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Hinsinger G, Du Trieu De Terdonck L, Urbach S, Salvetat N, Rival M, Galoppin M, Ripoll C, Cezar R, Laurent-Chabalier S, Demattei C, Agherbi H, Castelnovo G, Lehmann S, Rigau V, Marin P, Thouvenot E. CD138 as a Specific CSF Biomarker of Multiple Sclerosis. Neurol Neuroimmunol Neuroinflamm 2024; 11:e200230. [PMID: 38669615 DOI: 10.1212/nxi.0000000000200230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
BACKGROUND AND OBJECTIVES The aim of this study was to identify novel biomarkers for multiple sclerosis (MS) diagnosis and prognosis, addressing the critical need for specific and prognostically valuable markers in the field. METHODS We conducted an extensive proteomic investigation, combining analysis of (1) CSF proteome from symptomatic controls, fast and slow converters after clinically isolated syndromes, and patients with relapsing-remitting MS (n = 10 per group) using label-free quantitative proteomics and (2) oligodendrocyte secretome changes under proinflammatory or proapoptotic conditions using stable isotope labeling by amino acids in cell culture. Proteins exhibiting differential abundance in both proteomic analyses were combined with other putative MS biomarkers, yielding a comprehensive list of 87 proteins that underwent quantification through parallel reaction monitoring (PRM) in a novel cohort, comprising symptomatic controls, inflammatory neurologic disease controls, and patients with MS at various disease stages (n = 10 per group). The 11 proteins that passed this qualification step were subjected to a new PRM assay within an expanded cohort comprising 158 patients with either MS at different disease stages or other inflammatory or noninflammatory neurologic disease controls. RESULTS This study unveiled a promising biomarker signature for MS, including previously established candidates, such as chitinase 3-like protein 1, chitinase 3-like protein 2, chitotriosidase, immunoglobulin kappa chain region C, neutrophil gelatinase-associated lipocalin, and CD27. In addition, we identified novel markers, namely cat eye syndrome critical region protein 1 (adenosine deaminase 2, a therapeutic target in multiple sclerosis) and syndecan-1, a proteoglycan, also known as plasma cell surface marker CD138 and acting as chitinase 3-like protein 1 receptor implicated in inflammation and cancer signaling. CD138 exhibited good diagnostic accuracy in distinguishing MS from inflammatory neurologic disorders (area under the curve [AUC] = 0.85, CI 0.75-0.95). CD138 immunostaining was also observed in the brains of patients with MS and cultured oligodendrocyte precursor cells but was absent in astrocytes. DISCUSSION These findings identify CD138 as a specific CSF biomarker for MS and suggest the selective activation of the chitinase 3-like protein 1/CD138 pathway within the oligodendrocyte lineage in MS. They offer promising prospects for improving MS diagnosis and prognosis by providing much-needed specificity and clinical utility. CLASSIFICATION OF EVIDENCE This study provides Class II evidence that CD138 distinguishes multiple sclerosis from other inflammatory neurologic disorders with an AUC of 0.85 (95% CI 0.75-0.95).
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Affiliation(s)
- Geoffrey Hinsinger
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Lucile Du Trieu De Terdonck
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Serge Urbach
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Nicolas Salvetat
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Manon Rival
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Manon Galoppin
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Chantal Ripoll
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Renaud Cezar
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Sabine Laurent-Chabalier
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Christophe Demattei
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Hanane Agherbi
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Giovanni Castelnovo
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Sylvain Lehmann
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Valérie Rigau
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Philippe Marin
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Eric Thouvenot
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
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Salvetat N, Checa-Robles FJ, Delacrétaz A, Cayzac C, Dubuc B, Vetter D, Dainat J, Lang JP, Gamma F, Weissmann D. AI algorithm combined with RNA editing-based blood biomarkers to discriminate bipolar from major depressive disorders in an external validation multicentric cohort. J Affect Disord 2024; 356:385-393. [PMID: 38615844 DOI: 10.1016/j.jad.2024.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 04/02/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024]
Abstract
Bipolar disorder (BD) is a leading cause of disability worldwide, as it can lead to cognitive and functional impairment and premature mortality. The first episode of BD is usually a depressive episode and is often misdiagnosed as major depressive disorder (MDD). Growing evidence indicates that peripheral immune activation and inflammation are involved in the pathophysiology of BD and MDD. Recently, by developing a panel of RNA editing-based blood biomarkers able to discriminate MDD from depressive BD, we have provided clinicians a new tool to reduce the misdiagnosis delay observed in patients suffering from BD. The present study aimed at validating the diagnostic value of this panel in an external independent multicentric Switzerland-based cohort of 143 patients suffering from moderate to major depression. The RNA-editing based blood biomarker (BMK) algorithm developped allowed to accurately discriminate MDD from depressive BD in an external cohort, with high accuracy, sensitivity and specificity values (82.5 %, 86.4 % and 80.8 %, respectively). These findings further confirm the important role of RNA editing in the physiopathology of mental disorders and emphasize the possible clinical usefulness of the biomarker panel for optimization treatment delay in patients suffering from BD.
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Affiliation(s)
- Nicolas Salvetat
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | | | - Aurélie Delacrétaz
- Les Toises. Center for psychiatry and psychotherapy, Lausanne, Switzerland
| | - Christopher Cayzac
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Benjamin Dubuc
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Diana Vetter
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France
| | - Jacques Dainat
- 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
| | - Franziska Gamma
- Les Toises. Center for psychiatry and psychotherapy, Lausanne, Switzerland
| | - Dinah Weissmann
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Montpellier, France.
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Hayashi MAF, Salvetat N, Cayzac C, Checa-Robles FJ, Dubuc B, Mereuze S, Nani JV, Molina F, Brietzke E, Weissmann D. Euthymic and depressed bipolar patients are characterized by different RNA editing patterns in blood. Psychiatry Res 2023; 328:115422. [PMID: 37643531 DOI: 10.1016/j.psychres.2023.115422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 08/13/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023]
Abstract
Bipolar disorder (BD) is a worldwide leading cause of disability. Inflammation roles in this disease is well established. ADAR1-mediated RNA editing is one of the key mechanisms regulating the inflammatory response. We have identified a panel of RNA editing-based blood biomarkers which allowed to discriminate unipolar from BD depression with high accuracy. We confirmed here the diagnostic value of this panel in a new cohort of BD patients recruited in Brazil. We also identified new combinations which allow a clear discrimination of BD from healthy controls and among BD subgroups, confirming that RNA editing is a key mechanism in BD.
