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Schneider N, Steinberg R, Ben-David A, Valensi J, David-Kadoch G, Rosenwasser Z, Banin E, Levanon EY, Sharon D, Ben-Aroya S. A pipeline for identifying guide RNA sequences that promote RNA editing of nonsense mutations that cause inherited retinal diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102130. [PMID: 38375504 PMCID: PMC10875612 DOI: 10.1016/j.omtn.2024.102130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 01/24/2024] [Indexed: 02/21/2024]
Abstract
Adenosine deaminases acting on RNA (ADARs) are endogenous enzymes catalyzing the deamination of adenosines to inosines, which are then read as guanosines during translation. This ability to recode makes ADAR an attractive therapeutic tool to edit genetic mutations and reprogram genetic information at the mRNA level. Using the endogenous ADARs and guiding them to a selected target has promising therapeutic potential. Indeed, different studies have reported several site-directed RNA-editing approaches for making targeted base changes in RNA molecules. The basic strategy has been to use guide RNAs (gRNAs) that hybridize and form a double-stranded RNA (dsRNA) structure with the desired RNA target because of ADAR activity in regions of dsRNA formation. Here we report on a novel pipeline for identifying disease-causing variants as candidates for RNA editing, using a yeast-based screening system to select efficient gRNAs for editing of nonsense mutations, and test them in a human cell line reporter system. We have used this pipeline to modify the sequence of transcripts carrying nonsense mutations that cause inherited retinal diseases in the FAM161A, KIZ, TRPM1, and USH2A genes. Our approach can serve as a basis for gene therapy intervention in knockin mouse models and ultimately in human patients.
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Affiliation(s)
- Nina Schneider
- Division of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Ricky Steinberg
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Room B-840, Ramat Gan 52900, Israel
| | - Amit Ben-David
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Room B-840, Ramat Gan 52900, Israel
| | - Johanna Valensi
- Division of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Galit David-Kadoch
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Room B-840, Ramat Gan 52900, Israel
| | - Zohar Rosenwasser
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Room B-840, Ramat Gan 52900, Israel
| | - Eyal Banin
- Division of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Erez Y. Levanon
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Room B-840, Ramat Gan 52900, Israel
| | - Dror Sharon
- Division of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Shay Ben-Aroya
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Room B-840, Ramat Gan 52900, Israel
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Jacobsen CS, Salvador P, Yung JF, Kragness S, Mendoza HG, Mandel G, Beal PA. Library Screening Reveals Sequence Motifs That Enable ADAR2 Editing at Recalcitrant Sites. ACS Chem Biol 2023; 18:2188-2199. [PMID: 37040436 PMCID: PMC10581013 DOI: 10.1021/acschembio.3c00107] [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] [Indexed: 04/13/2023]
Abstract
Adenosine deaminases acting on RNA (ADARs) catalyze the hydrolytic deamination of adenosine to inosine in duplex RNA. The inosine product preferentially base pairs with cytidine resulting in an effective A-to-G edit in RNA. ADAR editing can result in a recoding event alongside other alterations to RNA function. A consequence of ADARs' selective activity on duplex RNA is that guide RNAs (gRNAs) can be designed to target an adenosine of interest and promote a desired recoding event. One of ADAR's main limitations is its preference to edit adenosines with specific 5' and 3' nearest neighbor nucleotides (e.g., 5' U, 3' G). Current rational design approaches are well-suited for this ideal sequence context, but limited when applied to difficult-to-edit sites. Here we describe a strategy for the in vitro evaluation of very large libraries of ADAR substrates (En Masse Evaluation of RNA Guides, EMERGe). EMERGe allows for a comprehensive screening of ADAR substrate RNAs that complements current design approaches. We used this approach to identify sequence motifs for gRNAs that enable editing in otherwise difficult-to-edit target sites. A guide RNA bearing one of these sequence motifs enabled the cellular repair of a premature termination codon arising from mutation of the MECP2 gene associated with Rett Syndrome. EMERGe provides an advancement in screening that not only allows for novel gRNA design, but also furthers our understanding of ADARs' specific RNA-protein interactions.
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Affiliation(s)
- Casey S. Jacobsen
- Department of Chemistry, University of California, Davis, Davis, CA, USA, 95616
| | - Prince Salvador
- Department of Chemistry, University of California, Davis, Davis, CA, USA, 95616
| | - John F. Yung
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA, 97239
| | - Sabrina Kragness
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA, 97239
| | - Herra G. Mendoza
- Department of Chemistry, University of California, Davis, Davis, CA, USA, 95616
| | - Gail Mandel
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA, 97239
| | - Peter A. Beal
- Department of Chemistry, University of California, Davis, Davis, CA, USA, 95616
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Broni E, Ashley C, Velazquez M, Khan S, Striegel A, Sakyi PO, Peracha S, Bebla K, Sodhi M, Kwofie SK, Ademokunwa A, Miller WA. In Silico Discovery of Potential Inhibitors Targeting the RNA Binding Loop of ADAR2 and 5-HT2CR from Traditional Chinese Natural Compounds. Int J Mol Sci 2023; 24:12612. [PMID: 37628792 PMCID: PMC10454645 DOI: 10.3390/ijms241612612] [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: 07/01/2023] [Revised: 08/02/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
Adenosine deaminase acting on RNA 2 (ADAR2) is an important enzyme involved in RNA editing processes, particularly in the conversion of adenosine to inosine in RNA molecules. Dysregulation of ADAR2 activity has been implicated in various diseases, including neurological disorders (including schizophrenia), inflammatory disorders, viral infections, and cancers. Therefore, targeting ADAR2 with small molecules presents a promising therapeutic strategy for modulating RNA editing and potentially treating associated pathologies. However, there are limited compounds that effectively inhibit ADAR2 reactions. This study therefore employed computational approaches to virtually screen natural compounds from the traditional Chinese medicine (TCM) library. The shortlisted compounds demonstrated a stronger binding affinity to the ADAR2 (<-9.5 kcal/mol) than the known inhibitor, 8-azanebularine (-6.8 kcal/mol). The topmost compounds were also observed to possess high binding affinity towards 5-HT2CR with binding energies ranging from -7.8 to -12.9 kcal/mol. Further subjecting the top ADAR2-ligand complexes to molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations revealed that five potential hit compounds comprising ZINC000014637370, ZINC000085593577, ZINC000042890265, ZINC000039183320, and ZINC000101100339 had favorable binding free energies of -174.911, -137.369, -117.236, -67.023, and -64.913 kJ/mol, respectively, with the human ADAR2 protein. Residues Lys350, Cys377, Glu396, Cys451, Arg455, Ser486, Gln488, and Arg510 were also predicted to be crucial in ligand recognition and binding. This finding will provide valuable insights into the molecular interactions between ADAR2 and small molecules, aiding in the design of future ADAR2 inhibitors with potential therapeutic applications. The potential lead compounds were also profiled to have insignificant toxicities. A structural similarity search via DrugBank revealed that ZINC000039183320 and ZINC000014637370 were similar to naringin and naringenin, which are known adenosine deaminase (ADA) inhibitors. These potential novel ADAR2 inhibitors identified herein may be beneficial in treating several neurological disorders, cancers, viral infections, and inflammatory disorders caused by ADAR2 after experimental validation.
