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AYAZ A, GEZDIRICI A, YILMAZ GULEC E, OZALP Ö, KOSEOGLU AH, DOGRU Z, YALCINTEPE S. Diagnostic Value of Microarray Method in Autism Spectrum Disorder, Intellectual Disability, and Multiple Congenital Anomalies and Some Candidate Genes for Autism: Experience of Two Centers. Medeni Med J 2022; 37:180-193. [PMID: 35735171 PMCID: PMC9234369 DOI: 10.4274/mmj.galenos.2022.70962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Objective: This study aimed to demonstrate the diagnostic value of microarray testing in autism spectrum disorder, intellectual disability, and multiple congenital anomalies of unknown etiology, as well as to report some potential candidate genes for autism. Methods: Microarray analysis records between January 2016 and December 2017 from two Genetic Diagnostic Centers in Turkey, Kanuni Sultan Suleyman and Adana Numune Training and Research Hospital, were compiled. Detected copy number variations (CNVs) were classified as benign, likely benign, variants of uncertain significance (VUS), likely pathogenic, and pathogenic according to American College of Medical Genetics and Genomics guidelines. The clinical findings of the some patients and the literature data were compared. Results: In 109 (24.5%) of 445 patients, a total of 163 CNVs with reporting criterion feature were detected. Sixty-nine (42%) and 8 (5%) of these were evaluated as pathogenic and likely pathogenic, respectively. Fifteen (9%) CNVs were also evaluated as VUS. Pathogenic or likely pathogenic CNVs were detected in 61 (13.6%) of 445 patients. Conclusions: We found that the probability of elucidating the etiology of microarray method in autism spectrum disorder, intellectual disability, and multiple congenital anomalies is 13.6% with a percentage similar to the literature. We suggest that the MYT1L, PXDN, TPO, and AUTS2 genes are all strong candidate genes for autism spectrum disorders. We detailed the clinical findings of the cases and reported that some CNV regions in the genome may be associated with autism.
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Syme TE, Grill M, Hayashida E, Viengkhou B, Campbell IL, Hofer MJ. Strawberry notch homolog 2 regulates the response to interleukin-6 in the central nervous system. J Neuroinflammation 2022; 19:126. [PMID: 35624480 PMCID: PMC9145108 DOI: 10.1186/s12974-022-02475-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The cytokine interleukin-6 (IL-6) modulates a variety of inflammatory processes and, context depending, can mediate either pro- or anti-inflammatory effects. Excessive IL-6 signalling in the brain is associated with chronic inflammation resulting in neurodegeneration. Strawberry notch homolog 2 (Sbno2) is an IL-6-regulated gene whose function is largely unknown. Here we aimed to address this issue by investigating the impact of Sbno2 disruption in mice with IL-6-mediated neuroinflammation. METHODS Mice with germline disruption of Sbno2 (Sbno2-/-) were generated and crossed with transgenic mice with chronic astrocyte production of IL-6 (GFAP-IL6). Phenotypic, molecular and transcriptomic analyses were performed on tissues and primary cell cultures to clarify the role of SBNO2 in IL-6-mediated neuroinflammation. RESULTS We found Sbno2-/- mice to be viable and overtly normal. By contrast GFAP-IL6 × Sbno2-/- mice had more severe disease compared with GFAP-IL6 mice. This was evidenced by exacerbated neuroinflammation and neurodegeneration and enhanced IL-6-responsive gene expression. Cell culture experiments on primary astrocytes from Sbno2-/- mice further showed elevated and sustained transcript levels of a number of IL-6 stimulated genes. Notably, despite enhanced disease in vivo and gene expression both in vivo and in vitro, IL-6-stimulated gp130 pathway activation was reduced when Sbno2 is disrupted. CONCLUSION Based on these results, we propose a role for SBNO2 as a novel negative feedback regulator of IL-6 that restrains the excessive inflammatory actions of this cytokine in the brain.
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Affiliation(s)
- Taylor E Syme
- School of Life and Environmental Sciences and the Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Magdalena Grill
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, 8010, Graz, Austria
- Division of Phoniatrics, Department of Otorhinolaryngology, Medical University of Graz, 8036, Graz, Austria
| | - Emina Hayashida
- School of Life and Environmental Sciences and the Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Barney Viengkhou
- School of Life and Environmental Sciences and the Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Iain L Campbell
- School of Life and Environmental Sciences and the Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Markus J Hofer
- School of Life and Environmental Sciences and the Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia.
