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Carneiro BA, Franco Guerreiro-Costa LN, Lins-Silva D, Faria Guimaraes D, Souza LS, Leal GC, Caliman-Fontes AT, Beanes G, Costa RDS, Quarantini LC. MicroRNAs as Diagnostic Biomarkers and Predictors of Antidepressant Response in Major Depressive Disorder: A Systematic Review. Cureus 2024; 16:e56910. [PMID: 38665721 PMCID: PMC11043793 DOI: 10.7759/cureus.56910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2024] [Indexed: 04/28/2024] Open
Abstract
Despite the hardships of major depressive disorder (MDD), biomarkers for the diagnosis and pharmacological management of this condition are lacking. MicroRNAs are epigenetic mechanisms that could provide promising MDD biomarkers. Our aim was to summarize the findings and provide validation for the selection and use of specific microRNAs as biomarkers in the diagnosis and treatment of MDD. A systematic review was conducted using the PubMed/Medline, Cochrane, PsycINFO, Embase, and LILACS databases from March 2022 to November 2023, with clusters of terms based on "microRNA" and "antidepressant". Studies involving human subjects, animal models, and cell cultures were included, whereas those that evaluated herbal medicines, non-pharmacological therapies, or epigenetic mechanisms other than miRNA were excluded. The review revealed differences in the expression of various microRNAs when considering the time of assessment (before or after antidepressant treatment) and the population studied. However, due to the heterogeneity of the microRNAs investigated, the limited size of the samples, and the wide variety of antidepressants used, few conclusions could be made. Despite the observed heterogeneity, the following microRNAs were determined to be important factors in MDD and the antidepressant response: mir-1202, mir-135, mir-124, and mir-16. The findings indicate the potential for the use of microRNAs as biomarkers for the diagnosis and treatment of MDD; however, more homogeneous studies are needed.
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Affiliation(s)
- Beatriz A Carneiro
- Medicine, Laboratório de Neuropsicofarmacologia, Serviço de Psiquiatria do Hospital Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, BRA
| | | | - Daniel Lins-Silva
- Medicine, Laboratório de Neuropsicofarmacologia, Serviço de Psiquiatria do Hospital Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, BRA
| | - Daniela Faria Guimaraes
- Medicine, Laboratório de Neuropsicofarmacologia, Serviço de Psiquiatria do Hospital Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, BRA
| | - Lucca S Souza
- Medicine, Laboratório de Neuropsicofarmacologia, Serviço de Psiquiatria do Hospital Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, BRA
| | - Gustavo C Leal
- Medicine, Programa de Pós-Graduação em Medicina e Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, BRA
| | - Ana Teresa Caliman-Fontes
- Medicine, Programa de Pós-Graduação em Medicina e Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador, BRA
| | - Graziele Beanes
- Medicine, Laboratório de Neuropsicofarmacologia, Serviço de Psiquiatria do Hospital Universitário Professor Edgard Santos, Universidade Federal da Bahia, Salvador, BRA
| | - Ryan Dos S Costa
- Medicine, Laboratório de Imunofarmacologia e Biologia Molecular, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, BRA
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Yuan M, Yang B, Rothschild G, Mann JJ, Sanford LD, Tang X, Huang C, Wang C, Zhang W. Epigenetic regulation in major depression and other stress-related disorders: molecular mechanisms, clinical relevance and therapeutic potential. Signal Transduct Target Ther 2023; 8:309. [PMID: 37644009 PMCID: PMC10465587 DOI: 10.1038/s41392-023-01519-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 05/14/2023] [Accepted: 05/31/2023] [Indexed: 08/31/2023] Open
Abstract
Major depressive disorder (MDD) is a chronic, generally episodic and debilitating disease that affects an estimated 300 million people worldwide, but its pathogenesis is poorly understood. The heritability estimate of MDD is 30-40%, suggesting that genetics alone do not account for most of the risk of major depression. Another factor known to associate with MDD involves environmental stressors such as childhood adversity and recent life stress. Recent studies have emerged to show that the biological impact of environmental factors in MDD and other stress-related disorders is mediated by a variety of epigenetic modifications. These epigenetic modification alterations contribute to abnormal neuroendocrine responses, neuroplasticity impairment, neurotransmission and neuroglia dysfunction, which are involved in the pathophysiology of MDD. Furthermore, epigenetic marks have been associated with the diagnosis and treatment of MDD. The evaluation of epigenetic modifications holds promise for further understanding of the heterogeneous etiology and complex phenotypes of MDD, and may identify new therapeutic targets. Here, we review preclinical and clinical epigenetic findings, including DNA methylation, histone modification, noncoding RNA, RNA modification, and chromatin remodeling factor in MDD. In addition, we elaborate on the contribution of these epigenetic mechanisms to the pathological trait variability in depression and discuss how such mechanisms can be exploited for therapeutic purposes.
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Affiliation(s)
- Minlan Yuan
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Biao Yang
- Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Gerson Rothschild
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - J John Mann
- Department of Psychiatry, Columbia University, New York, NY, 10032, USA
- Molecular Imaging and Neuropathology Division, New York State Psychiatric Institute, New York, NY, 10032, USA
- Department of Radiology, Columbia University, New York, NY, 10032, USA
| | - Larry D Sanford
- Sleep Research Laboratory, Center for Integrative Neuroscience and Inflammatory Diseases, Pathology and Anatomy, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Xiangdong Tang
- Sleep Medicine Center, Department of Respiratory and Critical Care Medicine, Mental Health Center, Translational Neuroscience Center, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Canhua Huang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Chuang Wang
- Department of Pharmacology, and Provincial Key Laboratory of Pathophysiology in School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China.
| | - Wei Zhang
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Medical Big Data Center, Sichuan University, Chengdu, 610041, China.
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3
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Ryan KM, Smyth P, Blackshields G, Kranaster L, Sartorius A, Sheils O, McLoughlin DM. Electroconvulsive Stimulation in Rats Induces Alterations in the Hippocampal miRNome: Translational Implications for Depression. Mol Neurobiol 2023; 60:1150-1163. [PMID: 36414911 DOI: 10.1007/s12035-022-03131-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/09/2022] [Indexed: 11/24/2022]
Abstract
MicroRNAs (miRNAs) may contribute to the development of depression and its treatment. Here, we used the hypothesis-neutral approach of next-generation sequencing (NGS) to gain comprehensive understanding of the effects of a course of electroconvulsive stimulation (ECS), the animal model equivalent of electroconvulsive therapy (ECT), on rat hippocampal miRNAs. Significant differential expression (p < 0.001) of six hippocampal miRNAs was noted following NGS, after correcting for multiple comparisons. Three of these miRNAs were upregulated (miR-132, miR-212, miR-331) and three downregulated (miR-204, miR-483, miR-301a). qRT-PCR confirmed significant changes in four of the six miRNAs (miR-132, miR-212, miR-204, miR-483). miR-483 was also significantly reduced in frontal cortex, though no other significant alterations were noted in frontal cortex, cerebellum, or whole blood. Assessing the translatability of the results, miR-132 and miR-483 were significantly reduced in whole blood samples from medicated patients with depression (n = 50) compared to healthy controls (n = 45), though ECT had no impact on miRNA levels. Notably, pre-ECT miR-204 levels moderately positively correlated with depression severity at baseline and moderately negatively correlated with mood score reduction post-ECT. miRNAs were also examined in cerebrospinal fluid and serum from a separate cohort of patients (n = 8) treated with ECT; no significant changes were noted post-treatment. However, there was a large positive correlation between changes in miR-212 and mood score post-ECT in serum. Though replication studies using larger sample sizes are required, alterations in miRNA expression may be informative about the mechanism of action of ECS/ECT and in turn might give insight into the neurobiology of depression.
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Affiliation(s)
- Karen M Ryan
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland. .,Department of Psychiatry, Trinity College Dublin, St Patrick's University Hospital, Dublin 8, Ireland.
| | - Paul Smyth
- Department of Histopathology, Trinity Translational Medicine Institute, Trinity College Dublin, St. James's Hospital, Dublin, Ireland
| | - Gordon Blackshields
- Department of Histopathology, Trinity Translational Medicine Institute, Trinity College Dublin, St. James's Hospital, Dublin, Ireland
| | - Laura Kranaster
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty, Mannheim/Heidelberg University, Mannheim, Germany
| | - Alexander Sartorius
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty, Mannheim/Heidelberg University, Mannheim, Germany
| | - Orla Sheils
- Department of Histopathology, Trinity Translational Medicine Institute, Trinity College Dublin, St. James's Hospital, Dublin, Ireland
| | - Declan M McLoughlin
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland.,Department of Psychiatry, Trinity College Dublin, St Patrick's University Hospital, Dublin 8, Ireland
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4
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Tsermpini EE, Kalogirou CI, Kyriakopoulos GC, Patrinos GP, Stathopoulos C. miRNAs as potential diagnostic biomarkers and pharmacogenomic indicators in psychiatric disorders. THE PHARMACOGENOMICS JOURNAL 2022; 22:211-222. [PMID: 35725816 DOI: 10.1038/s41397-022-00283-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/23/2022] [Accepted: 06/08/2022] [Indexed: 12/11/2022]
Abstract
The heterogeneity of psychiatric disorders and the lack of reliable biomarkers for prediction and treatments follow-up pose difficulties towards recognition and understanding of the molecular basis of psychiatric diseases. However, several studies based on NGS approaches have shown that miRNAs could regulate gene expression during onset and disease progression and could serve as potential diagnostic and pharmacogenomics biomarkers during treatment. We provide herein a detailed overview of circulating miRNAs and their expression profiles as biomarkers in schizophrenia, bipolar disorder and major depressive disorder and their role in response to specific treatments. Bioinformatics analysis of miR-34a, miR-106, miR-134 and miR-132, which are common among SZ, BD and MDD patients, showed brain enrichment and involvement in the modulation of critical signaling pathways, which are often deregulated in psychiatric disorders. We propose that specific miRNAs support accurate diagnosis and effective precision treatment of psychiatric disorders.
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Affiliation(s)
- Evangelia Eirini Tsermpini
- Pharmacogenetics Laboratory, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Christina I Kalogirou
- Department of Biochemistry, School of Medicine, University of Patras, Patras, Greece
| | | | - George P Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, School of Health Sciences, Department of Pharmacy, University of Patras, Patras, Greece
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Emerging role of microRNAs as novel targets of antidepressants. Asian J Psychiatr 2021; 66:102906. [PMID: 34740127 DOI: 10.1016/j.ajp.2021.102906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/20/2021] [Indexed: 12/31/2022]
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6
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Ortega MA, Alvarez-Mon MA, García-Montero C, Fraile-Martinez O, Lahera G, Monserrat J, Muñoz-Merida L, Mora F, Rodríguez-Jiménez R, Fernandez-Rojo S, Quintero J, Álvarez-Mon M. MicroRNAs as Critical Biomarkers of Major Depressive Disorder: A Comprehensive Perspective. Biomedicines 2021; 9:biomedicines9111659. [PMID: 34829888 PMCID: PMC8615526 DOI: 10.3390/biomedicines9111659] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/05/2021] [Accepted: 11/08/2021] [Indexed: 12/23/2022] Open
Abstract
Major Depressive Disorder (MDD) represents a major global health concern, a body-mind malady of rising prevalence worldwide nowadays. The complex network of mechanisms involved in MDD pathophysiology is subjected to epigenetic changes modulated by microRNAs (miRNAs). Serum free or vesicles loaded miRNAs have starred numerous publications, denoting a key role in cell-cell communication, systematically and in brain structure and neuronal morphogenesis, activity and plasticity. Upregulated or downregulated expression of these signaling molecules may imply the impairment of genes implicated in pathways of MDD etiopathogenesis (neuroinflammation, brain-derived neurotrophic factor (BDNF), neurotransmitters, hypothalamic-pituitary-adrenal (HPA) axis, oxidative stress, circadian rhythms...). In addition, these miRNAs could serve as potential biomarkers with diagnostic, prognostic and predictive value, allowing to classify severity of the disease or to make decisions in clinical management. They have been considered as promising therapy targets as well and may interfere with available antidepressant treatments. As epigenetic malleable regulators, we also conclude emphasizing lifestyle interventions with physical activity, mindfulness and diet, opening the door to new clinical management considerations.
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Affiliation(s)
- Miguel A. Ortega
- Department of Medicine and Medical Specialities, University of Alcala, 28801 Alcalá de Henares, Spain; (M.A.O.); (C.G.-M.); (O.F.-M.); (G.L.); (J.M.); (L.M.-M.); (M.Á.-M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
- Cancer Registry and Pathology Department, Hospital Universitario Principe de Asturias, 28806 Alcalá de Henares, Spain; (F.M.); (S.F.-R.); (J.Q.)
| | - Miguel Angel Alvarez-Mon
- Department of Medicine and Medical Specialities, University of Alcala, 28801 Alcalá de Henares, Spain; (M.A.O.); (C.G.-M.); (O.F.-M.); (G.L.); (J.M.); (L.M.-M.); (M.Á.-M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
- Department of Psychiatry and Mental Health, Hospital Universitario Infanta Leonor, 28031 Madrid, Spain
- Correspondence:
| | - Cielo García-Montero
- Department of Medicine and Medical Specialities, University of Alcala, 28801 Alcalá de Henares, Spain; (M.A.O.); (C.G.-M.); (O.F.-M.); (G.L.); (J.M.); (L.M.-M.); (M.Á.-M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Oscar Fraile-Martinez
- Department of Medicine and Medical Specialities, University of Alcala, 28801 Alcalá de Henares, Spain; (M.A.O.); (C.G.-M.); (O.F.-M.); (G.L.); (J.M.); (L.M.-M.); (M.Á.-M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Guillermo Lahera
- Department of Medicine and Medical Specialities, University of Alcala, 28801 Alcalá de Henares, Spain; (M.A.O.); (C.G.-M.); (O.F.-M.); (G.L.); (J.M.); (L.M.-M.); (M.Á.-M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
- Psychiatry Service, Center for Biomedical Research in the Mental Health Network, University Hospital Príncipe de Asturias, 28806 Alcalá de Henares, Spain
| | - Jorge Monserrat
- Department of Medicine and Medical Specialities, University of Alcala, 28801 Alcalá de Henares, Spain; (M.A.O.); (C.G.-M.); (O.F.-M.); (G.L.); (J.M.); (L.M.-M.); (M.Á.-M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
| | - Luis Muñoz-Merida
- Department of Medicine and Medical Specialities, University of Alcala, 28801 Alcalá de Henares, Spain; (M.A.O.); (C.G.-M.); (O.F.-M.); (G.L.); (J.M.); (L.M.-M.); (M.Á.-M.)
| | - Fernando Mora
- Cancer Registry and Pathology Department, Hospital Universitario Principe de Asturias, 28806 Alcalá de Henares, Spain; (F.M.); (S.F.-R.); (J.Q.)
