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Piazzi M, Bavelloni A, Salucci S, Faenza I, Blalock WL. Alternative Splicing, RNA Editing, and the Current Limits of Next Generation Sequencing. Genes (Basel) 2023; 14:1386. [PMID: 37510291 PMCID: PMC10379330 DOI: 10.3390/genes14071386] [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: 06/08/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
The advent of next generation sequencing (NGS) has fostered a shift in basic analytic strategies of a gene expression analysis in diverse pathologies for the purposes of research, pharmacology, and personalized medicine. What was once highly focused research on individual signaling pathways or pathway members has, from the time of gene expression arrays, become a global analysis of gene expression that has aided in identifying novel pathway interactions, the discovery of new therapeutic targets, and the establishment of disease-associated profiles for assessing progression, stratification, or a therapeutic response. But there are significant caveats to this analysis that do not allow for the construction of the full picture. The lack of timely updates to publicly available databases and the "hit and miss" deposition of scientific data to these databases relegate a large amount of potentially important data to "garbage", begging the question, "how much are we really missing?" This brief perspective aims to highlight some of the limitations that RNA binding/modifying proteins and RNA processing impose on our current usage of NGS technologies as relating to cancer and how not fully appreciating the limitations of current NGS technology may negatively affect therapeutic strategies in the long run.
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Affiliation(s)
- Manuela Piazzi
- "Luigi Luca Cavalli-Sforza" Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 40136 Bologna, Italy
- IRCCS, Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Alberto Bavelloni
- Laboratorio di Oncologia Sperimentale, IRCCS, Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Sara Salucci
- Dipartimento di Scienze Biomediche e Neuromotorie (DIBINEM), Università di Bologna, 40126 Bologna, Italy
| | - Irene Faenza
- Dipartimento di Scienze Biomediche e Neuromotorie (DIBINEM), Università di Bologna, 40126 Bologna, Italy
| | - William L Blalock
- "Luigi Luca Cavalli-Sforza" Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 40136 Bologna, Italy
- IRCCS, Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
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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: 7] [Impact Index Per Article: 3.5] [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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Chaytow H, Sethw Hassan I, Akbar S, Popplewell L, Dickson G, Chen PE. A new strategy to increase RNA editing at the Q/R site of GluA2 AMPA receptor subunits by targeting alternative splicing patterns of ADAR2. J Neurosci Methods 2021; 364:109357. [PMID: 34536489 PMCID: PMC8573265 DOI: 10.1016/j.jneumeth.2021.109357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 08/25/2021] [Accepted: 09/09/2021] [Indexed: 11/27/2022]
Abstract
Background The GluA2 subunit of AMPA receptors (AMPARs) undergoes RNA editing at a specific base mediated by the enzyme ADAR2, changing the coded amino acid from a glutamine to arginine at the so-called Q/R site, which is critical for regulating calcium permeability. ADAR2 exists as multiple alternatively-spliced variants within mammalian cells with differing editing efficiency. New method In this study, phosphorodiamidate morpholino oligomers (PMOs) were used to increase Q/R site editing, by affecting the alternative splicing of ADAR2. Results PMOs targeting the ADAR2 pre-mRNA transcript successfully induced alternative splicing around the AluJ cassette leading to expression of a more active isoform with increased editing of the GluA2 subunit compared to control. Comparison with existing method(s) Previously PMOs have been used to disrupt RNA editing via steric hindrance of the GluA2 RNA duplex. In contrast we report PMOs that can increase the expression of more catalytically active variants of ADAR2, leading to enhanced GluA2 Q/R RNA editing. Conclusions Using PMOs to increase Q/R site editing is presented here as a validated method that would allow investigation of downstream cellular processes implicated in altered ADAR2 activity. Aberrant RNA editing has been linked to a number of neurodegenerative diseases. Phosphorodiamidate morpholino oligomers (PMOs) were targeted to ADAR2 pre-mRNA. These PMOs increased expression of ADAR2 isoforms with higher editing efficiency. These PMOs significantly increased Q/R editing in HeLa and SH-SY5Y cell lines.
