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Salvetat N, Checa-Robles FJ, Patel V, Cayzac C, Dubuc B, Chimienti F, Abraham JD, Dupré P, Vetter D, Méreuze S, Lang JP, Kupfer DJ, Courtet P, Weissmann D. A game changer for bipolar disorder diagnosis using RNA editing-based biomarkers. Transl Psychiatry 2022; 12:182. [PMID: 35504874 PMCID: PMC9064541 DOI: 10.1038/s41398-022-01938-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/30/2022] [Accepted: 04/19/2022] [Indexed: 11/08/2022] Open
Abstract
In clinical practice, differentiating Bipolar Disorder (BD) from unipolar depression is a challenge due to the depressive symptoms, which are the core presentations of both disorders. This misdiagnosis during depressive episodes results in a delay in proper treatment and a poor management of their condition. In a first step, using A-to-I RNA editome analysis, we discovered 646 variants (366 genes) differentially edited between depressed patients and healthy volunteers in a discovery cohort of 57 participants. After using stringent criteria and biological pathway analysis, candidate biomarkers from 8 genes were singled out and tested in a validation cohort of 410 participants. Combining the selected biomarkers with a machine learning approach achieved to discriminate depressed patients (n = 267) versus controls (n = 143) with an AUC of 0.930 (CI 95% [0.879-0.982]), a sensitivity of 84.0% and a specificity of 87.1%. In a second step by selecting among the depressed patients those with unipolar depression (n = 160) or BD (n = 95), we identified a combination of 6 biomarkers which allowed a differential diagnosis of bipolar disorder with an AUC of 0.935 and high specificity (Sp = 84.6%) and sensitivity (Se = 90.9%). The association of RNA editing variants modifications with depression subtypes and the use of artificial intelligence allowed developing a new tool to identify, among depressed patients, those suffering from BD. This test will help to reduce the misdiagnosis delay of bipolar patients, leading to an earlier implementation of a proper treatment.
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Affiliation(s)
- Nicolas Salvetat
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | | | - Vipul Patel
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Christopher Cayzac
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Benjamin Dubuc
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Fabrice Chimienti
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | | | - Pierrick Dupré
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Diana Vetter
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Sandie Méreuze
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Jean-Philippe Lang
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
- Les Toises. Center for Psychiatry and Psychotherapy, Lausanne, Switzerland
| | - David J Kupfer
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Philippe Courtet
- Department of Psychiatric Emergency & Acute Care, Lapeyronie Hospital, CHU Montpellier, Montpellier, France
| | - Dinah Weissmann
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France.
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2
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Karagianni K, Pettas S, Christoforidou G, Kanata E, Bekas N, Xanthopoulos K, Dafou D, Sklaviadis T. A Systematic Review of Common and Brain-Disease-Specific RNA Editing Alterations Providing Novel Insights into Neurological and Neurodegenerative Disease Manifestations. Biomolecules 2022; 12:biom12030465. [PMID: 35327657 PMCID: PMC8946084 DOI: 10.3390/biom12030465] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/08/2022] [Accepted: 03/15/2022] [Indexed: 02/05/2023] Open
Abstract
RNA editing contributes to transcriptome diversification through RNA modifications in relation to genome-encoded information (RNA–DNA differences, RDDs). The deamination of Adenosine (A) to Inosine (I) or Cytidine (C) to Uridine (U) is the most common type of mammalian RNA editing. It occurs as a nuclear co- and/or post-transcriptional event catalyzed by ADARs (Adenosine deaminases acting on RNA) and APOBECs (apolipoprotein B mRNA editing enzyme catalytic polypeptide-like genes). RNA editing may modify the structure, stability, and processing of a transcript. This review focuses on RNA editing in psychiatric, neurological, neurodegenerative (NDs), and autoimmune brain disorders in humans and rodent models. We discuss targeted studies that focus on RNA editing in specific neuron-enriched transcripts with well-established functions in neuronal activity, and transcriptome-wide studies, enabled by recent technological advances. We provide comparative editome analyses between human disease and corresponding animal models. Data suggest RNA editing to be an emerging mechanism in disease development, displaying common and disease-specific patterns. Commonly edited RNAs represent potential disease-associated targets for therapeutic and diagnostic values. Currently available data are primarily descriptive, calling for additional research to expand global editing profiles and to provide disease mechanistic insights. The potential use of RNA editing events as disease biomarkers and available tools for RNA editing identification, classification, ranking, and functional characterization that are being developed will enable comprehensive analyses for a better understanding of disease(s) pathogenesis and potential cures.
