano LE, Milham L, Hoang M, Zinn R, Chesworth R, Tan RP, Royle GA, Clark I, Petrou S, Abraham WC, Vissel B. The Q/R editing site of AMPA receptor GluA2 subunit acts as an epigenetic switch regulating dendritic spines, neurodegeneration and cognitive deficits in Alzheimer's disease. Mol Neurodegener 2023; 18:65. [PMID: 37759260 PMCID: PMC10537207 DOI: 10.1186/s13024-023-00632-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/03/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND RNA editing at the Q/R site of GluA2 occurs with ~99% efficiency in the healthy brain, so that the majority of AMPARs contain GluA2(R) instead of the exonically encoded GluA2(Q). Reduced Q/R site editing infcreases AMPA receptor calcium permeability and leads to dendritic spine loss, neurodegeneration, seizures and learning impairments. Furthermore, GluA2 Q/R site editing is impaired in Alzheimer's disease (AD), raising the possibility that unedited GluA2(Q)-containing AMPARs contribute to synapse loss and neurodegeneration in AD. If true, then inhibiting expression of unedited GluA2(Q), while maintaining expression of GluA2(R), may be a novel strategy of preventing synapse loss and neurodegeneration in AD. METHODS We engineered mice with the 'edited' arginine codon (CGG) in place of the unedited glutamine codon (CAG) at position 607 of the Gria2 gene. We crossbred this line with the J20 mouse model of AD and conducted anatomical, electrophysiological and behavioural assays to determine the impact of eliminating unedited GluA2(Q) expression on AD-related phenotypes. RESULTS Eliminating unedited GluA2(Q) expression in AD mice prevented dendritic spine loss and hippocampal CA1 neurodegeneration as well as improved working and reference memory in the radial arm maze. These phenotypes were improved independently of Aβ pathology and ongoing seizure susceptibility. Surprisingly, our data also revealed increased spine density in non-AD mice with exonically encoded GluA2(R) as compared to their wild-type littermates, suggesting an unexpected and previously unknown role for unedited GluA2(Q) in regulating dendritic spines. CONCLUSION The Q/R editing site of the AMPA receptor subunit GluA2 may act as an epigenetic switch that regulates dendritic spines, neurodegeneration and memory deficits in AD.
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Affiliation(s)
- Amanda L Wright
- St Vincent's Clinical School, St Vincent's Hospital Sydney, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, 2010, Australia
- School of Rural Medicine, Charles Sturt University, Orange, NSW, 2800, Australia
| | - Lyndsey M Konen
- Centre for Neuroscience and Regenerative Medicine, St Vincent's Centre for Applied Medical Research, St Vincent's Hospital Sydney, Darlinghurst, NSW, 2010, Australia
| | - Bruce G Mockett
- Department of Psychology, Brain Health Research Centre, Brain Research New Zealand, University of Otago, Box 56, Dunedin, 9054, New Zealand
| | - Gary P Morris
- Centre for Neuroscience and Regenerative Medicine, St Vincent's Centre for Applied Medical Research, St Vincent's Hospital Sydney, Darlinghurst, NSW, 2010, Australia
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, TAS, 7005, Australia
| | - Anurag Singh
- Department of Psychology, Brain Health Research Centre, Brain Research New Zealand, University of Otago, Box 56, Dunedin, 9054, New Zealand
| | - Lisseth Estefania Burbano
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Luke Milham
- St Vincent's Clinical School, St Vincent's Hospital Sydney, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, 2010, Australia
- Centre for Neuroscience and Regenerative Medicine, St Vincent's Centre for Applied Medical Research, St Vincent's Hospital Sydney, Darlinghurst, NSW, 2010, Australia
| | - Monica Hoang
- School of Pharmacy, University of Waterloo, Kitchener, ON, N2G 1C5, Canada
| | - Raphael Zinn
- Centre for Neuroscience and Regenerative Medicine, St Vincent's Centre for Applied Medical Research, St Vincent's Hospital Sydney, Darlinghurst, NSW, 2010, Australia
| | - Rose Chesworth
- School of Medicine, Western Sydney University, Campbelltown, NSW, 2560, Australia
| | - Richard P Tan
- Chronic Diseases, School of Medical Sciences, Faculty of Health and Medicine, University of Sydney, Sydney, NSW, 2050, Australia
- Charles Perkins Centre, University of Sydney, Sydney, NSW, 2006, Australia
| | - Gordon A Royle
- Middlemore Hospital, Counties Manukau DHB, Otahuhu, Auckland, 1062, New Zealand
- Faculty of Medical and Health Sciences, University of Auckland, Grafton, Auckland, 1023, New Zealand
| | - Ian Clark
- Research School of Biology, Australian National University, Canberra, ACT, 0200, Australia
| | - Steven Petrou
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Anatomy and Neuroscience, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Wickliffe C Abraham
- Department of Psychology, Brain Health Research Centre, Brain Research New Zealand, University of Otago, Box 56, Dunedin, 9054, New Zealand
| | - Bryce Vissel
- St Vincent's Clinical School, St Vincent's Hospital Sydney, Faculty of Medicine, University of New South Wales, Darlinghurst, NSW, 2010, Australia.
- Centre for Neuroscience and Regenerative Medicine, St Vincent's Centre for Applied Medical Research, St Vincent's Hospital Sydney, Darlinghurst, NSW, 2010, Australia.
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Habib MZ, Elnahas EM, Aboul-Ela YM, Ebeid MA, Tarek M, Sadek DR, Negm EA, Abdelhakam DA, Aboul-Fotouh S. Risperidone impedes glutamate excitotoxicity in a valproic acid rat model of autism: Role of ADAR2 in AMPA GluA2 RNA editing. Eur J Pharmacol 2023; 955:175916. [PMID: 37460052 DOI: 10.1016/j.ejphar.2023.175916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023]
Abstract
Several reports indicate a plausible role of calcium (Ca2+) permeable AMPA glutamate receptors (with RNA hypo-editing at the GluA2 Q/R site) and the subsequent excitotoxicity-mediated neuronal death in the pathogenesis of a wide array of neurological disorders including autism spectrum disorder (ASD). This study was designed to examine the effects of chronic risperidone treatment on the expression of adenosine deaminase acting on RNA 2 (Adar2), the status of AMPA glutamate receptor GluA2 editing, and its effects on oxidative/nitrosative stress and excitotoxicity-mediated neuronal death in the prenatal valproic acid (VPA) rat model of ASD. Prenatal VPA exposure was associated with autistic-like behaviors accompanied by an increase in the apoptotic marker "caspase-3" and a decrease in the antiapoptotic marker "BCL2" alongside a reduction in the Adar2 relative gene expression and an increase in GluA2 Q:R ratio in the hippocampus and the prefrontal cortex. Risperidone, at doses of 1 and 3 mg, improved the VPA-induced behavioral deficits and enhanced the Adar2 relative gene expression and the subsequent GluA2 subunit editing. This was reflected on the cellular level where risperidone impeded VPA-induced oxidative/nitrosative stress and neurodegenerative changes. In conclusion, the present study confirms a possible role for Adar2 downregulation and the subsequent hypo-editing of the GluA2 subunit in the pathophysiology of the prenatal VPA rat model of autism and highlights the favorable effect of risperidone on reversing the RNA editing machinery deficits, giving insights into a new possible mechanism of risperidone in autism.
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Affiliation(s)
- Mohamed Z Habib
- Clinical Pharmacology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt.
| | - Esraa M Elnahas
- Clinical Pharmacology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Yasmin M Aboul-Ela
- Clinical Pharmacology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mai A Ebeid
- Clinical Pharmacology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Marwa Tarek
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Doaa R Sadek
- Histology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Eman A Negm
- Histology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Dina A Abdelhakam
- Clinical Pathology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Sawsan Aboul-Fotouh
- Clinical Pharmacology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt; Clinical Pharmacology Unit, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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Neves D, Salazar IL, Almeida RD, Silva RM. Molecular mechanisms of ischemia and glutamate excitotoxicity. Life Sci 2023; 328:121814. [PMID: 37236602 DOI: 10.1016/j.lfs.2023.121814] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/05/2023] [Accepted: 05/23/2023] [Indexed: 05/28/2023]
Abstract
Excitotoxicity is classically defined as the neuronal damage caused by the excessive release of glutamate, and subsequent activation of excitatory plasma membrane receptors. In the mammalian brain, this phenomenon is mainly driven by excessive activation of glutamate receptors (GRs). Excitotoxicity is common to several chronic disorders of the Central Nervous System (CNS) and is considered the primary mechanism of neuronal loss of function and cell death in acute CNS diseases (e.g. ischemic stroke). Multiple mechanisms and pathways lead to excitotoxic cell damage including pro-death signaling cascade events downstream of glutamate receptors, calcium (Ca2+) overload, oxidative stress, mitochondrial impairment, excessive glutamate in the synaptic cleft as well as altered energy metabolism. Here, we review the current knowledge on the molecular mechanisms that underlie excitotoxicity, emphasizing the role of Nicotinamide Adenine Dinucleotide (NAD) metabolism. We also discuss novel and promising therapeutic strategies to treat excitotoxicity, highlighting recent clinical trials. Finally, we will shed light on the ongoing search for stroke biomarkers, an exciting and promising field of research, which may improve stroke diagnosis, prognosis and allow better treatment options.
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Affiliation(s)
- Diogo Neves
- iBiMED - Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Ivan L Salazar
- Multidisciplinary Institute of Ageing, MIA - Portugal, University of Coimbra, Coimbra, Portugal
| | - Ramiro D Almeida
- iBiMED - Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal; CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.
| | - Raquel M Silva
- iBiMED - Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal; Universidade Católica Portuguesa, Faculdade de Medicina Dentária, Centro de Investigação Interdisciplinar em Saúde, Viseu, Portugal.
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9
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Qiu L, Jing Q, Li Y, Han J. RNA modification: mechanisms and therapeutic targets. MOLECULAR BIOMEDICINE 2023; 4:25. [PMID: 37612540 PMCID: PMC10447785 DOI: 10.1186/s43556-023-00139-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023] Open
Abstract
RNA modifications are dynamic and reversible chemical modifications on substrate RNA that are regulated by specific modifying enzymes. They play important roles in the regulation of many biological processes in various diseases, such as the development of cancer and other diseases. With the help of advanced sequencing technologies, the role of RNA modifications has caught increasing attention in human diseases in scientific research. In this review, we briefly summarized the basic mechanisms of several common RNA modifications, including m6A, m5C, m1A, m7G, Ψ, A-to-I editing and ac4C. Importantly, we discussed their potential functions in human diseases, including cancer, neurological disorders, cardiovascular diseases, metabolic diseases, genetic and developmental diseases, as well as immune disorders. Through the "writing-erasing-reading" mechanisms, RNA modifications regulate the stability, translation, and localization of pivotal disease-related mRNAs to manipulate disease development. Moreover, we also highlighted in this review all currently available RNA-modifier-targeting small molecular inhibitors or activators, most of which are designed against m6A-related enzymes, such as METTL3, FTO and ALKBH5. This review provides clues for potential clinical therapy as well as future study directions in the RNA modification field. More in-depth studies on RNA modifications, their roles in human diseases and further development of their inhibitors or activators are needed for a thorough understanding of epitranscriptomics as well as diagnosis, treatment, and prognosis of human diseases.
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Affiliation(s)
- Lei Qiu
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Qian Jing
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Yanbo Li
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Junhong Han
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China.