- Department of Legal Medicine and Psychiatry, Complutense University, 28040 Madrid, Spain;
| | - Roberto Rodríguez-Jiménez
- Department of Legal Medicine and Psychiatry, Complutense University, 28040 Madrid, Spain;
- Institute for Health Research Hospital 12 de Octubre (imas 12), CIBERSAM, 28041 Madrid, Spain
| | - Sonia Fernandez-Rojo
- Cancer Registry and Pathology Department, Hospital Universitario Principe de Asturias, 28806 Alcalá de Henares, Spain; (F.M.); (S.F.-R.); (J.Q.)
- Department of Legal Medicine and Psychiatry, Complutense University, 28040 Madrid, Spain;
| | - Javier Quintero
- Cancer Registry and Pathology Department, Hospital Universitario Principe de Asturias, 28806 Alcalá de Henares, Spain; (F.M.); (S.F.-R.); (J.Q.)
- Department of Legal Medicine and Psychiatry, Complutense University, 28040 Madrid, Spain;
| | - Melchor Álvarez-Mon
- Department of Medicine and Medical Specialities, University of Alcala, 28801 Alcalá de Henares, Spain; (M.A.O.); (C.G.-M.); (O.F.-M.); (G.L.); (J.M.); (L.M.-M.); (M.Á.-M.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain
- Immune System Diseases-Rheumatology, Oncology Service an Internal Medicine, University Hospital Príncipe de Asturias, (CIBEREHD), 28806 Alcalá de Henares, Spain
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RETRACTED ARTICLE: MiR-151-3p transferred by cancer-associated fibroblast-derived extracellular vesicles promotes osteosarcoma progression through the CHL1/integrin 1β/TGF-β axis. Cancer Gene Ther 2021; 28:1390. [PMID: 33723405 PMCID: PMC8636259 DOI: 10.1038/s41417-021-00304-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 01/19/2021] [Accepted: 02/01/2021] [Indexed: 11/18/2022]
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The Importance of Epigenetics in Diagnostics and Treatment of Major Depressive Disorder. J Pers Med 2021; 11:jpm11030167. [PMID: 33804455 PMCID: PMC7999864 DOI: 10.3390/jpm11030167] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/09/2021] [Accepted: 02/17/2021] [Indexed: 12/15/2022] Open
Abstract
Recent studies imply that there is a tight association between epigenetics and a molecular mechanism of major depressive disorder (MDD). Epigenetic modifications, i.e., DNA methylation, post-translational histone modification and interference of microRNA (miRNA) or long non-coding RNA (lncRNA), are able to influence the severity of the disease and the outcome of the therapy. This article summarizes the most recent literature data on this topic, i.e., usage of histone deacetylases as therapeutic agents with an antidepressant effect and miRNAs or lncRNAs as markers of depression. Due to the noteworthy potential of the role of epigenetics in MDD diagnostics and therapy, we have gathered the most relevant data in this area.
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Jonchhe S, Selvam S, Karna D, Mandal S, Wales-McGrath B, Mao H. Ensemble Sensing Using Single-Molecule DNA Copolymers. Anal Chem 2020; 92:13126-13133. [PMID: 32829637 PMCID: PMC7757751 DOI: 10.1021/acs.analchem.0c02196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While single-molecule sensing has offered ultimate mass sensitivity at the precision of individual molecules, it requires a longer time to detect analytes at lower concentrations when analyte binding to single-molecule probes becomes diffusion-limited. Here, we solved this accuracy problem in the concentration sensitivity determination by using single-molecule DNA homopolymers, in which up to 473 identical sensing elements (DNA hairpins) were introduced by rolling circle amplification. Surprisingly, the DNA homopolymers containing as few as 10 tandem hairpins displayed ensemble unfolding/refolding transitions, which were exploited to recognize microRNAs (miRNAs) that populated unfolded hairpins. Within 20 min, the femtomolar detection limit for miRNAs was observed, 6 orders of magnitude better than standalone hairpins. By incorporating different hairpin probes in an alternating DNA copolymer, multiplex recognition of different miRNAs was demonstrated. These DNA co-polymers represent new materials for innovative sensing strategies that combine the single-molecule precision with the accuracy of ensemble assays to determine concentration sensitivities.
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Affiliation(s)
- Sagun Jonchhe
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, United States
| | - Sangeetha Selvam
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, United States
| | - Deepak Karna
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, United States
| | - Shankar Mandal
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, United States
| | - Benjamin Wales-McGrath
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, United States
| | - Hanbin Mao
- Department of Chemistry & Biochemistry and School of Biomedical Sciences, Kent State University, Kent, Ohio 44242, United States
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Barakat AK, Scholl C, Steffens M, Brandenburg K, Ising M, Lucae S, Holsboer F, Laje G, Kalayda GV, Jaehde U, Stingl JC. Citalopram-induced pathways regulation and tentative treatment-outcome-predicting biomarkers in lymphoblastoid cell lines from depression patients. Transl Psychiatry 2020; 10:210. [PMID: 32612257 PMCID: PMC7329820 DOI: 10.1038/s41398-020-00900-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 06/08/2020] [Accepted: 06/16/2020] [Indexed: 12/17/2022] Open
Abstract
Antidepressant therapy is still associated with delays in symptomatic improvement and low response rates. Incomplete understanding of molecular mechanisms underlying antidepressant effects hampered the identification of objective biomarkers for antidepressant response. In this work, we studied transcriptome-wide expression followed by pathway analysis in lymphoblastoid cell lines (LCLs) derived from 17 patients documented for response to SSRI antidepressants from the Munich Antidepressant Response Signatures (MARS) study upon short-term incubation (24 and 48 h) with citalopram. Candidate transcripts were further validated with qPCR in MARS LCLs from responders (n = 33) vs. non-responders (n = 36) and afterward in an independent cohort of treatment-resistant patients (n = 20) vs. first-line responders (n = 24) from the STAR*D study. In MARS cohort we observed significant associations of GAD1 (glutamate decarboxylase 1; p = 0.045), TBC1D9 (TBC1 Domain Family Member 9; p = 0.014-0.021) and NFIB (nuclear factor I B; p = 0.015-0.025) expression with response status, remission status and improvement in depression scale, respectively. Pathway analysis of citalopram-altered gene expression indicated response-status-dependent transcriptional reactions. Whereas in clinical responders neural function pathways were primarily up- or downregulated after incubation with citalopram, deregulated pathways in non-responders LCLs mainly involved cell adhesion and immune response. Results from the STAR*D study showed a marginal association of treatment-resistant depression with NFIB (p = 0.068) but not with GAD1 (p = 0.23) and TBC1D9 (p = 0.27). Our results propose the existence of distinct pathway regulation mechanisms in responders vs. non-responders and suggest GAD1, TBC1D9, and NFIB as tentative predictors for clinical response, full remission, and improvement in depression scale, respectively, with only a weak overlap in predictors of different therapy outcome phenotypes.
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Affiliation(s)
- Abdul Karim Barakat
- grid.414802.b0000 0000 9599 0422Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany ,grid.10388.320000 0001 2240 3300Department of Clinical Pharmacy, University of Bonn, Bonn, Germany
| | - Catharina Scholl
- grid.414802.b0000 0000 9599 0422Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany
| | - Michael Steffens
- grid.414802.b0000 0000 9599 0422Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany
| | - Kerstin Brandenburg
- grid.414802.b0000 0000 9599 0422Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany
| | - Marcus Ising
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, Munich, Germany
| | - Susanne Lucae
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, Munich, Germany
| | - Florian Holsboer
- grid.419548.50000 0000 9497 5095Max Planck Institute of Psychiatry, Munich, Germany
| | - Gonzalo Laje
- Washington Behavioral Medicine Associates LLC, Chevy Chase, MD USA
| | - Ganna V. Kalayda
- grid.10388.320000 0001 2240 3300Department of Clinical Pharmacy, University of Bonn, Bonn, Germany
| | - Ulrich Jaehde
- grid.10388.320000 0001 2240 3300Department of Clinical Pharmacy, University of Bonn, Bonn, Germany
| | - Julia Carolin Stingl
- Institute of Clinical Pharmacology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany.
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Downregulation of Adhesion Molecule CHL1 in B Cells but Not T Cells of Patients with Major Depression and in the Brain of Mice with Chronic Stress. Neurotox Res 2020; 38:914-928. [PMID: 32557322 DOI: 10.1007/s12640-020-00234-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/25/2020] [Accepted: 05/29/2020] [Indexed: 12/19/2022]
Abstract
Depression is a common serious mental disorder with unclear pathogenesis. Currently, specific diagnostic biomarkers are yet to be characterized. The close homolog of L1 (CHL1) is a L1 family cell adhesion molecule involved in the regulation of neuronal survival and growth. Although genome-wide expression profiling of human lymphoblastoid cell lines (LCLs) reported neural cell adhesion molecule (NCAM) L1 as a tentative biomarker for selective serotonin reuptake inhibitor (SSRI) antidepressant response, the involvement of CHL1 in depression is unclear. In this study, using a well-established chronic unpredictable mild stress (CUMS) depression mouse model, we examined the mRNA and protein expression of CHL1 in normal control, CUMS, vehicle (VEH), fluoxetine (FLU), and clozapine (CLO) groups. We found that in the CUMS group, both mRNA and protein expression of CHL1 were downregulated in both the hippocampus and the cortex. Treatment of CUMS mice with FLU and CLO reversed CHL1 mRNA and protein expression. In the human study, we showed that CHL1 expression was significantly downregulated in monocytes of unipolar and bipolar depressive patients compared with healthy donors (HD) at both mRNA and protein levels. Consistently, ELISA showed that CHL1 levels in the serum of patients with depression were reduced and negatively correlated with their HRSD-21 scores. Further flow cytometry studies showed that the reduced number of CHL1 positive CD19+ and CD20+ B cells of patients with depression was subsequently reversed with antidepressant treatment. Our findings suggested that downregulation of CHL1 from both immune cells and the brain may be linked to the immunopathogenesis of depression. In conclusion, CHL1 may be an important predictive marker for both diagnosis and treatment outcome of depression.
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12
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Lin CC, Huang TL. Brain-derived neurotrophic factor and mental disorders. Biomed J 2020; 43:134-142. [PMID: 32386841 PMCID: PMC7283564 DOI: 10.1016/j.bj.2020.01.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 01/21/2020] [Accepted: 01/21/2020] [Indexed: 12/26/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) is a neurotrophin that modulates neuroplasticity in the brain, and is one of the most widely investigated molecule in psychiatric disorders. The researches of BDNF emcompassed the advance of investigative techniques of past decades. BDNF researches ranged from protein quantilization, to RNA expression measurements, to DNA sequencing, and lately but not lastly, epigenetic studies. In this review, we will briefly address findings on BDNF protein levels, mRNA expression, Val66Met polymorphism, and epigenetic modifications, in schizophrenia, major depressive disorder (MDD), and bipolar disorder.
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Affiliation(s)
- Chin-Chuen Lin
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tiao-Lai Huang
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan; Genomic and Proteomic Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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13
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Sun N, Yang C, He X, Liu Z, Liu S, Li X, Wang Y, Jin R, Zhang K. Impact of Expression and Genetic Variation of microRNA-34b/c on Cognitive Dysfunction in Patients with Major Depressive Disorder. Neuropsychiatr Dis Treat 2020; 16:1543-1554. [PMID: 32606706 PMCID: PMC7311205 DOI: 10.2147/ndt.s247787] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/17/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Patients suffering from major depressive disorder (MDD) commonly demonstrate lower performance across multiple cognitive domains. Cognitive impairment is an intrinsic characteristic of MDD status and is often influenced by genetic factors. microRNAs (miRNAs or miRs) have been shown to have important implications in the etiology of MDD. Therefore, we aimed to identify and analyze the impact of expression and genetic variation of miR-34b/c on cognitive dysfunction in MDD. METHODS First, we analyzed miR-34c-5p expression in 48 cases of MDD and 54 healthy controls in a Chinese population using qRT-PCR. We assessed the relationship between the level of miR-34c-5p expression and cognitive performance by Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) and the Trail Making Test (TMT). Second, in order to characterize allelic effects of miR-34b/c on cognitive performance in MDD patients, we performed genetic association analysis of single-nucleotide polymorphism (SNP) loci of the MIR34B/C genes with cognitive function in a second group consisting of 531 MDD patients and 267 healthy controls. RESULTS We found a significant negative correlation between the level of miR-34c-5p expression and both the language and delayed memory index scores in patients with MDD. We also found a significant positive correlation between the level of miR-34c-5p expression and the time required to complete tests A and B of the TMT. The interaction between the rs2187473 genotype and the disease was significant for both immediate memory and delayed memory. In the patient group, the rs2187473 CC genotype was significantly associated with higher performance on immediate memory (F = 6.683, p < 0.05) and delayed memory tasks (F = 4.221, p < 0.05). CONCLUSION Our findings suggest that changes in miR-34c expression level have important impacts on cognitive function in patients with MDD. In particular, the polymorphism rs2187473 is a potential genetic risk factor for cognitive function in MDD, which may be of clinical use.