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Affiliation(s)
- Korina Karagianni
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece; (K.K.); (S.P.); (G.C.); (N.B.)
| | - Spyros Pettas
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece; (K.K.); (S.P.); (G.C.); (N.B.)
| | - Georgia Christoforidou
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece; (K.K.); (S.P.); (G.C.); (N.B.)
| | - Eirini Kanata
- Neurodegenerative Diseases Research Group, Department of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece; (E.K.); (K.X.); (T.S.)
| | - Nikolaos Bekas
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece; (K.K.); (S.P.); (G.C.); (N.B.)
| | - Konstantinos Xanthopoulos
- Neurodegenerative Diseases Research Group, Department of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece; (E.K.); (K.X.); (T.S.)
| | - Dimitra Dafou
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece; (K.K.); (S.P.); (G.C.); (N.B.)
- Correspondence:
| | - Theodoros Sklaviadis
- Neurodegenerative Diseases Research Group, Department of Pharmacy, School of Health Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece; (E.K.); (K.X.); (T.S.)
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3
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Ruan H, Li Q, Liu Y, Liu Y, Lussier C, Diao L, Han L. GPEdit: the genetic and pharmacogenomic landscape of A-to-I RNA editing in cancers. Nucleic Acids Res 2021; 50:D1231-D1237. [PMID: 34534336 PMCID: PMC8728115 DOI: 10.1093/nar/gkab810] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/27/2021] [Accepted: 09/06/2021] [Indexed: 12/24/2022] Open
Abstract
Altered A-to-I RNA editing has been widely observed in many human cancers and some editing sites are associated with drug sensitivity, implicating its therapeutic potential. Increasing evidence has demonstrated that a quantitative trait loci mapping approach is effective to understanding the genetic basis of RNA editing. We systematically performed RNA editing quantitative trait loci (edQTL) analysis in 33 human cancer types for >10 000 cancer samples and identified 320 029 edQTLs. We also identified 1688 ed-QTLs associated with patient overall survival and 4672 ed-QTLs associated with GWAS risk loci. Furthermore, we demonstrated the associations between RNA editing and >1000 anti-cancer drug response with ∼3.5 million significant associations. We developed GPEdit (https://hanlab.uth.edu/GPEdit/) to facilitate a global map of the genetic and pharmacogenomic landscape of RNA editing. GPEdit is a user-friendly and comprehensive database that provides an opportunity for a better understanding of the genetic impact and the effects on drug response of RNA editing in cancers.
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Affiliation(s)
- Hang Ruan
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Qiang Li
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Yuan Liu
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA
| | - Yaoming Liu
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Charles Lussier
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA.,Department of Computer Science and Statistics, Rice University, Houston, TX 77030, USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.,Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030, USA.,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA
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Salvetat N, Van der Laan S, Vire B, Chimienti F, Cleophax S, Bronowicki JP, Doffoel M, Bourlière M, Schwan R, Lang JP, Pujol JF, Weissmann D. RNA editing blood biomarkers for predicting mood alterations in HCV patients. J Neurovirol 2019; 25:825-836. [PMID: 31332697 PMCID: PMC6920238 DOI: 10.1007/s13365-019-00772-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 03/13/2019] [Accepted: 06/03/2019] [Indexed: 12/19/2022]
Abstract
Treatment-emergent depression is a common complication in patients with chronic hepatitis C virus (HCV) infection undergoing antiviral combination therapy with IFN-α and ribavirin. It has recently been shown that changes in A-to-I RNA editing rates are associated with various pathologies such as inflammatory disorders, depression and suicide. Interestingly, IFN-α induces gene expression of the RNA editing enzyme ADAR1-1 (ADAR1a-p150) and alters overall RNA editing activity. In this study, we took advantage of the high prevalence of pharmacologically induced depression in patients treated with IFN-α and ribavirin to test the interest of RNA editing–related biomarkers in white blood cells of patients. In this 16-week longitudinal study, a