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10
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Chen J, Jin J, Jiang J, Wang Y. Adenosine deaminase acting on RNA 1 (ADAR1) as crucial regulators in cardiovascular diseases: structures, pathogenesis, and potential therapeutic approach. Front Pharmacol 2023; 14:1194884. [PMID: 37663249 PMCID: PMC10469703 DOI: 10.3389/fphar.2023.1194884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/11/2023] [Indexed: 09/05/2023] Open
Abstract
Cardiovascular diseases (CVDs) are a group of diseases that have a major impact on global health and are the leading cause of death. A large number of chemical base modifications in ribonucleic acid (RNA) are associated with cardiovascular diseases. A variety of ribonucleic acid modifications exist in cells, among which adenosine deaminase-dependent modification is one of the most common ribonucleic acid modifications. Adenosine deaminase acting on ribonucleic acid 1 (Adenosine deaminase acting on RNA 1) is a widely expressed double-stranded ribonucleic acid adenosine deaminase that forms inosine (A-to-I) by catalyzing the deamination of adenosine at specific sites of the target ribonucleic acid. In this review, we provide a comprehensive overview of the structure of Adenosine deaminase acting on RNA 1 and summarize the regulatory mechanisms of ADAR1-mediated ribonucleic acid editing in cardiovascular diseases, indicating Adenosine deaminase acting on RNA 1 as a promising therapeutic target in cardiovascular diseases.
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Affiliation(s)
- Jieying Chen
- Department of Cardiology ofThe Second Affiliated Hospital, School of Medicine Zhejiang University, Hangzhou, China
| | - Junyan Jin
- Department of Cardiology ofThe Second Affiliated Hospital, School of Medicine Zhejiang University, Hangzhou, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China
| | - Jun Jiang
- Department of Cardiology ofThe Second Affiliated Hospital, School of Medicine Zhejiang University, Hangzhou, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China
| | - Yaping Wang
- Department of Cardiology ofThe Second Affiliated Hospital, School of Medicine Zhejiang University, Hangzhou, China
- Cardiovascular Key Laboratory of Zhejiang Province, Hangzhou, China
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11
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Coombs I, Bats C, Sexton CA, Studniarczyk D, Cull-Candy SG, Farrant M. Enhanced functional detection of synaptic calcium-permeable AMPA receptors using intracellular NASPM. eLife 2023; 12:e66765. [PMID: 37042655 PMCID: PMC10168695 DOI: 10.7554/elife.66765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/11/2023] [Indexed: 04/13/2023] Open
Abstract
Calcium-permeable AMPA-type glutamate receptors (CP-AMPARs) contribute to many forms of synaptic plasticity and pathology. They can be distinguished from GluA2-containing calcium-impermeable AMPARs by the inward rectification of their currents, which reflects voltage-dependent channel block by intracellular spermine. However, the efficacy of this weakly permeant blocker is differentially altered by the presence of AMPAR auxiliary subunits - including transmembrane AMPAR regulatory proteins, cornichons, and GSG1L - which are widely expressed in neurons and glia. This complicates the interpretation of rectification as a measure of CP-AMPAR expression. Here, we show that the inclusion of the spider toxin analog 1-naphthylacetyl spermine (NASPM) in the intracellular solution results in a complete block of GluA1-mediated outward currents irrespective of the type of associated auxiliary subunit. In neurons from GluA2-knockout mice expressing only CP-AMPARs, intracellular NASPM, unlike spermine, completely blocks outward synaptic currents. Thus, our results identify a functional measure of CP-AMPARs, that is unaffected by their auxiliary subunit content.
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Affiliation(s)
- Ian Coombs
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondonUnited Kingdom
| | - Cécile Bats
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondonUnited Kingdom
| | - Craig A Sexton
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondonUnited Kingdom
| | - Dorota Studniarczyk
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondonUnited Kingdom
| | - Stuart G Cull-Candy
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondonUnited Kingdom
| | - Mark Farrant
- Department of Neuroscience, Physiology and Pharmacology, University College LondonLondonUnited Kingdom
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12
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RNA Editing Therapeutics: Advances, Challenges and Perspectives on Combating Heart Disease. Cardiovasc Drugs Ther 2023; 37:401-411. [PMID: 36239832 PMCID: PMC9561330 DOI: 10.1007/s10557-022-07391-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/01/2022] [Indexed: 11/15/2022]
Abstract
Cardiovascular disease still remains the leading cause of morbidity and mortality worldwide. Current pharmacological or interventional treatments help to tackle symptoms and even reduce mortality, but cardiovascular disease cases continue to rise. The emergence of novel therapeutic strategies that precisely and efficiently combat cardiovascular disease is therefore deemed more essential than ever. RNA editing, the cell-intrinsic deamination of adenosine or cytidine RNA residues, changes the molecular identity of edited nucleotides, severely altering the fate of RNA molecules involved in key biological processes. The most common type of RNA editing is the deamination of adenosine residue to inosine (A-to-I), which is catalysed by adenosine deaminases acting on RNA (ADARs). Recent efforts have convincingly liaised RNA editing-based mechanisms to the pathophysiology of the cardiovascular system. In this review, we will briefly introduce the basic concepts of the RNA editing field of research. We will particularly focus our discussion on the therapeutic exploitation of RNA editing as a novel therapeutic tool as well as the future perspectives for its use in cardiovascular disease treatment.
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13
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Lu H, Chen S, Nie Q, Xue Q, Fan H, Wang Y, Fan S, Zhu J, Shen H, Li H, Fang Q, Ni J, Chen G. Synaptotagmin-3 interactions with GluA2 mediate brain damage and impair functional recovery in stroke. Cell Rep 2023; 42:112233. [PMID: 36892998 DOI: 10.1016/j.celrep.2023.112233] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 01/20/2023] [Accepted: 02/23/2023] [Indexed: 03/10/2023] Open
Abstract
Synaptotagmin III (Syt3) is a Ca2+-dependent membrane-traffic protein that is highly concentrated in synaptic plasma membranes and affects synaptic plasticity by regulating post-synaptic receptor endocytosis. Here, we show that Syt3 is upregulated in the penumbra after ischemia/reperfusion (I/R) injury. Knockdown of Syt3 protects against I/R injury, promotes recovery of motor function, and inhibits cognitive decline. Overexpression of Syt3 exerts the opposite effects. Mechanistically, I/R injury augments Syt3-GluA2 interactions, decreases GluA2 surface expression, and promotes the formation of Ca2+-permeable AMPA receptors (CP-AMPARs). Using a CP-AMPAR antagonist or dissociating the Syt3-GluA2 complex via TAT-GluA2-3Y peptide promotes recovery from neurological impairments and improves cognitive function. Furthermore, Syt3 knockout mice are resistant to cerebral ischemia because they show high-level expression of surface GluA2 and low-level expression of CP-AMPARs after I/R. Our results indicate that Syt3-GluA2 interactions, which regulate the formation of CP-AMPARs, may be a therapeutic target for ischemic insults.
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Affiliation(s)
- Haifeng Lu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu, China; Institute of Stroke Research, Soochow University, Suzhou 215006, Jiangsu, China
| | - Shujun Chen
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu, China; Institute of Stroke Research, Soochow University, Suzhou 215006, Jiangsu, China
| | - Qianqian Nie
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu, China; Institute of Stroke Research, Soochow University, Suzhou 215006, Jiangsu, China
| | - Qun Xue
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu, China; Institute of Stroke Research, Soochow University, Suzhou 215006, Jiangsu, China.
| | - Hua Fan
- The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471000, Henan, China
| | - Yiqing Wang
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu, China; Institute of Stroke Research, Soochow University, Suzhou 215006, Jiangsu, China
| | - Shenghao Fan
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu, China; Institute of Stroke Research, Soochow University, Suzhou 215006, Jiangsu, China
| | - Juehua Zhu
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu, China; Institute of Stroke Research, Soochow University, Suzhou 215006, Jiangsu, China
| | - Haitao Shen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu, China; Institute of Stroke Research, Soochow University, Suzhou 215006, Jiangsu, China
| | - Haiying Li
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu, China; Institute of Stroke Research, Soochow University, Suzhou 215006, Jiangsu, China
| | - Qi Fang
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu, China; Institute of Stroke Research, Soochow University, Suzhou 215006, Jiangsu, China
| | - Jianqiang Ni
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu, China; Institute of Stroke Research, Soochow University, Suzhou 215006, Jiangsu, China
| | - Gang Chen
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu, China; Institute of Stroke Research, Soochow University, Suzhou 215006, Jiangsu, China.
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14
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Gaidin SG, Maiorov SA, Laryushkin DP, Zinchenko VP, Kosenkov AM. A novel approach for vital visualization and studying of neurons containing Ca 2+ -permeable AMPA receptors. J Neurochem 2023; 164:583-597. [PMID: 36415923 DOI: 10.1111/jnc.15729] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 10/19/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022]
Abstract
Calcium-permeable AMPA receptors (CP-AMPARs) play a pivotal role in brain functioning in health and disease. They are involved in synaptic plasticity, synaptogenesis, and neuronal circuits development. However, the functions of neurons expressing CP-AMPARs and their role in the modulation of network activity remain elusive since reliable and accurate visualization methods are absent. Here we developed an approach allowing the vital identification of neurons containing CP-AMPARs. The proposed method relies on evaluating Ca2+ influx in neurons during activation of AMPARs in the presence of NMDAR and KAR antagonists, and blockers of voltage-gated Ca2+ channels. Using this method, we studied the properties of CP-AMPARs-containing neurons. We showed that the overwhelming majority of neurons containing CP-AMPARs are GABAergic, and they are distinguished by higher amplitudes of the calcium responses to applications of the agonists. Furthermore, about 30% of CP-AMPARs-containing neurons demonstrate the presence of GluK1-containing KARs. Although CP-AMPARs-containing neurons are characterized by more significant Ca2+ influx during the activation of AMPARs than other neurons, AMPAR-mediated Na+ influx is similar in these two groups. We revealed that neurons containing CP-AMPARs demonstrate weak GABA(A)R-mediated inhibition because of the low percentage of GABAergic synapses on the soma of these cells. However, our data show that weak GABA(A)R-mediated inhibition is inherent to all GABAergic neurons in the culture and cannot be considered a unique feature of CP-AMPARs-containing neurons. We believe that the suggested approach will help to understand the role of CP-AMPARs in the mammalian nervous system in more detail.
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Affiliation(s)
- Sergei G Gaidin
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino, Russia
| | - Sergei A Maiorov
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino, Russia
| | - Denis P Laryushkin
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino, Russia
| | - Valery P Zinchenko
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino, Russia
| | - Artem M Kosenkov
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institute of Cell Biophysics of the Russian Academy of Sciences, Pushchino, Russia
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15
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Schackert F, Biedermann J, Abdolvand S, Minniberger S, Song C, Plested AJR, Carloni P, Sun H. Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel. J Chem Inf Model 2023; 63:1293-1300. [PMID: 36758214 PMCID: PMC9976283 DOI: 10.1021/acs.jcim.2c01494] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) are neurotransmitter-activated cation channels ubiquitously expressed in vertebrate brains. The regulation of calcium flux through the channel pore by RNA-editing is linked to synaptic plasticity while excessive calcium influx poses a risk for neurodegeneration. Unfortunately, the molecular mechanisms underlying this key process are mostly unknown. Here, we investigated calcium conduction in calcium-permeable AMPAR using Molecular Dynamics (MD) simulations with recently introduced multisite force-field parameters for Ca2+. Our calculations are consistent with experiment and explain the distinct calcium permeability in different RNA-edited forms of GluA2. For one of the identified metal binding sites, multiscale Quantum Mechanics/Molecular Mechanics (QM/MM) simulations further validated the results from MD and revealed small but reproducible charge transfer between the metal ion and its first solvation shell. In addition, the ion occupancy derived from MD simulations independently reproduced the Ca2+ binding profile in an X-ray structure of an NaK channel mimicking the AMPAR selectivity filter. This integrated study comprising X-ray crystallography, multisite MD, and multiscale QM/MM simulations provides unprecedented insights into Ca2+ permeation mechanisms in AMPARs, and paves the way for studying other biological processes in which Ca2+ plays a pivotal role.