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Affiliation(s)
- Ning Sun
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China.,Nursing College of Shanxi Medical University, Taiyuan, People's Republic of China
| | - Chunxia Yang
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China
| | - Xiaoting He
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China.,University-Town Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Zhifen Liu
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China
| | - Sha Liu
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China
| | - Xinrong Li
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China
| | - Yanfang Wang
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China
| | - Ruihua Jin
- Nursing College of Shanxi Medical University, Taiyuan, People's Republic of China
| | - Kerang Zhang
- Department of Psychiatry, First Hospital of Shanxi Medical University, Taiyuan, People's Republic of China
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14
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Xu YY, Xia QH, Xia QR, Zhang XL, Liang J. MicroRNA-Based Biomarkers in the Diagnosis and Monitoring of Therapeutic Response in Patients with Depression. Neuropsychiatr Dis Treat 2019; 15:3583-3597. [PMID: 31920318 PMCID: PMC6939173 DOI: 10.2147/ndt.s237116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 12/16/2019] [Indexed: 12/25/2022] Open
Abstract
Depression is a debilitating mental illness that affects up to 120 million people worldwide; it is currently determined based on subjective diagnostic schemes that are limited by high uncertainty. Hence, there is an urgent need to identify effective and reliable biomarkers to increase diagnostic accuracy. MicroRNAs (miRNAs) constitute a recently discovered class of non-coding RNAs that play a key role in the regulation of gene expression by modulating translation, messenger RNA (mRNA) degradation, or stability of mRNA targets. Dysregulated expression of miRNAs is being investigated as a clinical biomarker for a variety of diseases, including depression. Accumulating evidence has shown that miRNAs participate in many aspects of neural plasticity, neurogenesis, and the stress response. This is supported by more direct studies based on human postmortem brain tissue that strongly indicate that miRNAs not only play a key role in the pathogenesis of major depressive disorder, but also present potential for the development of therapeutic targets. miRNAs in the peripheral and central nervous system are being considered as potential biomarkers in the diagnosis of depression and in monitoring the therapeutic response to antidepressants, owing to their stability, tissue-specificity, and disease-specific expression. In this review, we focus on various miRNAs in tissues and fluids that could be employed as diagnostic and therapeutic biomarkers in patients with depression.
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Affiliation(s)
- Ya-Yun Xu
- Department of Pharmacy, Hefei Fourth People’s Hospital, Hefei230000, People’s Republic of China
- CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei230022, People’s Republic of China
- Department of Psychopharmacology, Anhui Mental Health Center, Hefei230000, People’s Republic of China
- Department of Clinical Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei230000, People’s Republic of China
| | - Qian-Hui Xia
- School of Pharmacy, Wannan Medical College, Wuhu241002, People’s Republic of China
| | - Qing-Rong Xia
- Department of Pharmacy, Hefei Fourth People’s Hospital, Hefei230000, People’s Republic of China
- Department of Psychopharmacology, Anhui Mental Health Center, Hefei230000, People’s Republic of China
- Department of Clinical Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei230000, People’s Republic of China
| | - Xu-Lai Zhang
- Department of Geriatric Psychology, Hefei Fourth People’s Hospital, Hefei230000, People’s Republic of China
- Clinical School of Mental Health, Anhui Medical University, Hefei230000, People’s Republic of China
| | - Jun Liang
- Department of Pharmacy, Hefei Fourth People’s Hospital, Hefei230000, People’s Republic of China
- Department of Psychopharmacology, Anhui Mental Health Center, Hefei230000, People’s Republic of China
- Department of Clinical Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei230000, People’s Republic of China
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15
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Pfau ML, Menard C, Cathomas F, Desland F, Kana V, Chan KL, Shimo Y, LeClair K, Flanigan ME, Aleyasin H, Walker DM, Bouchard S, Mack M, Hodes GE, Merad MM, Russo SJ. Role of Monocyte-Derived MicroRNA106b∼25 in Resilience to Social Stress. Biol Psychiatry 2019; 86:474-482. [PMID: 31101319 PMCID: PMC6717005 DOI: 10.1016/j.biopsych.2019.02.023] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 02/13/2019] [Accepted: 02/28/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Clinical studies suggest that heightened peripheral inflammation contributes to the pathogenesis of stress-related disorders, including major depressive disorder. However, the molecular mechanisms within peripheral immune cells that mediate enhanced stress vulnerability are not well known. Because microRNAs (miRs) are important regulators of immune response, we sought to examine their role in mediating inflammatory and behavioral responses to repeated social defeat stress (RSDS), a mouse model of stress vulnerability that produces susceptible and resilient phenotypes. METHODS We isolated Ly6chigh monocytes via fluorescence-activated cell sorting in the blood of susceptible and resilient mice following RSDS and profiled miR expression via quantitative real-time polymerase chain reaction. Bone marrow chimeric mice were generated to confirm a causal role of the miR-106b∼25 cluster in bone marrow-derived leukocytes in mediating stress resilience versus susceptibility. RESULTS We found that RSDS produces an increase in circulating Ly6chigh inflammatory monocytes in both susceptible and resilient mice. We next investigated whether intrinsic leukocyte posttranscriptional mechanisms contribute to individual differences in stress response and the resilient phenotype. Of the miRs profiled in our panel, eight were significantly regulated by RSDS within Ly6chigh monocytes, including miR-25-3p, a member of the miR-106b∼25 cluster. Selective knockout of the miR-106b∼25 cluster in peripheral leukocytes promoted behavioral resilience to RSDS. CONCLUSIONS Our results identify the miR-106b∼25 cluster as a key regulator of stress-induced inflammation and depression that may represent a novel therapeutic target for drug development.
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Affiliation(s)
- Madeline L Pfau
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Center for Affective Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Caroline Menard
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry and Neuroscience, Faculty of Medicine and Cervo Brain Research Center, Université Laval, Quebec City, Quebec, Canada
| | - Flurin Cathomas
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Center for Affective Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Fiona Desland
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Oncological Science, Tisch Cancer Institute and Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Veronika Kana
- Department of Oncological Science, Tisch Cancer Institute and Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kenny L Chan
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Center for Affective Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yusuke Shimo
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Center for Affective Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Katherine LeClair
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Center for Affective Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Meghan E Flanigan
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Center for Affective Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Hossein Aleyasin
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Center for Affective Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Deena M Walker
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Center for Affective Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sylvain Bouchard
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Matthias Mack
- Department of Internal Medicine II, University Hospital Regensburg, Regensburg, Germany
| | - Georgia E Hodes
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
| | - Miriam M Merad
- Department of Oncological Science, Tisch Cancer Institute and Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Scott J Russo
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Center for Affective Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York.
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16
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miRNAs in depression vulnerability and resilience: novel targets for preventive strategies. J Neural Transm (Vienna) 2019; 126:1241-1258. [PMID: 31350592 PMCID: PMC6746676 DOI: 10.1007/s00702-019-02048-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 07/11/2019] [Indexed: 02/06/2023]
Abstract
The exposure to stressful experiences during the prenatal period and through the first years of life is known to affect the brain developmental trajectories, leading to an enhanced vulnerability for the development of several psychiatric disorders later in life. However, not all the subjects exposed to the same stressful experience develop a pathologic condition, as some of them, activating coping strategies, become more resilient. The disclosure of mechanisms associated with stress vulnerability or resilience may allow the identification of novel biological processes and potential molecules that, if properly targeted, may prevent susceptibility or potentiate resilience. Over the last years, miRNAs have been proposed as one of the epigenetic mechanisms mediating the long-lasting effects of stress. Accordingly, they are associated with the development of stress vulnerability or resilience-related strategies. Moreover, miRNAs have been proposed as possible biomarkers able to identify subjects at high risk to develop depression and to predict the response to pharmacological treatments. In this review, we aimed to provide an overview of findings from studies in rodents and humans focused on the involvement of miRNAs in the mechanisms of stress response with the final goal to identify distinct sets of miRNAs involved in stress vulnerability or resilience. In addition, we reviewed studies on alterations of miRNAs in the context of depression, showing data on the involvement of miRNAs in the pathogenesis of the disease and in the efficacy of pharmacological treatments, discussing the potential utility of miRNAs as peripheral biomarkers able to predict the treatment response.
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17
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Tang C, Zhou H, Zheng X, Zhang Y, Sha X. Dual Laplacian regularized matrix completion for microRNA-disease associations prediction. RNA Biol 2019; 16:601-611. [PMID: 30676207 PMCID: PMC6546388 DOI: 10.1080/15476286.2019.1570811] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 11/30/2018] [Accepted: 01/03/2019] [Indexed: 01/21/2023] Open
Abstract
Since lots of miRNA-disease associations have been verified, it is meaningful to discover more miRNA-disease associations for serving disease diagnosis and prevention of human complex diseases. However, it is not practical to identify potential associations using traditional biological experimental methods since the process is expensive and time consuming. Therefore, it is necessary to develop efficient computational methods to accomplish this task. In this work, we introduced a matrix completion model with dual Laplacian regularization (DLRMC) to infer unknown miRNA-disease associations in heterogeneous omics data. Specifically, DLRMC transformed the task of miRNA-disease association prediction into a matrix completion problem, in which the potential missing entries of the miRNA-disease association matrix were calculated, the missing association can be obtained based on the prediction scores after the completion procedure. Meanwhile, the miRNA functional similarity and the disease semantic similarity were fully exploited to serve the miRNA-disease association matrix completion by using a dual Laplacian regularization term. In the experiments, we conducted global and local Leave-One-Out Cross Validation (LOOCV) and case studies to evaluate the efficacy of DLRMC on the Human miRNA-disease associations dataset obtained from the HMDDv2.0 database. As a result, the AUCs of DLRMC is 0.9174 and 0.8289 in global LOOCV and local LOOCV, respectively, which significantly outperform a variety of previous methods. In addition, in the case studies on four significant diseases related to human health including Colon Neoplasms, Kidney neoplasms, Lymphoma and Prostate neoplasms, 90%, 92%, 92% and 94% out of the top 50 predicted miRNAs has been confirmed, respectively.
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Affiliation(s)
- Chang Tang
- School of Computer Science, China University of Geosciences, Wuhan, China
| | - Hua Zhou
- Department of Hematology, The Affiliated Huai’an Hospital of Xuzhou Medical University, Huai’an, China
| | - Xiao Zheng
- Wuhan University of Technology Hospital, Wuhan University of Technology, Wuhan, China
| | - Yanming Zhang
- Department of Hematology, The Affiliated Huai’an Hospital of Xuzhou Medical University, Huai’an, China
| | - Xiaofeng Sha
- Department of Oncology, Huai’an Hongze District People’s Hospital, Huai’an, China
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18
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Fries GR, Zhang W, Benevenuto D, Quevedo J. MicroRNAs in Major Depressive Disorder. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1118:175-190. [PMID: 30747423 DOI: 10.1007/978-3-030-05542-4_9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Major depressive disorder (MDD) is a severe and chronic psychiatric disorder with a high prevalence in the population. Although our understanding of its pathophysiological mechanisms has significantly increased over the years, available treatments still present several limitations and are not effective to all MDD patients. Epigenetic mechanisms have recently been suggested to play key roles in MDD pathogenesis and treatment, including the effects of small noncoding RNAs known as microRNAs (miRNAs). miRNAs can modulate gene expression posttranscriptionally by interfering with the stability and translation of messenger RNA molecules and are also known to cross-talk with other epigenetic mechanisms. In this review, we will summarize and discuss recent findings of alterations in miRNAs in tissues of patients with MDD and evidence of treatment-induced effects in these molecules.
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Affiliation(s)
- Gabriel R Fries
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Wei Zhang
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Deborah Benevenuto
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - Joao Quevedo
- Translational Psychiatry Program, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA.
- Center of Excellence on Mood Disorders, Department of Psychiatry and Behavioral Sciences, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA.
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.
- Translational Psychiatry Laboratory, Graduate Program in Health Sciences, University of Southern Santa Catarina (UNESC), Criciúma, SC, Brazil.
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19
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MiR-155 is involved in major depression disorder and antidepressant treatment via targeting SIRT1. Biosci Rep 2018; 38:BSR20181139. [PMID: 30482883 PMCID: PMC6435510 DOI: 10.1042/bsr20181139] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 11/14/2018] [Accepted: 11/21/2018] [Indexed: 12/26/2022] Open
Abstract
Major depressive disorder (MDD) is a common mood disorder, and the treatment of MDD requires a variety of biopsychosocial approaches. The role of Silent information regulator 1 (SIRT1) in the regulation of MDD has recently been implicated. Here, we aimed to explore and elucidate the therapeutic effects of a microRNA, miR-155, in the treatment of MDD. With quantitative real-time PCR (qRT-PCR) analysis, we confirmed that cellular and serum levels of miR-155 were up-regulated in individuals with depression compared with those in healthy controls. TargetScan analysis indicated that SIRT1 is a target of miR-155, which was confirmed by dual-luciferase assay, qRT-PCR and Western blot analyses. Treatment of human neural progenitor cells with the antidepressant drug citalopram down-regulated miR-155 expression and up-regulated SIRT1 expression. These results suggest that miR-155 is an important factor in the pathophysiology of depression. miR-155 is a potential target for the development of new antidepressant treatments.