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Affiliation(s)
- Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Carolyn Ashley
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Miriam Velazquez
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Sufia Khan
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
| | - Andrew Striegel
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Chemical and Biochemistry, College of Science, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Patrick O. Sakyi
- Department of Chemistry, School of Physical and Mathematical Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 56, Ghana
- Department of Chemical Sciences, School of Sciences, University of Energy and Natural Resources, Sunyani P.O. Box 214, Ghana
| | - Saqib Peracha
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Kristeen Bebla
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Monsheel Sodhi
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Adesanya Ademokunwa
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Cognitive and Behavioral Neuroscience, Loyola University Chicago, Chicago, IL 60660, USA
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
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Broni E, Striegel A, Ashley C, Sakyi PO, Peracha S, Velazquez M, Bebla K, Sodhi M, Kwofie SK, Ademokunwa A, Khan S, Miller WA. Molecular Docking and Dynamics Simulation Studies Predict Potential Anti-ADAR2 Inhibitors: Implications for the Treatment of Cancer, Neurological, Immunological and Infectious Diseases. Int J Mol Sci 2023; 24:ijms24076795. [PMID: 37047766 PMCID: PMC10095294 DOI: 10.3390/ijms24076795] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023] Open
Abstract
Altered RNA editing has been linked to several neurodevelopmental disorders, including autism spectrum disorder (ASD) and intellectual disability, in addition to depression, schizophrenia, some cancers, viral infections and autoimmune disorders. The human ADAR2 is a potential therapeutic target for managing these various disorders due to its crucial role in adenosine to inosine editing. This study applied consensus scoring to rank potential ADAR2 inhibitors after performing molecular docking with AutoDock Vina and Glide (Maestro), using a library of 35,161 compounds obtained from traditional Chinese medicine. A total of 47 compounds were predicted to be good binders of the human ADAR2 and had insignificant toxicity concerns. Molecular dynamics (MD) simulations, including the molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) procedure, also emphasized the binding of the shortlisted compounds. The potential compounds had plausible binding free energies ranging from −81.304 to −1068.26 kJ/mol from the MM/PBSA calculations. ZINC000085511995, a naphthoquinone had more negative binding free energy (−1068.26 kJ/mol) than inositol hexakisphosphate (IHP) [−873.873 kJ/mol], an agonist and a strong binder of ADAR2. The potential displacement of IHP by ZINC000085511995 in the IHP binding site of ADAR2 could be explored for possible deactivation of ADAR2. Bayesian-based biological activity prediction corroborates the neuropharmacological, antineoplastic and antiviral activity of the potential lead compounds. All the potential lead compounds, except ZINC000014612330 and ZINC000013462928, were predicted to be inhibitors of various deaminases. The potential lead compounds also had probability of activity (Pa) > 0.442 and probability of inactivity (Pi) < 0.116 values for treating acute neurologic disorders, except for ZINC000085996580 and ZINC000013462928. Pursuing these compounds for their anti-ADAR2 activities holds a promising future, especially against neurological disorders, some cancers and viral infections caused by RNA viruses. Molecular interaction, hydrogen bond and per-residue decomposition analyses predicted Arg400, Arg401, Lys519, Trp687, Glu689, and Lys690 as hot-spot residues in the ADAR2 IHP binding site. Most of the top compounds were observed to have naphthoquinone, indole, furanocoumarin or benzofuran moieties. Serotonin and tryptophan, which are beneficial in digestive regulation, improving sleep cycle and mood, are indole derivatives. These chemical series may have the potential to treat neurological disorders, prion diseases, some cancers, specific viral infections, metabolic disorders and eating disorders through the disruption of ADAR2 pathways. A total of nine potential lead compounds were shortlisted as plausible modulators of ADAR2.
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Affiliation(s)
- Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Andrew Striegel
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Chemical and Biochemistry, College of Science, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Carolyn Ashley
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Patrick O. Sakyi
- Department of Chemistry, School of Physical and Mathematical Sciences, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 56, Ghana
- Department of Chemical Sciences, School of Sciences, University of Energy and Natural Resources, Sunyani P.O. Box 214, Ghana
| | - Saqib Peracha
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Miriam Velazquez
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Kristeen Bebla
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Monsheel Sodhi
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Samuel K. Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 77, Ghana
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Adesanya Ademokunwa
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Cognitive and Behavioral Neuroscience, Loyola University Chicago, Chicago, IL 60660, USA
| | - Sufia Khan
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
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Avram-Shperling A, Kopel E, Twersky I, Gabay O, Ben-David A, Karako-Lampert S, Rosenthal JJC, Levanon EY, Eisenberg E, Ben-Aroya S. Identification of exceptionally potent adenosine deaminases RNA editors from high body temperature organisms. PLoS Genet 2023; 19:e1010661. [PMID: 36877730 PMCID: PMC10019624 DOI: 10.1371/journal.pgen.1010661] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 03/16/2023] [Accepted: 02/08/2023] [Indexed: 03/07/2023] Open
Abstract
The most abundant form of RNA editing in metazoa is the deamination of adenosines into inosines (A-to-I), catalyzed by ADAR enzymes. Inosines are read as guanosines by the translation machinery, and thus A-to-I may lead to protein recoding. The ability of ADARs to recode at the mRNA level makes them attractive therapeutic tools. Several approaches for Site-Directed RNA Editing (SDRE) are currently under development. A major challenge in this field is achieving high on-target editing efficiency, and thus it is of much interest to identify highly potent ADARs. To address this, we used the baker yeast Saccharomyces cerevisiae as an editing-naïve system. We exogenously expressed a range of heterologous ADARs and identified the hummingbird and primarily mallard-duck ADARs, which evolved at 40-42°C, as two exceptionally potent editors. ADARs bind to double-stranded RNA structures (dsRNAs), which in turn are temperature sensitive. Our results indicate that species evolved to live with higher core body temperatures have developed ADAR enzymes that target weaker dsRNA structures and would therefore be more effective than other ADARs. Further studies may use this approach to isolate additional ADARs with an editing profile of choice to meet specific requirements, thus broadening the applicability of SDRE.