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Affiliation(s)
- Florian
Karl Schackert
- Computational
Biomedicine (IAS-5/INM-9), Forschungszentrum
Jülich GmbH, 52428 Jülich, Germany,Department
of Physics, RWTH Aachen University, 52062 Aachen, Germany
| | - Johann Biedermann
- Institute
of Biology, Cellular Biophysics, Humboldt
Universität zu Berlin, 10115 Berlin, Germany,Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Saeid Abdolvand
- Institute
of Biology, Cellular Biophysics, Humboldt
Universität zu Berlin, 10115 Berlin, Germany,Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Sonja Minniberger
- Institute
of Biology, Cellular Biophysics, Humboldt
Universität zu Berlin, 10115 Berlin, Germany,Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Chen Song
- Center
for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China,Peking-Tsinghua
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Andrew J. R. Plested
- Institute
of Biology, Cellular Biophysics, Humboldt
Universität zu Berlin, 10115 Berlin, Germany,Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Paolo Carloni
- Computational
Biomedicine (IAS-5/INM-9), Forschungszentrum
Jülich GmbH, 52428 Jülich, Germany,Department
of Physics, RWTH Aachen University, 52062 Aachen, Germany,
| | - Han Sun
- Leibniz
Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany,Institute
of Chemistry, TU Berlin, Straße des 17 Juni 135, 10623 Berlin, Germany,
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16
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Hajji K, Sedmík J, Cherian A, Amoruso D, Keegan LP, O'Connell MA. ADAR2 enzymes: efficient site-specific RNA editors with gene therapy aspirations. RNA (NEW YORK, N.Y.) 2022; 28:1281-1297. [PMID: 35863867 PMCID: PMC9479739 DOI: 10.1261/rna.079266.122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The adenosine deaminase acting on RNA (ADAR) enzymes are essential for neuronal function and innate immune control. ADAR1 RNA editing prevents aberrant activation of antiviral dsRNA sensors through editing of long, double-stranded RNAs (dsRNAs). In this review, we focus on the ADAR2 proteins involved in the efficient, highly site-specific RNA editing to recode open reading frames first discovered in the GRIA2 transcript encoding the key GLUA2 subunit of AMPA receptors; ADAR1 proteins also edit many of these sites. We summarize the history of ADAR2 protein research and give an up-to-date review of ADAR2 structural studies, human ADARBI (ADAR2) mutants causing severe infant seizures, and mouse disease models. Structural studies on ADARs and their RNA substrates facilitate current efforts to develop ADAR RNA editing gene therapy to edit disease-causing single nucleotide polymorphisms (SNPs). Artificial ADAR guide RNAs are being developed to retarget ADAR RNA editing to new target transcripts in order to correct SNP mutations in them at the RNA level. Site-specific RNA editing has been expanded to recode hundreds of sites in CNS transcripts in Drosophila and cephalopods. In Drosophila and C. elegans, ADAR RNA editing also suppresses responses to self dsRNA.
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Affiliation(s)
- Khadija Hajji
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | - Jiří Sedmík
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | - Anna Cherian
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | | | - Liam P Keegan
- CEITEC Masaryk University, Brno 62500, Czech Republic
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17
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Ji B, Wojtaś B, Skup M. Molecular Identification of Pro-Excitogenic Receptor and Channel Phenotypes of the Deafferented Lumbar Motoneurons in the Early Phase after SCT in Rats. Int J Mol Sci 2022; 23:ijms231911133. [PMID: 36232433 PMCID: PMC9569670 DOI: 10.3390/ijms231911133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/19/2022] [Accepted: 09/19/2022] [Indexed: 02/07/2023] Open
Abstract
Spasticity impacts the quality of life of patients suffering spinal cord injury and impedes the recovery of locomotion. At the cellular level, spasticity is considered to be primarily caused by the hyperexcitability of spinal α-motoneurons (MNs) within the spinal stretch reflex circuit. Here, we hypothesized that after a complete spinal cord transection in rats, fast adaptive molecular responses of lumbar MNs develop in return for the loss of inputs. We assumed that early loss of glutamatergic afferents changes the expression of glutamatergic AMPA and NMDA receptor subunits, which may be the forerunners of the developing spasticity of hindlimb muscles. To better understand its molecular underpinnings, concomitant expression of GABA and Glycinergic receptors and serotoninergic and noradrenergic receptors, which regulate the persistent inward currents crucial for sustained discharges in MNs, were examined together with voltage-gated ion channels and cation-chloride cotransporters. Using quantitative real-time PCR, we showed in the tracer-identified MNs innervating extensor and flexor muscles of the ankle joint multiple increases in transcripts coding for AMPAR and 5-HTR subunits, along with a profound decrease in GABAAR, GlyR subunits, and KCC2. Our study demonstrated that both MNs groups similarly adapt to a more excitable state, which may increase the occurrence of extensor and flexor muscle spasms.
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Affiliation(s)
- Benjun Ji
- Group of Restorative Neurobiology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland
| | - Bartosz Wojtaś
- Laboratory of Sequencing, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland
| | - Małgorzata Skup
- Group of Restorative Neurobiology, Nencki Institute of Experimental Biology, 02-093 Warsaw, Poland
- Correspondence:
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18
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Sikorski V, Vento A, Kankuri E. Emerging roles of the RNA modifications N6-methyladenosine and adenosine-to-inosine in cardiovascular diseases. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:426-461. [PMID: 35991314 PMCID: PMC9366019 DOI: 10.1016/j.omtn.2022.07.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cardiovascular diseases lead the mortality and morbidity disease metrics worldwide. A multitude of chemical base modifications in ribonucleic acids (RNAs) have been linked with key events of cardiovascular diseases and metabolic disorders. Named either RNA epigenetics or epitranscriptomics, the post-transcriptional RNA modifications, their regulatory pathways, components, and downstream effects substantially contribute to the ways our genetic code is interpreted. Here we review the accumulated discoveries to date regarding the roles of the two most common epitranscriptomic modifications, N6-methyl-adenosine (m6A) and adenosine-to-inosine (A-to-I) editing, in cardiovascular disease.
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Affiliation(s)
- Vilbert Sikorski
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Antti Vento
- Heart and Lung Center, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Esko Kankuri
- Department of Pharmacology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
- Corresponding author Esko Kankuri, M.D. Ph.D., Faculty of Medicine, Department of Pharmacology, PO Box 63 (Haartmaninkatu 8), FIN-00014 University of Helsinki, 00014 Helsinki, Finland.
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19
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Zhai J, Koh JH, Soong TW. RNA editing of ion channels and receptors in physiology and neurological disorders. OXFORD OPEN NEUROSCIENCE 2022; 1:kvac010. [PMID: 38596706 PMCID: PMC11003377 DOI: 10.1093/oons/kvac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/14/2022] [Accepted: 05/15/2022] [Indexed: 04/11/2024]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a post-transcriptional modification that diversifies protein functions by recoding RNA or alters protein quantity by regulating mRNA level. A-to-I editing is catalyzed by adenosine deaminases that act on RNA. Millions of editing sites have been reported, but they are mostly found in non-coding sequences. However, there are also several recoding editing sites in transcripts coding for ion channels or transporters that have been shown to play important roles in physiology and changes in editing level are associated with neurological diseases. These editing sites are not only found to be evolutionary conserved across species, but they are also dynamically regulated spatially, developmentally and by environmental factors. In this review, we discuss the current knowledge of A-to-I RNA editing of ion channels and receptors in the context of their roles in physiology and pathological disease. We also discuss the regulation of editing events and site-directed RNA editing approaches for functional study that offer a therapeutic pathway for clinical applications.
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Affiliation(s)
- Jing Zhai
- Department of Physiology, National University of Singapore, Singapore 117593, Singapore
| | - Joanne Huifen Koh
- Department of Physiology, National University of Singapore, Singapore 117593, Singapore
| | - Tuck Wah Soong
- Department of Physiology, National University of Singapore, Singapore 117593, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore,
Singapore 117456, Singapore
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20
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Kokot KE, Kneuer JM, John D, Rebs S, Möbius-Winkler MN, Erbe S, Müller M, Andritschke M, Gaul S, Sheikh BN, Haas J, Thiele H, Müller OJ, Hille S, Leuschner F, Dimmeler S, Streckfuss-Bömeke K, Meder B, Laufs U, Boeckel JN. Reduction of A-to-I RNA editing in the failing human heart regulates formation of circular RNAs. Basic Res Cardiol 2022; 117:32. [PMID: 35737129 PMCID: PMC9226085 DOI: 10.1007/s00395-022-00940-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 01/31/2023]
Abstract
Alterations of RNA editing that affect the secondary structure of RNAs can cause human diseases. We therefore studied RNA editing in failing human hearts. Transcriptome sequencing showed that adenosine-to-inosine (A-to-I) RNA editing was responsible for 80% of the editing events in the myocardium. Failing human hearts were characterized by reduced RNA editing. This was primarily attributable to Alu elements in introns of protein-coding genes. In the failing left ventricle, 166 circRNAs were upregulated and 7 circRNAs were downregulated compared to non-failing controls. Most of the upregulated circRNAs were associated with reduced RNA editing in the host gene. ADAR2, which binds to RNA regions that are edited from A-to-I, was decreased in failing human hearts. In vitro, reduction of ADAR2 increased circRNA levels suggesting a causal effect of reduced ADAR2 levels on increased circRNAs in the failing human heart. To gain mechanistic insight, one of the identified upregulated circRNAs with a high reduction of editing in heart failure, AKAP13, was further characterized. ADAR2 reduced the formation of double-stranded structures in AKAP13 pre-mRNA, thereby reducing the stability of Alu elements and the circularization of the resulting circRNA. Overexpression of circAKAP13 impaired the sarcomere regularity of human induced pluripotent stem cell-derived cardiomyocytes. These data show that ADAR2 mediates A-to-I RNA editing in the human heart. A-to-I RNA editing represses the formation of dsRNA structures of Alu elements favoring canonical linear mRNA splicing and inhibiting the formation of circRNAs. The findings are relevant to diseases with reduced RNA editing and increased circRNA levels and provide insights into the human-specific regulation of circRNA formation.
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Affiliation(s)
- Karoline E Kokot
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - Jasmin M Kneuer
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - David John
- Institute for Cardiovascular Regeneration, Goethe-University Hospital, Theodor Stern Kai 7, Frankfurt, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Sabine Rebs
- Institute of Pharmacology and Toxicology, Versbacher-Str. 9, Würzburg, Germany
- Heartcenter - Clinic for Cardiology and Pneumology, University Medicine Goettingen, Robert-Koch-Str. 40, Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Göttingen, Göttingen, Germany
| | | | - Stephan Erbe
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - Marion Müller
- Department of General and Interventional Cardiology/Angiology, Ruhr University of Bochum, Heart-and Diabetes Center North Rhine-Westphalia, Bad Oeynhausen, Germany
| | - Michael Andritschke
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - Susanne Gaul
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - Bilal N Sheikh
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Jan Haas
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Heidelberg, Heidelberg, Germany
| | - Holger Thiele
- Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute, Leipzig, Germany
| | - Oliver J Müller
- Department of Internal Medicine III, University of Kiel, Kiel, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Kiel, Germany
| | - Susanne Hille
- Department of Internal Medicine III, University of Kiel, Kiel, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Hamburg/Kiel/Lübeck, Kiel, Germany
| | - Florian Leuschner
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Heidelberg, Heidelberg, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Goethe-University Hospital, Theodor Stern Kai 7, Frankfurt, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Katrin Streckfuss-Bömeke
- Institute of Pharmacology and Toxicology, Versbacher-Str. 9, Würzburg, Germany
- Heartcenter - Clinic for Cardiology and Pneumology, University Medicine Goettingen, Robert-Koch-Str. 40, Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Göttingen, Göttingen, Germany
| | - Benjamin Meder
- Department of Internal Medicine III, University of Heidelberg, Heidelberg, Germany
- German Centre for Cardiovascular Research (DZHK), Partner site Heidelberg, Heidelberg, Germany
| | - Ulrich Laufs
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany
| | - Jes-Niels Boeckel
- Klinik und Poliklinik für Kardiologie, Universitätsklinikum Leipzig, Liebigstrasse 20, Leipzig, Germany.