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20
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Lin CC, Tsai MC, Lee CT, Sun MH, Huang TL. Antidepressant treatment increased serum miR-183 and miR-212 levels in patients with major depressive disorder. Psychiatry Res 2018; 270:232-237. [PMID: 30269040 DOI: 10.1016/j.psychres.2018.09.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 09/12/2018] [Accepted: 09/12/2018] [Indexed: 11/29/2022]
Abstract
Major depressive disorder (MDD) had been associated with brain-derived neurotrophic factor (BDNF). Studies had shown that patients with MDD were associated with lower BDNF protein levels, which could be reversed by antidepressant treatment. BDNF expression had also been affected by a number of microRNAs (miRNA). BDNF and miRNA in MDD had been investigated widely in the recent years, but the relationships between miRNAs and antidepressants were less studied. From November 2015 to October 2017, inpatients diagnosed with MDD were recruited. Serum miR-16, miR-30, miR-34, miR-128, miR-132, miR-134, miR-182, miR-183, miR-185, miR-212 levels were measured before and after four weeks of antidepressant treatment of either selective serotonin reuptake inhibitor (SSRI) or serotonin-norepinephrine reuptake inhibitor (SNRI). Thirty-three patients with MDD were recruited. After treatment, miR-183 and miR-212 levels increased significantly. In patients treated with SSRI (n = 13), miR-16 levels increased significantly after treatment. Therefore, miR-183 and miR-212 levels increased significantly after four weeks of antidepressant treatment. In the SSRI group, significantly increased miR-16 levels were found, but not in SNRI group, suggesting that different types of antidepressants might affect different sets of miRNAs.
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Affiliation(s)
- Chin-Chuen Lin
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Meng-Chang Tsai
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chien-Te Lee
- Division of Nephrology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ming-Hsiang Sun
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Tiao-Lai Huang
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.
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21
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Calabrò M, Mandelli L, Crisafulli C, Lee SJ, Jun TY, Wang SM, Patkar AA, Masand PS, Benedetti F, Han C, Pae CU, Serretti A. Neuroplasticity, Neurotransmission and Brain-Related Genes in Major Depression and Bipolar Disorder: Focus on Treatment Outcomes in an Asiatic Sample. Adv Ther 2018; 35:1656-1670. [PMID: 30178121 PMCID: PMC6182627 DOI: 10.1007/s12325-018-0781-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Indexed: 02/06/2023]
Abstract
Introduction Mood disorders are common and disabling disorders. Despite the availability of over 100 psychotropic compounds, only one-third of patients benefit from first-line treatments. Over the past 20 years, many studies have focused on the biological factors modulating disease risk and response to treatments, but with still inconclusive data. In order to improve our current knowledge, in this study, we investigated the role of a set of genes involved in different pathways (neurotransmission, neuroplasticity, circadian rhythms, transcription factors, signal transduction and cellular metabolism) in the treatment outcome of major depressive disorder (MDD) and bipolar disorder (BD) after naturalistic pharmacological treatment. Methods Totals of 242 MDD, 132 BD patients and 326 healthy controls of Asian ethnicity (Koreans) were genotyped for polymorphisms within 19 genes. Response and remission after 6–8 weeks of treatment with antidepressants and mood stabilizers were evaluated. In secondary analyses, genetic associations with disease risk and some disease-associated features (age of onset, suicide attempt and psychotic BD) were also tested. Results None of the variants within the investigated genes was significantly associated with treatment outcomes. Some marginal association (uncorrected p < 0.01) was observed for HTR2A, BDNF, CHL1, RORA and HOMER1 SNPs. In secondary analyses, HTR2A (rs643627, p = 0.002) and CHL1 (rs4003413, p = 0.002) were found associated with risk for BD, HOMER1 (rs6872497, p = 0.002) with lifetime history of suicide attempt in patients, and RORA with early onset and presence of psychotic features in BD. Marginal results were also observed for ST8SIA2 and COMT. Discussion Despite limitations linked to multiple testing on small samples, methodological shortcomings and small significance of the findings, this study may support the involvement of some candidate genes in the outcomes of treatments for mood disorders, as well as in BD risk and other disease features. Electronic supplementary material The online version of this article (10.1007/s12325-018-0781-2) contains supplementary material, which is available to authorized users.
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22
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Liu S, Zhou B, Wang L, Hu H, Yao C, Cai Z, Cui X. Therapeutic Antidepressant Potential of NONHSAG045500 in Regulating Serotonin Transporter in Major Depressive Disorder. Med Sci Monit 2018; 24:4465-4473. [PMID: 29955033 PMCID: PMC6055515 DOI: 10.12659/msm.908543] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background Major depressive disorder (MDD) is a chronic, life-threatening, highly disabling disease. Standardized treatment with fewer adverse effects, quick onset, and long-term maintenance of the effects of brief treatment for MDD is always being pursued. Long non-coding RNAs (lncRNAs) are highly expressed in the central nervous system and are involved in the occurrence and development of neurodegenerative and psychiatric diseases. This study aimed to investigate whether the overexpression and interference of 3 differentially down-regulated lncRNAs (NONHSAT142707, NONHSAG045500, and ENST00000517573) in MDD can affect the expression of central neurotransmitter serotonin (5-hydroxytryptamine) transporter (SERT) in vitro. Material/Methods First, we synthesized and validated the effect of 3 lncRNA plasmids and small interfering RNAs (siRNAs); next, we transfected the plasmids and siRNAs that caused significant overexpression or interference in SK-N-SH cells, and tested the expression of SERT by qRT-PCR. Results The results showed that 3 lncRNA plasmids and siRNAs2 caused overexpression and interference, respectively. Only the overexpression of NONHSAG045500 could significantly inhibit the expression of SERT; interference with NONHSAG045500 could significantly strengthen the expression of SERT. Conclusions This study indicated that the expression of SERT could be regulated by up-regulating or down-regulating NONHSAG045500 expression and suggested that NONHSAG045500 could potentially be established as a new therapeutic target of MDD. Future work may be needed to definitively determine the correlation between NONHSAG045500 and SERT in vivo.
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Affiliation(s)
- Song Liu
- College of Economy and Management, Changzhou Institute of Technology, Changzhou, Jiangsu, China (mainland)
| | - Beibei Zhou
- Department of Health, Changzhou Maternity and Child Health Care Hospital Affiliated with Nanjing Medical University, Changzhou, Jiangsu, China (mainland)
| | - Li Wang
- Department of Medical Section, Changzhou Maternity and Child Health Care Hospital Affiliated with Nanjing Medical University, Changzhou, Jiangsu, China (mainland)
| | - Huiwen Hu
- Department of Health, Maternity and Child Health Care Hospital Affiliated with Nanjing Medical University, Changzhou, Jiangsu, China (mainland)
| | - Chanjuan Yao
- Department of Health, Changzhou Maternity and Child Health Care Hospital Affiliated with Nanjing Medical University, Changzhou, Jiangsu, China (mainland)
| | - Zhengmao Cai
- Department of Administration, Changzhou Maternity and Child Health Care Hospital Affiliated with Nanjing Medical University, Changzhou, Jiangsu, China (mainland)
| | - Xuelian Cui
- Department of Health, Changzhou Maternity and Child Health Care Hospital Affiliated with Nanjing Medical University, Changzhou, Jiangsu, China (mainland)
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Hadar A, Milanesi E, Walczak M, Puzianowska-Kuźnicka M, Kuźnicki J, Squassina A, Niola P, Chillotti C, Attems J, Gozes I, Gurwitz D. SIRT1, miR-132 and miR-212 link human longevity to Alzheimer's Disease. Sci Rep 2018; 8:8465. [PMID: 29855513 PMCID: PMC5981646 DOI: 10.1038/s41598-018-26547-6] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/15/2018] [Indexed: 01/13/2023] Open
Abstract
Alzheimer's Disease (AD) is the most common cause of dementia in the elderly. Centenarians - reaching the age of >100 years while maintaining good cognitive skills - seemingly have unique biological features allowing healthy aging and protection from dementia. Here, we studied the expression of SIRT1 along with miR-132 and miR-212, two microRNAs known to regulate SIRT1, in lymphoblastoid cell lines (LCLs) from 45 healthy donors aged 21 to 105 years and 24 AD patients, and in postmortem olfactory bulb and hippocampus tissues from 14 AD patients and 20 age-matched non-demented individuals. We observed 4.0-fold (P = 0.001) lower expression of SIRT1, and correspondingly higher expression of miR-132 (1.7-fold; P = 0.014) and miR-212 (2.1-fold; P = 0.036), in LCLs from AD patients compared with age-matched healthy controls. Additionally, SIRT1 expression was 2.2-fold (P = 0.001) higher in centenarian LCLs compared with LCLs from individuals aged 56-82 years; while centenarian LCLs miR-132 and miR-212 indicated 7.6-fold and 4.1-fold lower expression, respectively. Correlations of SIRT1, miR-132 and miR-212 expression with cognitive scores were observed for AD patient-derived LCLs and postmortem AD olfactory bulb and hippocampus tissues, suggesting that higher SIRT1 expression, possibly mediated by lower miR-132 and miR-212, may protect aged individuals from dementia and is reflected in their peripheral tissues.
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Affiliation(s)
- A Hadar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - E Milanesi
- Department of Cellular and Molecular Medicine, Victor Babes National Institute of Pathology, Bucharest, Romania
| | - M Walczak
- Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Warsaw, Poland
| | - M Puzianowska-Kuźnicka
- Department of Human Epigenetics, Mossakowski Medical Research Centre, Warsaw, Poland
- Department of Geriatrics and Gerontology, Medical Centre of Postgraduate Education, Warsaw, Poland
| | - J Kuźnicki
- The International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - A Squassina
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - P Niola
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - C Chillotti
- Unit of Clinical Pharmacology, University Hospital of Cagliari, Cagliari, Italy
| | - J Attems
- Institute of Neuroscience and Newcastle University Institute of Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - I Gozes
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
- Adams Super Center for Brain Studies, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
| | - D Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
- Adams Super Center for Brain Studies, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel.
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24
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Chen X, Zhou Z, Zhao Y. ELLPMDA: Ensemble learning and link prediction for miRNA-disease association prediction. RNA Biol 2018; 15:807-818. [PMID: 29619882 DOI: 10.1080/15476286.2018.1460016] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Recently, accumulating evidences have indicated miRNAs play critical roles in the progression and development of various human complex diseases, which pointed out that identifying miRNA-disease association could enable us to understand diseases at miRNA level. Thus, revealing more and more potential miRNA-disease associations is a vital topic in biomedical domain. However, it will be extremely expensive and time-consuming if we examine all the possible miRNA-disease pairs. Therefore, more accurate and efficient methods are being highly requested to detect potential miRNA-disease associations. In this study, we developed a computational model of Ensemble Learning and Link Prediction for miRNA-Disease Association prediction (ELLPMDA) to achieve this goal. By integrating miRNA functional similarity, disease semantic similarity, miRNA-disease association and Gaussian profile kernel similarity for miRNAs and diseases, we constructed a similarity network and utilized ensemble learning to combine rank results given by three classic similarity-based algorithms. To evaluate the performance of ELLPMDA, we exploited global and local Leave-One-Out Cross Validation (LOOCV), 5-fold Cross Validation (CV) and three kinds of case studies. As a result, the AUCs of ELLPMDA is 0.9181, 0.8181 and 0.9193+/-0.0002 in global LOOCV, local LOOCV and 5-fold CV, respectively, which significantly exceed almost all the previous methods. Moreover, in three distinct kinds of case studies for Kidney Neoplasms, Lymphoma, Prostate Neoplasms, Colon Neoplasms and Esophageal Neoplasms, 88%, 92%, 86%, 98% and 98% out of the top 50 predicted miRNAs has been confirmed, respectively. Besides, ELLPMDA is based on global similarity measure and applicable to new diseases without any known related miRNAs.
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Affiliation(s)
- Xing Chen
- a School of Information and Control Engineering, China University of Mining and Technology , Xuzhou , China
| | - Zhihan Zhou
- b School of Mathematical Science, Zhejiang University , Hangzhou , China
| | - Yan Zhao
- a School of Information and Control Engineering, China University of Mining and Technology , Xuzhou , China
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25
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Oved K, Farberov L, Gilam A, Israel I, Haguel D, Gurwitz D, Shomron N. MicroRNA-Mediated Regulation of ITGB3 and CHL1 Is Implicated in SSRI Action. Front Mol Neurosci 2017; 10:355. [PMID: 29163031 PMCID: PMC5682014 DOI: 10.3389/fnmol.2017.00355] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 10/18/2017] [Indexed: 01/05/2023] Open
Abstract
Background: Selective serotonin reuptake inhibitor (SSRI) antidepressant drugs are the first-line of treatment for major depressive disorder (MDD) but are effective in <70% of patients. Our earlier genome-wide studies indicated that two genes encoding for cell adhesion proteins, close homolog of L1 (CHL1) and integrin beta-3 (ITGB3), and microRNAs, miR-151a-3p and miR-221/222, are implicated in the variable sensitivity and response of human lymphoblastoid cell lines (LCL) from unrelated individuals to SSRI drugs. Methods: The microRNAs miR-221, miR-222, and miR-151-a-3p, along with their target gene binding sites, were explored in silico using miRBase, TargetScan, microRNAviewer, and the UCSC Genome Browser. Luciferase reporter assays were conducted for demonstrating the direct functional regulation of ITGB3 and CHL1 expression by miR-221/222 and miR-151a-3p, respectively. A human LCL exhibiting low sensitivity to paroxetine was utilized for studying the phenotypic effect of CHL1 regulation by miR-151a-3p on SSRI response. Results: By showing direct regulation of CHL1 and ITGB3 by miR-151a-3p and miR-221/222, respectively, we link these microRNAs and genes with cellular SSRI sensitivity phenotypes. We report that miR-151a-3p increases cell sensitivity to paroxetine via down-regulating CHL1 expression. Conclusions: miR-151a-3p, miR-221/222 and their (here confirmed) respective target-genes, CHL1 and ITGB3, are implicated in SSRI responsiveness, and possibly in the clinical response to antidepressant drugs.