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Affiliation(s)
- Adi Avram-Shperling
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Kopel
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Itamar Twersky
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Orshay Gabay
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Amit Ben-David
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | | | - Joshua J. C. Rosenthal
- The Eugene Bell Center, The Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - Erez Y. Levanon
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- The Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Eisenberg
- Raymond and Beverly Sackler School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (EE); (SB-A)
| | - Shay Ben-Aroya
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- * E-mail: (EE); (SB-A)
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6
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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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7
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Katrekar D, Xiang Y, Palmer N, Saha A, Meluzzi D, Mali P. Comprehensive interrogation of the ADAR2 deaminase domain for engineering enhanced RNA editing activity and specificity. eLife 2022; 11:75555. [PMID: 35044296 PMCID: PMC8809894 DOI: 10.7554/elife.75555] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 01/18/2022] [Indexed: 11/17/2022] Open
Abstract
Adenosine deaminases acting on RNA (ADARs) can be repurposed to enable programmable RNA editing, however their exogenous delivery leads to transcriptome-wide off-targeting, and additionally, enzymatic activity on certain RNA motifs, especially those flanked by a 5’ guanosine is very low thus limiting their utility as a transcriptome engineering toolset. Towards addressing these issues, we first performed a novel deep mutational scan of the ADAR2 deaminase domain, directly measuring the impact of every amino acid substitution across 261 residues, on RNA editing. This enabled us to create a domain-wide mutagenesis map while also revealing a novel hyperactive variant with improved enzymatic activity at 5’-GAN-3’ motifs. As overexpression of ADAR enzymes, especially hyperactive variants, can lead to significant transcriptome-wide off-targeting, we next engineered a split-ADAR2 deaminase which resulted in >100-fold more specific RNA editing as compared to full-length deaminase overexpression. Taken together, we anticipate this systematic engineering of the ADAR2 deaminase domain will enable broader utility of the ADAR toolset for RNA biotechnology applications.
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Affiliation(s)
| | - Yichen Xiang
- Department of Bioengineering, University of California, San Diego
| | - Nathan Palmer
- Division of Biological Sciences, University of California, San Diego
| | - Anushka Saha
- Department of Bioengineering, University of California, San Diego
| | - Dario Meluzzi
- Department of Bioengineering, University of California, San Diego
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego
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8
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Hanscom M, Loane DJ, Aubretch T, Leser J, Molesworth K, Hedgekar N, Ritzel RM, Abulwerdi G, Shea-Donohue T, Faden AI. Acute colitis during chronic experimental traumatic brain injury in mice induces dysautonomia and persistent extraintestinal, systemic, and CNS inflammation with exacerbated neurological deficits. J Neuroinflammation 2021; 18:24. [PMID: 33461596 PMCID: PMC7814749 DOI: 10.1186/s12974-020-02067-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Disruptions of brain-gut axis have been implicated in the progression of a variety of gastrointestinal (GI) disorders and central nervous system (CNS) diseases and injuries, including traumatic brain injury (TBI). TBI is a chronic disease process characterized by persistent secondary injury processes which can be exacerbated by subsequent challenges. Enteric pathogen infection during chronic TBI worsened cortical lesion volume; however, the pathophysiological mechanisms underlying the damaging effects of enteric challenge during chronic TBI remain unknown. This preclinical study examined the effect of intestinal inflammation during chronic TBI on associated neurobehavioral and neuropathological outcomes, systemic inflammation, and dysautonomia. METHODS Dextran sodium sulfate (DSS) was administered to adult male C57BL/6NCrl mice 28 days following craniotomy (Sham) or TBI for 7 days to induce intestinal inflammation, followed by a return to normal drinking water for an additional 7 to 28 days for recovery; uninjured animals (Naïve) served as an additional control group. Behavioral testing was carried out prior to, during, and following DSS administration to assess changes in motor and cognitive function, social behavior, and mood. Electrocardiography was performed to examine autonomic balance. Brains were collected for histological and molecular analyses of injury lesion, neurodegeneration, and neuroinflammation. Blood, colons, spleens, mesenteric lymph nodes (mLNs), and thymus were collected for morphometric analyses and/or immune characterization by flow cytometry. RESULTS Intestinal inflammation 28 days after craniotomy or TBI persistently induced, or exacerbated, respectively, deficits in fine motor coordination, cognition, social behavior, and anxiety-like behavior. Behavioral changes were associated with an induction, or exacerbation, of hippocampal neuronal cell loss and microglial activation in Sham and TBI mice administered DSS, respectively. Acute DSS administration resulted in a sustained systemic immune response with increases in myeloid cells in blood and spleen, as well as myeloid cells and lymphocytes in mesenteric lymph nodes. Dysautonomia was also induced in Sham and TBI mice administered DSS, with increased sympathetic tone beginning during DSS administration and persisting through the first recovery week. CONCLUSION Intestinal inflammation during chronic experimental TBI causes a sustained systemic immune response and altered autonomic balance that are associated with microglial activation, increased neurodegeneration, and persistent neurological deficits.