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Affiliation(s)
- Helena Chaytow
- Centres of Gene and Cell Therapy and Biomedical Sciences, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - Ilda Sethw Hassan
- Centres of Gene and Cell Therapy and Biomedical Sciences, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - Sara Akbar
- Centres of Gene and Cell Therapy and Biomedical Sciences, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - Linda Popplewell
- Centres of Gene and Cell Therapy and Biomedical Sciences, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - George Dickson
- Centres of Gene and Cell Therapy and Biomedical Sciences, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
| | - Philip E Chen
- Centres of Gene and Cell Therapy and Biomedical Sciences, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK.
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Barbon A, Magri C. RNA Editing and Modifications in Mood Disorders. Genes (Basel) 2020; 11:genes11080872. [PMID: 32752036 PMCID: PMC7464464 DOI: 10.3390/genes11080872] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/23/2020] [Accepted: 07/30/2020] [Indexed: 12/18/2022] Open
Abstract
Major depressive disorder (MDD) is a major health problem with significant limitations in functioning and well-being. The World Health Organization (WHO) evaluates MDD as one of the most disabling disorders in the world and with very high social cost. Great attention has been given to the study of the molecular mechanism underpinning MDD at the genetic, epigenetic and proteomic level. However, the importance of RNA modifications has attracted little attention until now in this field. RNA molecules are extensively and dynamically altered by a variety of mechanisms. Similar to "epigenomic" changes, which modify DNA structure or histones, RNA alterations are now termed "epitranscriptomic" changes and have been predicted to have profound consequences for gene expression and cellular functionality. Two of these modifications, adenosine to inosine (A-to-I) RNA editing and m6A methylations, have fascinated researchers over the last years, showing a new level of complexity in gene expression. In this review, we will summary the studies that focus on the role of RNA editing and m6A methylation in MDD, trying to underline their potential breakthroughs and pitfalls.
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Piazzi M, Bavelloni A, Faenza I, Blalock W. Glycogen synthase kinase (GSK)-3 and the double-strand RNA-dependent kinase, PKR: When two kinases for the common good turn bad. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118769. [PMID: 32512016 PMCID: PMC7273171 DOI: 10.1016/j.bbamcr.2020.118769] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 01/08/2023]
Abstract
Glycogen synthase kinase (GSK)-3α/β and the double-stranded RNA-dependent kinase PKR are two sentinel kinases that carry-out multiple similar yet distinct functions in both the cytosol and the nucleus. While these kinases belong to separate signal transduction cascades, they demonstrate an uncanny propensity to regulate many of the same proteins either through direct phosphorylation or by altering transcription/translation, including: c-MYC, NF-κB, p53 and TAU, as well as each another. A significant number of studies centered on the GSK3 kinases have led to the identification of the GSK3 interactome and a number of substrates, which link GSK3 activity to metabolic control, translation, RNA splicing, ribosome biogenesis, cellular division, DNA repair and stress/inflammatory signaling. Interestingly, many of these same pathways and processes are controlled by PKR, but unlike the GSK3 kinases, a clear picture of proteins interacting with PKR and a complete listing of its substrates is still missing. In this review, we take a detailed look at what is known about the PKR and GSK3 kinases, how these kinases interact to influence common cellular processes (innate immunity, alternative splicing, translation, glucose metabolism) and how aberrant activation of these kinases leads to diseases such as Alzheimer's disease (AD), diabetes mellitus (DM) and cancer. GSK3α/β and PKR are major regulators of cellular homeostasis and the response to stress/inflammation and infection. GSK3α/β and PKR interact with and/or modify many of the same proteins and affect the expression of similar genes. A balance between AKT and PKR nuclear signaling may be responsible for regulating the activation of nuclear GSK3β. GSK3α/β- and PKR-dependent signaling influence major molecular mechanisms of the cell through similar intermediates. Aberrant activation of GSK3α/β and PKR is highly involved in cancer, metabolic disorders, and neurodegenerative diseases.