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Wöhr M, Fong WM, Janas JA, Mall M, Thome C, Vangipuram M, Meng L, Südhof TC, Wernig M. Myt1l haploinsufficiency leads to obesity and multifaceted behavioral alterations in mice. Mol Autism 2022; 13:19. [PMID: 35538503 PMCID: PMC9087967 DOI: 10.1186/s13229-022-00497-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 04/15/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The zinc finger domain containing transcription factor Myt1l is tightly associated with neuronal identity and is the only transcription factor known that is both neuron-specific and expressed in all neuronal subtypes. We identified Myt1l as a powerful reprogramming factor that, in combination with the proneural bHLH factor Ascl1, could induce neuronal fate in fibroblasts. Molecularly, we found it to repress many non-neuronal gene programs, explaining its supportive role to induce and safeguard neuronal identity in combination with proneural bHLH transcriptional activators. Moreover, human genetics studies found MYT1L mutations to cause intellectual disability and autism spectrum disorder often coupled with obesity. METHODS Here, we generated and characterized Myt1l-deficient mice. A comprehensive, longitudinal behavioral phenotyping approach was applied. RESULTS Myt1l was necessary for survival beyond 24 h but not for overall histological brain organization. Myt1l heterozygous mice became increasingly overweight and exhibited multifaceted behavioral alterations. In mouse pups, Myt1l haploinsufficiency caused mild alterations in early socio-affective communication through ultrasonic vocalizations. In adulthood, Myt1l heterozygous mice displayed hyperactivity due to impaired habituation learning. Motor performance was reduced in Myt1l heterozygous mice despite intact motor learning, possibly due to muscular hypotonia. While anxiety-related behavior was reduced, acoustic startle reactivity was enhanced, in line with higher sensitivity to loud sound. Finally, Myt1l haploinsufficiency had a negative impact on contextual fear memory retrieval, while cued fear memory retrieval appeared to be intact. LIMITATIONS In future studies, additional phenotypes might be identified and a detailed characterization of direct reciprocal social interaction behavior might help to reveal effects of Myt1l haploinsufficiency on social behavior in juvenile and adult mice. CONCLUSIONS Behavioral alterations in Myt1l haploinsufficient mice recapitulate several clinical phenotypes observed in humans carrying heterozygous MYT1L mutations and thus serve as an informative model of the human MYT1L syndrome.
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Affiliation(s)
- Markus Wöhr
- grid.168010.e0000000419368956Department of Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305 USA ,grid.5596.f0000 0001 0668 7884Research Unit Brain and Cognition, Laboratory of Biological Psychology, Social and Affective Neuroscience Research Group, Faculty of Psychology and Educational Sciences, KU Leuven, 3000 Leuven, Belgium ,grid.5596.f0000 0001 0668 7884Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium ,grid.10253.350000 0004 1936 9756Faculty of Psychology, Experimental and Biological Psychology, Behavioral Neuroscience, Philipps-University of Marburg, 35032 Marburg, Germany ,grid.10253.350000 0004 1936 9756Center for Mind, Brain and Behavior, Philipps-University of Marburg, 35032 Marburg, Germany
| | - Wendy M. Fong
- grid.168010.e0000000419368956Departments of Pathology and Chemical and Systems Biology, School of Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305 USA
| | - Justyna A. Janas
- grid.168010.e0000000419368956Departments of Pathology and Chemical and Systems Biology, School of Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305 USA
| | - Moritz Mall
- grid.168010.e0000000419368956Departments of Pathology and Chemical and Systems Biology, School of Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305 USA ,grid.7497.d0000 0004 0492 0584Present Address: Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany ,Present Address: HITBR Hector Institute for Translational Brain Research gGmbH, 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Present Address: Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159 Mannheim, Germany
| | - Christian Thome
- grid.168010.e0000000419368956Departments of Pathology and Chemical and Systems Biology, School of Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305 USA
| | - Madhuri Vangipuram
- grid.168010.e0000000419368956Departments of Pathology and Chemical and Systems Biology, School of Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305 USA
| | - Lingjun Meng
- grid.168010.e0000000419368956Departments of Pathology and Chemical and Systems Biology, School of Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305 USA
| | - Thomas C. Südhof
- grid.168010.e0000000419368956Department of Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305 USA ,grid.168010.e0000000419368956School of Medicine, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305 USA