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Affiliation(s)
- Marie Hanscom
- Department of Anesthesiology and Shock, Trauma and Anesthesiology Research (STAR) Center, University of Maryland School of Medicine, 685 West Baltimore Street, MSTF #6-016, Baltimore, MD, 21201, USA.
| | - David J Loane
- Department of Anesthesiology and Shock, Trauma and Anesthesiology Research (STAR) Center, University of Maryland School of Medicine, 685 West Baltimore Street, MSTF #6-016, Baltimore, MD, 21201, USA
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College, Dublin, Ireland
| | - Taryn Aubretch
- Department of Anesthesiology and Shock, Trauma and Anesthesiology Research (STAR) Center, University of Maryland School of Medicine, 685 West Baltimore Street, MSTF #6-016, Baltimore, MD, 21201, USA
| | - Jenna Leser
- Department of Anesthesiology and Shock, Trauma and Anesthesiology Research (STAR) Center, University of Maryland School of Medicine, 685 West Baltimore Street, MSTF #6-016, Baltimore, MD, 21201, USA
| | - Kara Molesworth
- Department of Anesthesiology and Shock, Trauma and Anesthesiology Research (STAR) Center, University of Maryland School of Medicine, 685 West Baltimore Street, MSTF #6-016, Baltimore, MD, 21201, USA
| | - Nivedita Hedgekar
- Department of Anesthesiology and Shock, Trauma and Anesthesiology Research (STAR) Center, University of Maryland School of Medicine, 685 West Baltimore Street, MSTF #6-016, Baltimore, MD, 21201, USA
| | - Rodney M Ritzel
- Department of Anesthesiology and Shock, Trauma and Anesthesiology Research (STAR) Center, University of Maryland School of Medicine, 685 West Baltimore Street, MSTF #6-016, Baltimore, MD, 21201, USA
| | - Gelareh Abulwerdi
- Department of Anesthesiology and Shock, Trauma and Anesthesiology Research (STAR) Center, University of Maryland School of Medicine, 685 West Baltimore Street, MSTF #6-016, Baltimore, MD, 21201, USA
| | - Terez Shea-Donohue
- Division of Translational Radiation Sciences (DTRS), Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alan I Faden
- Department of Anesthesiology and Shock, Trauma and Anesthesiology Research (STAR) Center, University of Maryland School of Medicine, 685 West Baltimore Street, MSTF #6-016, Baltimore, MD, 21201, USA
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9
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Co-stimulatory and co-inhibitory immune markers in solid tumors with MET alterations. Future Sci OA 2020; 7:FSO662. [PMID: 33437521 PMCID: PMC7787173 DOI: 10.2144/fsoa-2020-0159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The implication of MET alterations in solid tumors and the immune microenvironment remains elusive. Formalin-fixed, paraffin-embedded samples of 21 patients with solid tumors harboring MET alterations were used for immunohistochemical staining. Extracted RNA was analyzed with the NanoString nCounter human PanCancer immune profiling panel (NanoString Technologies, Inc., WA, USA). Patients were diagnosed with lung (n = 10), breast (n = 5), genitourinary (n = 3) or colorectal cancer (n = 3). Eleven had a MET missense mutation, four had an exon 14 splice site mutation and six had MET amplification. CD6, CCL19, CD40LG, XCR1, MAGEA1, ATM and CCL19 genes were significantly differentially expressed in MET-altered cancers. MET alterations may have a role in various solid tumors as potential therapeutic targets and combination therapy candidates with immune checkpoint inhibitors. MET is a receptor for growth signals that keeps cells alive and healthy. However, some tumors have changes in MET that allow for uncontrollable cell growth. Patients with MET-altered tumors may benefit from treatments targeting this gene, but eventually they become resistant to the treatments. Thus, there is a need to identify additional therapies for this patient population. The authors tested immune gene expression in tumors with MET alterations to determine if these patients would benefit from a new class of treatments called immunotherapies and found that patients with and without MET changes had differences in immune gene expression.
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10
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Van Goor A, Pasternak A, Walker K, Hong L, Malgarin C, MacPhee DJ, Harding JCS, Lunney JK. Differential responses in placenta and fetal thymus at 12 days post infection elucidate mechanisms of viral level and fetal compromise following PRRSV2 infection. BMC Genomics 2020; 21:763. [PMID: 33148169 PMCID: PMC7640517 DOI: 10.1186/s12864-020-07154-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/15/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND A pregnant gilt infected with porcine reproductive and respiratory syndrome virus (PRRSV) can transmit the virus to her fetuses across the maternal-fetal-interface resulting in varying disease outcomes. However, the mechanisms leading to variation in fetal outcome in response to PRRSV infection are not fully understood. Our objective was to assess targeted immune-related gene expression patterns and pathways in the placenta and fetal thymus to elucidate the molecular mechanisms involved in the resistance/tolerance and susceptibility of fetuses to PRRSV2 infection. Fetuses were grouped by preservation status and PRRS viral load (VL): mock infected control (CTRL), no virus detected (UNINF), virus detected in the placenta only with viable (PLCO-VIA) or meconium-stained fetus (PLCO-MEC), low VL with viable (LVL-VIA) or meconium-stained fetus (LVL-MEC), and high VL with viable (HVL-VIA) or meconium-stained fetus (HVL-MEC). RESULTS The host immune response was initiated only in fetuses with detectable levels of PRRSV. No differentially expressed genes (DEG) in either the placenta or thymus were identified in UNINF, PLCO-VIA, and PLCO-MEC when compared to CTRL fetuses. Upon fetal infection, a set of core responsive IFN-inducible genes (CXCL10, IFIH1, IFIT1, IFIT3, ISG15, and MX1) were strongly upregulated in both tissues. Gene expression in the thymus is a better differentiator of fetal VL; the strong downregulation of several innate and adaptive immune pathways (e.g., B Cell Development) are indicative of HVL. Gene expression in the placenta may be a better differentiator of fetal demise than the thymus, based-on principle component analysis clustering, gene expression patterns, and dysregulation of the Apoptosis and Ubiquitination pathways. CONCLUSION Our data supports the concept that fetal outcome in response to PRRSV2 infection is determined by fetal, and more significantly placental response, which is initiated only after fetal infection. This conceptual model represents a significant step forward in understanding the mechanisms underpinning fetal susceptibility to the virus.