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Affiliation(s)
- Keren Oved
- Faculty of Medicine, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Luba Farberov
- Faculty of Medicine, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Avial Gilam
- Faculty of Medicine, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Ifat Israel
- Faculty of Medicine, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Danielle Haguel
- Faculty of Medicine, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - David Gurwitz
- Faculty of Medicine, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Noam Shomron
- Faculty of Medicine, Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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26
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Li JQ, Rong ZH, Chen X, Yan GY, You ZH. MCMDA: Matrix completion for MiRNA-disease association prediction. Oncotarget 2017; 8:21187-21199. [PMID: 28177900 PMCID: PMC5400576 DOI: 10.18632/oncotarget.15061] [Citation(s) in RCA: 144] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/09/2017] [Indexed: 12/31/2022] Open
Abstract
Nowadays, researchers have realized that microRNAs (miRNAs) are playing a significant role in many important biological processes and they are closely connected with various complex human diseases. However, since there are too many possible miRNA-disease associations to analyze, it remains difficult to predict the potential miRNAs related to human diseases without a systematic and effective method. In this study, we developed a Matrix Completion for MiRNA-Disease Association prediction model (MCMDA) based on the known miRNA-disease associations in HMDD database. MCMDA model utilized the matrix completion algorithm to update the adjacency matrix of known miRNA-disease associations and furthermore predict the potential associations. To evaluate the performance of MCMDA, we performed leave-one-out cross validation (LOOCV) and 5-fold cross validation to compare MCMDA with three previous classical computational models (RLSMDA, HDMP, and WBSMDA). As a result, MCMDA achieved AUCs of 0.8749 in global LOOCV, 0.7718 in local LOOCV and average AUC of 0.8767+/−0.0011 in 5-fold cross validation. Moreover, the prediction results associated with colon neoplasms, kidney neoplasms, lymphoma and prostate neoplasms were verified. As a consequence, 84%, 86%, 78% and 90% of the top 50 potential miRNAs for these four diseases were respectively confirmed by recent experimental discoveries. Therefore, MCMDA model is superior to the previous models in that it improves the prediction performance although it only depends on the known miRNA-disease associations.
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Affiliation(s)
- Jian-Qiang Li
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Zhi-Hao Rong
- School of Software, Beihang University, Beijing, 100191, China
| | - Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China
| | - Gui-Ying Yan
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | - Zhu-Hong You
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Science, ürümqi, 830011, China
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Gurwitz D. Human iPSC-derived neurons and lymphoblastoid cells for personalized medicine research in neuropsychiatric disorders. DIALOGUES IN CLINICAL NEUROSCIENCE 2017. [PMID: 27757061 PMCID: PMC5067144 DOI: 10.31887/dcns.2016.18.3/dgurwitz] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The development and clinical implementation of personalized medicine crucially depends on the availability of high-quality human biosamples; animal models, although capable of modeling complex human diseases, cannot reflect the large variation in the human genome, epigenome, transcriptome, proteome, and metabolome. Although the biosamples available from public biobanks that store human tissues and cells may represent the large human diversity for most diseases, these samples are not always sufficient for developing biomarkers for patient-tailored therapies for neuropsychiatric disorders. Postmortem human tissues are available from many biobanks; nevertheless, collections of neuronal human cells from large patient cohorts representing the human diversity remain scarce. Two tools are gaining popularity for personalized medicine research on neuropsychiatric disorders: human induced pluripotent stem cell-derived neurons and human lymphoblastoid cell lines. This review examines and contrasts the advantages and limitations of each tool for personalized medicine research.
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Affiliation(s)
- David Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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28
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Dwivedi Y. microRNA-124: a putative therapeutic target and biomarker for major depression. Expert Opin Ther Targets 2017; 21:653-656. [PMID: 28490207 DOI: 10.1080/14728222.2017.1328501] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yogesh Dwivedi
- a Department of Psychiatry and Behavioral Neurobiology , University of Alabama at Birmingham , Birmingham , AL , USA
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29
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Breitfeld J, Scholl C, Steffens M, Laje G, Stingl JC. Gene expression and proliferation biomarkers for antidepressant treatment resistance. Transl Psychiatry 2017; 7:e1061. [PMID: 28291260 PMCID: PMC5416664 DOI: 10.1038/tp.2017.16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/09/2016] [Accepted: 12/30/2016] [Indexed: 02/07/2023] Open
Abstract
The neurotrophic hypothesis of depression suggests an association between effects on neuroplasticity and clinical response to antidepressant drug therapy. We studied individual variability in antidepressant drug effects on cell proliferation in lymphoblastoid cell lines (LCLs) from n=25 therapy-resistant patients versus n=25 first-line therapy responders from the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. Furthermore, the variability in gene expression of genes associated with cell proliferation was analyzed for tentative candidate genes for prediction of individual LCL donor's treatment response. Cell proliferation was quantified by EdU (5-ethynyl-2'-deoxyuridine) assays after 21-day incubation of LCLs with fluoxetine (0.5 ng μl-1) and citalopram (0.3 ng μl-1) as developed and described earlier. Gene expression of a panel of candidate genes derived from genome-wide expression analyses of antidepressant effects on cell proliferation of LCLs from the Munich Antidepressant Response Signature (MARS) study was analyzed by real-time PCR. Significant differences in in vitro cell proliferation effects were detected between the group of LCLs from first-line therapy responders and LCLs from treatment-resistant patients. Gene expression analysis of the candidate gene panel revealed and confirmed influence of the candidate genes ABCB1, FZD7 and WNT2B on antidepressant drug resistance. The potential of these genes as tentative biomarkers for antidepressant drug resistance was confirmed. In vitro cell proliferation testing may serve as functional biomarker for individual neuroplasticity effects of antidepressants.
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Affiliation(s)
- J Breitfeld
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany
| | - C Scholl
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany
| | - M Steffens
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany
| | - G Laje
- Washington Behavioral Medicine Associates, LLC, Chevy Chase, MD, USA
| | - J C Stingl
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany,Centre for Translational Medicine, University Bonn Medical Faculty, Bonn, Germany,Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, 53175 Bonn, Germany. E-mail:
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30
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Alural B, Genc S, Haggarty SJ. Diagnostic and therapeutic potential of microRNAs in neuropsychiatric disorders: Past, present, and future. Prog Neuropsychopharmacol Biol Psychiatry 2017; 73:87-103. [PMID: 27072377 PMCID: PMC5292013 DOI: 10.1016/j.pnpbp.2016.03.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/28/2016] [Accepted: 03/30/2016] [Indexed: 12/12/2022]
Abstract
Neuropsychiatric disorders are common health problems affecting approximately 1% of the population. Twin, adoption, and family studies have displayed a strong genetic component for many of these disorders; however, the underlying pathophysiological mechanisms and neural substrates remain largely unknown. Given the critical need for new diagnostic markers and disease-modifying treatments, expanding the focus of genomic studies of neuropsychiatric disorders to include the role of non-coding RNAs (ncRNAs) is of growing interest. Of known types of ncRNAs, microRNAs (miRNAs) are 20-25-nucleotide, single-stranded, molecules that regulate gene expression through post-transcriptional mechanisms and have the potential to coordinately regulate complex regulatory networks. In this review, we summarize the current knowledge on miRNA alteration/dysregulation in neuropsychiatric disorders, with a special emphasis on schizophrenia (SCZ), bipolar disorder (BD), and major depressive disorder (MDD). With an eye toward the future, we also discuss the diagnostic and prognostic potential of miRNAs for neuropsychiatric disorders in the context of personalized treatments and network medicine.
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Affiliation(s)
- Begum Alural
- Department of Neuroscience, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylul University, Izmir, Turkey
| | - Sermin Genc
- Department of Neuroscience, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylul University, Izmir, Turkey
| | - Stephen J Haggarty
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Chemical Neurobiology Laboratory, Departments of Neurology and Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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31
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Genetic Contributions of Inflammation to Depression. Neuropsychopharmacology 2017; 42:81-98. [PMID: 27555379 PMCID: PMC5143493 DOI: 10.1038/npp.2016.169] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/04/2016] [Accepted: 08/08/2016] [Indexed: 01/05/2023]
Abstract
This paper describes the effects of immune genes genetic variants and mRNA expression on depression's risk, severity, and response to antidepressant treatment, through a systematic review on all papers published between 2000 and 2016. Our results, based largely on case-control studies, suggest that common genetic variants and gene-expression pathways are involved in both immune activation and depression. The most replicated and relevant genetic variants include polymorphisms in the genes for interleukin (IL)-1β, IL-6, IL-10, monocyte chemoattractant protein-1, tumor necrosis factor-alpha, C-reactive protein, and phospholipase A2. Moreover, increased blood cytokines mRNA expression (especially of IL-1β) identifies patients that are less likely to respond to conventional antidepressants. However, even for the most replicated findings there are inconsistent results, not only between studies, but also between the immune effects of the genetic variants and the resulting effects on depression. We find evidence that these discrepant findings may be explained, at least in part, by the heterogeneity of the depression immunophenotype, by environmental influences and gene × environment interactions, and by the complex interfacing of genetic variants with gene expression. Indeed, some of the most robust findings have been obtained in patients developing depression in the context of treatment with interferon-alpha, a widely used model to mimic depression in the context of inflammation. Further 'omics' approaches, through GWAS and transcriptomics, will finally shed light on the interaction between immune genes, their expression, and the influence of the environment, in the pathogenesis of depression.
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32
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Breitfeld J, Scholl C, Steffens M, Brandenburg K, Probst-Schendzielorz K, Efimkina O, Gurwitz D, Ising M, Holsboer F, Lucae S, Stingl JC. Proliferation rates and gene expression profiles in human lymphoblastoid cell lines from patients with depression characterized in response to antidepressant drug therapy. Transl Psychiatry 2016; 6:e950. [PMID: 27845776 PMCID: PMC5314111 DOI: 10.1038/tp.2016.185] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 08/02/2016] [Accepted: 08/03/2016] [Indexed: 12/25/2022] Open
Abstract
The current therapy success of depressive disorders remains in need of improvement due to low response rates and a delay in symptomatic improvement. Reliable functional biomarkers would be necessary to predict the individual treatment outcome. On the basis of the neurotrophic hypothesis of antidepressant's action, effects of antidepressant drugs on proliferation may serve as tentative individual markers for treatment efficacy. We studied individual differences in antidepressant drug effects on cell proliferation and gene expression in lymphoblastoid cell lines (LCLs) derived from patients treated for depression with documented clinical treatment outcome. Cell proliferation was characterized by EdU (5-ethynyl-2'-deoxyuridine) incorporation assays following a 3-week incubation with therapeutic concentrations of fluoxetine. Genome-wide expression profiling was conducted by microarrays, and candidate genes such as betacellulin-a gene involved in neuronal stem cell regeneration-were validated by quantitative real-time PCR. Ex vivo assessment of proliferation revealed large differences in fluoxetine-induced proliferation inhibition between donor LCLs, but no association with clinical response was observed. Genome-wide expression analyses followed by pathway and gene ontology analyses identified genes with different expression before vs after 21-day incubation with fluoxetine. Significant correlations between proliferation and gene expression of WNT2B, FZD7, TCF7L2, SULT4A1 and ABCB1 (all involved in neurogenesis or brain protection) were also found. Basal gene expression of SULT4A1 (P=0.029), and gene expression fold changes of WNT2B by ex vivo fluoxetine (P=0.025) correlated with clinical response and clinical remission, respectively. Thus, we identified potential gene expression biomarkers eventually being useful as baseline predictors or as longitudinal targets in antidepressant therapy.
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Affiliation(s)
- J Breitfeld
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany
| | - C Scholl
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany
| | - M Steffens
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany
| | - K Brandenburg
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany
| | - K Probst-Schendzielorz
- Institute of Clinical Pharmacology and Pharmacology of Natural Products, University of Ulm, Ulm, Germany
| | - O Efimkina
- Institute of Clinical Pharmacology and Pharmacology of Natural Products, University of Ulm, Ulm, Germany
| | - D Gurwitz
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - M Ising
- Max Planck Institute of Psychiatry, Munich, Germany
| | - F Holsboer
- Max Planck Institute of Psychiatry, Munich, Germany,HMNC Holding GmbH, Munich, Germany
| | - S Lucae
- Max Planck Institute of Psychiatry, Munich, Germany
| | - J C Stingl
- Research Division, Federal Institute for Drugs and Medical Devices (BfArM), Bonn, Germany,Center for Translational Medicine, Bonn University Medical School, Bonn, Germany,Federal Institute for Drugs and Medical Devices, Kurt-Georg-Kiesinger-Allee 3, 53175 Bonn, Germany. E-mail:
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Enatescu VR, Papava I, Enatescu I, Antonescu M, Anghel A, Seclaman E, Sirbu IO, Marian C. Circulating Plasma Micro RNAs in Patients with Major Depressive Disorder Treated with Antidepressants: A Pilot Study. Psychiatry Investig 2016; 13:549-557. [PMID: 27757134 PMCID: PMC5067350 DOI: 10.4306/pi.2016.13.5.549] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 12/22/2015] [Accepted: 12/22/2015] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVE Significant progress was made in the understanding etiopathogenic factors related to MDD, including through research on the role of micro RNAs (miRs). We investigated plasma miRs as potential markers for MDD in patients treated with antidepressants. METHODS At the initiation and at the end of twelve weeks of treatment, blood samples were collected and a structured diagnostic interview and a standardized depression rating scale for the presence and severity of major depression were done. The average decrease in HAMD score was 76.89%. Plasma miR expression profiling was performed by real time PCR. The lists of up-regulated (cut-off=2) and down-regulated miRs were imported into the miRWalk2.0 algorithm and used for target predictions. KEGG database pathways analysis was used to retrieve the pathways significantly targeted by at least two of the miRs. RESULTS Of the 222 miRs detected in plasma samples of MDD patients, 40 were differentially expressed after treatment. Twenty-three miRs were significantly overexpressed with fold changes between 1.85 and 25.42, and 17 miRs were significantly downregulated with fold changes from 0.28 to 0.68. Pathway analysis revealed a list of 29 pathways for up-regulated miRs, and 20 pathways for down-regulated miRs. Six dysregulated miRs are common to all the top five pathways (Wnt signaling, Cancer, Endocytosis, Axon guidance, MAPK signaling): miR-146a-5p, miR-146b-5p, miR-221-3p, miR-24-3p, miR-26a-5p. CONCLUSION Overall, our miRWalk analysis of changes in plasma microRNAs after treatment of patients with major depression might open a new avenue for the understanding of Escitalopram mode of action and for its side effects.