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21
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The Role of Mitochondrial Dynamin in Stroke. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:2504798. [PMID: 35571256 PMCID: PMC9106451 DOI: 10.1155/2022/2504798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/17/2022] [Indexed: 11/25/2022]
Abstract
Stroke is one of the leading causes of death and disability in the world. However, the pathophysiological process of stroke is still not fully clarified. Mitochondria play an important role in promoting nerve survival and are an important drug target for the treatment of stroke. Mitochondrial dysfunction is one of the hallmarks of stroke. Mitochondria are in a state of continuous fission and fusion, which are termed as mitochondrial dynamics. Mitochondrial dynamics are very important for maintaining various functions of mitochondria. In this review, we will introduce the structure and functions of mitochondrial fission and fusion related proteins and discuss their role in the pathophysiologic process of stroke. A better understanding of mitochondrial dynamin in stroke will pave way for the development of new therapeutic options.
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22
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Chokkalla AK, Mehta SL, Vemuganti R. Epitranscriptomic Modifications Modulate Normal and Pathological Functions in CNS. Transl Stroke Res 2022; 13:1-11. [PMID: 34224107 PMCID: PMC8727632 DOI: 10.1007/s12975-021-00927-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 05/28/2021] [Accepted: 06/24/2021] [Indexed: 12/13/2022]
Abstract
RNA is more than just a combination of four genetically encoded nucleobases as it carries extra information in the form of epitranscriptomic modifications. Diverse chemical groups attach covalently to RNA to enhance the plasticity of cellular transcriptome. The reversible and dynamic nature of epitranscriptomic modifications allows RNAs to achieve rapid and context-specific gene regulation. Dedicated cellular machinery comprising of writers, erasers, and readers drives the epitranscriptomic signaling. Epitranscriptomic modifications control crucial steps of mRNA metabolism such as splicing, export, localization, stability, degradation, and translation. The majority of the epitranscriptomic modifications are highly abundant in the brain and contribute to activity-dependent gene expression. Thus, they regulate the vital physiological processes of the brain, such as synaptic plasticity, neurogenesis, and stress response. Furthermore, epitranscriptomic alterations influence the progression of several neurologic disorders. This review discussed the molecular mechanisms of epitranscriptomic regulation in neurodevelopmental and neuropathological conditions with the goal to identify novel therapeutic targets.
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Affiliation(s)
- Anil K Chokkalla
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin, Madison, WI, USA
- Department of Neurological Surgery, University of Wisconsin-Madison, 600 Highland Ave, Madison, WI, 53792, USA
| | - Suresh L Mehta
- Department of Neurological Surgery, University of Wisconsin-Madison, 600 Highland Ave, Madison, WI, 53792, USA
| | - Raghu Vemuganti
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin, Madison, WI, USA.
- Department of Neurological Surgery, University of Wisconsin-Madison, 600 Highland Ave, Madison, WI, 53792, USA.
- William S. Middleton Memorial Veteran Administration Hospital, Madison, WI, USA.
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Hosaka T, Tsuji H, Kwak S. RNA Editing: A New Therapeutic Target in Amyotrophic Lateral Sclerosis and Other Neurological Diseases. Int J Mol Sci 2021; 22:ijms222010958. [PMID: 34681616 PMCID: PMC8536083 DOI: 10.3390/ijms222010958] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/29/2021] [Accepted: 10/08/2021] [Indexed: 12/24/2022] Open
Abstract
The conversion of adenosine to inosine in RNA editing (A-to-I RNA editing) is recognized as a critical post-transcriptional modification of RNA by adenosine deaminases acting on RNAs (ADARs). A-to-I RNA editing occurs predominantly in mammalian and human central nervous systems and can alter the function of translated proteins, including neurotransmitter receptors and ion channels; therefore, the role of dysregulated RNA editing in the pathogenesis of neurological diseases has been speculated. Specifically, the failure of A-to-I RNA editing at the glutamine/arginine (Q/R) site of the GluA2 subunit causes excessive permeability of α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptors to Ca2+, inducing fatal status epilepticus and the neurodegeneration of motor neurons in mice. Therefore, an RNA editing deficiency at the Q/R site in GluA2 due to the downregulation of ADAR2 in the motor neurons of sporadic amyotrophic lateral sclerosis (ALS) patients suggests that Ca2+-permeable AMPA receptors and the dysregulation of RNA editing are suitable therapeutic targets for ALS. Gene therapy has recently emerged as a new therapeutic opportunity for many heretofore incurable diseases, and RNA editing dysregulation can be a target for gene therapy; therefore, we reviewed neurological diseases associated with dysregulated RNA editing and a new therapeutic approach targeting dysregulated RNA editing, especially one that is effective in ALS.
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Affiliation(s)
- Takashi Hosaka
- Department of Neurology, Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Ibaraki, Japan; (T.H.); (H.T.)
- Department of Internal Medicine, Tsukuba University Hospital Kensei Area Medical Education Center, Chikusei 308-0813, Ibaraki, Japan
- Department of Internal Medicine, Ibaraki Western Medical Center, Chikusei 308-0813, Ibaraki, Japan
| | - Hiroshi Tsuji
- Department of Neurology, Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Ibaraki, Japan; (T.H.); (H.T.)
| | - Shin Kwak
- Department of Neurology, Tokyo Medical University, Shinjuku-ku, Tokyo 160-0023, Japan
- Correspondence: ; Tel.: +81-3-3342-6111
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Xie KY, Chien SJ, Tan BCM, Chen YW. RNA editing of 5-HT 2C R impairs insulin secretion of pancreatic beta cells via altered store-operated calcium entry. FASEB J 2021; 35:e21929. [PMID: 34553421 DOI: 10.1096/fj.202100265rr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 08/20/2021] [Accepted: 08/31/2021] [Indexed: 11/11/2022]
Abstract
Recent studies emphasize the importance of 5-HT2C receptor (5-HT2C R) signaling in the regulation of energy homeostasis. The 5-HT2C R is the only G-protein-coupled receptor known to undergo post-transcriptional adenosine to inosine (A-to-I) editing by adenosine deaminase acting on RNA (ADAR). 5-HT2C R has emerged as an important role in the modulation of pancreatic β cell functions. This study investigated mechanisms behind the effects of palmitic acid (PA) on insulin secretion in different overexpressed 5-HT2C R edited isoforms in pancreatic MIN6 β cells. Results showed that the expressions of 5HT2C R and ADAR2 were upregulated in the pancreatic islets of mice fed with high-fat diet (HFD) compared to control mice. PA treatment significantly induced the expressions of 5-HT2C R and ADAR2 in pancreatic MIN6 β cells. PA treatment significantly induced the editing of 5-HT2C R in pancreatic MIN6 β cells. There was no significant difference in cell viability between naïve cells and three overexpressed 5-HT2C R edited isoforms in pancreatic MIN6 β cells. Overexpressed 5-HT2C R edited isoforms showed reduced glucose-stimulated insulin secretion (GSIS) compared with green fluorescent protein (GFP) expressed cells. Moreover, 5-HT2C R edited isoforms displayed reduced endoplasmic reticulum (ER) calcium release and store-operated calcium entry (SOCE) activation, probably through inhibition of stromal interaction molecule 1 trafficking under PA treatment. Altogether, our results show that PA-mediated editing of 5-HT2C R modulates GSIS through alteration of ER calcium release and SOCE activation in pancreatic MIN6 β cells.
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Affiliation(s)
- Ke-Yun Xie
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shao-Ju Chien
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Bertrand Chin-Ming Tan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, Linkou Medical Center, Chang Gung Memorial Hospital, Linkou, Taiwan.,Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan
| | - Yun-Wen Chen
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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Guo C, Ma YY. Calcium Permeable-AMPA Receptors and Excitotoxicity in Neurological Disorders. Front Neural Circuits 2021; 15:711564. [PMID: 34483848 PMCID: PMC8416103 DOI: 10.3389/fncir.2021.711564] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022] Open
Abstract
Excitotoxicity is one of the primary mechanisms of cell loss in a variety of diseases of the central and peripheral nervous systems. Other than the previously established signaling pathways of excitotoxicity, which depend on the excessive release of glutamate from axon terminals or over-activation of NMDA receptors (NMDARs), Ca2+ influx-triggered excitotoxicity through Ca2+-permeable (CP)-AMPA receptors (AMPARs) is detected in multiple disease models. In this review, both acute brain insults (e.g., brain trauma or spinal cord injury, ischemia) and chronic neurological disorders, including Epilepsy/Seizures, Huntington’s disease (HD), Parkinson’s disease (PD), Alzheimer’s disease (AD), amyotrophic lateral sclerosis (ALS), chronic pain, and glaucoma, are discussed regarding the CP-AMPAR-mediated excitotoxicity. Considering the low expression or absence of CP-AMPARs in most cells, specific manipulation of the CP-AMPARs might be a more plausible strategy to delay the onset and progression of pathological alterations with fewer side effects than blocking NMDARs.
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Affiliation(s)
- Changyong Guo
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Yao-Ying Ma
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States.,Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States
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Ge Y, Wang YT. GluA1-homomeric AMPA receptor in synaptic plasticity and neurological diseases. Neuropharmacology 2021; 197:108708. [PMID: 34274350 DOI: 10.1016/j.neuropharm.2021.108708] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/28/2021] [Accepted: 07/08/2021] [Indexed: 11/17/2022]
Abstract
Synaptic transmission is one of the fundamental processes that all brain functions are based on. Changes in the strength of synaptic transmission among neurons are crucial for information processing in the central nervous system. The α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid subtype of ionotropic glutamate receptors (AMPARs) mediate the majority of the fast excitatory synaptic transmission in the mammalian brain. Rapid trafficking of AMPARs in and out of the postsynaptic membrane is proposed to be a major mechanism for synaptic plasticity, and learning and memory. Defects in the regulated AMPAR trafficking have been shown to be involved in the pathogenesis of certain psychiatric and neurodegenerative diseases. Studies accumulated in the past 30 years have provided a detailed molecular insight on how the trafficking of AMPARs is modulated in a subunit-specific manner. In particular, emerging evidence supports that the regulated expression and trafficking of Ca2+-permeable, GluA1-homomeric subtype of AMPARs mediates diverse types of synaptic plasticity, thereby playing critical roles in brain function and dysfunction. In this review, we will discuss the current knowledge of AMPAR subunit-specific trafficking, with a particular emphasis on the involvement of GluA1-homomeric receptor trafficking in synaptic plasticity and brain disorders.
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Affiliation(s)
- Yuan Ge
- Djavad Mowafaghian Centre for Brain Health and Department of Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada; Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, BC, V6T 2B5, Canada
| | - Yu Tian Wang
- Djavad Mowafaghian Centre for Brain Health and Department of Medicine, University of British Columbia, Vancouver, BC, V6T 2B5, Canada.
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Vesely C, Jantsch MF. An I for an A: Dynamic Regulation of Adenosine Deamination-Mediated RNA Editing. Genes (Basel) 2021; 12:1026. [PMID: 34356042 PMCID: PMC8304401 DOI: 10.3390/genes12071026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
RNA-editing by adenosine deaminases acting on RNA (ADARs) converts adenosines to inosines in structured RNAs. Inosines are read as guanosines by most cellular machineries. A to I editing has two major functions: first, marking endogenous RNAs as "self", therefore helping the innate immune system to distinguish repeat- and endogenous retrovirus-derived RNAs from invading pathogenic RNAs; and second, recoding the information of the coding RNAs, leading to the translation of proteins that differ from their genomically encoded versions. It is obvious that these two important biological functions of ADARs will differ during development, in different tissues, upon altered physiological conditions or after exposure to pathogens. Indeed, different levels of ADAR-mediated editing have been observed in different tissues, as a response to altered physiology or upon pathogen exposure. In this review, we describe the dynamics of A to I editing and summarize the known and likely mechanisms that will lead to global but also substrate-specific regulation of A to I editing.