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Affiliation(s)
- Angelica Van Goor
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, ARS, USDA, Beltsville, MD, USA
| | - Alex Pasternak
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kristen Walker
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, ARS, USDA, Beltsville, MD, USA
| | - Linjun Hong
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Carolina Malgarin
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Daniel J MacPhee
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - John C S Harding
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Joan K Lunney
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, ARS, USDA, Beltsville, MD, USA.
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11
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Park S, Doherty EE, Xie Y, Padyana AK, Fang F, Zhang Y, Karki A, Lebrilla CB, Siegel JB, Beal PA. High-throughput mutagenesis reveals unique structural features of human ADAR1. Nat Commun 2020; 11:5130. [PMID: 33046702 PMCID: PMC7550611 DOI: 10.1038/s41467-020-18862-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 09/11/2020] [Indexed: 01/06/2023] Open
Abstract
Adenosine Deaminases that act on RNA (ADARs) are enzymes that catalyze adenosine to inosine conversion in dsRNA, a common form of RNA editing. Mutations in the human ADAR1 gene are known to cause disease and recent studies have identified ADAR1 as a potential therapeutic target for a subset of cancers. However, efforts to define the mechanistic effects for disease associated ADAR1 mutations and the rational design of ADAR1 inhibitors are limited by a lack of structural information. Here, we describe the combination of high throughput mutagenesis screening studies, biochemical characterization and Rosetta-based structure modeling to identify unique features of ADAR1. Importantly, these studies reveal a previously unknown zinc-binding site on the surface of the ADAR1 deaminase domain which is important for ADAR1 editing activity. Furthermore, we present structural models that explain known properties of this enzyme and make predictions about the role of specific residues in a surface loop unique to ADAR1.
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Affiliation(s)
- SeHee Park
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Erin E Doherty
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Yixuan Xie
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | | | | | - Yue Zhang
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Agya Karki
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
| | - Justin B Siegel
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
- Genome Center, University of California Davis, Davis, CA, USA
| | - Peter A Beal
- Department of Chemistry, University of California, Davis, Davis, CA, USA.
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12
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Wang Y, Chung DH, Monteleone LR, Li J, Chiang Y, Toney MD, Beal PA. RNA binding candidates for human ADAR3 from substrates of a gain of function mutant expressed in neuronal cells. Nucleic Acids Res 2020; 47:10801-10814. [PMID: 31552420 PMCID: PMC6846710 DOI: 10.1093/nar/gkz815] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 08/26/2019] [Accepted: 09/16/2019] [Indexed: 12/18/2022] Open
Abstract
Human ADAR3 is a catalytically inactive member of the Adenosine Deaminase Acting on RNA (ADAR) protein family, whose active members catalyze A-to-I RNA editing in metazoans. Until now, the reasons for the catalytic incapability of ADAR3 has not been defined and its biological function rarely explored. Yet, its exclusive expression in the brain and involvement in learning and memory suggest a central role in the nervous system. Here we describe the engineering of a catalytically active ADAR3 enzyme using a combination of computational design and functional screening. Five mutations (A389V, V485I, E527Q, Q549R and Q733D) engender RNA deaminase in human ADAR3. By way of its catalytic activity, the ADAR3 pentamutant was used to identify potential binding targets for wild type ADAR3 in a human glioblastoma cell line. Novel ADAR3 binding sites discovered in this manner include the 3'-UTRs of the mRNAs encoding early growth response 1 (EGR1) and dual specificity phosphatase 1 (DUSP1); both known to be activity-dependent immediate early genes that respond to stimuli in the brain. Further studies reveal that the wild type ADAR3 protein can regulate transcript levels for DUSP1 and EGR1, suggesting a novel role ADAR3 may play in brain function.
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Affiliation(s)
- Yuru Wang
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA
| | - Dong Hee Chung
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA
| | - Leanna R Monteleone
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA
| | - Jie Li
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA
| | - Yao Chiang
- Department of Chemistry, University of California, One Shields Ave, Davis, CA 95616, USA
| | - Michael D Toney
- 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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13
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Park HK, Lim SD, Kwon GY. mRNA expressions of androgen receptor and its variants in matched hormone-sensitive and castration-resistant prostate cancer. Scand J Urol 2019; 53:365-371. [PMID: 31809622 DOI: 10.1080/21681805.2019.1697359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Objectives: Androgen receptor splice variants (AR-Vs), especially androgen receptor splice variant 7 (AR-V7), are considered as important factors in developing castration-resistance of prostate cancer and also as candidate predictive factors. Our aim was to evaluate changes in the mRNA expression of full-length AR (AR-FL) and AR-Vs in the primary prostate cancers from the same patients before and after ADT.Methods: We compared morphologic differences and evaluated AR-FL, AR-V7, AR-V4, ARv567es, AR-V3 and AR8 mRNA expression in matched samples of primary hormone-sensitive and castration-resistant prostate cancer (CRPC) from 19 patients.Results: mRNA expression of AR-FL, AR-V7, ARv567es and AR-V3 was present in hormone sensitive prostate cancer (HSPC) and was significantly increased in CRPC in 81.2% (13/16). There were strong positive correlations between AR-FL and AR-V7 (r = 0.93, p < .001), ARv567es (r = 0.72, p < .001) and AR-V3 (r = 0.81, p < .001) mRNA expression. AR-V7/AR-FL ratio was more significantly (>30%) increased after ADT in 25% (4/16) of the patients, who showed significantly (p < .001) worse overall survival. Neuroendocrine differentiation was seen in one patient (5.3%) and the Gleason score was increased in 10 (52.6%) patients.Conclusion: We demonstrated that the expression of AR-V7 is present at low levels in HSPC and is increased in CRPC and the increase is an active process possibly related to aggressive clinical course.