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Affiliation(s)
- Mirian A F Hayashi
- Department of Pharmacology, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Rua 3 de maio 100, Ed. INFAR, 3rd floor, SP CEP 04044-020, Brazil; National Institute for Translational Medicine (INCT-TM, CNPq/FAPESP/CAPES), Ribeirão Preto, Brazil.
| | - Nicolas Salvetat
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, 1682 rue de la Valsière, Montpellier 34184, France
| | - Christopher Cayzac
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, 1682 rue de la Valsière, Montpellier 34184, France
| | | | - Benjamin Dubuc
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, 1682 rue de la Valsière, Montpellier 34184, France
| | - Sandie Mereuze
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, 1682 rue de la Valsière, Montpellier 34184, France
| | - João V Nani
- Department of Pharmacology, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), Rua 3 de maio 100, Ed. INFAR, 3rd floor, SP CEP 04044-020, Brazil; National Institute for Translational Medicine (INCT-TM, CNPq/FAPESP/CAPES), Ribeirão Preto, Brazil
| | - Franck Molina
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, 1682 rue de la Valsière, Montpellier 34184, France
| | - Elisa Brietzke
- Department of Psychiatry, Queen's University School of Medicine, Kingston, Canada
| | - Dinah Weissmann
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, 1682 rue de la Valsière, Montpellier 34184, France.
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Abraham JD, Salvetat N, Guerra P, Ferrari M, Le Guen P, Biglia O, Henry C, Kessing L, Haro J, Vieta E, Weissmann D. Clinical validation of EDIT-B test for the diagnosis of bipolar disorder. Eur Psychiatry 2022. [PMCID: PMC9565526 DOI: 10.1192/j.eurpsy.2022.1047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Introduction Bipolar disorder (BD) is a psychiatric disorder characterized by alternating episodes of high mood and low mood similar to depression. To differentiate BD patients from unipolar (UN) depressed patients remains a challenge and the clinical scales available failed to distinguish these 2 populations. ALCEDIAG developed EDIT-B, the first blood test able to make a differential diagnosis of BD. Based on RNA editing modifications measurement and AI, the test requires a simple blood draw and equipment available in most central laboratories. A first study on 160 UN and 95 BD patients allowed a differential diagnosis with an AUC of 0.935 and high specificity (Sp=84.6%) and sensitivity (Se=90.9%). A multicentric clinical study has been set up to validate these performances. Objectives The objective of this project is to run a multicentric clinical study in Europe and assess the performances of the test. Methods The EDIT-B project, led by Alcediag, is supported by EIT-Health grant (European institute of Innovation and Technology) and gathers 4 clinical centers in 3 countries (France, Spain, Danemark), a CRO for the clinical study management (Aixial), a CRO for the development of a diagnostic kit (Veracyte), a diagnostic lab for molecular biology analyses (Synlab), and a regulatory company (PLG). Results At the end of the study, the EDIT-B performance will be confirmed and the test will be CE-marked. Conclusions This test will address the needs of millions of patients suffering from misdiagnosis and therefore allow them to receive the correct treatment. Disclosure JDA, NS and DW are employees of Alcediag.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Schneider FS, Molina L, Picot MC, L'Helgoualch N, Espeut J, Champigneux P, Alali M, Baptiste J, Cardeur L, Carniel C, Davy M, Dedisse D, Dubuc B, Fenech H, Foulongne V, Gaillard CF, Galtier F, Makinson A, Marin G, Santos RM, Morquin D, Ouedraogo A, Lejeune AP, Quenot M, Keiflin P, Robles FC, Rego CR, Salvetat N, Trento C, Vetter D, Molina F, Reynes J. Performances of rapid and connected salivary RT-LAMP diagnostic test for SARS-CoV-2 infection in ambulatory screening. Sci Rep 2022; 12:2843. [PMID: 35181680 PMCID: PMC8857239 DOI: 10.1038/s41598-022-04826-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/22/2021] [Indexed: 12/27/2022] Open
Abstract
In the context of social events reopening and economic relaunch, sanitary surveillance of SARS-CoV-2 infection is still required. Here, we evaluated the diagnostic performances of a rapid, extraction-free and connected reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay on saliva. Nasopharyngeal (NP) swabs and saliva from 443 outpatients were collected simultaneously and tested by reverse-transcription quantitative PCR (RT-qPCR) as reference standard test. Seventy-one individuals (16.0%) were positive by NP and/or salivary RT-qPCR. Sensitivity and specificity of salivary RT-LAMP were 85.9% (95%CI 77.8–94.0%) and 99.5% (98.7–100%), respectively. Performances were similar for symptomatic and asymptomatic participants. Moreover, SARS-CoV-2 genetic variants were analyzed and no dominant mutation in RT-LAMP primer region was observed during the period of the study. We demonstrated that this RT-LAMP test on self-collected saliva is reliable for SARS-CoV-2 detection. This simple connected test with optional automatic results transfer to health authorities is unique and opens the way to secure professional and social events in actual context of economics restart.
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Affiliation(s)
- Francisco Santos Schneider
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France.,SkillCell, Montpellier, France
| | - Laurence Molina
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France
| | - Marie-Christine Picot
- Clinical Research and Epidemiology Unit, Department of Medical Information, Montpellier University Hospital, University of Montpellier, Montpellier, France.,INSERM Centre Investigation Clinique 1411, University Hospital, Montpellier, France
| | - Nicolas L'Helgoualch
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France
| | - Julien Espeut
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France.,SkillCell, Montpellier, France
| | - Pierre Champigneux
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France
| | - Mellis Alali
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France
| | - Julie Baptiste
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France.,SkillCell, Montpellier, France
| | - Lise Cardeur
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France
| | | | - Martin Davy
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France.,SkillCell, Montpellier, France
| | | | - Benjamin Dubuc
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France
| | - Hugo Fenech
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France
| | - Vincent Foulongne
- PCCEI, Univ Montpellier, INSERM, EFS, Univ Antilles, Montpellier, France
| | - Carole Fruchart Gaillard
- CEA, INRAE, Department of Medicines and Healthcare Technologies (DMTS), University of Paris-Saclay, SIMoS, Gif-sur-Yvette, France
| | - Florence Galtier
- INSERM Centre Investigation Clinique 1411, University Hospital, Montpellier, France
| | - Alain Makinson
- Infectious Diseases Department, Montpellier University Hospital, Montpellier, France.,TransVIHMI, IRD, INSERM, University of Montpellier, Montpellier, France
| | - Grégory Marin
- Clinical Research and Epidemiology Unit, Department of Medical Information, Montpellier University Hospital, University of Montpellier, Montpellier, France
| | - Raissa Medina Santos
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France.,Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - David Morquin
- Infectious Diseases Department, Montpellier University Hospital, Montpellier, France.,TransVIHMI, IRD, INSERM, University of Montpellier, Montpellier, France
| | - Alimata Ouedraogo
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France
| | - Alexandra Prieux Lejeune
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France.,SkillCell, Montpellier, France
| | - Marine Quenot
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France
| | | | - Francisco Checa Robles
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France
| | - Carolina Rodrigues Rego
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France.,Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Nicolas Salvetat
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France
| | - Charline Trento
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France
| | - Diana Vetter
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France
| | - Franck Molina
- Sys2Diag UMR9005 CNRS ALCEN, Cap Gamma, Parc Euromédecine, 1682 rue de la Valsière, CS 40182, 34184, Montpellier, CEDEX 4, France.