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Affiliation(s)
| | - Michael F. Jantsch
- Division of Cell & Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17, A-1090 Vienna, Austria;
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Gabriel L, Srinivasan B, Kuś K, Mata JF, João Amorim M, Jansen LET, Athanasiadis A. Enrichment of Zα domains at cytoplasmic stress granules is due to their innate ability to bind to nucleic acids. J Cell Sci 2021; 134:268376. [PMID: 34037233 DOI: 10.1242/jcs.258446] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/08/2021] [Indexed: 01/14/2023] Open
Abstract
Zα domains recognize the left-handed helical Z conformation of double-stranded nucleic acids. They are found in proteins involved in the nucleic acid sensory pathway of the vertebrate innate immune system and host evasion by viral pathogens. Previously, it has been demonstrated that ADAR1 (encoded by ADAR in humans) and DAI (also known as ZBP1) localize to cytoplasmic stress granules (SGs), and this localization is mediated by their Zα domains. To investigate the mechanism, we determined the interactions and localization pattern for the N-terminal region of human DAI (ZαβDAI), which harbours two Zα domains, and for a ZαβDAI mutant deficient in nucleic acid binding. Electrophoretic mobility shift assays demonstrated the ability of ZαβDAI to bind to hyperedited nucleic acids, which are enriched in SGs. Furthermore, using immunofluorescence and immunoprecipitation coupled with mass spectrometry, we identified several interacting partners of the ZαβDAI-RNA complex in vivo under conditions of arsenite-induced stress. These interactions are lost upon loss of nucleic acid-binding ability or upon RNase treatment. Thus, we posit that the mechanism for the translocation of Zα domain-containing proteins to SGs is mainly mediated by the nucleic acid-binding ability of their Zα domains. This article has an associated First Person interview with Bharath Srinivasan, joint first author of the paper.
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Affiliation(s)
- Luisa Gabriel
- Instituto Gulbenkian de Ciência, Rua Quinta Grande 6, Oeiras 2781-156, Portugal
| | - Bharath Srinivasan
- Instituto Gulbenkian de Ciência, Rua Quinta Grande 6, Oeiras 2781-156, Portugal
| | - Krzysztof Kuś
- Instituto Gulbenkian de Ciência, Rua Quinta Grande 6, Oeiras 2781-156, Portugal
| | - João F Mata
- Instituto Gulbenkian de Ciência, Rua Quinta Grande 6, Oeiras 2781-156, Portugal
| | - Maria João Amorim
- Instituto Gulbenkian de Ciência, Rua Quinta Grande 6, Oeiras 2781-156, Portugal
| | - Lars E T Jansen
- Instituto Gulbenkian de Ciência, Rua Quinta Grande 6, Oeiras 2781-156, Portugal
| | - Alekos Athanasiadis
- Instituto Gulbenkian de Ciência, Rua Quinta Grande 6, Oeiras 2781-156, Portugal
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29
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Zhou G, Wang Y, Gao S, Fu X, Cao Y, Peng Y, Zhuang J, Hu J, Shao A, Wang L. Potential Mechanisms and Perspectives in Ischemic Stroke Treatment Using Stem Cell Therapies. Front Cell Dev Biol 2021; 9:646927. [PMID: 33869200 PMCID: PMC8047216 DOI: 10.3389/fcell.2021.646927] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/05/2021] [Indexed: 12/12/2022] Open
Abstract
Ischemic stroke (IS) remains one of the major causes of death and disability due to the limited ability of central nervous system cells to regenerate and differentiate. Although several advances have been made in stroke therapies in the last decades, there are only a few approaches available to improve IS outcome. In the acute phase of IS, mechanical thrombectomy and the administration of tissue plasminogen activator have been widely used, while aspirin or clopidogrel represents the main therapy used in the subacute or chronic phase. However, in most cases, stroke patients fail to achieve satisfactory functional recovery under the treatments mentioned above. Recently, cell therapy, especially stem cell therapy, has been considered as a novel and potential therapeutic strategy to improve stroke outcome through mechanisms, including cell differentiation, cell replacement, immunomodulation, neural circuit reconstruction, and protective factor release. Different stem cell types, such as mesenchymal stem cells, marrow mononuclear cells, and neural stem cells, have also been considered for stroke therapy. In recent years, many clinical and preclinical studies on cell therapy have been carried out, and numerous results have shown that cell therapy has bright prospects in the treatment of stroke. However, some cell therapy issues are not yet fully understood, such as its optimal parameters including cell type choice, cell doses, and injection routes; therefore, a closer relationship between basic and clinical research is needed. In this review, the role of cell therapy in stroke treatment and its mechanisms was summarized, as well as the function of different stem cell types in stroke treatment and the clinical trials using stem cell therapy to cure stroke, to reveal future insights on stroke-related cell therapy, and to guide further studies.
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Affiliation(s)
- Guoyang Zhou
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yongjie Wang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shiqi Gao
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiongjie Fu
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yang Cao
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yucong Peng
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jianfeng Zhuang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Junwen Hu
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Anwen Shao
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lin Wang
- Department of Neurosurgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Abstract
The brain is one of the organs that are preferentially targeted by adenosine-to-inosine (A-to-I) RNA editing, a posttranscriptional modification. This chemical modification affects neuronal development and functions at multiple levels, leading to normal brain homeostasis by increasing the complexity of the transcriptome. This includes modulation of the properties of ion channel and neurotransmitter receptors by recoding, redirection of miRNA targets by changing sequence complementarity, and suppression of immune response by altering RNA structure. Therefore, from another perspective, it appears that the brain is highly vulnerable to dysregulation of A-to-I RNA editing. Here, we focus on how aberrant A-to-I RNA editing is involved in neurological and neurodegenerative diseases of humans including epilepsy, amyotrophic lateral sclerosis, psychiatric disorders, developmental disorders, brain tumors, and encephalopathy caused by autoimmunity. In addition, we provide information regarding animal models to better understand the mechanisms behind disease phenotype.
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Affiliation(s)
- Pedro Henrique Costa Cruz
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yukio Kawahara
- Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, Osaka, Japan.
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31
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Fukushima Y, Uchida S, Imai H, Nakatomi H, Kataoka K, Saito N, Itaka K. Treatment of ischemic neuronal death by introducing brain-derived neurotrophic factor mRNA using polyplex nanomicelle. Biomaterials 2021; 270:120681. [PMID: 33517206 DOI: 10.1016/j.biomaterials.2021.120681] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/12/2021] [Accepted: 01/16/2021] [Indexed: 12/19/2022]
Abstract
Ischemic neuronal death causes serious lifelong neurological deficits; however, there is no proven effective treatment that can prevent neuronal death after the ischemia. We investigated the feasibility of mRNA therapeutics for preventing the neuronal death in a rat model of transient global ischemia (TGI). By intraventricular administration of mRNA encoding brain-derived neurotrophic factor (BDNF) using a polymer-based carrier, polyplex nanomicelle, the mRNA significantly increased the survival rate of hippocampal neurons after TGI, with a rapid rise of BDNF in the hippocampus. Interestingly, mRNA administration on Day 2 after TGI provided significantly better survival rate than the administration immediately after TGI. Eventually, dosing twice on Day 2 and 5 exerted long-term therapeutic effects, which were confirmed by a Y-maze behavioral test demonstrating improved spatial memory compared with untreated rats on Day 20. Immunohistochemical analysis showed that astrocytes were chief targets of the BDNF mRNA-loaded nanomicelles, suggesting that the augmented BDNF secretion from astrocytes creates a supportive microenvironment for the neurons to tolerate changes caused by ischemic stresses, and terminate the process of progressive neuronal death after the ischemic attack. Overall, the unique mechanism of action of mRNA therapeutics provide a promising approach for preventing ischemic neuronal death.
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Affiliation(s)
- Yuta Fukushima
- Department of Biofunction Research, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 1010062, Tokyo, Japan; Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, 1138655, Tokyo, Japan; Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 2100821, Kawasaki, Kanagawa, Japan
| | - Satoshi Uchida
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 2100821, Kawasaki, Kanagawa, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 1138656, Tokyo, Japan
| | - Hideaki Imai
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, 1138655, Tokyo, Japan
| | - Hirofumi Nakatomi
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, 1138655, Tokyo, Japan
| | - Kazunori Kataoka
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 2100821, Kawasaki, Kanagawa, Japan; Institute for Future Initiatives, The University of Tokyo, 1130033, Tokyo, Japan
| | - Nobuhito Saito
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, 1138655, Tokyo, Japan
| | - Keiji Itaka
- Department of Biofunction Research, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 1010062, Tokyo, Japan; Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 2100821, Kawasaki, Kanagawa, Japan.
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Wu D, Zang YY, Shi YY, Ye C, Cai WM, Tang XH, Zhao L, Liu Y, Gan Z, Chen GQ, Xu Y, Yang JJ, Shi YS. Distant coupling between RNA editing and alternative splicing of the osmosensitive cation channel Tmem63b. J Biol Chem 2020; 295:18199-18212. [PMID: 33100268 PMCID: PMC7939439 DOI: 10.1074/jbc.ra120.016049] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/17/2020] [Indexed: 11/06/2022] Open
Abstract
Post-transcriptional modifications of pre-mRNAs expand the diversity of proteomes in higher eukaryotes. In the brain, these modifications diversify the functional output of many critical neuronal signal molecules. In this study, we identified a brain-specific A-to-I RNA editing that changed glutamine to arginine (Q/R) at exon 20 and an alternative splicing of exon 4 in Tmem63b, which encodes a ubiquitously expressed osmosensitive cation channel. The channel isoforms lacking exon 4 occurred in ∼80% of Tmem63b mRNAs in the brain but were not detected in other tissues, suggesting a brain-specific splicing. We found that the Q/R editing was catalyzed by Adar2 (Adarb1) and required an editing site complementary sequence located in the proximal 5' end of intron 20. Moreover, the Q/R editing was almost exclusively identified in the splicing isoform lacking exon 4, indicating a coupling between the editing and the splicing. Elimination of the Q/R editing in brain-specific Adar2 knockout mice did not affect the splicing efficiency of exon 4. Furthermore, transfection with the splicing isoform containing exon 4 suppressed the Q/R editing in primary cultured cerebellar granule neurons. Thus, our study revealed a coupling between an RNA editing and a distant alternative splicing in the Tmem63b pre-mRNA, in which the splicing plays a dominant role. Finally, physiological analysis showed that the splicing and the editing coordinately regulate Ca2+ permeability and osmosensitivity of channel proteins, which may contribute to their functions in the brain.
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Affiliation(s)
- Dan Wu
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Yan-Yu Zang
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Yong-Yun Shi
- Department of Orthopaedics, Luhe People's Hospital Affiliated to Yangzhou University, Nanjing, China
| | - Chang Ye
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Wen-Min Cai
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Xiao-Hui Tang
- Department of Anesthesiology and Perioperative Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China; School of Medicine, Southeast University, Nanjing, China
| | - Liyun Zhao
- Translational Science and Clinical Biomarker, BeiGene (Shanghai) Co., Ltd., Shanghai, China
| | - Yong Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Zhenji Gan
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China
| | - Gui-Quan Chen
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China; Institute for Brain Sciences, Nanjing University, Nanjing, China
| | - Yun Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China; Institute for Brain Sciences, Nanjing University, Nanjing, China
| | - Jian-Jun Yang
- Department of Anesthesiology and Perioperative Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Yun Stone Shi
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Medical School, Nanjing University, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Department of Neurology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing University, Nanjing, China; Institute for Brain Sciences, Nanjing University, Nanjing, China; Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China.