| | - Marius Wernig
- grid.168010.e0000000419368956Departments of Pathology and Chemical and Systems Biology, School of Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305 USA
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Sabaie H, Mazaheri Moghaddam M, Mazaheri Moghaddam M, Amirinejad N, Asadi MR, Daneshmandpour Y, Hussen BM, Taheri M, Rezazadeh M. Long non-coding RNA-associated competing endogenous RNA axes in the olfactory epithelium in schizophrenia: a bioinformatics analysis. Sci Rep 2021; 11:24497. [PMID: 34969953 PMCID: PMC8718521 DOI: 10.1038/s41598-021-04326-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/21/2021] [Indexed: 12/26/2022] Open
Abstract
The etiology of schizophrenia (SCZ), as a serious mental illness, is unknown. The significance of genetics in SCZ pathophysiology is yet unknown, and newly identified mechanisms involved in the regulation of gene transcription may be helpful in determining how these changes affect SCZ development and progression. In the current work, we used a bioinformatics approach to describe the role of long non-coding RNA (lncRNA)-associated competing endogenous RNAs (ceRNAs) in the olfactory epithelium (OE) samples in order to better understand the molecular regulatory processes implicated in SCZ disorders in living individuals. The Gene Expression Omnibus database was used to obtain the OE microarray dataset (GSE73129) from SCZ sufferers and control subjects, which contained information about both lncRNAs and mRNAs. The limma package of R software was used to identify the differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs). RNA interaction pairs were discovered using the Human MicroRNA Disease Database, DIANA-LncBase, and miRTarBase databases. In this study, the Pearson correlation coefficient was utilized to find positive correlations between DEmRNAs and DElncRNAs in the ceRNA network. Eventually, lncRNA-associated ceRNA axes were developed based on co-expression relations and DElncRNA-miRNA-DEmRNA interactions. This work found six potential DElncRNA-miRNA-DEmRNA loops in SCZ pathogenesis, including, SNTG2-AS1/hsa-miR-7-5p/SLC7A5, FLG-AS1/hsa-miR-34a-5p/FOSL1, LINC00960/hsa-miR-34a-5p/FOSL1, AQP4-AS1/hsa-miR-335-5p/FMN2, SOX2-OT/hsa-miR-24-3p/NOS3, and CASC2/hsa-miR-24-3p/NOS3. According to the findings, ceRNAs in OE might be promising research targets for studying SCZ molecular mechanisms. This could be a great opportunity to examine different aspects of neurodevelopment that may have been hampered early in SCZ patients.
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Affiliation(s)
- Hani Sabaie
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Madiheh Mazaheri Moghaddam
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences (ZUMS), Zanjan, Iran
| | - Nazanin Amirinejad
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mohammad Reza Asadi
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yousef Daneshmandpour
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq
| | - Mohammad Taheri
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Maryam Rezazadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran. .,Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran.
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Pol-Fuster J, Cañellas F, Ruiz-Guerra L, Medina-Dols A, Bisbal-Carrió B, Ortega-Vila B, Llinàs J, Hernandez-Rodriguez J, Lladó J, Olmos G, Strauch K, Heine-Suñer D, Vives-Bauzà C, Flaquer A. The conserved ASTN2/BRINP1 locus at 9q33.1-33.2 is associated with major psychiatric disorders in a large pedigree from Southern Spain. Sci Rep 2021; 11:14529. [PMID: 34267256 PMCID: PMC8282839 DOI: 10.1038/s41598-021-93555-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/21/2021] [Indexed: 11/11/2022] Open
Abstract
We investigated the genetic causes of major mental disorders (MMDs) including schizophrenia, bipolar disorder I, major depressive disorder and attention deficit hyperactive disorder, in a large family pedigree from Alpujarras, South of Spain, a region with high prevalence of psychotic disorders. We applied a systematic genomic approach based on karyotyping (n = 4), genotyping by genome-wide SNP array (n = 34) and whole-genome sequencing (n = 12). We performed genome-wide linkage analysis, family-based association analysis and polygenic risk score estimates. Significant linkage was obtained at chromosome 9 (9q33.1–33.2, LOD score = 4.11), a suggestive region that contains five candidate genes ASTN2, BRINP1, C5, TLR4 and TRIM32, previously associated with MMDs. Comprehensive analysis associated the MMD phenotype with genes of the immune system with dual brain functions. Moreover, the psychotic phenotype was enriched for genes involved in synapsis. These results should be considered once studying the genetics of psychiatric disorders in other families, especially the ones from the same region, since founder effects may be related to the high prevalence.