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Affiliation(s)
- Hyung Kyu Park
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - So Dug Lim
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Ghee Young Kwon
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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14
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McQuerry JA, Jenkins DF, Yost SE, Zhang Y, Schmolze D, Johnson WE, Yuan Y, Bild AH. Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes. BMC Cancer 2019; 19:881. [PMID: 31488082 PMCID: PMC6727561 DOI: 10.1186/s12885-019-6052-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022] Open
Abstract
Background Gene expression profiling of rare cancers has proven challenging due to limited access to patient materials and requirement of intact, non-degraded RNA for next-generation sequencing. We customized a gene expression panel compatible with degraded RNA from formalin-fixed, paraffin-embedded (FFPE) patient cancer samples and investigated its utility in pathway activity profiling in patients with metaplastic breast cancer (MpBC). Methods Activity of various biological pathways was profiled in samples from nineteen patients with MpBC and 8 patients with invasive ductal carcinoma with triple negative breast cancer (TNBC) phenotype using a custom gene expression-based assay of 345 genes. Results MpBC samples of mesenchymal (chondroid and/or osteoid) histology demonstrated increased SNAI1 and BCL2L11 pathway activity compared to samples with non-mesenchymal histology. Additionally, late cornified envelope and keratinization genes were downregulated in MpBC compared to TNBC, and epithelial-to-mesenchymal transition (EMT) and collagen genes were upregulated in MpBC. Patients with high activity of an invasiveness gene expression signature, as well as high expression of the mesenchymal marker and extracellular matrix glycoprotein gene SPARC, experienced worse outcomes than those with low invasiveness activity and low SPARC expression. Conclusions This study demonstrates the utility of gene expression profiling of metaplastic breast cancer FFPE samples with a custom counts-based assay. Gene expression patterns identified by this assay suggest that, although often histologically triple negative, patients with MpBC have distinct pathway activation compared to patients with invasive ductal TNBC. Incorporation of targeted therapies may lead to improved outcome for MpBC patients, especially in those patients expressing increased activity of invasiveness pathways. Electronic supplementary material The online version of this article (10.1186/s12885-019-6052-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jasmine A McQuerry
- Department of Oncological Sciences, School of Medicine, University of Utah, 2000 Circle of Hope Drive, Salt Lake City, UT, 84112, USA.,Department of Medical Oncology and Therapeutics Research, City of Hope, 1218 S Fifth Ave, Monrovia, CA, 91016, USA
| | - David F Jenkins
- Division of Computational Biomedicine, School of Medicine, Boston University, 72 East Concord Street, Boston, MA, 02218, USA
| | - Susan E Yost
- Department of Medical Oncology and Therapeutics, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Yuqing Zhang
- Division of Computational Biomedicine, School of Medicine, Boston University, 72 East Concord Street, Boston, MA, 02218, USA
| | - Daniel Schmolze
- Department of Pathology, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - W Evan Johnson
- Division of Computational Biomedicine, School of Medicine, Boston University, 72 East Concord Street, Boston, MA, 02218, USA
| | - Yuan Yuan
- Department of Medical Oncology and Therapeutics, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
| | - Andrea H Bild
- Department of Medical Oncology and Therapeutics Research, City of Hope, 1218 S Fifth Ave, Monrovia, CA, 91016, USA.
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15
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Fritzell K, Xu LD, Otrocka M, Andréasson C, Öhman M. Sensitive ADAR editing reporter in cancer cells enables high-throughput screening of small molecule libraries. Nucleic Acids Res 2019; 47:e22. [PMID: 30590609 PMCID: PMC6393238 DOI: 10.1093/nar/gky1228] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/19/2018] [Accepted: 12/21/2018] [Indexed: 12/22/2022] Open
Abstract
Adenosine to inosine editing is common in the human transcriptome and changes of this essential activity is associated with disease. Children with ADAR1 mutations develop fatal Aicardi-Goutières syndrome characterized by aberrant interferon expression. In contrast, ADAR1 overexpression is associated with increased malignancy of breast, lung and liver cancer. ADAR1 silencing in breast cancer cells leads to increased apoptosis, suggesting an anti-apoptotic function that promotes cancer progression. Yet, suitable high-throughput editing assays are needed to efficiently screen chemical libraries for modifiers of ADAR1 activity. We describe the development of a bioluminescent reporter system that facilitates rapid and accurate determination of endogenous editing activity. The system is based on the highly sensitive and quantitative Nanoluciferase that is conditionally expressed upon reporter-transcript editing. Stably introduced into cancer cell lines, the system reports on elevated endogenous ADAR1 editing activity induced by interferon as well as knockdown of ADAR1 and ADAR2. In a single-well setup we used the reporter in HeLa cells to screen a small molecule library of 33 000 compounds. This yielded a primary hit rate of 0.9% at 70% inhibition of editing. Thus, we provide a key tool for high-throughput identification of modifiers of A-to-I editing activity in cancer cells.
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Affiliation(s)
- Kajsa Fritzell
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden
| | - Li-Di Xu
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden
| | - Magdalena Otrocka
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden
| | - Marie Öhman
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden
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16
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Abudayyeh OO, Gootenberg JS, Franklin B, Koob J, Kellner MJ, Ladha A, Joung J, Kirchgatterer P, Cox DBT, Zhang F. A cytosine deaminase for programmable single-base RNA editing. Science 2019; 365:382-386. [PMID: 31296651 DOI: 10.1126/science.aax7063] [Citation(s) in RCA: 275] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/29/2019] [Indexed: 12/16/2022]
Abstract
Programmable RNA editing enables reversible recoding of RNA information for research and disease treatment. Previously, we developed a programmable adenosine-to-inosine (A-to-I) RNA editing approach by fusing catalytically inactivate RNA-targeting CRISPR-Cas13 (dCas13) with the adenine deaminase domain of ADAR2. Here, we report a cytidine-to-uridine (C-to-U) RNA editor, referred to as RNA Editing for Specific C-to-U Exchange (RESCUE), by directly evolving ADAR2 into a cytidine deaminase. RESCUE doubles the number of mutations targetable by RNA editing and enables modulation of phosphosignaling-relevant residues. We apply RESCUE to drive β-catenin activation and cellular growth. Furthermore, RESCUE retains A-to-I editing activity, enabling multiplexed C-to-U and A-to-I editing through the use of tailored guide RNAs.