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Activity Dependent Inhibition of AMPA Receptors by Zn 2. J Neurosci 2020; 40:8629-8636. [PMID: 33046551 DOI: 10.1523/jneurosci.1481-20.2020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/01/2020] [Accepted: 10/01/2020] [Indexed: 11/21/2022] Open
Abstract
Zn2+ has been shown to have a wide range of modulatory effects on neuronal AMPARs. However, the mechanism of modulation is largely unknown. Here we show that Zn2+ inhibits GluA2(Q) homomeric receptors in an activity- and voltage-dependent manner, indicating a pore block mechanism. The rate of inhibition is slow, in the hundreds of milliseconds at millimolar Zn2+ concentrations; hence, the inhibition is only observed in the residual nondesensitizing currents. Consequently, the inhibition is higher for GluA2 receptors in complex with auxiliary subunits γ2 and γ8 where the residual activation is larger. The extent of inhibition is also dependent on charge at site 607, the site that undergoes RNA editing in GluA2 subunits replacing glutamine to arginine, with the percent inhibition being lower and IC50 being higher for the edited GluA2(R) relative to unedited GluA2(Q) and to GluA2(Q607E), a mutation observed in the genetic screen of a patient exhibiting developmental delays. We also show that Zn2+ inhibition is significant during rapid repetitive activity with pulses of millimolar concentrations of glutamate in both receptors expressed in HEK cells as well as in native receptors in cortical neurons of C57BL/6J mice of either sex, indicating a physiological relevance of this inhibition.SIGNIFICANCE STATEMENT Zn2+ is present along with glutamate in synaptic vesicles and coreleased during synaptic transmission, modulating the postsynaptic ionotropic glutamate receptors. While Zn2+ inhibition of the NMDA subtype of the ionotropic glutamate receptors is well characterized, the mechanism of modulation of the AMPA subtype is much less known. Here we have systematically studied Zn2+ inhibition of AMPARs by varying calcium permeability, auxiliary subunits, and activation levels and show that Zn2+ inhibits AMPARs in an activity-dependent manner, opening up this pathway as a means to pharmacologically modulate the receptors.
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34
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Non-Coding RNA Editing in Cancer Pathogenesis. Cancers (Basel) 2020; 12:cancers12071845. [PMID: 32650588 PMCID: PMC7408896 DOI: 10.3390/cancers12071845] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
In the last two decades, RNA post-transcriptional modifications, including RNA editing, have been the subject of increasing interest among the scientific community. The efforts of the Human Genome Project combined with the development of new sequencing technologies and dedicated bioinformatic approaches created to detect and profile RNA transcripts have served to further our understanding of RNA editing. Investigators have determined that non-coding RNA (ncRNA) A-to-I editing is often deregulated in cancer. This discovery has led to an increased number of published studies in the field. However, the eventual clinical application for these findings remains a work in progress. In this review, we provide an overview of the ncRNA editing phenomenon in cancer. We discuss the bioinformatic strategies for RNA editing detection as well as the potential roles for ncRNA A to I editing in tumor immunity and as clinical biomarkers.
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35
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Charsouei S, Jabalameli MR, Karimi-Moghadam A. Molecular insights into the role of AMPA receptors in the synaptic plasticity, pathogenesis and treatment of epilepsy: therapeutic potentials of perampanel and antisense oligonucleotide (ASO) technology. Acta Neurol Belg 2020; 120:531-544. [PMID: 32152997 DOI: 10.1007/s13760-020-01318-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Accepted: 02/27/2020] [Indexed: 02/07/2023]
Abstract
Glutamate is considered as the predominant excitatory neurotransmitter in the mammalian central nervous systems (CNS). Alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) are the main glutamate-gated ionotropic channels that mediate the majority of fast synaptic excitation in the brain. AMPARs are highly dynamic that constitutively move into and out of the postsynaptic membrane. Changes in the postsynaptic number of AMPARs play a key role in controlling synaptic plasticity and also brain functions such as memory formation and forgetting development. Impairments in the regulation of AMPAR function, trafficking, and signaling pathway may also contribute to neuronal hyperexcitability and epileptogenesis process, which offers AMPAR as a potential target for epilepsy therapy. Over the last decade, various types of AMPAR antagonists such as perampanel and talampanel have been developed to treat epilepsy, but they usually show limited efficacy at low doses and produce unwanted cognitive and motor side effects when administered at higher doses. In the present article, the latest findings in the field of molecular mechanisms controlling AMPAR biology, as well as the role of these mechanism dysfunctions in generating epilepsy will be reviewed. Also, a comprehensive summary of recent findings from clinical trials with perampanel, in treating epilepsy, glioma-associated epilepsy and Parkinson's disease is provided. Finally, antisense oligonucleotide therapy as an alternative strategy for the efficient treatment of epilepsy is discussed.
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Affiliation(s)
- Saeid Charsouei
- Department of Neurology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, IR, Iran
| | - M Reza Jabalameli
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Amin Karimi-Moghadam
- Division of Genetics, Department of Biology, Faculty of Science, University of Isfahan, Isfahan, IR, Iran.
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36
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Han J, An O, Hong H, Chan THM, Song Y, Shen H, Tang SJ, Lin JS, Ng VHE, Tay DJT, Molias FB, Pitcheshwar P, Tan HQ, Yang H, Chen L. Suppression of adenosine-to-inosine (A-to-I) RNA editome by death associated protein 3 (DAP3) promotes cancer progression. SCIENCE ADVANCES 2020; 6:eaba5136. [PMID: 32596459 PMCID: PMC7299630 DOI: 10.1126/sciadv.aba5136] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/06/2020] [Indexed: 05/02/2023]
Abstract
RNA editing introduces nucleotide changes in RNA sequences. Recent studies have reported that aberrant A-to-I RNA editing profiles are implicated in cancers. Albeit changes in expression and activity of ADAR genes are thought to have been responsible for the dysregulated RNA editome in diseases, they are not always correlated, indicating the involvement of secondary regulators. Here, we uncover DAP3 as a potent repressor of editing and a strong oncogene in cancer. DAP3 mainly interacts with the deaminase domain of ADAR2 and represses editing via disrupting association of ADAR2 with its target transcripts. PDZD7, an exemplary DAP3-repressed editing target, undergoes a protein recoding editing at stop codon [Stop →Trp (W)]. Because of editing suppression by DAP3, the unedited PDZD7WT, which is more tumorigenic than edited PDZD7Stop518W, is accumulated in tumors. In sum, cancer cells may acquire malignant properties for their survival advantage through suppressing RNA editome by DAP3.
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Affiliation(s)
- Jian Han
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - HuiQi Hong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117549, Singapore
| | - Tim Hon Man Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Haoqing Shen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Sze Jing Tang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Jaymie Siqi Lin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Vanessa Hui En Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Daryl Jin Tai Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Fernando Bellido Molias
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Priyankaa Pitcheshwar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Hui Qing Tan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117549, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
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37
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Jung S, Ballheimer YE, Brackmann F, Zoglauer D, Geppert CI, Hartmann A, Trollmann R. Seizure-induced neuronal apoptosis is related to dysregulation of the RNA-edited GluR2 subunit in the developing mouse brain. Brain Res 2020; 1735:146760. [PMID: 32142720 DOI: 10.1016/j.brainres.2020.146760] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 02/27/2020] [Accepted: 03/02/2020] [Indexed: 12/28/2022]
Abstract
Ca2+-permeable AMPA receptors (AMPAR) which crucially modify maturational programs of the developing brain are involved in seizure-induced glutamate excitotoxicity and apoptosis. Regulatory effects on AMPAR subunit composition and RNA-editing in the developing brain and their significance as therapeutic targets are not well understood. Here, we analyzed acute effects of recurrent pilocarpine-induced neonatal seizures on age- and region-specific expression of AMPAR subunits and adenosine deaminases (ADAR) in the developing mouse brain (P10). After recurrent seizure activity and regeneration periods of 6-72 h cerebral mRNA levels of GluR (glutamate receptor subunit) 1, GluR2, GluR3, and GluR4 were unaffected compared to controls. However, ratio of GluR2 and GluR4 to pooled GluR1-4 mRNA concentration significantly decreased in seizure-exposed brains in comparison to controls. After a regeneration period of 24-72 h ADAR1 and ADAR2 mRNA expression was significantly lower in seizure-exposed brains than in those of controls. This was confirmed at the protein level in the hippocampal CA3 region. We observed a regionally increased apoptosis (TUNEL+ and CC3+ cells) in the hippocampus, parietal cortex and subventricular zone of seizure-exposed brains in comparison to controls. Together, present in vivo data demonstrate the maturational age-specific, functional role of RNA-edited GluR2 in seizure-induced excitotoxicity in the developing mouse brain. In response to recurrent seizure activity, we observed reduced expression of GluR2 and the GluR2 mRNA-editing enzymes ADAR1 and ADAR2 accompanied by increased apoptosis in a region-specific manner. Thus, AMPA receptor subtype-specific mRNA editing is assessed as a promising target of novel neuroprotective treatment strategies in consideration of age-related developmental mechanisms.
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Affiliation(s)
- Susan Jung
- Department of Pediatrics, Division of Neuropediatrics, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Yili E Ballheimer
- Department of Pediatrics, Division of Neuropediatrics, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Florian Brackmann
- Department of Pediatrics, Division of Neuropediatrics, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Daniel Zoglauer
- Department of Pediatrics, Division of Neuropediatrics, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Carol-Immanuel Geppert
- Institute of Pathology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Regina Trollmann
- Department of Pediatrics, Division of Neuropediatrics, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.
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38
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Konen LM, Wright AL, Royle GA, Morris GP, Lau BK, Seow PW, Zinn R, Milham LT, Vaughan CW, Vissel B. A new mouse line with reduced GluA2 Q/R site RNA editing exhibits loss of dendritic spines, hippocampal CA1-neuron loss, learning and memory impairments and NMDA receptor-independent seizure vulnerability. Mol Brain 2020; 13:27. [PMID: 32102661 PMCID: PMC7045468 DOI: 10.1186/s13041-020-0545-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/05/2020] [Indexed: 11/18/2022] Open
Abstract
Calcium (Ca2+)-permeable AMPA receptors may, in certain circumstances, contribute to normal synaptic plasticity or to neurodegeneration. AMPA receptors are Ca2+-permeable if they lack the GluA2 subunit or if GluA2 is unedited at a single nucleic acid, known as the Q/R site. In this study, we examined mice engineered with a point mutation in the intronic editing complementary sequence (ECS) of the GluA2 gene, Gria2. Mice heterozygous for the ECS mutation (named GluA2+/ECS(G)) had a ~ 20% reduction in GluA2 RNA editing at the Q/R site. We conducted an initial phenotypic analysis of these mice, finding altered current-voltage relations (confirming expression of Ca2+-permeable AMPA receptors at the synapse). Anatomically, we observed a loss of hippocampal CA1 neurons, altered dendritic morphology and reductions in CA1 pyramidal cell spine density. Behaviourally, GluA2+/ECS(G) mice exhibited reduced motor coordination, and learning and memory impairments. Notably, the mice also exhibited both NMDA receptor-independent long-term potentiation (LTP) and vulnerability to NMDA receptor-independent seizures. These NMDA receptor-independent seizures were rescued by the Ca2+-permeable AMPA receptor antagonist IEM-1460. In summary, unedited GluA2(Q) may have the potential to drive NMDA receptor-independent processes in brain function and disease. Our study provides an initial characterisation of a new mouse model for studying the role of unedited GluA2(Q) in synaptic and dendritic spine plasticity in disorders where unedited GluA2(Q), synapse loss, neurodegeneration, behavioural impairments and/or seizures are observed, such as ischemia, seizures and epilepsy, Huntington’s disease, amyotrophic lateral sclerosis, astrocytoma, cocaine seeking behaviour and Alzheimer’s disease.