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Affiliation(s)
- Josep Pol-Fuster
- Department of Biology, University of Balearic Islands (UIB), Institut Universitari d'Investigacions en Ciències de la Salut (IUNICS), Palma, Spain.,Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain
| | - Francesca Cañellas
- Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain.,Department of Psychiatry, HUSE, IdISBa, Palma, Spain
| | - Laura Ruiz-Guerra
- Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain
| | - Aina Medina-Dols
- Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain
| | - Bàrbara Bisbal-Carrió
- Department of Biology, University of Balearic Islands (UIB), Institut Universitari d'Investigacions en Ciències de la Salut (IUNICS), Palma, Spain.,Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain
| | - Bernat Ortega-Vila
- Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain.,Molecular Diagnostics and Clinical Genetics Unit (UDMGC) and Genomics of Health Research Group, Hospital Universitari Son Espases (HUSE) and Institut d'Investigacions Sanitaries de Balears (IDISBA), Palma, Spain
| | - Jaume Llinàs
- Department of Biology, University of Balearic Islands (UIB), Institut Universitari d'Investigacions en Ciències de la Salut (IUNICS), Palma, Spain
| | - Jessica Hernandez-Rodriguez
- Molecular Diagnostics and Clinical Genetics Unit (UDMGC) and Genomics of Health Research Group, Hospital Universitari Son Espases (HUSE) and Institut d'Investigacions Sanitaries de Balears (IDISBA), Palma, Spain
| | - Jerònia Lladó
- Department of Biology, University of Balearic Islands (UIB), Institut Universitari d'Investigacions en Ciències de la Salut (IUNICS), Palma, Spain.,Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain
| | - Gabriel Olmos
- Department of Biology, University of Balearic Islands (UIB), Institut Universitari d'Investigacions en Ciències de la Salut (IUNICS), Palma, Spain.,Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain
| | - Konstantin Strauch
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany.,Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, LMU Munich, Munich, Germany
| | - Damià Heine-Suñer
- Molecular Diagnostics and Clinical Genetics Unit (UDMGC) and Genomics of Health Research Group, Hospital Universitari Son Espases (HUSE) and Institut d'Investigacions Sanitaries de Balears (IDISBA), Palma, Spain
| | - Cristòfol Vives-Bauzà
- Department of Biology, University of Balearic Islands (UIB), Institut Universitari d'Investigacions en Ciències de la Salut (IUNICS), Palma, Spain. .,Neurobiology Laboratory, Research Unit, Son Espases University Hospital (HUSE), Health Research Institute of Balearic Islands (IdISBa), Floor -1, Module F, R-805, Palma, Spain.
| | - Antònia Flaquer
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany.,Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, LMU Munich, Munich, Germany
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Reiner BC, Doyle GA, Weller AE, Levinson RN, Rao AM, Davila Perea E, Namoglu E, Pigeon A, Arauco-Shapiro G, Weickert CS, Turecki G, Crist RC, Berrettini WH. Inherited L1 Retrotransposon Insertions Associated With Risk for Schizophrenia and Bipolar Disorder. SCHIZOPHRENIA BULLETIN OPEN 2021; 2:sgab031. [PMID: 34901866 PMCID: PMC8650070 DOI: 10.1093/schizbullopen/sgab031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Studies of the genetic heritability of schizophrenia and bipolar disorder examining single nucleotide polymorphisms (SNPs) and copy number variations have failed to explain a large portion of the genetic liability, resulting in substantial missing heritability. Long interspersed element 1 (L1) retrotransposons are a type of inherited polymorphic variant that may be associated with risk for schizophrenia and bipolar disorder. We performed REBELseq, a genome wide assay for L1 sequences, on DNA from male and female persons with schizophrenia and controls (n = 63 each) to identify inherited L1 insertions and validated priority insertions. L1 insertions of interest were genotyped in DNA from a replication cohort of persons with schizophrenia, bipolar disorder, and controls (n = 2268 each) to examine differences in carrier frequencies. We identified an inherited L1 insertion in ARHGAP24 and a quadallelic SNP (rs74169643) inside an L1 insertion in SNTG2 that are associated with risk for developing schizophrenia and bipolar disorder (all odds ratios ~1.2). Pathway analysis identified 15 gene ontologies that were differentially affected by L1 burden, including multiple ontologies related to glutamatergic signaling and immune function, which have been previously associated with schizophrenia. These findings provide further evidence supporting the role of inherited repetitive genetic elements in the heritability of psychiatric disorders.