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Affiliation(s)
- Virgil Radu Enatescu
- Victor Babes University of Medicine and Pharmacy Timisoara-Discipline of Psychiatry, Timisoara, Romania
- Eduard Pamfil Psychiatry Clinic, Timisoara County Hospital, Timisoara, Romania
| | - Ion Papava
- Victor Babes University of Medicine and Pharmacy Timisoara-Discipline of Psychiatry, Timisoara, Romania
- Eduard Pamfil Psychiatry Clinic, Timisoara County Hospital, Timisoara, Romania
| | - Ileana Enatescu
- Victor Babes University of Medicine and Pharmacy Timisoara-Department of Neonatology and Puericulture, Timisoara, Romania
| | - Mirela Antonescu
- Victor Babes University of Medicine and Pharmacy Timisoara-Department of Biochemistry, Timisoara, Romania
| | - Andrei Anghel
- Victor Babes University of Medicine and Pharmacy Timisoara-Department of Biochemistry, Timisoara, Romania
| | - Edward Seclaman
- Victor Babes University of Medicine and Pharmacy Timisoara-Department of Biochemistry, Timisoara, Romania
| | - Ioan Ovidiu Sirbu
- Victor Babes University of Medicine and Pharmacy Timisoara-Department of Biochemistry, Timisoara, Romania
| | - Catalin Marian
- Victor Babes University of Medicine and Pharmacy Timisoara-Department of Biochemistry, Timisoara, Romania
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Sun N, Lei L, Wang Y, Yang C, Liu Z, Li X, Zhang K. Preliminary comparison of plasma notch-associated microRNA-34b and -34c levels in drug naive, first episode depressed patients and healthy controls. J Affect Disord 2016; 194:109-14. [PMID: 26807671 DOI: 10.1016/j.jad.2016.01.017] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/04/2016] [Accepted: 01/08/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Major depressive disorder (MDD) is a common debilitating disease of unknown etiology. The expression of miRNA is closely related to depression and efficacy of antidepressant therapy. However, whether Notch-associated miRNAs expressions involved in first-episode of MDD are still unknown. METHODS In this study, the expression levels of Notch1, Hes1 mRNA and 5 miRNAs (miR-369-3p, miR-34b-5p, miR-34c-5p, miR-381 and miR-107) in peripheral blood leukocytes of 32 MDD patients and 32 healthy controls were detected using qRT-PCR method. We also assessed the severity of depressive symptom, suicide risk level, negative life events and event-related potential P300. RESULTS The expression levels of miR-34b-5p (62.49 as the median of cases group and 38.62 as median of control group) and miR-34c-5p (7.17 as the median of cases group and 5.45 as median of control group) in MDD patients were significantly higher than these in control subjects. NOTCH1 gene were significantly lower in MDD patients (5.35 as the median of cases group and 6.80 as median of control group), and was negatively correlated with the expression miR-34c-5p and miR-34b-5p. The expression level of miR-34b-5p and miR-369-3p were significantly lower in patients with suicide idea. N1 latency of P300 were positive correlated with miR-34c-5p, miR-107 and miR-381, and P2 latency of P300 were positive correlated with miR-34c-5p, miR-107 and miR-381. LIMITATIONS The sample size was small and the role of candidate miRNAs in the regulation of Notch1 gene and cognitive function are still need to be further investigated. CONCLUSIONS Differentially Notch-associated miRNAs expressions in peripheral blood might be involved in MDD, and the miR-34b-5p and miR-34c-5p levels in peripheral blood leukocytes are closely related to MDD, suicide idea and cognitive function, further studies with large sample size are warranted to test the feasibility of these miRNAs serving as biomarkers for MDD.
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Affiliation(s)
- Ning Sun
- Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, Shanxi, China; Nuring College of Shanxi Medical University, 030001 Taiyuan, Shanxi, China
| | - Lei Lei
- Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, Shanxi, China
| | - Yanfang Wang
- Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, Shanxi, China
| | - Chunxia Yang
- Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, Shanxi, China
| | - Zhifen Liu
- Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, Shanxi, China
| | - Xinrong Li
- Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, Shanxi, China
| | - Kerang Zhang
- Department of Psychiatry, First Hospital of Shanxi Medical University, 030001 Taiyuan, Shanxi, China.
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Lin E, Tsai SJ. Genome-wide microarray analysis of gene expression profiling in major depression and antidepressant therapy. Prog Neuropsychopharmacol Biol Psychiatry 2016; 64:334-40. [PMID: 25708651 DOI: 10.1016/j.pnpbp.2015.02.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 02/13/2015] [Accepted: 02/15/2015] [Indexed: 12/21/2022]
Abstract
Major depressive disorder (MDD) is a serious health concern worldwide. Currently there are no predictive tests for the effectiveness of any particular antidepressant in an individual patient. Thus, doctors must prescribe antidepressants based on educated guesses. With the recent advent of scientific research, genome-wide gene expression microarray studies are widely utilized to analyze hundreds of thousands of biomarkers by high-throughput technologies. In addition to the candidate-gene approach, the genome-wide approach has recently been employed to investigate the determinants of MDD as well as antidepressant response to therapy. In this review, we mainly focused on gene expression studies with genome-wide approaches using RNA derived from peripheral blood cells. Furthermore, we reviewed their limitations and future directions with respect to the genome-wide gene expression profiling in MDD pathogenesis as well as in antidepressant therapy.
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Affiliation(s)
- Eugene Lin
- Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan; Vita Genomics, Inc., Taipei, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan; Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan.
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36
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Kalueff AV, Stewart AM, Nguyen M, Song C, Gottesman II. Targeting drug sensitivity predictors: New potential strategies to improve pharmacotherapy of human brain disorders. Prog Neuropsychopharmacol Biol Psychiatry 2015; 63:76-82. [PMID: 25976211 DOI: 10.1016/j.pnpbp.2015.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/05/2015] [Accepted: 05/06/2015] [Indexed: 02/07/2023]
Abstract
One of the main challenges in medicine is the lack of efficient drug therapies for common human disorders. For example, although depressed patients receive powerful antidepressants, many often remain resistant to psychopharmacotherapy. The growing recognition of complex interplay between the drug targets and the predictors of drug sensitivity requires an improved understanding of these two key aspects of drug action and their potentially shared molecular networks. Here, we apply the concept of endophenotypes and their interplay to drug action and sensitivity. Based on these analyses, we postulate that novel drugs may be developed by targeting specific molecular pathways that integrate drug targets with drug sensitivity predictors.
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Affiliation(s)
- Allan V Kalueff
- Research Institute for Marine Drugs and Nutrition, College for Food Science and Technology, Guangdong Ocean University, Zhanjiang, Guangdong 524025, China; ZENEREI Institute, 309 Palmer Court, Slidell, LA 70458, USA; Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199034, Russia.
| | | | - Michael Nguyen
- ZENEREI Institute, 309 Palmer Court, Slidell, LA 70458, USA
| | - Cai Song
- Research Institute for Marine Drugs and Nutrition, College for Food Science and Technology, Guangdong Ocean University, Zhanjiang, Guangdong 524025, China
| | - Irving I Gottesman
- Department of Psychology, University of Minnesota, Elliot Hall, Minneapolis, MN 55455, USA
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Su M, Hong J, Zhao Y, Liu S, Xue X. MeCP2 controls hippocampal brain-derived neurotrophic factor expression via homeostatic interactions with microRNA‑132 in rats with depression. Mol Med Rep 2015; 12:5399-406. [PMID: 26239616 DOI: 10.3892/mmr.2015.4104] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 06/03/2015] [Indexed: 11/06/2022] Open
Abstract
Major depressive disorder (MDD) is a considerable public health concern, which affects patients worldwide. MDD is associated with psychosocial impairment, poor quality of life, and significant disability, morbidity and mortality. Stress is a major factor in depression, which impairs the structural and functional plasticity of the hippocampus. Previous studies have demonstrated that chronic unpredictable mild stress is able to downregulate the expression of brain‑derived neurotrophic factor (BDNF) and methyl‑CpG‑binding protein 2 (MeCP2), and alter the expression levels of certain microRNAs (miR). The aim of the present study was to investigate the regulatory association between BDNF, MeCP2 and miR-132 in an animal model of chronic stress‑induced depression. ELISA, western blot and qPCR were used to detect the expression levels of BDNF, MeCP2 and miR-132 in the peripheral blood samples of patients with MDD and in the hippocampi of depressed animals. In addition, a dual luciferase reporter gene system was used to determine whether miR-132 directly targets BDNF or MeCP2. The present study demonstrated that, as compared with normal subjects, miR‑132 expression was increased in the peripheral blood samples of patients with MDD, whereas the expression of MeCP2 and BDNF was decreased; thus, the expression levels of MeCP2 and BDNF were negatively correlated with those of miR‑132. In addition, in an animal model of chronic stress‑induced depression, increased expression levels of miR‑132, and decreased levels of MeCP2 and BDNF were detected in the hippocampi. Furthermore, knockdown of MeCP2 expression in primary hippocampal neurons increased the expression of miR‑132 and decreased the expression levels of BDNF. The results of the present study demonstrated that miR‑132 may directly target MeCP2, but not BDNF, and control its expression at the transcriptional and translational level. miR‑132 was also shown to negatively regulate BDNF expression. The reduced expression levels of BDNF, as induced by MeCP2 knockdown, were enhanced by miR‑132 mimics, and were rescued by miR‑132 inhibitors. These results suggested that homeostatic interactions between MeCP2 and miR‑132 may regulate hippocampal BDNF levels, which may have a role in the pathogenesis of MDD.
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Affiliation(s)
- Meilei Su
- Department of Psychology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Jun Hong
- Department of Psychology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Yongzhi Zhao
- Department of Psychology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Shuai Liu
- Department of Psychology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Xiang Xue
- Department of Psychology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
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38
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Song MF, Dong JZ, Wang YW, He J, Ju X, Zhang L, Zhang YH, Shi JF, Lv YY. CSF miR-16 is decreased in major depression patients and its neutralization in rats induces depression-like behaviors via a serotonin transmitter system. J Affect Disord 2015; 178:25-31. [PMID: 25779937 DOI: 10.1016/j.jad.2015.02.022] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/30/2015] [Accepted: 02/19/2015] [Indexed: 01/16/2023]
Abstract
BACKGROUND Animal and cell line studies demonstrated that miR-16 may be associated with major depressive disorder (MDD) via regulation of the expression of serotonin transporter (SERT) gene. However, human studies about miR-16 of patients with MDD are still lacking. The aim of this study was to investigate the possible involvement of miR-16 in the mechanism of MDD in humans. METHODS Thirty-six drug-free patients with MDD and 30 healthy controls aged between 18 and 45 years old were recruited. 24-item Hamilton depression scale test was performed for each subject. MiR-16 in cerebrospinal fluid (CSF) and blood, as well as serotonin in CSF were assayed by the qRT-PCR or ELISA method. To confirm the role of CSF miR-16 in MDD, animal study about intracerebroventricular injection of anti-miR-16 was also performed. Depression-like behaviors, CSF miR-16 and serotonin, blood miR-16, and raphe SERT protein of rats were also tested. RESULTS CSF miR-16 in MDD patients was significantly lower than that in controls. It was negatively correlated with Hamilton scores and positively associated with CSF serotonin. However, blood miR-16 was not significantly different between two groups and it was not statistically correlated with CSF miR-16. In animal study, anti-miR-16-treated rats were evaluated to exhibit depression-like behaviors, extremely lower CSF miR-16, significantly higher CSF serotonin, and obviously higher raphe SERT protein than control rats. LIMITATION We did not detect SERT protein in human brain due to the impossibility of sample collection. CONCLUSION Our study suggested that CSF miR-16 participated in the physiopathology of MDD via the modulation of serotonin transmitter system in brain.
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Affiliation(s)
- Ming-Fen Song
- Molecular Biology Laboratory, Hangzhou Seventh People's Hospital, 305 Tianmushan Road, Hangzhou 310013, Zhejiang, China
| | - Jie-Zheng Dong
- Department of Psychiatry, Hangzhou Seventh People's Hospital, 305 Tianmushan Road, Hangzhou 310013, Zhejiang, China
| | - Yu-Wen Wang
- Department of Pharmacy, Hangzhou Seventh People's Hospital, 305 Tianmushan Road, Hangzhou 310013, Zhejiang, China
| | - Jun He
- Department of Pharmacy, Hangzhou Seventh People's Hospital, 305 Tianmushan Road, Hangzhou 310013, Zhejiang, China
| | - Xuan Ju
- Department of Psychiatry, Hangzhou Seventh People's Hospital, 305 Tianmushan Road, Hangzhou 310013, Zhejiang, China
| | - Long Zhang
- Molecular Biology Laboratory, Hangzhou Seventh People's Hospital, 305 Tianmushan Road, Hangzhou 310013, Zhejiang, China
| | - Yong-Hua Zhang
- Department of Psychiatry, Hangzhou Seventh People's Hospital, 305 Tianmushan Road, Hangzhou 310013, Zhejiang, China
| | - Jian-Fei Shi
- Department of Psychiatry, Hangzhou Seventh People's Hospital, 305 Tianmushan Road, Hangzhou 310013, Zhejiang, China
| | - Ya-Ying Lv
- Department of Human Resources, Hangzhou Seventh People's Hospital, 305 Tianmushan Road, Hangzhou 310013, Zhejiang, China.