| | - Jacques Reynes
- Infectious Diseases Department, Montpellier University Hospital, Montpellier, France.,TransVIHMI, IRD, INSERM, University of Montpellier, Montpellier, France
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7
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Salvetat N, Chimienti F, Cayzac C, Dubuc B, Checa-Robles F, Dupre P, Mereuze S, Patel V, Genty C, Lang JP, Pujol JF, Courtet P, Weissmann D. Phosphodiesterase 8A to discriminate in blood samples depressed patients and suicide attempters from healthy controls based on A-to-I RNA editing modifications. Transl Psychiatry 2021; 11:255. [PMID: 33931591 PMCID: PMC8087806 DOI: 10.1038/s41398-021-01377-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 03/19/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Mental health issues, including major depressive disorder, which can lead to suicidal behavior, are considered by the World Health Organization as a major threat to global health. Alterations in neurotransmitter signaling, e.g., serotonin and glutamate, or inflammatory response have been linked to both MDD and suicide. Phosphodiesterase 8A (PDE8A) gene expression is significantly decreased in the temporal cortex of major depressive disorder (MDD) patients. PDE8A specifically hydrolyzes adenosine 3',5'-cyclic monophosphate (cAMP), which is a key second messenger involved in inflammation, cognition, and chronic antidepressant treatment. Moreover, alterations of RNA editing in PDE8A mRNA has been described in the brain of depressed suicide decedents. Here, we investigated PDE8A A-to-I RNA editing-related modifications in whole blood of depressed patients and suicide attempters compared to age-matched and sex-matched healthy controls. We report significant alterations of RNA editing of PDE8A in the blood of depressed patients and suicide attempters with major depression, for which the suicide attempt took place during the last month before sample collection. The reported RNA editing modifications in whole blood were similar to the changes observed in the brain of suicide decedents. Furthermore, analysis and combinations of different edited isoforms allowed us to discriminate between suicide attempters and control groups. Altogether, our results identify PDE8A as an immune response-related marker whose RNA editing modifications translate from brain to blood, suggesting that monitoring RNA editing in PDE8A in blood samples could help to evaluate depressive state and suicide risk.
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Affiliation(s)
- Nicolas Salvetat
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Fabrice Chimienti
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Christopher Cayzac
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Benjamin Dubuc
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Francisco Checa-Robles
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Pierrick Dupre
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Sandie Mereuze
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Vipul Patel
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Catherine Genty
- Department of Emergency Psychiatry and Acute Care, University Hospital/INSERM U1061, 191 Av. du Doyen Gaston Giraud, Montpellier, 34295 France
| | - Jean-Philippe Lang
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Jean-François Pujol
- grid.4444.00000 0001 2112 9282ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184 France
| | - Philippe Courtet
- Department of Emergency Psychiatry and Acute Care, University Hospital/INSERM U1061, 191 Av. du Doyen Gaston Giraud, Montpellier, 34295 France
| | - Dinah Weissmann
- ALCEDIAG/Sys2Diag, CNRS UMR 9005, Parc Euromédecine, Cap Delta, 1682 Rue de la Valsière, Montpellier, 34184, France.
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8
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Abraham JD, Salvetat N, Checa-Robles F, Patel V, Cayzac C, Dubuc B, Vetter D, Lang JP, Courtet P, Kupfer D, Weissmann D. Game changer in the diagnosis of bipolar disorder using RNA editing-based blood biomarkers. Eur Psychiatry 2021. [PMCID: PMC9471217 DOI: 10.1192/j.eurpsy.2021.235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Introduction In clinical practice, differentiating Bipolar Disorder (BD) from unipolar depression is challenging due to the depressive symptoms, which are the core presentations of both disorders. Patients with BD are often misdiagnosed during depressive episodes resulting in a delay in proper treatment and a poor management of their condition. Objectives The aim of the present study is to discriminate between unipolar depression and BD using a panel of RNA edited blood biomarkers. Methods Depressed patients were classified according to clinical scores in MADRS and IDSC-30 depression scales. After blood collection and RNA extraction, we used whole-transcriptome sequencing to identify differential A-to-I editing events, and Targeted Next Generation Sequencing to validate those biomarkers. Results We discovered 646 variants differentially edited between depressed patients and control in a discovery cohort of 57 participants. After using stringent criteria and biological pathway analysis, 6 biomarker candidates were singled out and tested in a validation cohort of 160 patients suffering from unipolar depression and 95 BD patients in a depressive episode, which allowed a differential diagnosis of BD with an AUC of 0.935 and high specificity (Sp=84.6%) and sensitivity (Se=90.9%). Conclusions We have shown that a combination of 6 blood RNA editing-related biomarkers allows to discriminate unipolar and bipolar depression This 6 BMKs panel may be crucial to improve BD diagnosis and orientate the treatment therefore addressing the needs of millions of patients suffering from misdiagnosis and incorrect treatment for their diseases. This will change the game for the management of patients. Disclosure No significant relationships.