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Affiliation(s)
- Benjamin C Reiner
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Glenn A Doyle
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew E Weller
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rachel N Levinson
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aditya M Rao
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emilie Davila Perea
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Esin Namoglu
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alicia Pigeon
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gabriella Arauco-Shapiro
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cyndi Shannon Weickert
- Schizophrenia Research Laboratory, Neuroscience Research Australia & School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Department of Neuroscience & Physiology, Upstate Medical University, Syracuse, NY, USA
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Canada
| | - Richard C Crist
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wade H Berrettini
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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7
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Mansfield P, Constantino JN, Baldridge D. MYT1L: A systematic review of genetic variation encompassing schizophrenia and autism. Am J Med Genet B Neuropsychiatr Genet 2020; 183:227-233. [PMID: 32267091 PMCID: PMC7605444 DOI: 10.1002/ajmg.b.32781] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/23/2020] [Accepted: 02/03/2020] [Indexed: 02/03/2023]
Abstract
Variations in MYT1L, a gene encoding a transcription factor expressed in the brain, have been associated with autism, intellectual disability, and schizophrenia. Here we provide an updated review of published reports of neuropsychiatric correlates of loss of function and duplication of MYT1L. Of 27 duplications all were partial; 33% were associated exclusively with schizophrenia, and the chromosomal locations of schizophrenia-associated duplications exhibited a distinct difference in pattern-of-location from those associated with autism and/or intellectual disability. Of 51 published heterozygous loss of function variants, all but one were associated with intellectual disability, autism, or both, and one resulted in no neuropsychiatric diagnosis. There were no reports of schizophrenia associated with loss of function variants of MYT1L (Fisher's exact p < .00001, for contrast with all reported duplications). Although the precise function of the various mutations remains unspecified, these data collectively establish the candidacy of MYT1L as a reciprocal mutation, in which schizophrenia may be engendered by partial duplications, typically involving the 3' end of the gene, while developmental disability-notably autism-is associated with both loss of function and partial duplication. Future research on the specific effects of contrasting mutations in MYT1L may provide insight into the causal origins of autism and schizophrenia.
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Affiliation(s)
| | - John N. Constantino
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, Missouri,Department of Pediatrics, Washington University School of Medicine, Saint Louis, Missouri
| | - Dustin Baldridge
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, Missouri
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8
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Castronovo P, Baccarin M, Ricciardello A, Picinelli C, Tomaiuolo P, Cucinotta F, Frittoli M, Lintas C, Sacco R, Persico AM. Phenotypic spectrum of NRXN1 mono- and bi-allelic deficiency: A systematic review. Clin Genet 2019; 97:125-137. [PMID: 30873608 DOI: 10.1111/cge.13537] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/01/2019] [Accepted: 03/10/2019] [Indexed: 01/13/2023]
Abstract
Neurexins are presynaptic cell adhesion molecules critically involved in synaptogenesis and vesicular neurotransmitter release. They are encoded by three genes (NRXN1-3), each yielding a longer alpha (α) and a shorter beta (β) transcript. Deletions spanning the promoter and the initial exons of the NRXN1 gene, located in chromosome 2p16.3, are associated with a variety of neurodevelopmental, psychiatric, neurological and neuropsychological phenotypes. We have performed a systematic review to define (a) the clinical phenotypes most associated with mono-allelic exonic NRXN1 deletions, and (b) the phenotypic features of NRXN1 bi-allelic deficiency due to compound heterozygous deletions/mutations. Clinically, three major conclusions can be drawn: (a) incomplete penetrance and pleiotropy do not allow reliable predictions of clinical outcome following prenatal detection of mono-allelic exonic NRXN1 deletions. Newborn carriers should undergo periodic neuro-behavioral observations for the timely detection of warning signs and the prescription of early behavioral intervention; (b) the presence of additional independent genetic risk factors should always be sought, as they may influence prognosis; (c) children with exonic NRXN1 deletions displaying early-onset, severe psychomotor delay in the context of a Pitt-Hopkins-like syndrome 2 phenotype, should undergo DNA sequencing of the spared NRXN1 allele in search for mutations or very small insertions/deletions.