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Affiliation(s)
- Manuela Piazzi
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche (IGM-CNR), Bologna, Italy; IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Alberto Bavelloni
- Laboratoria di Oncologia Sperimentale, IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Irene Faenza
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
| | - William Blalock
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", Consiglio Nazionale delle Ricerche (IGM-CNR), Bologna, Italy; IRCCS, Istituto Ortopedico Rizzoli, Bologna, Italy.
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Tan TY, Sedmík J, Fitzgerald MP, Halevy RS, Keegan LP, Helbig I, Basel-Salmon L, Cohen L, Straussberg R, Chung WK, Helal M, Maroofian R, Houlden H, Juusola J, Sadedin S, Pais L, Howell KB, White SM, Christodoulou J, O'Connell MA. Bi-allelic ADARB1 Variants Associated with Microcephaly, Intellectual Disability, and Seizures. Am J Hum Genet 2020; 106:467-483. [PMID: 32220291 DOI: 10.1016/j.ajhg.2020.02.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/26/2020] [Indexed: 11/15/2022] Open
Abstract
The RNA editing enzyme ADAR2 is essential for the recoding of brain transcripts. Impaired ADAR2 editing leads to early-onset epilepsy and premature death in a mouse model. Here, we report bi-allelic variants in ADARB1, the gene encoding ADAR2, in four unrelated individuals with microcephaly, intellectual disability, and epilepsy. In one individual, a homozygous variant in one of the double-stranded RNA-binding domains (dsRBDs) was identified. In the others, variants were situated in or around the deaminase domain. To evaluate the effects of these variants on ADAR2 enzymatic activity, we performed in vitro assays with recombinant proteins in HEK293T cells and ex vivo assays with fibroblasts derived from one of the individuals. We demonstrate that these ADAR2 variants lead to reduced editing activity on a known ADAR2 substrate. We also demonstrate that one variant leads to changes in splicing of ADARB1 transcript isoforms. These findings reinforce the importance of RNA editing in brain development and introduce ADARB1 as a genetic etiology in individuals with intellectual disability, microcephaly, and epilepsy.
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Affiliation(s)
- Tiong Yang Tan
- Victorian Clinical Genetics Services, Melbourne 3052, Australia; Murdoch Children's Research Institute, Melbourne 3052, Australia; Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia.
| | - Jiří Sedmík
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, A35, Brno 62500, Czech Republic
| | - Mark P Fitzgerald
- Division of Neurology, Departments of Neurology and Pediatrics, The Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Rivka Sukenik Halevy
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petah Tikva 49100, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Liam P Keegan
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, A35, Brno 62500, Czech Republic
| | - Ingo Helbig
- Division of Neurology, Departments of Neurology and Pediatrics, The Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA; The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lina Basel-Salmon
- Raphael Recanati Genetic Institute, Rabin Medical Center-Beilinson Hospital, Petah Tikva 49100, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Felsenstein Medical Research Center, Petah Tikva 49100, Israel
| | - Lior Cohen
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petah Tikva 49100, Israel
| | - Rachel Straussberg
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Pediatric Neurology Unit, Schneider Children's Medical Center of Israel, Petah Tikva 49100, Israel
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Mayada Helal
- Department of Pediatrics, Columbia University Medical Center, New York, NY 10032, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | | | - Simon Sadedin
- Victorian Clinical Genetics Services, Melbourne 3052, Australia; Murdoch Children's Research Institute, Melbourne 3052, Australia
| | - Lynn Pais
- Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Katherine B Howell
- Murdoch Children's Research Institute, Melbourne 3052, Australia; Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia; Department of Neurology, Royal Children's Hospital, Parkville 3052, Australia
| | - Susan M White
- Victorian Clinical Genetics Services, Melbourne 3052, Australia; Murdoch Children's Research Institute, Melbourne 3052, Australia; Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia
| | - John Christodoulou
- Victorian Clinical Genetics Services, Melbourne 3052, Australia; Murdoch Children's Research Institute, Melbourne 3052, Australia; Department of Pediatrics, University of Melbourne, Melbourne 3052, Australia
| | - Mary A O'Connell
- Central European Institute of Technology, Masaryk University, Kamenice 735/5, A35, Brno 62500, Czech Republic.
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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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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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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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