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9
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Castro-Severyn J, Pardo-Esté C, Sulbaran Y, Cabezas C, Gariazzo V, Briones A, Morales N, Séveno M, Decourcelle M, Salvetat N, Remonsellez F, Castro-Nallar E, Molina F, Molina L, Saavedra CP. Arsenic Response of Three Altiplanic Exiguobacterium Strains With Different Tolerance Levels Against the Metalloid Species: A Proteomics Study. Front Microbiol 2019; 10:2161. [PMID: 31611848 PMCID: PMC6775490 DOI: 10.3389/fmicb.2019.02161] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/03/2019] [Indexed: 12/23/2022] Open
Abstract
Exiguobacterium is a polyextremophile bacterial genus with a physiology that allows it to develop in different adverse environments. The Salar de Huasco is one of these environments due to its altitude, atmospheric pressure, solar radiation, temperature variations, pH, salinity, and the presence of toxic compounds such as arsenic. However, the physiological and/or molecular mechanisms that enable them to prosper in these environments have not yet been described. Our research group has isolated several strains of Exiguobacterium genus from different sites of Salar de Huasco, which show different resistance levels to As(III) and As(V). In this work, we compare the protein expression patterns of the three strains in response to arsenic by a proteomic approach; strains were grown in absence of the metalloid and in presence of As(III) and As(V) sublethal concentrations and the protein separation was carried out in 2D electrophoresis gels (2D-GE). In total, 999 spots were detected, between 77 and 173 of which showed significant changes for As(III) among the three strains, and between 90 and 143 for As(V), respectively, compared to the corresponding control condition. Twenty-seven of those were identified by mass spectrometry (MS). Among these identified proteins, the ArsA [ATPase from the As(III) efflux pump] was found to be up-regulated in response to both arsenic conditions in the three strains, as well as the Co-enzyme A disulfide reductase (Cdr) in the two more resistant strains. Interestingly, in this genus the gene that codifies for Cdr is found within the genic context of the ars operon. We suggest that this protein could be restoring antioxidants molecules, necessary for the As(V) reduction. Additionally, among the proteins that change their expression against As, we found several with functions relevant to stress response, e.g., Hpf, LuxS, GLpX, GlnE, and Fur. This study allowed us to shed light into the physiology necessary for these bacteria to be able to tolerate the toxicity and stress generated by the presence of arsenic in their niche.
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Affiliation(s)
- Juan Castro-Severyn
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Coral Pardo-Esté
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Yoelvis Sulbaran
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Carolina Cabezas
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Valentina Gariazzo
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Alan Briones
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Naiyulin Morales
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Martial Séveno
- BioCampus Montpellier, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Mathilde Decourcelle
- BioCampus Montpellier, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | | | - Francisco Remonsellez
- Laboratorio de Microbiología Aplicada y Extremófilos, Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile.,Centro de Investigación Tecnológica del Agua en el Desierto (CEITSAZA), Universidad Católica del Norte, Antofagasta, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Franck Molina
- Sys2Diag, UMR9005 CNRS ALCEDIAG, Montpellier, France
| | | | - Claudia P Saavedra
- Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Chimienti F, Cavarec L, Vincent L, Salvetat N, Arango V, Underwood MD, Mann JJ, Pujol JF, Weissmann D. Correction: Brain region-specific alterations of RNA editing in PDE8A mRNA in suicide decedents. Transl Psychiatry 2019; 9:112. [PMID: 30872571 PMCID: PMC6418082 DOI: 10.1038/s41398-019-0453-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Author forgot to attach a supplementary doc file which includes the supplementary methods and supplementary figure legends.
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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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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van der Laan S, Salvetat N, Weissmann D, Molina F. Emerging RNA editing biomarkers will foster drug development. Drug Discov Today 2017; 22:1056-1063. [PMID: 28188894 DOI: 10.1016/j.drudis.2017.01.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/19/2016] [Accepted: 01/30/2017] [Indexed: 01/02/2023]
Abstract
Unanticipated adverse drug reactions (ADRs) on the central nervous system are a major cause of clinical attrition and market withdrawal. Current practices for their prospective assessment still lean on extensive analysis of rodent behaviour despite their highly controversial predictive value. Human-derived in vitro models that objectively quantify mechanism-related biomarkers can greatly contribute to better ADR prediction at early developmental stages. Adenosine-to-inosine RNA editing constitutes a physiological cellular process that translates environmental cues by regulating protein function at the synaptic level in health and disease. Robust solutions based on NGS-based quantification of RNA editing biomarkers have emerged to predict the likelihood of treatment-related suicidal ideation and behaviour allowing cost-effective high-throughput drug screening as a strategy for risk mitigation.
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Affiliation(s)
- Siem van der Laan
- Sys2Diag FRE3690 CNRS/ALCEDIAG, Complex System Modeling and Engineering for Diagnosis, Cap delta/Parc Euromédecine, 1682 rue de la Valsière CS 61003, 34184 Montpellier Cedex 4, France.
| | - Nicolas Salvetat
- Sys2Diag FRE3690 CNRS/ALCEDIAG, Complex System Modeling and Engineering for Diagnosis, Cap delta/Parc Euromédecine, 1682 rue de la Valsière CS 61003, 34184 Montpellier Cedex 4, France
| | - Dinah Weissmann
- Sys2Diag FRE3690 CNRS/ALCEDIAG, Complex System Modeling and Engineering for Diagnosis, Cap delta/Parc Euromédecine, 1682 rue de la Valsière CS 61003, 34184 Montpellier Cedex 4, France
| | - Franck Molina
- Sys2Diag FRE3690 CNRS/ALCEDIAG, Complex System Modeling and Engineering for Diagnosis, Cap delta/Parc Euromédecine, 1682 rue de la Valsière CS 61003, 34184 Montpellier Cedex 4, France.
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Malaud E, Merle D, Piquer D, Molina L, Salvetat N, Rubrecht L, Dupaty E, Galea P, Cobo S, Blanc A, Saussine M, Marty-Ané C, Albat B, Meilhac O, Rieunier F, Pouzet A, Molina F, Laune D, Fareh J. Local carotid atherosclerotic plaque proteins for the identification of circulating biomarkers in coronary patients. Atherosclerosis 2014; 233:551-558. [PMID: 24530963 DOI: 10.1016/j.atherosclerosis.2013.12.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/18/2013] [Accepted: 12/09/2013] [Indexed: 10/25/2022]
Abstract
OBJECTIVE To identify circulating biomarkers that originate from atherosclerotic vulnerable plaques and that could predict future cardiovascular events. METHODS After a protein enrichment step (combinatorial peptide ligand library approach), we performed a two-dimensional electrophoresis comparative analysis on human carotid plaque protein extracts (fibrotic and hemorrhagic atherosclerotic plaques). In silico analysis of the biological processes was applied on proteomic data. Luminex xMAP assays were used to quantify inflammatory components in carotid plaques. The systemic quantification of proteins originating from vulnerable plaques in blood samples from patients with stable and unstable coronary disease was evaluated. RESULTS A total of 118 proteins are differentially expressed in fibrotic and hemorrhagic plaques, and allowed the identification of three biological processes related to atherosclerosis (platelet degranulation, vascular autophagy and negative regulation of fibrinolysis). The multiplex assays revealed an increasing expression of VEGF, IL-6, IL-8, IP-10 and RANTES in hemorrhagic as compared to fibrotic plaques (p<0.05). Measurement of protein expressions in plasmas from patients with stable and unstable coronary disease identified a combination of biomarkers, including proteins of the smooth muscle cell integrity (Calponin-1), oxidative stress (DJ-1) and inflammation (IL-8), that allows the accurate classification of patients at risk (p=0.0006). CONCLUSION Using tissue protein enrichment technology, we validated proteins that are differentially expressed in hemorrhagic plaques as potential circulating biomarkers of coronary patients. Combinations of such circulating biomarkers could be used to stratify coronary patients.