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Affiliation(s)
- Paola Castronovo
- Laboratory for Pervasive Developmental Disorders, Mafalda Luce Center, Milan, Italy
| | - Marco Baccarin
- Laboratory for Pervasive Developmental Disorders, Mafalda Luce Center, Milan, Italy
| | - Arianna Ricciardello
- Interdepartmental Program "Autism 0-90", "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
| | - Chiara Picinelli
- Laboratory for Pervasive Developmental Disorders, Mafalda Luce Center, Milan, Italy
| | - Pasquale Tomaiuolo
- Laboratory for Pervasive Developmental Disorders, Mafalda Luce Center, Milan, Italy
| | - Francesca Cucinotta
- Interdepartmental Program "Autism 0-90", "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
| | - Myriam Frittoli
- Laboratory for Pervasive Developmental Disorders, Mafalda Luce Center, Milan, Italy
| | - Carla Lintas
- Service for Neurodevelopmental Disorders & Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy
| | - Roberto Sacco
- Service for Neurodevelopmental Disorders & Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy
| | - Antonio M Persico
- Interdepartmental Program "Autism 0-90", "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
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9
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Abstract
Schizophrenia and other types of psychosis incur suffering, high health care costs and loss of human potential, due to the combination of early onset and poor response to treatment. Our ability to prevent or cure psychosis depends on knowledge of causal mechanisms. Molecular genetic studies show that thousands of common and rare variants contribute to the genetic risk for psychosis. Epidemiological studies have identified many environmental factors associated with increased risk of psychosis. However, no single genetic or environmental factor is sufficient to cause psychosis on its own. The risk of developing psychosis increases with the accumulation of many genetic risk variants and exposures to multiple adverse environmental factors. Additionally, the impact of environmental exposures likely depends on genetic factors, through gene-environment interactions. Only a few specific gene-environment combinations that lead to increased risk of psychosis have been identified to date. An example of replicable gene-environment interaction is a common polymorphism in the AKT1 gene that makes its carriers sensitive to developing psychosis with regular cannabis use. A synthesis of results from twin studies, molecular genetics, and epidemiological research outlines the many genetic and environmental factors contributing to psychosis. The interplay between these factors needs to be considered to draw a complete picture of etiology. To reach a more complete explanation of psychosis that can inform preventive strategies, future research should focus on longitudinal assessments of multiple environmental exposures within large, genotyped cohorts beginning early in life.
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Affiliation(s)
- Alyson Zwicker
- Department of Pathology,Dalhousie University,Halifax,NS,Canada
| | | | - Rudolf Uher
- Department of Pathology,Dalhousie University,Halifax,NS,Canada
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10
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Clinical significance of germline copy number variation in susceptibility of human diseases. J Genet Genomics 2018; 45:3-12. [PMID: 29396143 DOI: 10.1016/j.jgg.2018.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 12/27/2017] [Accepted: 01/02/2018] [Indexed: 02/06/2023]
Abstract
Germline copy number variation (CNV) is considered to be an important form of human genetic polymorphisms. Previous studies have identified amounts of CNVs in human genome by advanced technologies, such as comparative genomic hybridization, single nucleotide genotyping, and high-throughput sequencing. CNV is speculated to be derived from multiple mechanisms, such as nonallelic homologous recombination (NAHR) and nonhomologous end-joining (NHEJ). CNVs cover a much larger genome scale than single nucleotide polymorphisms (SNPs), and may alter gene expression levels by means of gene dosage, gene fusion, gene disruption, and long-range regulation effects, thus affecting individual phenotypes and playing crucial roles in human pathogenesis. The number of studies linking CNVs with common complex diseases has increased dramatically in recent years. Here, we provide a comprehensive review of the current understanding of germline CNVs, and summarize the association of germline CNVs with the susceptibility to a wide variety of human diseases that were identified in recent years. We also propose potential issues that should be addressed in future studies.