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Affiliation(s)
- Lyndsey M Konen
- Centre for Neuroscience and Regenerative Medicine (CNRM), Faculty of Science, University of Technology Sydney, PO Box 123 Broadway, Sydney, NSW, 2007, Australia.,St Vincent's Centre for Applied Medical Research, Sydney, 2011, Australia
| | - Amanda L Wright
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Gordon A Royle
- Middlemore Hospital, Counties Manukau DHB, Otahuhu, Auckland, 1062, New Zealand.,The University of Auckland, Faculty of Medical and Health Sciences, School of Medicine, Grafton, Auckland, 1023, New Zealand
| | - Gary P Morris
- Centre for Neuroscience and Regenerative Medicine (CNRM), Faculty of Science, University of Technology Sydney, PO Box 123 Broadway, Sydney, NSW, 2007, Australia.,St Vincent's Centre for Applied Medical Research, Sydney, 2011, Australia
| | - Benjamin K Lau
- Kolling Institute of Medical Research, Royal North Shore Hospital, The University of Sydney, Sydney, 2065, Australia
| | - Patrick W Seow
- Kolling Institute of Medical Research, Royal North Shore Hospital, The University of Sydney, Sydney, 2065, Australia
| | - Raphael Zinn
- Centre for Neuroscience and Regenerative Medicine (CNRM), Faculty of Science, University of Technology Sydney, PO Box 123 Broadway, Sydney, NSW, 2007, Australia.,St Vincent's Centre for Applied Medical Research, Sydney, 2011, Australia
| | - Luke T Milham
- Centre for Neuroscience and Regenerative Medicine (CNRM), Faculty of Science, University of Technology Sydney, PO Box 123 Broadway, Sydney, NSW, 2007, Australia.,St Vincent's Centre for Applied Medical Research, Sydney, 2011, Australia
| | - Christopher W Vaughan
- Kolling Institute of Medical Research, Royal North Shore Hospital, The University of Sydney, Sydney, 2065, Australia
| | - Bryce Vissel
- Centre for Neuroscience and Regenerative Medicine (CNRM), Faculty of Science, University of Technology Sydney, PO Box 123 Broadway, Sydney, NSW, 2007, Australia. .,St Vincent's Centre for Applied Medical Research, Sydney, 2011, Australia.
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39
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Vargas EJM, Matamoros AJ, Qiu J, Jan CH, Wang Q, Gorczyca D, Han TW, Weissman JS, Jan YN, Banerjee S, Song Y. The microtubule regulator ringer functions downstream from the RNA repair/splicing pathway to promote axon regeneration. Genes Dev 2020; 34:194-208. [PMID: 31919191 PMCID: PMC7000917 DOI: 10.1101/gad.331330.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/10/2019] [Indexed: 12/17/2022]
Abstract
In this study, Vargas et al. set out to elucidate the downstream effectors of the Rtca-mediated RNA repair/splicing pathway. Using genome-wide transcriptome analysis, the authors demonstrate that the microtubule-associated protein (MAP) tubulin polymerization-promoting protein (TPPP) ringer functions downstream from and is suppressed by Rtca via Xbp1-dependent transcription. Ringer cell-autonomously promotes axon regeneration in the peripheral and central nervous system. Promoting axon regeneration in the central and peripheral nervous system is of clinical importance in neural injury and neurodegenerative diseases. Both pro- and antiregeneration factors are being identified. We previously reported that the Rtca mediated RNA repair/splicing pathway restricts axon regeneration by inhibiting the nonconventional splicing of Xbp1 mRNA under cellular stress. However, the downstream effectors remain unknown. Here, through transcriptome profiling, we show that the tubulin polymerization-promoting protein (TPPP) ringmaker/ringer is dramatically increased in Rtca-deficient Drosophila sensory neurons, which is dependent on Xbp1. Ringer is expressed in sensory neurons before and after injury, and is cell-autonomously required for axon regeneration. While loss of ringer abolishes the regeneration enhancement in Rtca mutants, its overexpression is sufficient to promote regeneration both in the peripheral and central nervous system. Ringer maintains microtubule stability/dynamics with the microtubule-associated protein futsch/MAP1B, which is also required for axon regeneration. Furthermore, ringer lies downstream from and is negatively regulated by the microtubule-associated deacetylase HDAC6, which functions as a regeneration inhibitor. Taken together, our findings suggest that ringer acts as a hub for microtubule regulators that relays cellular status information, such as cellular stress, to the integrity of microtubules in order to instruct neuroregeneration.
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Affiliation(s)
- Ernest J Monahan Vargas
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Andrew J Matamoros
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jingyun Qiu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Calvin H Jan
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94158, USA.,Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94158, USA
| | - Qin Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - David Gorczyca
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94158, USA.,Department of Physiology, University of California at San Francisco, San Francisco, California 94158, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Tina W Han
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94158, USA.,Department of Physiology, University of California at San Francisco, San Francisco, California 94158, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94158, USA.,Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94158, USA
| | - Yuh Nung Jan
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, California 94158, USA.,Department of Physiology, University of California at San Francisco, San Francisco, California 94158, USA.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Swati Banerjee
- Department of Cellular and Integrative Physiology, Long School of Medicine, University of Texas Health Science Center, San Antonio, Texas 78229, USA
| | - Yuanquan Song
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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40
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Huang H, Kapeli K, Jin W, Wong YP, Arumugam TV, Koh JH, Srimasorn S, Mallilankaraman K, Chua JJE, Yeo GW, Soong TW. Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9. Nucleic Acids Res 2019; 46:7323-7338. [PMID: 29733375 PMCID: PMC6101491 DOI: 10.1093/nar/gky348] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/30/2018] [Indexed: 12/31/2022] Open
Abstract
Adenosine DeAminases acting on RNA (ADAR) catalyzes adenosine-to-inosine (A-to-I) conversion within RNA duplex structures. While A-to-I editing is often dynamically regulated in a spatial-temporal manner, the mechanisms underlying its tissue-selective restriction remain elusive. We have previously reported that transcripts of voltage-gated calcium channel CaV1.3 are subject to brain-selective A-to-I RNA editing by ADAR2. Here, we show that editing of CaV1.3 mRNA is dependent on a 40 bp RNA duplex formed between exon 41 and an evolutionarily conserved editing site complementary sequence (ECS) located within the preceding intron. Heterologous expression of a mouse minigene that contained the ECS, intermediate intronic sequence and exon 41 with ADAR2 yielded robust editing. Interestingly, editing of CaV1.3 was potently inhibited by serine/arginine-rich splicing factor 9 (SRSF9). Mechanistically, the inhibitory effect of SRSF9 required direct RNA interaction. Selective down-regulation of SRSF9 in neurons provides a basis for the neuron-specific editing of CaV1.3 transcripts.
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Affiliation(s)
- Hua Huang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.,Neurobiology/Ageing Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Katannya Kapeli
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Wenhao Jin
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Yuk Peng Wong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.,Neurobiology/Ageing Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
| | - Thiruma Valavan Arumugam
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Joanne Huifen Koh
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Sumitra Srimasorn
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Karthik Mallilankaraman
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - John Jia En Chua
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.,Neurobiology/Ageing Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Gene W Yeo
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.,Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, USA.,Molecular Engineering Laboratory, A*STAR, Singapore, Singapore
| | - Tuck Wah Soong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.,Neurobiology/Ageing Programme, Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore
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Cesarini V, Silvestris DA, Tassinari V, Tomaselli S, Alon S, Eisenberg E, Locatelli F, Gallo A. ADAR2/miR-589-3p axis controls glioblastoma cell migration/invasion. Nucleic Acids Res 2019; 46:2045-2059. [PMID: 29267965 PMCID: PMC5829642 DOI: 10.1093/nar/gkx1257] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/05/2017] [Indexed: 12/26/2022] Open
Abstract
Recent studies have reported the emerging role of microRNAs (miRNAs) in human cancers. We systematically characterized miRNA expression and editing in the human brain, which displays the highest number of A-to-I RNA editing sites among human tissues, and in de novo glioblastoma brain cancer. We identified 299 miRNAs altered in their expression and 24 miRNAs differently edited in human brain compared to glioblastoma tissues. We focused on the editing site within the miR-589–3p seed. MiR-589–3p is a unique miRNA almost fully edited (∼100%) in normal brain and with a consistent editing decrease in glioblastoma. The edited version of miR-589–3p inhibits glioblastoma cell proliferation, migration and invasion, while the unedited version boosts cell proliferation and motility/invasion, thus being a potential cancer-promoting factor. We demonstrated that the editing of this miRNA is mediated by ADAR2, and retargets miR-589–3p from the tumor-suppressor PCDH9 to ADAM12, which codes for the metalloproteinase 12 promoting glioblastoma invasion. Overall, our study dissects the role of a unique brain-specific editing site within miR-589–3p, with important anticancer features, and highlights the importance of RNA editing as an essential player not only for diversifying the genomic message but also for correcting not-tolerable/critical genomic coding sites.
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Affiliation(s)
- Valeriana Cesarini
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy
| | - Domenico A Silvestris
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy
| | - Valentina Tassinari
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy
| | - Sara Tomaselli
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy
| | - Shahar Alon
- Media Laboratory and McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Franco Locatelli
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy.,Department of Pediatric Science, University of Pavia, 27100 Pavia, Italy
| | - Angela Gallo
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo, 15, 00146 Rome, Italy
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42
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Shanmugam R, Zhang F, Srinivasan H, Charles Richard JL, Liu KI, Zhang X, Woo CWA, Chua ZHM, Buschdorf JP, Meaney MJ, Tan MH. SRSF9 selectively represses ADAR2-mediated editing of brain-specific sites in primates. Nucleic Acids Res 2019; 46:7379-7395. [PMID: 29992293 PMCID: PMC6101530 DOI: 10.1093/nar/gky615] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 06/26/2018] [Indexed: 02/05/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing displays diverse spatial patterns across different tissues. However, the human genome encodes only two catalytically active editing enzymes (ADAR1 and ADAR2), suggesting that other regulatory factors help shape the editing landscape. Here, we show that the splicing factor SRSF9 selectively controls the editing of many brain-specific sites in primates. SRSF9 is more lowly expressed in the brain than in non-brain tissues. Gene perturbation experiments and minigene analysis of candidate sites demonstrated that SRSF9 could robustly repress A-to-I editing by ADAR2. We found that SRSF9 biochemically interacted with ADAR2 in the nucleus via its RRM2 domain. This interaction required the presence of the RNA substrate and disrupted the formation of ADAR2 dimers. Transcriptome-wide location analysis and RNA sequencing revealed 1328 editing sites that are controlled directly by SRSF9. This regulon is significantly enriched for brain-specific sites. We further uncovered a novel motif in the ADAR2-dependent SRSF9 binding sites and provided evidence that the splicing factor prevents loss of cell viability by inhibiting ADAR2-mediated editing of genes involved in proteostasis, energy metabolism, the cell cycle and DNA repair. Collectively, our results highlight the importance of SRSF9 as an editing regulator and suggest potential roles for other splicing factors.