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Affiliation(s)
- Eric Malaud
- UMR3145 CNRS Bio-Rad, SysDiag, Montpellier, France
| | | | | | | | | | | | | | | | - Sandra Cobo
- UMR3145 CNRS Bio-Rad, SysDiag, Montpellier, France
| | | | - Max Saussine
- Vascular Surgery Department, Arnaud de Villeneuve Hospital, CHU Montpellier, France
| | - Charles Marty-Ané
- Vascular Surgery Department, Arnaud de Villeneuve Hospital, CHU Montpellier, France
| | - Bernard Albat
- Vascular Surgery Department, Arnaud de Villeneuve Hospital, CHU Montpellier, France
| | | | | | - Agnes Pouzet
- Bio-Rad Laboratories, Marnes la Coquette, France
| | | | - Daniel Laune
- UMR3145 CNRS Bio-Rad, SysDiag, Montpellier, France
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Roubille F, Delseny D, Cristol JP, Merle D, Salvetat N, Larue C, Davy JM, Leclercq F, Pasquie JL, Guerrier L, Fareh J, Dupuy AM. Depletion of proBNP1-108 in patients with heart failure prevents cross-reactivity with natriuretic peptides. PLoS One 2013; 8:e75174. [PMID: 24069392 PMCID: PMC3775813 DOI: 10.1371/journal.pone.0075174] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 08/12/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND After synthesis by cardiomyocytes, precursor proBNP1-108 is cleaved into NT-proBNP and BNP. Recently, cross-reactivity between these assays was discussed. The aim of this study was to characterize the cross-reactivities, through a new biochemical innovative approach consisting in the total depletion of the circulating proBNP1-108 in patients with heart failure (HF). METHODS This prospective study included 180 patients with chronic HF. BNP and NT-proBNP were dosed with commercial kits. ProBNP1-108 was determined using an ELISA research assay specific to the precursor. ProBNP1-108 depletion was performed by immunocapture with a specific antibody targeting exclusively the ProBNP1-108 hinge region. ProBNP1-108, BNP and NT-proBNP levels were determined before and after depletion using this process in HF patients. RESULTS Mean age was 74.34 +/-12.5 y, and 69% of patients were males. NYHA classes II and III were the most frequent (32% and 45% respectively). Before depletion, ProBNP1-108, NT-proBNP and BNP levels were 316.8+/-265.9 pg/ml; 6,054.0+/-11,539 pg/ml and 684.3+/-82.1 pg/ml respectively, and were closely correlated with NHYA classes. After immuno-depletion, proBNP1-108 was decreased in mean by 96% (p<0.0001), BNP by 53% (p<0.0001) and NT-proBNP by 5%. The relationship between BNP or NT-proBNP and NHYA classes remained unchanged. CONCLUSION Current BNP and NT-proBNP assays measured as well proBNP molecule. This cross reactivity percentage has been controversial. Thanks to the removal of circulating proBNP1-108 with our immunodepletion process, we are now able to assess the remaining "true" BNP and NT-proBNP molecules and further evaluate their clinical relevance.
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Affiliation(s)
- François Roubille
- Cardiology Department, University Hospital of Montpellier, Université de Montpellier 1, Montpellier, France
- Research Center, Montreal Heart Institute, Université de Montréal, Montreal, Quebec, Canada
- * E-mail:
| | - Delphine Delseny
- Cardiology Department, University Hospital of Montpellier, Université de Montpellier 1, Montpellier, France
| | - Jean-Paul Cristol
- Department of Biochemistry, University Hospital of Montpellier, Université de Montpellier 1, Montpellier, France
| | | | | | | | - Jean-Marc Davy
- Cardiology Department, University Hospital of Montpellier, Université de Montpellier 1, Montpellier, France
| | - Florence Leclercq
- Cardiology Department, University Hospital of Montpellier, Université de Montpellier 1, Montpellier, France
| | - Jean-Luc Pasquie
- Cardiology Department, University Hospital of Montpellier, Université de Montpellier 1, Montpellier, France
| | - Luc Guerrier
- Bio-Rad Laboratories, Marnes la Coquette, France
| | | | - Anne-Marie Dupuy
- Department of Biochemistry, University Hospital of Montpellier, Université de Montpellier 1, Montpellier, France
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Roubille F, Delseny D, Cristol JP, Salvetat N, Larue C, Davy JM, Leclercq F, Guerrier L, Fareh J, Dupuy AM. Depletion of proBNP1-108 in HF patients prevents cross-reactivity with natriuretic peptides. Is it clinically relevant? Eur Heart J 2013. [DOI: 10.1093/eurheartj/eht309.p4237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abraham JD, Promé S, Salvetat N, Rubrecht L, Cobo S, du Paty E, Galéa P, Mathieu-Dupas E, Ranaldi S, Caillava C, Crémer GA, Rieunier F, Robert P, Molina F, Laune D, Checler F, Fareh J. Cerebrospinal Aβ11-x and 17-x levels as indicators of mild cognitive impairment and patients' stratification in Alzheimer's disease. Transl Psychiatry 2013; 3:e281. [PMID: 23860482 PMCID: PMC3731790 DOI: 10.1038/tp.2013.58] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 05/25/2013] [Indexed: 01/08/2023] Open
Abstract
In the present work, the concentrations of Aβ11-x and Aβ17-x peptides (x=40 or 42), which result from the combined cleavages of β-amyloid precursor protein (AβPP) by β'/α or α/γ-secretases, respectively, were assessed in cerebrospinal fluid (CSF) samples from patients with Alzheimer's disease (AD) or mild cognitive impairment (MCI). Specific multiplexed assays were set up using new anti-40 and anti-42 monoclonal antibodies (mAbs) for the capture of these N-truncated Aβ peptides and anti-11 or anti-17 mAbs for their detection. The specificity, sensitivity and reproducibility of such assays were assessed using synthetic peptides and human cell models. Aβ11-x and Aβ17-x were then measured in CSF samples from patients with AD (n=23), MCI (n=23) and controls with normal cognition (n=21). Aβ11-x levels were significantly lower in patients with MCI than in controls. Compared with the combined quantification of Aβ1-42, total Tau (T-Tau) and phosphorylated Tau (P-Tau; AlzBio3, Innogenetics), the association of Aβ11-40, Aβ17-40 and T-Tau improved the discrimination between MCI and controls. Furthermore, when patients with MCI were classified into two subgroups (MCI ≤1.5 or ≥2 based on their CDR-SB (Cognitive Dementia Rating-Sum of Boxes) score), the CSF Aβ17-40/Aβ11-40 ratio was significantly higher in patients with CDR-SB ≤1.5 than in controls, whereas neither Aβ1-42, T-Tau nor P-Tau allowed the detection of this subpopulation. These results need to be confirmed in a larger clinical prospective cohort.