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Affiliation(s)
- Omar O Abudayyeh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jonathan S Gootenberg
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian Franklin
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jeremy Koob
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Max J Kellner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alim Ladha
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Julia Joung
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - David B T Cox
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. .,McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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17
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Navas-Delgado I, García-Nieto J, López-Camacho E, Rybinski M, Lavado R, Berciano Guerrero MÁ, Aldana-Montes JF. VIGLA-M: visual gene expression data analytics. BMC Bioinformatics 2019; 20:150. [PMID: 30999846 PMCID: PMC6472185 DOI: 10.1186/s12859-019-2695-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Background The analysis of gene expression levels is used in many clinical studies to know how patients evolve or to find new genetic biomarkers that could help in clinical decision making. However, the techniques and software available for these analyses are not intended for physicians, but for geneticists. However, enabling physicians to make initial discoveries on these data would benefit in the clinical assay development. Results Melanoma is a highly immunogenic tumor. Therefore, in recent years physicians have incorporated immune system altering drugs into their therapeutic arsenal against this disease, revolutionizing the treatment of patients with an advanced stage of the cancer. This has led us to explore and deepen our knowledge of the immunology surrounding melanoma, in order to optimize the approach. Within this project we have developed a database for collecting relevant clinical information for melanoma patients, including the storage of patient gene expression levels obtained from the NanoString platform (several samples are taken from each patient). The Immune Profiling Panel is used in this case. This database is being exploited through the analysis of the different expression profiles of the patients. This analysis is being done with Python, and a parallel version of the algorithms is available with Apache Spark to provide scalability as needed. Conclusions VIGLA-M, the visual analysis tool for gene expression levels in melanoma patients is available at http://khaos.uma.es/melanoma/. The platform with real clinical data can be accessed with a demo user account, physician, using password physician_test_7634 (if you encounter any problems, contact us at this email address: mailto: khaos@lcc.uma.es). The initial results of the analysis of gene expression levels using these tools are providing first insights into the patients’ evolution. These results are promising, but larger scale tests must be developed once new patients have been sequenced, to discover new genetic biomarkers.
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Affiliation(s)
- Ismael Navas-Delgado
- Khaos Research, Universidad de Málaga, Málaga, Spain, Arquitecto Francisco Peñalosa 18, Málaga, 29071, Spain.
| | - José García-Nieto
- Khaos Research, Universidad de Málaga, Málaga, Spain, Arquitecto Francisco Peñalosa 18, Málaga, 29071, Spain
| | - Esteban López-Camacho
- Khaos Research, Universidad de Málaga, Málaga, Spain, Arquitecto Francisco Peñalosa 18, Málaga, 29071, Spain
| | - Maciej Rybinski
- Khaos Research, Universidad de Málaga, Málaga, Spain, Arquitecto Francisco Peñalosa 18, Málaga, 29071, Spain
| | - Rocio Lavado
- Unidad de Oncología Intercentros, Hospitales Univesitarios Regional y Virgen de la Victoria de Málaga, Instituto de Investigaciones Biomédicas (IBIMA), Málaga, Spain, Málaga, Spain
| | - Miguel Ángel Berciano Guerrero
- Unidad de Oncología Intercentros, Hospitales Univesitarios Regional y Virgen de la Victoria de Málaga, Instituto de Investigaciones Biomédicas (IBIMA), Málaga, Spain, Málaga, Spain
| | - José F Aldana-Montes
- Khaos Research, Universidad de Málaga, Málaga, Spain, Arquitecto Francisco Peñalosa 18, Málaga, 29071, Spain
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18
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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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19
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Cary GA, Wolff A, Zueva O, Pattinato J, Hinman VF. Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa. BMC Biol 2019; 17:16. [PMID: 30795750 PMCID: PMC6385403 DOI: 10.1186/s12915-019-0633-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 02/04/2019] [Indexed: 12/16/2022] Open
Abstract
Background Metazoan lineages exhibit a wide range of regenerative capabilities that vary among developmental stage and tissue type. The most robust regenerative abilities are apparent in the phyla Cnidaria, Platyhelminthes, and Echinodermata, whose members are capable of whole-body regeneration (WBR). This phenomenon has been well characterized in planarian and hydra models, but the molecular mechanisms of WBR are less established within echinoderms, or any other deuterostome system. Thus, it is not clear to what degree aspects of this regenerative ability are shared among metazoa. Results We characterize regeneration in the larval stage of the Bat Star (Patiria miniata). Following bisection along the anterior-posterior axis, larvae progress through phases of wound healing and re-proportioning of larval tissues. The overall number of proliferating cells is reduced following bisection, and we find evidence for a re-deployment of genes with known roles in embryonic axial patterning. Following axial respecification, we observe a significant localization of proliferating cells to the wound region. Analyses of transcriptome data highlight the molecular signatures of functions that are common to regeneration, including specific signaling pathways and cell cycle controls. Notably, we find evidence for temporal similarities among orthologous genes involved in regeneration from published Platyhelminth and Cnidarian regeneration datasets. Conclusions These analyses show that sea star larval regeneration includes phases of wound response, axis respecification, and wound-proximal proliferation. Commonalities of the overall process of regeneration, as well as gene usage between this deuterostome and other species with divergent evolutionary origins reveal a deep similarity of whole-body regeneration among the metazoa. Electronic supplementary material The online version of this article (10.1186/s12915-019-0633-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gregory A Cary
- Department of Biological Sciences, Carnegie Mellon University, Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Andrew Wolff
- Department of Biological Sciences, Carnegie Mellon University, Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Olga Zueva
- Department of Biological Sciences, Carnegie Mellon University, Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Joseph Pattinato
- Department of Biological Sciences, Carnegie Mellon University, Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA.