small cohort of patients was clinically evaluated using standard assessment methods prior to and during antiviral therapy and blood samples were collected to analyse RNA editing modifications. A-I RNA editing activity on the phosphodiesterase 8A (PDE8A) gene, a previously identified RNA editing hotspot in the context of lupus erythematosus, was quantified by using an ultra-deep next-generation sequencing approach. We also monitored gene expression levels of the ADAR enzymes and the PDE8A gene during treatment by qPCR. As expected, psychiatric evaluation could track treatment-emergent depression, which occurred in 30% of HCV patients. We show that PDE8A RNA editing is increased in all patients following interferon treatment, but differently in 30% of patients. This effect was mimicked in a cellular model using SHSY-5Y neuroblastoma cells. By combining the data of A-I RNA editing and gene expression, we generated an algorithm that allowed discrimination between the group of patients who developed a treatment-emergent depression and those who did not. The current model of drug-induced depression identified A-I RNA editing biomarkers as useful tools for the identification of individuals at risk of developing depression in an objective, quantifiable biological blood test.
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Affiliation(s)
- N Salvetat
- ALCEDIAG, Sys2Diag / CNRS UMR9005, Parc Euromédecine Cap Delta, 1682 Rue de la Valsière, 34184, Montpellier Cedex 4, France.
| | - S Van der Laan
- ALCEDIAG, Sys2Diag / CNRS UMR9005, Parc Euromédecine Cap Delta, 1682 Rue de la Valsière, 34184, Montpellier Cedex 4, France
| | - B Vire
- ALCEDIAG, Sys2Diag / CNRS UMR9005, Parc Euromédecine Cap Delta, 1682 Rue de la Valsière, 34184, Montpellier Cedex 4, France
| | - F Chimienti
- ALCEDIAG, Sys2Diag / CNRS UMR9005, Parc Euromédecine Cap Delta, 1682 Rue de la Valsière, 34184, Montpellier Cedex 4, France
| | - S Cleophax
- Biocortech, rue de la Croix Jarry, 75013, Paris, France.,Etablissement Français du Sang, 2 avenue Ile de France, 95300, Pontoise, France
| | - J P Bronowicki
- Hepato-Gastroenterology, Hopital Brabois- CHU Nancy, 54511, Vandoeuvre-les-Nancy, France
| | - M Doffoel
- Université de Strasbourg, Hopital Universitaire de Strasbourg, 67000, Strasbourg, France
| | - M Bourlière
- Hepato-Gastroenterology, Hopital Saint Joseph, 13285, Marseille, France
| | - R Schwan
- Hepato-Gastroenterology, Hopital Brabois- CHU Nancy, 54511, Vandoeuvre-les-Nancy, France
| | - J P Lang
- Université de Strasbourg, Hopital Universitaire de Strasbourg, 67000, Strasbourg, France.,Les Toises, Centre de psychiatrie et psychothérapie, Lausanne, Switzerland
| | - J F Pujol
- ALCEDIAG, Sys2Diag / CNRS UMR9005, Parc Euromédecine Cap Delta, 1682 Rue de la Valsière, 34184, Montpellier Cedex 4, France.,Biocortech, rue de la Croix Jarry, 75013, Paris, France
| | - D Weissmann
- ALCEDIAG, Sys2Diag / CNRS UMR9005, Parc Euromédecine Cap Delta, 1682 Rue de la Valsière, 34184, Montpellier Cedex 4, France.,Biocortech, rue de la Croix Jarry, 75013, Paris, France
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5
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Piontkivska H, Plonski NM, Miyamoto MM, Wayne ML. Explaining Pathogenicity of Congenital Zika and Guillain-Barré Syndromes: Does Dysregulation of RNA Editing Play a Role? Bioessays 2019; 41:e1800239. [PMID: 31106880 PMCID: PMC6699488 DOI: 10.1002/bies.201800239] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/28/2019] [Indexed: 12/11/2022]
Abstract
Previous studies of Zika virus (ZIKV) pathogenesis have focused primarily on virus-driven pathology and neurotoxicity, as well as host-related changes in cell proliferation, autophagy, immunity, and uterine function. It is now hypothesized that ZIKV pathogenesis arises instead as an (unintended) consequence of host innate immunity, specifically, as the side effect of an otherwise well-functioning machine. The hypothesis presented here suggests a new way of thinking about the role of host immune mechanisms in disease pathogenesis, focusing on dysregulation of post-transcriptional RNA editing as a candidate driver of a broad range of observed neurodevelopmental defects and neurodegenerative clinical symptoms in both infants and adults linked with ZIKV infections. The authors collect and synthesize existing evidence of ZIKV-mediated changes in the expression of adenosine deaminases acting on RNA (ADARs), known links between abnormal RNA editing and pathogenesis, as well as ideas for future research directions, including potential treatment strategies.