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Affiliation(s)
- J-D Abraham
- SysDiag CNRS/Bio-Rad UMR3145, Montpellier, France.
| | - S Promé
- SysDiag CNRS/Bio-Rad UMR3145, Montpellier, France
| | - N Salvetat
- SysDiag CNRS/Bio-Rad UMR3145, Montpellier, France
| | - L Rubrecht
- SysDiag CNRS/Bio-Rad UMR3145, Montpellier, France
| | - S Cobo
- SysDiag CNRS/Bio-Rad UMR3145, Montpellier, France
| | - E du Paty
- SysDiag CNRS/Bio-Rad UMR3145, Montpellier, France
| | - P Galéa
- SysDiag CNRS/Bio-Rad UMR3145, Montpellier, France
| | | | - S Ranaldi
- SysDiag CNRS/Bio-Rad UMR3145, Montpellier, France
| | - C Caillava
- Institut de Pharmacologie Moléculaire et Cellulaire, UMR7275, team labelized by the ‘Fondation pour la Recherche Médicale' and LABEX (Laboratory of Excellence), Valbonne, France
| | - G-A Crémer
- Bio-Rad Laboratories, Marnes la Coquette, France
| | - F Rieunier
- Bio-Rad Laboratories, Marnes la Coquette, France
| | - P Robert
- CMRR, Memory Center, EA CoBTeK, University of Nice Sophia-Antipolis, Nice, France
| | - F Molina
- SysDiag CNRS/Bio-Rad UMR3145, Montpellier, France
| | - D Laune
- SysDiag CNRS/Bio-Rad UMR3145, Montpellier, France
| | - F Checler
- Institut de Pharmacologie Moléculaire et Cellulaire, UMR7275, team labelized by the ‘Fondation pour la Recherche Médicale' and LABEX (Laboratory of Excellence), Valbonne, France
| | - J Fareh
- SysDiag CNRS/Bio-Rad UMR3145, Montpellier, France
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Molina L, Fasquelle L, Nouvian R, Salvetat N, Scott HS, Guipponi M, Molina F, Puel JL, Delprat B. Tmprss3 loss of function impairs cochlear inner hair cell Kcnma1 channel membrane expression. Hum Mol Genet 2012; 22:1289-99. [PMID: 23255163 DOI: 10.1093/hmg/dds532] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Before acquiring their mature state, cochlear hair cells undergo a series of changes in expression of ion channels. How this complex mechanism is achieved is not fully understood. Tmprss3, a type II serine protease expressed in hair cells, is required for their proper functioning at the onset of hearing. To unravel the role of Tmprss3 in the acquisition of mature K(+) currents, we compared their function by patch-clamp technique in wild-type Tmprss3(WT) and Tmprss3(Y260X)-mutant mice. Interestingly, only outward K(+) currents were altered in Tmprss3(Y260X)-mutant mice. To determine by which mechanism this occurred, we compared the protein network of Tmprss3(WT) and Tmprss3(Y260X)-mutant mice using proteomic analysis. This led to the identification of a pathway related to potassium Kcnma1 channels. This pathway was validated by immunohistochemistry, focusing on the most downregulated protein that was identified as a cochlear Kcnma1-associated protein, APOA1. Finally, we show that, in contrast to Tmprss3(WT), Kcnma1 channels were absent at the neck of inner hair cells (IHCs) in Tmprss3(Y260X)-mutant mice. In conclusion, our data suggest that lack of Tmprss3 leads to a decrease in Kcnma1 potassium channels expression in (IHCs).
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Affiliation(s)
- Laurence Molina
- SysDiag UMR 3145 CNRS/Bio-Rad, Cap Delta/Parc Euromédecine, 1682 rue de la Valsière, Cedex 4,Montpellier, France
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Cavarec L, Vincent L, Le Borgne C, Plusquellec C, Ollivier N, Normandie-Levi P, Allemand F, Salvetat N, Mathieu-Dupas E, Molina F, Weissmann D, Pujol JF. In vitro screening for drug-induced depression and/or suicidal adverse effects: a new toxicogenomic assay based on CE-SSCP analysis of HTR2C mRNA editing in SH-SY5Y cells. Neurotox Res 2012; 23:49-62. [PMID: 22528247 DOI: 10.1007/s12640-012-9324-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 03/28/2012] [Accepted: 03/30/2012] [Indexed: 02/02/2023]
Abstract
Many drugs in clinical trials, or already on the market, can have psychiatric side effects, independently of their therapeutic indication (e.g., Acomplia, Taranabant, and Roaccutane). There is currently no in vitro or in vivo approved test for the detection/prediction of such adverse effects, and the Food and Drugs Administration (FDA) can only issue general alerts on specific therapeutic classes. The development of a screening assay is therefore of real interest. The anti-viral and anti-tumor action of human interferon-alpha (hIFNα) is associated with a variety of neuropsychiatric side effects, including major depression, suicidal ideation and suicide. RNA editing of the serotonin 2C receptor (HTR2C) by adenosine deaminases acting on RNA (ADARs) is a post-transcriptional modification, the regulation of which is altered in depressed suicide victims. In this study, we show that in the SH-SY5Y neuroblastoma cell line, hIFNα specifically activates the ADAR1a isoform and thereby modifies the HTR2C mRNA editing profile. As this hIFNα-induced altered profile partly overlaps with that observed in the brain of depressed suicide victims, we investigated whether it could be used as a signature to identify drugs with depression and/or suicidal side effects. By means of the Biocortech proprietary screening assay, which allows the relative quantification of all the edited HTR2C isoforms in a sample, we blind-tested the effect of 50 marketed molecules on HTR2C mRNA editing in SH-SY5Y cells and identified 17 compounds with an IFN-like editing profile. This new toxicogenomic assay can identify compounds with potential psychiatric adverse events with a positive predictive value of 90 %.