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Affiliation(s)
- Raghuvaran Shanmugam
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore.,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Fan Zhang
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Harini Srinivasan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore.,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | | | - Kaiwen I Liu
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Xiujun Zhang
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore.,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Cheok Wei A Woo
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
| | - Zi Hao M Chua
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore.,School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore 599489, Singapore
| | - Jan Paul Buschdorf
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore 117609, Singapore
| | - Michael J Meaney
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore 117609, Singapore.,Douglas Mental Health University Institute, McGill University, Montreal (Quebec) H4H 1R3, Canada
| | - Meng How Tan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637459, Singapore.,Genome Institute of Singapore, Agency for Science Technology and Research, Singapore 138672, Singapore
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43
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Jiang W, Tian X, Yang P, Li J, Xiao L, Liu J, Liu C, Tan W, Tu H. Enolase1 Alleviates Cerebral Ischemia-Induced Neuronal Injury via Its Enzymatic Product Phosphoenolpyruvate. ACS Chem Neurosci 2019; 10:2877-2889. [PMID: 30943007 DOI: 10.1021/acschemneuro.9b00103] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Stroke is a leading cause of disability and the second leading cause of death among adults worldwide, while the mechanisms underlying neuronal death and dysfunction remain poorly understood. Here, we investigated the differential proteomic profiles of mouse brain homogenate with 3 h of middle cerebral artery occlusion (MCAO) ischemia, or sham, using Coomassie Brilliant Blue staining, followed by mass spectrometry. We identified enolase1 (ENO1), a key glycolytic enzyme, as a potential mediator of neuronal injury in MCAO ischemic model. Reverse transcription polymerase chain reaction and western blotting data showed that ENO1 was ubiquitously expressed in various tissues, distinct regions of brain, and different postnatal age. Immunohistochemical analysis revealed that ENO1 is localized in neuronal cytoplasm and dendrites. Interestingly, the expression level of ENO1 was significantly increased in the early stage, but dramatically decreased in the late stage, of cerebral ischemia in vivo. This dynamic change was consistent with our finding in cultured hippocampal neurons treated with oxygen/glucose deprivation (OGD) in vitro. Importantly, ENO1 overexpression in cultured neurons alleviated dendritic and spinal loss caused by OGD treatment. Furthermore, the enzymatic product of ENO1, phosphoenolpyruvate (PEP), was also synchronously changed along with the dynamic ENO1 level. The neuronal injury caused by OGD treatment in vitro or ischemia in vivo was mitigated by the application of PEP. Taken together, our data revealed that ENO1 plays a novel and protective role in cerebral ischemia-induced neuronal injury, highlighting a potential of ENO1 as a therapeutic target of neuronal protection from cerebral ischemia.
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Affiliation(s)
| | | | | | | | | | | | | | - Weihong Tan
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute University of Florida, Gainesville, Florida 32611, United States
| | - Haijun Tu
- Shenzhen Research Institute, Hunan University, Shenzhen, Guangdong 518000, China
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44
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Liu C, Jiang W, Tian X, Yang P, Xiao L, Li J, Qiu L, Tu H, Tan W. Identification of Vigilin as a Potential Ischemia Biomarker by Brain Slice-Based Systematic Evolution of Ligands by Exponential Enrichment. Anal Chem 2019; 91:6675-6681. [PMID: 30993971 PMCID: PMC6625766 DOI: 10.1021/acs.analchem.9b00609] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Stroke is one of the leading causes of disability and death among adults worldwide and results in numerous biochemical alterations. However, few efficient biomarkers are clinically available to diagnose stroke because of the limitations of biomarkers and their probes. In this work, we utilized frozen brain slices of middle cerebral artery occlusion (MCAO) in a mouse model of ischemia to select a specific binding aptamer, termed LCW17, by tissue-based SELEX (systematic evolution of ligands by exponential enrichment). LCW17 was enhanced in binding in ischemic brain slices compared to sham control. We identified the binding target of LCW17 as vigilin. Vigilin is increased in ischemia brain slices and exhibits enhanced release from cultured hippocampal neurons after oxygen glucose deprivation in vitro. Taken together, ischemic brain slice-based aptamer selection will enable identification of more probes and potential target molecules for diagnosis and therapy of ischemic stroke. Aptamer LCW17 and vigilin may potentially be applied to define the molecular mechanism underlying ischemic stroke, as well as its diagnosis.
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Affiliation(s)
- Chao Liu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
| | - Wei Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
| | - Xibin Tian
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
| | - Peng Yang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
| | - Le Xiao
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
| | - Jianglin Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
| | - Haijun Tu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University Changsha, Hunan, 410082, China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611, United States
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45
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Harries LW. RNA Biology Provides New Therapeutic Targets for Human Disease. Front Genet 2019; 10:205. [PMID: 30906315 PMCID: PMC6418379 DOI: 10.3389/fgene.2019.00205] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 02/26/2019] [Indexed: 12/11/2022] Open
Abstract
RNA is the messenger molecule that conveys information from the genome and allows the production of biomolecules required for life in a responsive and regulated way. Most genes are able to produce multiple mRNA products in response to different internal or external environmental signals, in different tissues and organs, and at specific times in development or later life. This fine tuning of gene expression is dependent on the coordinated effects of a large and intricate set of regulatory machinery, which together orchestrate the genomic output at each locus and ensure that each gene is expressed at the right amount, at the right time and in the correct location. This complexity of control, and the requirement for both sequence elements and the entities that bind them, results in multiple points at which errors may occur. Errors of RNA biology are common and found in association with both rare, single gene disorders, but also more common, chronic diseases. Fortunately, complexity also brings opportunity. The existence of many regulatory steps also offers multiple levels of potential therapeutic intervention which can be exploited. In this review, I will outline the specific points at which coding RNAs may be regulated, indicate potential means of intervention at each stage, and outline with examples some of the progress that has been made in this area. Finally, I will outline some of the remaining challenges with the delivery of RNA-based therapeutics but indicate why there are reasons for optimism.
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Affiliation(s)
- Lorna W. Harries
- RNA-Mediated Mechanisms of Disease, College of Medicine and Health, The Institute of Biomedical and Clinical Science, Medical School, University of Exeter, Exeter, United Kingdom
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46
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Sinigaglia K, Wiatrek D, Khan A, Michalik D, Sambrani N, Sedmík J, Vukić D, O'Connell MA, Keegan LP. ADAR RNA editing in innate immune response phasing, in circadian clocks and in sleep. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:356-369. [DOI: 10.1016/j.bbagrm.2018.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 10/12/2018] [Accepted: 10/27/2018] [Indexed: 01/24/2023]
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47
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Danesi C, Keinänen K, Castrén ML. Dysregulated Ca 2+-Permeable AMPA Receptor Signaling in Neural Progenitors Modeling Fragile X Syndrome. Front Synaptic Neurosci 2019; 11:2. [PMID: 30800064 PMCID: PMC6375879 DOI: 10.3389/fnsyn.2019.00002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/23/2019] [Indexed: 12/11/2022] Open
Abstract
Fragile X syndrome (FXS) is a neurodevelopmental disorder that represents a common cause of intellectual disability and is a variant of autism spectrum disorder (ASD). Studies that have searched for similarities in syndromic and non-syndromic forms of ASD have paid special attention to alterations of maturation and function of glutamatergic synapses. Copy number variations (CNVs) in the loci containing genes encoding alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptors (AMPARs) subunits are associated with ASD in genetic studies. In FXS, dysregulated AMPAR subunit expression and trafficking affect neural progenitor differentiation and synapse formation and neuronal plasticity in the mature brain. Decreased expression of GluA2, the AMPAR subunit that critically controls Ca2+-permeability, and a concomitant increase in Ca2+-permeable AMPARs (CP-AMPARs) in human and mouse FXS neural progenitors parallels changes in expression of GluA2-targeting microRNAs (miRNAs). Thus, posttranscriptional regulation of GluA2 by miRNAs and subsequent alterations in calcium signaling may contribute to abnormal synaptic function in FXS and, by implication, in some forms of ASD.
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Affiliation(s)
- Claudia Danesi
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kari Keinänen
- Research Program in Molecular and Integrative Biosciences, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Maija L Castrén
- Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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48
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Abstract
Noncoding RNAs (ncRNAs) have received much attention due to their central role in gene expression and translational regulation as well as due to their involvement in several biological processes and disease development. Small noncoding RNAs (sncRNAs), such as microRNAs and piwiRNAs, have been thoroughly investigated and functionally characterized. Long noncoding RNAs (lncRNAs), known to play an important role in chromatin-interacting transcription regulation, posttranscriptional regulation, cell-to-cell signaling, and protein regulation, are also being investigated to further elucidate their functional roles.Next-generation sequencing (NGS) technologies have greatly aided in characterizing the ncRNAome. Moreover, the coupling of NGS technology together with bioinformatics tools has been essential to the genome-wide detection of RNA modifications in ncRNAs. RNA editing, a common human co-transcriptional and posttranscriptional modification, is a dynamic biological phenomenon able to alter the sequence and the structure of primary transcripts (both coding and noncoding RNAs) during the maturation process, consequently influencing the biogenesis, as well as the function, of ncRNAs. In particular, the dysregulation of the RNA editing machineries have been associated with the onset of human diseases.In this chapter we discuss the potential functions of ncRNA editing and describe the knowledge base and bioinformatics resources available to investigate such phenomenon.
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49
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Gurung S, Evans AJ, Wilkinson KA, Henley JM. ADAR2-mediated Q/R editing of GluK2 regulates kainate receptor upscaling in response to suppression of synaptic activity. J Cell Sci 2018; 131:jcs222273. [PMID: 30559217 PMCID: PMC6307878 DOI: 10.1242/jcs.222273] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/19/2018] [Indexed: 12/29/2022] Open
Abstract
Kainate receptors (KARs) regulate neuronal excitability and network function. Most KARs contain the subunit GluK2 (also known as GRIK2), and the properties of these receptors are determined in part by ADAR2 (also known as ADARB1)-mediated mRNA editing of GluK2, which changes a genomically encoded glutamine residue into an arginine residue (Q/R editing). Suppression of synaptic activity reduces ADAR2-dependent Q/R editing of GluK2 with a consequential increase in GluK2-containing KAR surface expression. However, the mechanism underlying this reduction in GluK2 editing has not been addressed. Here, we show that induction of KAR upscaling, a phenomenon in which surface expression of receptors is increased in response to a chronic decrease in synaptic activity, results in proteasomal degradation of ADAR2, which reduces GluK2 Q/R editing. Because KARs incorporating unedited GluK2(Q) assemble and exit the ER more efficiently, this leads to an upscaling of KAR surface expression. Consistent with this, we demonstrate that partial ADAR2 knockdown phenocopies and occludes KAR upscaling. Moreover, we show that although the AMPA receptor (AMPAR) subunit GluA2 (also known as GRIA2) also undergoes ADAR2-dependent Q/R editing, this process does not mediate AMPAR upscaling. These data demonstrate that activity-dependent regulation of ADAR2 proteostasis and GluK2 Q/R editing are key determinants of KAR, but not AMPAR, trafficking and upscaling.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Sonam Gurung
- School of Biochemistry, Centre for Synaptic Plasticity, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Ashley J Evans
- School of Biochemistry, Centre for Synaptic Plasticity, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Kevin A Wilkinson
- School of Biochemistry, Centre for Synaptic Plasticity, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Jeremy M Henley
- School of Biochemistry, Centre for Synaptic Plasticity, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
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50
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Palumbo CM, Beal PA. Nucleoside analogs in the study of the epitranscriptome. Methods 2018; 156:46-52. [PMID: 30827466 DOI: 10.1016/j.ymeth.2018.10.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 09/27/2018] [Accepted: 10/13/2018] [Indexed: 01/15/2023] Open
Abstract
Over 150 unique RNA modifications are now known including several nonstandard nucleotides present in the body of messenger RNAs. These modifications can alter a transcript's function and are collectively referred to as the epitrancriptome. Chemically modified nucleoside analogs are poised to play an important role in the study of these epitranscriptomic marks. Introduced chemical features on nucleic acid strands provide unique structures or reactivity that can be used for downstream detection or quantification. Three methods are used in the field to synthesize RNA containing chemically modified nucleoside analogs. Nucleoside analogs can be introduced by metabolic labeling, via polymerases with modified nucleotide triphosphates or via phosphoramidite-based chemical synthesis. In this review, these methods for incorporation of nucleoside analogs will be discussed with specific recently published examples pertaining to the study of the epitranscriptome.
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Affiliation(s)
- Cody M Palumbo
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA
| | - Peter A Beal
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA.
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