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Probst-Schendzielorz K, Scholl C, Efimkina O, Ersfeld E, Viviani R, Serretti A, Fabbri C, Gurwitz D, Lucae S, Ising M, Paul AM, Lehmann ML, Steffens M, Crisafulli C, Calabrò M, Holsboer F, Stingl J. CHL1, ITGB3 and SLC6A4 gene expression and antidepressant drug response: results from the Munich Antidepressant Response Signature (MARS) study. Pharmacogenomics 2015; 16:689-701. [DOI: 10.2217/pgs.15.31] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Aim: The identification of antidepressant drugs (ADs) response biomarkers in depression is of high clinical importance. We explored CHL1 and ITGB3 expression as tentative response biomarkers. Materials & methods: In vitro sensitivity to ADs, as well as gene expression and genetic variants of the candidate genes CHL1, ITGB3 and SLC6A4 were measured in lymphoblastoid cell lines (LCLs) of 58 depressed patients. Results: An association between the clinical remission of depression and the basal expression of CHL1 and ITGB3 was discovered. Individuals whose LCLs expressed higher levels of CHL1 or ITGB3 showed a significantly better remission upon AD treatment. In addition individuals with the CHL1 rs1516338 TT genotype showed a significantly better remission after 5 weeks AD treatment than those carrying a CC genotype. No association between the in vitro sensitivity of LCLs toward AD and the clinical remission could be detected. Conclusion: CHL1 expression in patient-derived LCLs correlated with the clinical outcome. Thus, it could be a valid biomarker to predict the success of an antidepressant therapy. Original submitted 8 December 2014; Revision submitted 2 March 2015
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Affiliation(s)
| | - Catharina Scholl
- Research Division, Federal Institute for Drugs & Medical Devices, Bonn, Germany
- Medical Faculty, Faculty Centre for Translational Medicine, University Bonn, Bonn, Germany
| | - Olga Efimkina
- Institute for Pharmacology of Natural Products & Clinical Pharmacology, University Ulm, Ulm, Germany
| | - Eva Ersfeld
- Institute for Pharmacology of Natural Products & Clinical Pharmacology, University Ulm, Ulm, Germany
| | - Roberto Viviani
- Department of Psychiatry & Psychotherapy, University of Ulm, Ulm, Germany
| | - Alessandro Serretti
- Department of Biomedical & Neuromotor Sciences, University of Bologna, Italy
| | - Chiara Fabbri
- Department of Biomedical & Neuromotor Sciences, University of Bologna, Italy
| | - David Gurwitz
- Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | | | - Marcus Ising
- Max Planck Institute of Psychiatry, Munich, Germany
| | - Anna Maria Paul
- Research Division, Federal Institute for Drugs & Medical Devices, Bonn, Germany
- Medical Faculty, Faculty Centre for Translational Medicine, University Bonn, Bonn, Germany
| | - Marie-Louise Lehmann
- Research Division, Federal Institute for Drugs & Medical Devices, Bonn, Germany
- Medical Faculty, Faculty Centre for Translational Medicine, University Bonn, Bonn, Germany
| | - Michael Steffens
- Research Division, Federal Institute for Drugs & Medical Devices, Bonn, Germany
- Medical Faculty, Faculty Centre for Translational Medicine, University Bonn, Bonn, Germany
| | - Concetta Crisafulli
- Department of Biomedical Science & Morphological & Functional Images, University of Messina, Messina, Italy
| | - Marco Calabrò
- Department of Biomedical Science & Morphological & Functional Images, University of Messina, Messina, Italy
| | | | - Julia Stingl
- Research Division, Federal Institute for Drugs & Medical Devices, Bonn, Germany
- Medical Faculty, Faculty Centre for Translational Medicine, University Bonn, Bonn, Germany
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40
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Fabbri C, Crisafulli C, Gurwitz D, Stingl J, Calati R, Albani D, Forloni G, Calabrò M, Martines R, Kasper S, Zohar J, Juven-Wetzler A, Souery D, Montgomery S, Mendlewicz J, Girolamo GD, Serretti A. Neuronal cell adhesion genes and antidepressant response in three independent samples. THE PHARMACOGENOMICS JOURNAL 2015; 15:538-48. [PMID: 25850031 DOI: 10.1038/tpj.2015.15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 02/03/2015] [Accepted: 02/09/2015] [Indexed: 12/19/2022]
Abstract
Drug-effect phenotypes in human lymphoblastoid cell lines recently allowed to identify CHL1 (cell adhesion molecule with homology to L1CAM), GAP43 (growth-associated protein 43) and ITGB3 (integrin beta 3) as new candidates for involvement in the antidepressant effect. CHL1 and ITGB3 code for adhesion molecules, while GAP43 codes for a neuron-specific cytosolic protein expressed in neuronal growth cones; all the three gene products are involved in synaptic plasticity. Sixteen polymorphisms in these genes were genotyped in two samples (n=369 and 90) with diagnosis of major depressive episode who were treated with antidepressants in a naturalistic setting. Phenotypes were response, remission and treatment-resistant depression. Logistic regression including appropriate covariates was performed. Genes associated with outcomes were investigated in the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) genome-wide study (n=1861) as both individual genes and through a pathway analysis (Reactome and String databases). Gene-based analysis suggested CHL1 rs4003413, GAP43 rs283393 and rs9860828, ITGB3 rs3809865 as the top candidates due to their replication across the largest original sample and the STAR*D cohort. GAP43 molecular pathway was associated with both response and remission in the STAR*D, with ELAVL4 representing the gene with the highest percentage of single nucleotide polymorphisms (SNPs) associated with outcomes. Other promising genes emerging from the pathway analysis were ITGB1 and NRP1. The present study was the first to analyze cell adhesion genes and their molecular pathways in antidepressant response. Genes and biomarkers involved in neuronal adhesion should be considered by further studies aimed to identify predictors of antidepressant response.
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Affiliation(s)
- C Fabbri
- Department of Biomedical and NeuroMotor Sciences, University of Bologna, Bologna, Italy
| | - C Crisafulli
- Department of Biomedical Science and Morphological and Functional Images, University of Messina, Messina, Italy
| | - D Gurwitz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Italy
| | - J Stingl
- Federal Institute for Drugs and Medical Devices, University Bonn Medical School, Bonn, Germany
| | - R Calati
- Faculty Centre for Translational Medicine, University Bonn, Medical Faculty, Bonn, Germany
| | - D Albani
- Laboratory of Biology of Neurodegenerative Disorders, Department of Neuroscience, IRCCS Istituto di Ricerche Farmacologiche 'Mario Negri', Milan, Italy
| | - G Forloni
- Laboratory of Biology of Neurodegenerative Disorders, Department of Neuroscience, IRCCS Istituto di Ricerche Farmacologiche 'Mario Negri', Milan, Italy
| | - M Calabrò
- Department of Biomedical Science and Morphological and Functional Images, University of Messina, Messina, Italy.,Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - R Martines
- Department of Biomedical and NeuroMotor Sciences, University of Bologna, Bologna, Italy.,Laboratory of Biology of Neurodegenerative Disorders, Department of Neuroscience, IRCCS Istituto di Ricerche Farmacologiche 'Mario Negri', Milan, Italy
| | - S Kasper
- Department of Psychiatry and Psychotherapy, Medical University Vienna, Vienna, Austria
| | - J Zohar
- Department of Psychiatry, Sheba Medical Center, Tel Hashomer and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - A Juven-Wetzler
- Department of Psychiatry, Sheba Medical Center, Tel Hashomer and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - D Souery
- Laboratoire de Psychologie Medicale, Universitè Libre de Bruxelles and Psy Pluriel, Centre Européen de Psychologie Medicale, Brussels, Belgium
| | | | - J Mendlewicz
- Université Libre de Bruxelles, Brussels, Belgium
| | - G D Girolamo
- Faculty Centre for Translational Medicine, University Bonn, Medical Faculty, Bonn, Germany
| | - A Serretti
- Department of Biomedical and NeuroMotor Sciences, University of Bologna, Bologna, Italy
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41
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Garbett KA, Vereczkei A, Kálmán S, Brown JA, Taylor WD, Faludi G, Korade Ž, Shelton RC, Mirnics K. Coordinated messenger RNA/microRNA changes in fibroblasts of patients with major depression. Biol Psychiatry 2015; 77:256-265. [PMID: 25016317 PMCID: PMC4254393 DOI: 10.1016/j.biopsych.2014.05.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 04/30/2014] [Accepted: 05/22/2014] [Indexed: 12/22/2022]
Abstract
BACKGROUND Peripheral biomarkers for major psychiatric disorders have been an elusive target for the last half a century. Dermal fibroblasts are a simple, relevant, and much underutilized model for studying molecular processes of patients with affective disorders, as they share considerable similarity of signal transduction with neuronal tissue. METHODS Cultured dermal fibroblast samples from patients with major depressive disorder (MDD) and matched control subjects (n = 16 pairs, 32 samples) were assayed for genome-wide messenger RNA (mRNA) expression using microarrays. In addition, a simultaneous quantitative polymerase chain reaction-based assessment of >1000 microRNA (miRNA) species was performed. Finally, to test the relationship between the mRNA-miRNA expression changes, the two datasets were correlated with each other. RESULTS Our data revealed that MDD fibroblasts, when compared with matched control subjects, showed a strong mRNA gene expression pattern change in multiple molecular pathways, including cell-to-cell communication, innate/adaptive immunity, and cell proliferation. Furthermore, the same patient fibroblasts showed altered expression of a distinct panel of 38 miRNAs, which putatively targeted many of the differentially expressed mRNAs. The miRNA-mRNA expression changes appeared to be functionally connected, as the majority of the miRNA and mRNA changes were in the opposite direction. CONCLUSIONS Our data suggest that combined miRNA-mRNA assessments are informative about the disease process and that analyses of dermal fibroblasts might lead to the discovery of promising peripheral biomarkers of MDD that could be potentially used to aid the diagnosis and allow mechanistic testing of disturbed molecular pathways.
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Affiliation(s)
| | - Andrea Vereczkei
- Department of Psychiatry, Vanderbilt University, Nashville, Tennessee; Institute for Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest
| | - Sára Kálmán
- Department of Psychiatry, Vanderbilt University, Nashville, Tennessee; Department of Psychiatry, University of Szeged, Szeged
| | - Jacquelyn A Brown
- Department of Psychiatry, Vanderbilt University, Nashville, Tennessee
| | - Warren D Taylor
- Department of Psychiatry, Vanderbilt University, Nashville, Tennessee
| | - Gábor Faludi
- Department of Psychiatry, Kútvölgyi Clinical Centre, Semmelweis University, Budapest, Hungary
| | - Željka Korade
- Department of Psychiatry, Vanderbilt University, Nashville, Tennessee; Vanderbilt Kennedy Center for Research on Human Development (ZK, KM), Vanderbilt University, Nashville, Tennessee
| | - Richard C Shelton
- Department of Psychiatry, University of Alabama, Birmingham, Alabama
| | - Károly Mirnics
- Department of Psychiatry, Vanderbilt University, Nashville, Tennessee; Department of Psychiatry, University of Szeged, Szeged; Vanderbilt Kennedy Center for Research on Human Development (ZK, KM), Vanderbilt University, Nashville, Tennessee..
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42
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Dwivedi Y. Emerging role of microRNAs in major depressive disorder: diagnosis and therapeutic implications. DIALOGUES IN CLINICAL NEUROSCIENCE 2014. [PMID: 24733970 PMCID: PMC3984890 DOI: 10.31887/dcns.2014.16.1/ydwivedi] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Major depressive disorder (MDD) is a major public health concern. Despite tremendous advances, the pathogenic mechanisms associated with MDD are still unclear. Moreover, a significant number of MDD subjects do not respond to the currently available medication. MicroRNAs (miRNAs) are a class of small noncoding RNAs that control gene expression by modulating translation, messenger RNA (mRNA) degradation, or stability of mRNA targets. The role of miRNAs in disease pathophysiology is emerging rapidly. Recent studies demonstrating the involvement of miRNAs in several aspects of neural plasticity, neurogenesis, and stress response, and more direct studies in human postmortem brain provide strong evidence that miRNAs can not only play a critical role in MDD pathogenesis, but can also open up new avenues for the development of therapeutic targets. Circulating miRNAs are now being considered as possible biomarkers in disease pathogenesis and in monitoring therapeutic responses because of the presence and/or release of miRNAs in blood cells as well as in other peripheral tissues. In this review, these aspects are discussed in a comprehensive and critical manner.
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Affiliation(s)
- Yogesh Dwivedi
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Alabama, USA
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43
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Hommers LG, Domschke K, Deckert J. Heterogeneity and individuality: microRNAs in mental disorders. J Neural Transm (Vienna) 2014; 122:79-97. [PMID: 25395183 DOI: 10.1007/s00702-014-1338-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/07/2014] [Indexed: 12/21/2022]
Abstract
MicroRNAs are about 22 nucleotide long single-stranded RNA molecules, negatively regulating gene expression of a single gene or a gene network. In neural tissues, they have been implicated in developmental and neuroplasticity-related processes, such as neurogenesis, differentiation, apoptosis and long-term potentiation. Their molecular mode of action is reminiscent of findings of genome-wide association studies in mental disorders, unable to attribute the risk of disease to a specific gene, but rather to multiple genes, gene-networks and gene-environment interaction. As such, microRNAs are an attractive target for research. Here, we review clinical studies conducted in humans on microRNAs in mental disorders with a particular focus on schizophrenia, bipolar disorder, major depressive disorder and anxiety disorders. The majority of clinical studies have focused on schizophrenia. The most robust finding has been reported for rs1625579 located in MIR137HG, which was associated with schizophrenia on a genome-wide level. Concerning bipolar disorder, major depression and anxiety disorders, promising results have been published, but only a considerably smaller number of clinical studies is available and genome-wide association studies did not suggest a direct link to microRNAs so far. Expression of microRNAs as biomarkers of mental disorders and treatment response is currently emerging with preliminary results. Larger-scaled genetic and functional studies along with translational research are needed to enhance our understanding of microRNAs in mental disorders. These studies will aid in disentangling the complex genetic nature of these disorders and possibly contribute to the development of novel, individualized diagnostic and therapeutic approaches.