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Affiliation(s)
- Laurent Cavarec
- Biocortech SAS, 8 rue de la Croix de Jarry, BioPark, 75013 Paris, France
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Molina L, Salvetat N, Ameur RB, Peres S, Sommerer N, Jarraya F, Ayadi H, Molina F, Granier C. Analysis of the variability of human normal urine by 2D-GE reveals a “public” and a “private” proteome. J Proteomics 2011; 75:70-80. [DOI: 10.1016/j.jprot.2011.06.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 06/22/2011] [Accepted: 06/25/2011] [Indexed: 01/30/2023]
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Abraham JD, Calvayrac-Pawlowski S, Cobo S, Salvetat N, Vicat G, Molina L, Touchon J, Michel BF, Molina F, Verdier JM, Fareh J, Mourton-Gilles C. Combined measurement of PEDF, haptoglobin and tau in cerebrospinal fluid improves the diagnostic discrimination between alzheimer’s disease and other dementias. Biomarkers 2011; 16:161-71. [DOI: 10.3109/1354750x.2010.536995] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jean-Daniel Abraham
- SysDiag CNRS / Bio-Rad UMR3145, 1682 rue de la Valsiere, Montpellier, France
| | | | - Sandra Cobo
- SysDiag CNRS / Bio-Rad UMR3145, 1682 rue de la Valsiere, Montpellier, France
| | - Nicolas Salvetat
- SysDiag CNRS / Bio-Rad UMR3145, 1682 rue de la Valsiere, Montpellier, France
| | - Guillaume Vicat
- SysDiag CNRS / Bio-Rad UMR3145, 1682 rue de la Valsiere, Montpellier, France
| | - Laurence Molina
- SysDiag CNRS / Bio-Rad UMR3145, 1682 rue de la Valsiere, Montpellier, France
| | - Jacques Touchon
- Neurology Service, Gui de Chauliac Hospital, 80 Avenue Augustin Fliche, Montpellier, France
| | - Bernard-François Michel
- Univ. Montpellier 2, Montpellier, F-34095 France; Inserm, U710, Montpellier, F-34095 France; EPHE, Paris, F-75007 France
| | - Franck Molina
- SysDiag CNRS / Bio-Rad UMR3145, 1682 rue de la Valsiere, Montpellier, France
| | - Jean-Michel Verdier
- Univ. Montpellier 2, Montpellier, F-34095 France; Inserm, U710, Montpellier, F-34095 France; EPHE, Paris, F-75007 France
| | - Jeannette Fareh
- SysDiag CNRS / Bio-Rad UMR3145, 1682 rue de la Valsiere, Montpellier, France
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Batxelli-Molina I, Salvetat N, Andréoletti O, Guerrier L, Vicat G, Molina F, Mourton-Gilles C. Ovine serum biomarkers of early and late phase scrapie. BMC Vet Res 2010; 6:49. [PMID: 21044301 PMCID: PMC2988006 DOI: 10.1186/1746-6148-6-49] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 11/02/2010] [Indexed: 01/03/2023] Open
Abstract
Background Transmissible spongiform encephalopathies are fatal neurodegenerative disease occurring in animals and humans for which no ante-mortem diagnostic test in biological fluids is available. In such pathologies, detection of the pathological form of the prion protein (i.e., the causative factor) in blood is difficult and therefore identification of new biomarkers implicated in the pathway of prion infection is relevant. Methods In this study we used the SELDI-TOF MS technology to analyze a large number of serum samples from control sheep and animals with early phase or late phase scrapie. A few potential low molecular weight biomarkers were selected by statistical methods and, after a training analysis, a protein signature pattern, which discriminates between early phase scrapie samples and control sera was identified. Results The combination of early phase biomarkers showed a sensitivity of 87% and specificity of 90% for all studied sheep in the early stage of the disease. One of these potential biomarkers was identified and validated in a SELDI-TOF MS kinetic study of sera from Syrian hamsters infected by scrapie, by western blot analysis and ELISA quantitation. Conclusions Differential protein expression profiling allows establishing a TSE diagnostic in scrapie sheep, in the early phase of the disease. Some proteic differences observed in scrapie sheep exist in infected hamsters. Further studies are being performed to identify all the discriminant biomarkers of interest and to test our potential markers in a new cohort of animals.
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Affiliation(s)
- Isabelle Batxelli-Molina
- Complex system modeling and engineering for diagnosis, SysDiag - UMR 3145 CNRS/Bio-Rad, 34184 Montpellier Cedex 4, France.
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Pérès S, Molina L, Salvetat N, Granier C, Molina F. A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics. BMC Bioinformatics 2008; 9:460. [PMID: 18957120 PMCID: PMC2628390 DOI: 10.1186/1471-2105-9-460] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Accepted: 10/28/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In current comparative proteomics studies, the large number of images generated by 2D gels is currently compared using spot matching algorithms. Unfortunately, differences in gel migration and sample variability make efficient spot alignment very difficult to obtain, and, as consequence most of the software alignments return noisy gel matching which needs to be manually adjusted by the user. RESULTS We present Sili2DGel an algorithm for automatic spot alignment that uses data from recursive gel matching and returns meaningful Spot Alignment Positions (SAP) for a given set of gels. In the algorithm, the data are represented by a graph and SAP by specific subgraphs. The results are returned under various forms (clickable synthetic gel, text file, etc.). We have applied Sili2DGel to study the variability of the urinary proteome from 20 healthy subjects. CONCLUSION Sili2DGel performs noiseless automatic spot alignment for variability studies (as well as classical differential expression studies) of biological samples. It is very useful for typical clinical proteomic studies with large number of experiments.
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Affiliation(s)
- Sabine Pérès
- Sysdiag CNRS FRE 3009 BIO-RAD, Cap delta/Parc Euromédecine, 1682 rue de la Valsière, CS 61003, 34184 Montpellier Cedex 4, France.