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Monteleone LR, Matthews MM, Palumbo CM, Thomas JM, Zheng Y, Chiang Y, Fisher AJ, Beal PA. A Bump-Hole Approach for Directed RNA Editing. Cell Chem Biol 2019; 26:269-277.e5. [PMID: 30581135 PMCID: PMC6386613 DOI: 10.1016/j.chembiol.2018.10.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/28/2018] [Accepted: 10/26/2018] [Indexed: 12/17/2022]
Abstract
Molecules capable of directing changes to nucleic acid sequences are powerful tools for molecular biology and promising candidates for the therapeutic correction of disease-causing mutations. However, unwanted reactions at off-target sites complicate their use. Here we report selective combinations of mutant editing enzyme and directing oligonucleotide. Mutations in human ADAR2 (adenosine deaminase acting on RNA 2) that introduce aromatic amino acids at position 488 reduce background RNA editing. This residue is juxtaposed to the nucleobase that pairs with the editing site adenine, suggesting a steric clash for the bulky mutants. Replacing this nucleobase with a hydrogen atom removes the clash and restores editing activity. A crystal structure of the E488Y mutant bound to abasic site-containing RNA shows the accommodation of the tyrosine side chain. Finally, we demonstrate directed RNA editing in vitro and in human cells using mutant ADAR2 proteins and modified guide RNAs with reduced off-target activity.
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Affiliation(s)
- Leanna R Monteleone
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Melissa M Matthews
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Cody M Palumbo
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Justin M Thomas
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Yuxuan Zheng
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Yao Chiang
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Andrew J Fisher
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA; Department of Molecular and Cellular Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Peter A Beal
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA.
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Wang Y, Park S, Beal PA. Selective Recognition of RNA Substrates by ADAR Deaminase Domains. Biochemistry 2018; 57:1640-1651. [PMID: 29457714 DOI: 10.1021/acs.biochem.7b01100] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Adenosine deamination is one of the most prevalent post-transcriptional modifications in mRNA and is catalyzed by ADAR1 and ADAR2 in humans. ADAR1 and ADAR2 have different substrate selectivity, which is believed to mainly originate from the proteins' deaminase domains (hADAR1d and hADAR2d, respectively). RNA-seq of the Saccharomyces cerevisiae transcriptome subjected to ADAR-catalyzed RNA editing identified substrates with common secondary structure features preferentially edited by hADAR1d over hADAR2d. The relatively small size and efficient reaction of one of these substrates suggested it could be useful for further study of the hADAR1d reaction. Indeed, a short hairpin stem from the S. cerevisiae HER1 mRNA was efficiently deaminated by hADAR1d and used to generate an hADAR1d-specific fluorescent reporter of editing activity. Using substrates preferred by either hADAR1d or hADAR2d in vitro, we found that a chimeric protein bearing an RNA-binding loop from hADAR2d grafted onto hADAR1d showed ADAR2-like selectivity. Finally, a high-throughput mutagenesis analysis (Sat-FACS-Seq) of conserved residues in an RNA-binding loop of hADAR1d revealed essential amino acids for function, advancing our understanding of RNA recognition by this domain.
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Affiliation(s)
- Yuru Wang
- Department of Chemistry , University of California , One Shields Ave , Davis , California 95616 , United States
| | - SeHee Park
- Department of Chemistry , University of California , One Shields Ave , Davis , California 95616 , United States
| | - Peter A Beal
- Department of Chemistry , University of California , One Shields Ave , Davis , California 95616 , United States
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Abstract
Rett syndrome (RTT) is a debilitating neurological disorder caused by mutations in the gene encoding the transcription factor Methyl CpG Binding Protein 2 (MECP2). A distinct disorder results from MECP2 gene duplication, suggesting that therapeutic approaches must restore close to normal levels of MECP2. Here, we apply the approach of site-directed RNA editing to repair, at the mRNA level, a disease-causing guanosine to adenosine (G > A) mutation in the mouse MeCP2 DNA binding domain. To mediate repair, we exploit the catalytic domain of Adenosine Deaminase Acting on RNA (ADAR2) that deaminates A to inosine (I) residues that are subsequently translated as G. We fuse the ADAR2 domain, tagged with a nuclear localization signal, to an RNA binding peptide from bacteriophage lambda. In cultured neurons from mice that harbor an RTT patient G > A mutation and express engineered ADAR2, along with an appropriate RNA guide to target the enzyme, 72% of Mecp2 mRNA is repaired. Levels of MeCP2 protein are also increased significantly. Importantly, as in wild-type neurons, the repaired MeCP2 protein is enriched in heterochromatic foci, reflecting restoration of normal MeCP2 binding to methylated DNA. This successful use of site-directed RNA editing to repair an endogenous mRNA and restore protein function opens the door to future in vivo applications to treat RTT and other diseases.
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Abstract
Inosine is one of the most common modifications found in human RNAs and the Adenosine Deaminases that act on RNA (ADARs) are the main enzymes responsible for its production. ADARs were first discovered in the 1980s and since then our understanding of ADARs has advanced tremendously. For instance, it is now known that defective ADAR function can cause human diseases. Furthermore, recently solved crystal structures of the human ADAR2 deaminase bound to RNA have provided insights regarding the catalytic and substrate recognition mechanisms. In this chapter, we describe the occurrence of inosine in human RNAs and the newest perspective on the ADAR family of enzymes, including their substrate recognition, catalytic mechanism, regulation as well as the consequences of A-to-I editing, and their relation to human diseases.
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Thomas JM, Beal PA. How do ADARs bind RNA? New protein-RNA structures illuminate substrate recognition by the RNA editing ADARs. Bioessays 2017; 39. [PMID: 28217931 DOI: 10.1002/bies.201600187] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Deamination of adenosine in RNA to form inosine has wide ranging consequences on RNA function including amino acid substitution to give proteins not encoded in the genome. What determines which adenosines in an mRNA are subject to this modification reaction? The answer lies in an understanding of the mechanism and substrate recognition properties of adenosine deaminases that act on RNA (ADARs). Our recent publication of X-ray crystal structures of the human ADAR2 deaminase domain bound to RNA editing substrates shed considerable light on how the catalytic domains of these enzymes bind RNA and promote adenosine deamination. Here we review in detail the deaminase domain-RNA contact surfaces and present models of how full length ADARs, bearing double stranded RNA-binding domains (dsRBDs) and deaminase domains, could process naturally occurring substrate RNAs.
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Affiliation(s)
- Justin M Thomas
- Department of Chemistry, University of California, Davis, CA, USA
| | - Peter A Beal
- Department of Chemistry, University of California, Davis, CA, USA
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