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11
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Hansen RD, Christensen AF, Olesen J. Family studies to find rare high risk variants in migraine. J Headache Pain 2017; 18:32. [PMID: 28255817 PMCID: PMC5334193 DOI: 10.1186/s10194-017-0729-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/27/2017] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Migraine has long been known as a common complex disease caused by genetic and environmental factors. The pathophysiology and the specific genetic susceptibility are poorly understood. Common variants only explain a small part of the heritability of migraine. It is thought that rare genetic variants with bigger effect size may be involved in the disease. Since migraine has a tendency to cluster in families, a family approach might be the way to find these variants. This is also indicated by identification of migraine-associated loci in classical linkage-analyses in migraine families. A single migraine study using a candidate-gene approach was performed in 2010 identifying a rare mutation in the TRESK potassium channel segregating in a large family with migraine with aura, but this finding has later become questioned. The technologies of next-generation sequencing (NGS) now provides an affordable tool to investigate the genetic variation in the entire exome or genome. The family-based study design using NGS is described in this paper. We also review family studies using NGS that have been successful in finding rare variants in other common complex diseases in order to argue the promising application of a family approach to migraine. METHOD PubMed was searched to find studies that looked for rare genetic variants in common complex diseases through a family-based design using NGS, excluding studies looking for de-novo mutations, or using a candidate-gene approach and studies on cancer. All issues from Nature Genetics and PLOS genetics 2014, 2015 and 2016 (UTAI June) were screened for relevant papers. Reference lists from included and other relevant papers were also searched. For the description of the family-based study design using NGS an in-house protocol was used. RESULTS Thirty-two successful studies, which covered 16 different common complex diseases, were included in this paper. We also found a single migraine study. Twenty-three studies found one or a few family specific variants (less than five), while other studies found several possible variants. Not all of them were genome wide significant. Four studies performed follow-up analyses in unrelated cases and controls and calculated odds ratios that supported an association between detected variants and risk of disease. Studies of 11 diseases identified rare variants that segregated fully or to a large degree with the disease in the pedigrees. CONCLUSION It is possible to find rare high risk variants for common complex diseases through a family-based approach. One study using a family approach and NGS to find rare variants in migraine has already been published but with strong limitations. More studies are under way.
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Affiliation(s)
- Rikke Dyhr Hansen
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, University of Copenhagen, Glostrup, DK-2600 Denmark
| | - Anne Francke Christensen
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, University of Copenhagen, Glostrup, DK-2600 Denmark
| | - Jes Olesen
- Danish Headache Center, Department of Neurology, Rigshospitalet Glostrup, University of Copenhagen, Glostrup, DK-2600 Denmark
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12
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Di Gregorio E, Riberi E, Belligni EF, Biamino E, Spielmann M, Ala U, Calcia A, Bagnasco I, Carli D, Gai G, Giordano M, Guala A, Keller R, Mandrile G, Arduino C, Maffè A, Naretto VG, Sirchia F, Sorasio L, Ungari S, Zonta A, Zacchetti G, Talarico F, Pappi P, Cavalieri S, Giorgio E, Mancini C, Ferrero M, Brussino A, Savin E, Gandione M, Pelle A, Giachino DF, De Marchi M, Restagno G, Provero P, Cirillo Silengo M, Grosso E, Buxbaum JD, Pasini B, De Rubeis S, Brusco A, Ferrero GB. Copy number variants analysis in a cohort of isolated and syndromic developmental delay/intellectual disability reveals novel genomic disorders, position effects and candidate disease genes. Clin Genet 2017; 92:415-422. [PMID: 28295210 DOI: 10.1111/cge.13009] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Array-comparative genomic hybridization (array-CGH) is a widely used technique to detect copy number variants (CNVs) associated with developmental delay/intellectual disability (DD/ID). AIMS Identification of genomic disorders in DD/ID. MATERIALS AND METHODS We performed a comprehensive array-CGH investigation of 1,015 consecutive cases with DD/ID and combined literature mining, genetic evidence, evolutionary constraint scores, and functional information in order to assess the pathogenicity of the CNVs. RESULTS We identified non-benign CNVs in 29% of patients. Amongst the pathogenic variants (11%), detected with a yield consistent with the literature, we found rare genomic disorders and CNVs spanning known disease genes. We further identified and discussed 51 cases with likely pathogenic CNVs spanning novel candidate genes, including genes encoding synaptic components and/or proteins involved in corticogenesis. Additionally, we identified two deletions spanning potential Topological Associated Domain (TAD) boundaries probably affecting the regulatory landscape. DISCUSSION AND CONCLUSION We show how phenotypic and genetic analyses of array-CGH data allow unraveling complex cases, identifying rare disease genes, and revealing unexpected position effects.