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Affiliation(s)
- Helen Piontkivska
- Department of Biological Sciences and University, Kent, OH
44242, USA
- School of Biomedical Sciences, Kent State University, Kent,
OH 44242, USA
| | - Noel-Marie Plonski
- School of Biomedical Sciences, Kent State University, Kent,
OH 44242, USA
| | | | - Marta L. Wayne
- Department of Biology, University of Florida, Gainesville,
FL 32611, USA
- Emerging Pathogens Institute, University of Florida,
Gainesville, FL 32611, USA
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6
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Chimienti F, Cavarec L, Vincent L, Salvetat N, Arango V, Underwood MD, Mann JJ, Pujol JF, Weissmann D. Brain region-specific alterations of RNA editing in PDE8A mRNA in suicide decedents. Transl Psychiatry 2019; 9:91. [PMID: 30770787 PMCID: PMC6377659 DOI: 10.1038/s41398-018-0331-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/26/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022] Open
Abstract
Phosphodiesterases (PDE) are key modulators of signal transduction and are involved in inflammatory cell activation, memory and cognition. There is a two-fold decrease in the expression of phosphodiesterase 8A (PDE8A) in the temporal cortex of major depressive disorder (MDD) patients. Here, we studied PDE8A mRNA-editing profile in two architectonically distinct neocortical regions in a clinically well-characterized cohort of age- and sex-matched non-psychiatric drug-free controls and depressed suicide decedents. By using capillary electrophoresis single-stranded conformational polymorphism (CE-SSCP), a previously validated technique to identify A-to-I RNA modifications, we report the full editing profile of PDE8A in the brain, including identification of two novel editing sites. Editing of PDE8A mRNA displayed clear regional difference when comparing dorsolateral prefrontal cortex (BA9) and anterior cingulate cortex (BA24). Furthermore, we report significant intra-regional differences between non-psychiatric control individuals and depressed suicide decedents, which could discriminate the two populations. Taken together, our results (i) highlight the importance of immune/inflammatory markers in major depressive disorder and suicide and (ii) establish a direct relationship between A-to-I RNA modifications of peripheral markers and A-to-I RNA editing-related modifications in brain. This work provides the first immune response-related brain marker for suicide and could pave the way for the identification of a blood-based biomarker that predicts suicidal behavior.
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Affiliation(s)
- Fabrice Chimienti
- ALCEDIAG/ Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France.
| | - Laurent Cavarec
- grid.465535.4Genomic Vision, Green Square, 80-84 rue des Meuniers, 92220 Bagneux, France
| | - Laurent Vincent
- grid.457349.8Commissariat à l’Energie Atomique, Fontenay aux Roses, France
| | - Nicolas Salvetat
- ALCEDIAG/ Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Victoria Arango
- 0000 0000 8499 1112grid.413734.6Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY USA ,0000000419368729grid.21729.3fDepartment of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY USA
| | - Mark D. Underwood
- 0000 0000 8499 1112grid.413734.6Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY USA ,0000000419368729grid.21729.3fDepartment of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY USA
| | - J. John Mann
- 0000 0000 8499 1112grid.413734.6Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY USA ,0000000419368729grid.21729.3fDepartment of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY USA
| | | | - Dinah Weissmann
- ALCEDIAG/ Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
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