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Affiliation(s)
- Leif G Hommers
- Center of Mental Health, Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital Würzburg, Füchsleinstrasse 15, 97080, Würzburg, Germany,
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44
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Duan D, Yang X, Ya T, Chen L. Hippocampal gene expression in a rat model of depression after electroacupuncture at the Baihui and Yintang acupoints. Neural Regen Res 2014; 9:76-83. [PMID: 25206746 PMCID: PMC4146319 DOI: 10.4103/1673-5374.125333] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2013] [Indexed: 12/15/2022] Open
Abstract
Preliminary basic research and clinical findings have demonstrated that electroacupuncture therapy exhibits positive effects in ameliorating depression. However, most studies of the underlying mechanism are at the single gene level; there are few reports regarding the mechanism at the whole-genome level. Using a rat genomic gene-chip, we profiled hippocampal gene expression changes in rats after electroacupuncture therapy. Electroacupuncture therapy alleviated depression-related manifestations in the model rats. Using gene-chip analysis, we demonstrated that electroacupuncture at Baihui (DU20) and Yintang (EX-HN3) regulates the expression of 21 genes. Real-time PCR showed that the genes Vgf, Igf2, Tmp32, Loc500373, Hif1a, Folr1, Nmb, and Rtn were upregulated or downregulated in depression and that their expression tended to normalize after electroacupuncture therapy. These results indicate that electroacupuncture at Baihui and Yintang modulates depression by regulating the expression of particular genes.
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Affiliation(s)
- Dongmei Duan
- Department of Traditional Chinese Medicine of South Building, Chinese PLA General Hospital, Beijing, China
| | - Xiuyan Yang
- Institute of Health Maintenance, Beijing University of Chinese Medicine, Beijing, China
| | - Tu Ya
- School of Acupuncture and Moxibustion, Beijing University of Chinese Medicine, Beijing, China
| | - Liping Chen
- Department of Traditional Chinese Medicine of South Building, Chinese PLA General Hospital, Beijing, China
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Sun X, Zhang J. Identification of putative pathogenic SNPs implied in schizophrenia-associated miRNAs. BMC Bioinformatics 2014; 15:194. [PMID: 24934851 PMCID: PMC4072616 DOI: 10.1186/1471-2105-15-194] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 06/11/2014] [Indexed: 12/11/2022] Open
Abstract
Background Schizophrenia is a severe brain disorder, and SNPs (Single nucleotide polymorphism) in schizophrenia-associated miRNAs are believed to be one of the important reasons for dysregulation which might contribute to the altered expression of genes and ultimately result in the disease. Identification of causal SNPs in associated miRNAs may have certain significance in understanding the mechanism of schizophrenia. Results For the above purposes, a method based on detection of free energy change is proposed for identification of causal SNPs in schizophrenia-associated miRNAs. A miRNA is firstly segmented, and free energy change is computed after adding an SNP into a segment. The method discovers successfully 6 out of 32 known SNPs and some artificial SNPs could cause significant change in free energy, and among which, 6 known SNPs are supposed to be responsible for most cases of schizophrenia in population. Conclusions The proposed method is not only a convenient way to discover causal SNPs in schizophrenia-associated miRNAs without any biochemical assay or sample comparison between cases and controls, but it also has high resolution for causal SNPs even if the SNPs are not reported for their very rare cases in the population. Moreover, the method can be applied to discover the causal SNPs in miRNAs associated with other diseases.
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Affiliation(s)
| | - Junying Zhang
- School of Computer Science and Technology, Xidian University, Xi'an 710071, P, R, China.
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Stark AL, Hause RJ, Gorsic LK, Antao NN, Wong SS, Chung SH, Gill DF, Im HK, Myers JL, White KP, Jones RB, Dolan ME. Protein quantitative trait loci identify novel candidates modulating cellular response to chemotherapy. PLoS Genet 2014; 10:e1004192. [PMID: 24699359 PMCID: PMC3974641 DOI: 10.1371/journal.pgen.1004192] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 01/07/2014] [Indexed: 11/24/2022] Open
Abstract
Annotating and interpreting the results of genome-wide association studies (GWAS) remains challenging. Assigning function to genetic variants as expression quantitative trait loci is an expanding and useful approach, but focuses exclusively on mRNA rather than protein levels. Many variants remain without annotation. To address this problem, we measured the steady state abundance of 441 human signaling and transcription factor proteins from 68 Yoruba HapMap lymphoblastoid cell lines to identify novel relationships between inter-individual protein levels, genetic variants, and sensitivity to chemotherapeutic agents. Proteins were measured using micro-western and reverse phase protein arrays from three independent cell line thaws to permit mixed effect modeling of protein biological replicates. We observed enrichment of protein quantitative trait loci (pQTLs) for cellular sensitivity to two commonly used chemotherapeutics: cisplatin and paclitaxel. We functionally validated the target protein of a genome-wide significant trans-pQTL for its relevance in paclitaxel-induced apoptosis. GWAS overlap results of drug-induced apoptosis and cytotoxicity for paclitaxel and cisplatin revealed unique SNPs associated with the pharmacologic traits (at p<0.001). Interestingly, GWAS SNPs from various regions of the genome implicated the same target protein (p<0.0001) that correlated with drug induced cytotoxicity or apoptosis (p≤0.05). Two genes were functionally validated for association with drug response using siRNA: SMC1A with cisplatin response and ZNF569 with paclitaxel response. This work allows pharmacogenomic discovery to progress from the transcriptome to the proteome and offers potential for identification of new therapeutic targets. This approach, linking targeted proteomic data to variation in pharmacologic response, can be generalized to other studies evaluating genotype-phenotype relationships and provide insight into chemotherapeutic mechanisms. The central dogma of biology explains that DNA is transcribed to mRNA that is further translated into protein. Many genome-wide studies have implicated genetic variation that influences gene expression and that ultimately affect downstream complex traits including response to drugs. However, because of technical limitations, few studies have evaluated the contribution of genetic variation on protein expression and ensuing effects on downstream phenotypes. To overcome this challenge, we used a novel technology to simultaneously measure the baseline expression of 441 proteins in lymphoblastoid cell lines and compared them with publicly available genetic data. To further illustrate the utility of this approach, we compared protein-level measurements with chemotherapeutic induced apoptosis and cell-growth inhibition data. This study demonstrates the importance of using protein information to understand the functional consequences of genetic variants identified in genome-wide association studies. This protein data set will also have broad utility for understanding the relationship between other genome-wide studies of complex traits.
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Affiliation(s)
- Amy L. Stark
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
| | - Ronald J. Hause
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois, United States of America
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
| | - Lidija K. Gorsic
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
| | - Nirav N. Antao
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
| | - Shan S. Wong
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
| | - Sophie H. Chung
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
| | - Daniel F. Gill
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
| | - Hae K. Im
- Department of Health Studies, The University of Chicago, Chicago, Illinois, United States of America
| | - Jamie L. Myers
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
| | - Kevin P. White
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Richard Baker Jones
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Ben May Department for Cancer Research, The University of Chicago, Chicago, Illinois, United States of America
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Committee on Clinical Pharmacology and Pharmacogenomics, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (RBJ); (MED)
| | - M. Eileen Dolan
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago, Chicago, Illinois, United States of America
- Committee on Clinical Pharmacology and Pharmacogenomics, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (RBJ); (MED)
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Maffioletti E, Tardito D, Gennarelli M, Bocchio-Chiavetto L. Micro spies from the brain to the periphery: new clues from studies on microRNAs in neuropsychiatric disorders. Front Cell Neurosci 2014; 8:75. [PMID: 24653674 PMCID: PMC3949217 DOI: 10.3389/fncel.2014.00075] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 02/21/2014] [Indexed: 02/06/2023] Open
Abstract
microRNAs (miRNAs) are small non-coding RNAs (20-22 nucleotides) playing a major role in post-transcriptional regulation of gene expression. miRNAs are predicted to regulate more than 50% of all the protein-coding genes. Increasing evidence indicates that they may play key roles in the biological pathways that regulate neurogenesis and synaptic plasticity, as well as in neurotransmitter homeostasis in the adult brain. In this article we review recent studies suggesting that miRNAs may be involved in the pathophysiology of neuropsychiatric disorders and in the action of psychotropic drugs, in particular by analyzing the contribution of genomic studies in patients' peripheral tissues. Alterations in miRNA expression have been observed in schizophrenia, bipolar disorder, major depression, Parkinson's disease, Alzheimer's disease and other neuropsychiatric conditions. In particular, intriguing findings concern the identification of disease-associated miRNA signatures in peripheral tissues, or modifications in miRNA profiles induced by drug treatments. Furthermore, genetic variations in miRNA sequences and miRNA-related genes have been described in neuropsychiatric diseases. Overall, though still at a preliminary stage, several lines of evidence indicate an involvement of miRNAs in both the pathophysiology and pharmacotherapy of neuropsychiatric disorders. In this regard, the data obtained in peripheral tissues may provide further insights into the etiopathogenesis of several brain diseases and contribute to identify new biomarkers for diagnostic assessment improvement and treatment personalization.
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Affiliation(s)
- Elisabetta Maffioletti
- Genetic Unit, IRCCS Centro S. Giovanni di Dio FatebenefratelliBrescia, Italy
- Department of Molecular and Translational Medicine, University of BresciaBrescia, Italy
| | - Daniela Tardito
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di MilanoMilano, Italy
| | - Massimo Gennarelli
- Genetic Unit, IRCCS Centro S. Giovanni di Dio FatebenefratelliBrescia, Italy
- Department of Molecular and Translational Medicine, University of BresciaBrescia, Italy
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Dalton VS, Kolshus E, McLoughlin DM. Epigenetics and depression: return of the repressed. J Affect Disord 2014; 155:1-12. [PMID: 24238955 DOI: 10.1016/j.jad.2013.10.028] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 10/15/2013] [Accepted: 10/16/2013] [Indexed: 10/26/2022]
Abstract
INTRODUCTION Epigenetics has recently emerged as a potential mechanism by which adverse environmental stimuli can result in persistent changes in gene expression. Epigenetic mechanisms function alongside the DNA sequence to modulate gene expression and ultimately influence protein production. The current review provides an introduction and overview of epigenetics with a particular focus on preclinical and clinical studies relevant to major depressive disorder (MDD). METHODS PubMed and Web of Science databases were interrogated from January 1995 up to December 2012 using combinations of search terms, including "epigenetic", "microRNA" and "DNA methylation" cross referenced with "depression", "early life stress" and "antidepressant". RESULTS There is an association between adverse environmental stimuli, such as early life stress, and epigenetic modification of gene expression. Epigenetic changes have been reported in humans with MDD and may serve as biomarkers to improve diagnosis. Antidepressant treatments appear to reverse or initiate compensatory epigenetic alterations that may be relevant to their mechanism of action. LIMITATIONS As a narrative review, the current report was interpretive and qualitative in nature. CONCLUSION Epigenetic modification of gene expression provides a mechanism for understanding the link between long-term effects of adverse life events and the changes in gene expression that are associated with depression. Although still a developing field, in the future, epigenetic modifications of gene expression may provide novel biomarkers to predict future susceptibility and/or onset of MDD, improve diagnosis, and aid in the development of epigenetics-based therapies for depression.
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Affiliation(s)
- Victoria S Dalton
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland; Department of Psychiatry, Trinity College Dublin, St. Patrick's University Hospital, James's Street, Dublin 8, Ireland
| | - Erik Kolshus
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland; Department of Psychiatry, Trinity College Dublin, St. Patrick's University Hospital, James's Street, Dublin 8, Ireland
| | - Declan M McLoughlin
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland; Department of Psychiatry, Trinity College Dublin, St. Patrick's University Hospital, James's Street, Dublin 8, Ireland.
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Serafini G, Pompili M, Hansen KF, Obrietan K, Dwivedi Y, Amore M, Shomron N, Girardi P. MicroRNAs: fundamental regulators of gene expression in major affective disorders and suicidal behavior? Front Cell Neurosci 2013; 7:208. [PMID: 24298237 PMCID: PMC3828562 DOI: 10.3389/fncel.2013.00208] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 10/21/2013] [Indexed: 01/18/2023] Open
Affiliation(s)
- Gianluca Serafini
- Department of Neurosciences, Mental Health and Sensory Organs - Sant'Andrea Hospital, Sapienza University of Rome Rome, Italy
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Serafini G, Pompili M, Hansen KF, Obrietan K, Dwivedi Y, Shomron N, Girardi P. The involvement of microRNAs in major depression, suicidal behavior, and related disorders: a focus on miR-185 and miR-491-3p. Cell Mol Neurobiol 2013; 34:17-30. [PMID: 24213247 DOI: 10.1007/s10571-013-9997-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 10/12/2013] [Indexed: 01/08/2023]
Abstract
Major depressive disorders are common and disabling conditions associated with significant psychosocial impairment and suicide risk. At least 3-4 % of all depressive individuals die by suicide. Evidence suggests that small non-coding RNAs, in particular microRNAs (miRNAs), play a critical role in major affective disorders as well as suicide. We performed a detailed review of the current literature on miRNAs and their targets in major depression and related disorders as well as suicidal behavior, with a specific focus on miR-185 and miR-491-3p, which have been suggested to participate in the pathogenesis of major depression and/or suicide. miRNAs play a fundamental role in the development of the brain. Several miRNAs are reported to influence neuronal and circuit formation by negatively regulating gene expression. Global miRNA reduced expression was found in the prefrontal cortex of depressed suicide completers when compared to that of nonpsychiatric controls who died of other causes. One particular miRNA, miR-185, was reported to regulate TrkB-T1, which has been associated with suicidal behavior upon truncation. Furthermore, cAMP response element-binding protein-brain-derived neurotrophic factor pathways may regulate, through miRNAs, the homeostasis of neural and synaptic pathways playing a crucial role in major depression. miRNAs have gained attention as key players involved in nervous system development, physiology, and disease. Further evidence is needed to clarify the exact role that miRNAs play in major depression and related disorders and suicidal behavior.
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Affiliation(s)
- Gianluca Serafini
- Department of Neurosciences, Mental Health and Sensory Organs, Suicide Prevention Center, Sant'Andrea Hospital, Sapienza University of Rome, Via di Grottarossa 1037, 00189, Rome, Italy,
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