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Abraham JDD, Pawlowsky S, Cobo S, Mondon MCC, Vicat G, Salvetat N, Touchon J, Michel B, Verdier JMM, Fareh J, Mourton-Gilles C. P3-059: Combination of CSF PEDF, Haptoglobin and Tau measurements improves Alzheimer diagnosis. Alzheimers Dement 2008. [DOI: 10.1016/j.jalz.2008.05.1623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | | | - Sandra Cobo
- CNRS FRE3009 Bio-Rad SysDiag; Montpellier France
| | | | | | | | - Jacques Touchon
- Neurology Department; Gui de Chauliac Hospital; Montpellier France
| | - Bernard Michel
- INSERM UM2 EPHE U710, Montpellier 2 University; Montpellier France
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Chanrion M, Negre V, Fontaine H, Salvetat N, Bibeau F, Mac Grogan G, Mauriac L, Katsaros D, Molina F, Theillet C, Darbon JM. A gene expression signature that can predict the recurrence of tamoxifen-treated primary breast cancer. Clin Cancer Res 2008; 14:1744-52. [PMID: 18347175 DOI: 10.1158/1078-0432.ccr-07-1833] [Citation(s) in RCA: 138] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The identification of a molecular signature predicting the relapse of tamoxifen-treated primary breast cancers should help the therapeutic management of estrogen receptor-positive cancers. EXPERIMENTAL DESIGN A series of 132 primary tumors from patients who received adjuvant tamoxifen were analyzed for expression profiles at the whole-genome level by 70-mer oligonucleotide microarrays. A supervised analysis was done to identify an expression signature. RESULTS We defined a 36-gene signature that correctly classified 78% of patients with relapse and 80% of relapse-free patients (79% accuracy). Using 23 independent tumors, we confirmed the accuracy of the signature (78%) whose relevance was further shown by using published microarray data from 60 tamoxifen-treated patients (63% accuracy). Univariate analysis using the validation set of 83 tumors showed that the 36-gene classifier is more efficient in predicting disease-free survival than the traditional histopathologic prognostic factors and is as effective as the Nottingham Prognostic Index or the "Adjuvant!" software. Multivariate analysis showed that the molecular signature is the only independent prognostic factor. A comparison with several already published signatures demonstrated that the 36-gene signature is among the best to classify tumors from both training and validation sets. Kaplan-Meier analyses emphasized its prognostic power both on the whole cohort of patients and on a subgroup with an intermediate risk of recurrence as defined by the St. Gallen criteria. CONCLUSION This study identifies a molecular signature specifying a subgroup of patients who do not gain benefits from tamoxifen treatment. These patients may therefore be eligible for alternative endocrine therapies and/or chemotherapy.
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Affiliation(s)
- Maïa Chanrion
- U868 Institut National de la Sante et de la Recherche Medicale, Tumoral Identity and Plasticity, Cancer Research Center of Montpellier, Université Montpellier 1, CRLC Val d'Aurelle-Paul Lamarque, France
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Del Rio M, Molina F, Bascoul-Mollevi C, Copois V, Bibeau F, Chalbos P, Bareil C, Kramar A, Salvetat N, Fraslon C, Conseiller E, Granci V, Leblanc B, Pau B, Martineau P, Ychou M. Gene expression signature in advanced colorectal cancer patients select drugs and response for the use of leucovorin, fluorouracil, and irinotecan. J Clin Oncol 2007; 25:773-80. [PMID: 17327601 PMCID: PMC2257989 DOI: 10.1200/jco.2006.07.4187] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
PURPOSE In patients with advanced colorectal cancer, leucovorin, fluorouracil, and irinotecan (FOLFIRI) is considered as one of the reference first-line treatments. However, only about half of treated patients respond to this regimen, and there is no clinically useful marker that predicts response. A major clinical challenge is to identify the subset of patients who could benefit from this chemotherapy. We aimed to identify a gene expression profile in primary colon cancer tissue that could predict chemotherapy response. PATIENTS AND METHODS Tumor colon samples from 21 patients with advanced colorectal cancer were analyzed for gene expression profiling using Human Genome GeneChip arrays U133. At the end of the first-line treatment, the best observed response, according to WHO criteria, was used to define the responders and nonresponders. Discriminatory genes were first selected by the significance analysis of microarrays algorithm and the area under the receiver operating characteristic curve. A predictor classifier was then constructed using support vector machines. Finally, leave-one-out cross validation was used to estimate the performance and the accuracy of the output class prediction rule. RESULTS We determined a set of 14 predictor genes of response to FOLFIRI. Nine of nine responders (100% specificity) and 11 of 12 nonresponders (92% sensitivity) were classified correctly, for an overall accuracy of 95%. CONCLUSION After validation in an independent cohort of patients, our gene signature could be used as a decision tool to assist oncologists in selecting colorectal cancer patients who could benefit from FOLFIRI chemotherapy, both in the adjuvant and the first-line metastatic setting.
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Affiliation(s)
- Maguy Del Rio
- Centre National de la Recherche Scientifique Unité Mixte de Recherche 5160, Service d'Anatomie pathologique, Service d'Oncologie Digestive, Montpellier, France.
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Copois V, Bibeau F, Bascoul-Mollevi C, Salvetat N, Chalbos P, Bareil C, Candeil L, Fraslon C, Conseiller E, Granci V, Mazière P, Kramar A, Ychou M, Pau B, Martineau P, Molina F, Del Rio M. Impact of RNA degradation on gene expression profiles: assessment of different methods to reliably determine RNA quality. J Biotechnol 2006; 127:549-59. [PMID: 16945445 DOI: 10.1016/j.jbiotec.2006.07.032] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 07/21/2006] [Accepted: 07/27/2006] [Indexed: 11/24/2022]
Abstract
DNA microarray technology enables investigators to measure the expression of several 1000 mRNA species simultaneously in a biological specimen. However, the reliability of the microarray technology to detect transcriptional differences representative of the original samples is affected by the quality of the extracted RNA. Thus, it is of critical importance to standardize sample-handling protocols and to perform a quality assessment of RNA preparations. In this report, 59 human tissue samples were used to evaluate the relationships between RNA quality and gene expression. From Affymetrix GeneChip array data analysis of these samples, we compared the performance of the 28S/18S ratio, two computer methods (RIN and degradometer) and our in-house RNA quality scale (RQS) in assessing RNA quality. The optimal RNA reliability threshold was determined for each method using statistical discrimination measures. We showed that RQS, RIN and degradometer have a similar capacity to detect reliable RNA samples whereas the 28S/18S ratio leads to a misleading categorization. Furthermore, we developed a new approach, based on clustering analyses of full chip expression, to control RNA quality after hybridization experiments. The combination of these methods, allowing monitoring of RNA quality prior to and after the hybridization experiments, ensured reliable and reproducible microarray data.
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