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Affiliation(s)
- E Di Gregorio
- University of Torino, Department of Medical Sciences, Turin, Italy.,Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - E Riberi
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - E F Belligni
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - E Biamino
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - M Spielmann
- Research Group Mundlos, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - U Ala
- Computational Biology Unit, Molecular Biotechnology Center (MBC), Turin, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - A Calcia
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - I Bagnasco
- Neuropsichiatria Infantile, Martini Hospital, ASL TO1, Turin, Italy
| | - D Carli
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - G Gai
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - M Giordano
- Department of Health Sciences, Laboratory of Genetics, University of Eastern Piedmont and Interdisciplinary Research Center of Autoimmune Diseases, Novara, Italy
| | - A Guala
- SOC Pediatria, Castelli Hospital, Verbania, Italy
| | - R Keller
- Mental Health Department, ASL TO2, Adult Autism Center, Turin, Italy
| | - G Mandrile
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy.,Medical Genetics, San Luigi Gonzaga University Hospital, Orbassano (TO), Italy
| | - C Arduino
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - A Maffè
- Molecular Biology and Genetics Unit, Santa Croce e Carle Hospital, Cuneo, Italy
| | - V G Naretto
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - F Sirchia
- Molecular Biology and Genetics Unit, Santa Croce e Carle Hospital, Cuneo, Italy
| | - L Sorasio
- Pediatrics, Santa Croce e Carle Hospital, Cuneo, Italy
| | - S Ungari
- Molecular Biology and Genetics Unit, Santa Croce e Carle Hospital, Cuneo, Italy
| | - A Zonta
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - G Zacchetti
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy.,Department of Health Sciences, Laboratory of Genetics, University of Eastern Piedmont and Interdisciplinary Research Center of Autoimmune Diseases, Novara, Italy
| | - F Talarico
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - P Pappi
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - S Cavalieri
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - E Giorgio
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - C Mancini
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - M Ferrero
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - A Brussino
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - E Savin
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - M Gandione
- Department of Neuropsychiatry, University of Torino, Turin, Italy
| | - A Pelle
- Medical Genetics, San Luigi Gonzaga University Hospital, Orbassano (TO), Italy.,Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - D F Giachino
- Medical Genetics, San Luigi Gonzaga University Hospital, Orbassano (TO), Italy.,Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - M De Marchi
- Medical Genetics, San Luigi Gonzaga University Hospital, Orbassano (TO), Italy.,Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - G Restagno
- Laboratory of Molecular Genetics, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - P Provero
- Computational Biology Unit, Molecular Biotechnology Center (MBC), Turin, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - M Cirillo Silengo
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - E Grosso
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - J D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - B Pasini
- Molecular Biology and Genetics Unit, Santa Croce e Carle Hospital, Cuneo, Italy
| | - S De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - A Brusco
- University of Torino, Department of Medical Sciences, Turin, Italy.,Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - G B Ferrero
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
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13
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Besold AN, Michel SLJ. Neural Zinc Finger Factor/Myelin Transcription Factor Proteins: Metal Binding, Fold, and Function. Biochemistry 2015; 54:4443-52. [DOI: 10.1021/bi501371a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Angelique N. Besold
- Department of Pharmaceutical
Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Sarah L. J. Michel
- Department of Pharmaceutical
Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
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14
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Rudd DS, Axelsen M, Epping EA, Andreasen NC, Wassink TH. A genome-wide CNV analysis of schizophrenia reveals a potential role for a multiple-hit model. Am J Med Genet B Neuropsychiatr Genet 2014; 165B:619-26. [PMID: 25228354 DOI: 10.1002/ajmg.b.32266] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 07/21/2014] [Indexed: 12/30/2022]
Abstract
Schizophrenia is a chronic and severe psychiatric disorder that is highly heritable. While both common and rare genetic variants contribute to disease risk, many questions still remain about disease etiology. We performed a genome-wide analysis of copy number variants (CNVs) in 166 schizophrenia subjects and 52 psychiatrically healthy controls. First, overall CNV characteristics were compared between cases and controls. The only statistically significant finding was that deletions comprised a greater proportion of CNVs in cases. High interest CNVs were then identified as conservative using the following filtering criteria: (i) known deleterious CNVs; (ii) CNVs > 1 Mb that were novel (not found in a database of control individuals); and (iii) CNVs < 1 Mb that were novel and that overlapped the coding region of a gene of interest. Cases did not harbor a higher proportion of conservative CNVs in comparison to controls. However, similar to previous reports, cases had a slightly higher proportion of individuals with clinically significant CNVs (known deleterious or conservative CNVs > 1 Mb) or with multiple conservative CNVs. Two case individuals with the highest burden of conservative CNVs also share a recurrent 15q11.2 BP1-2 deletion, indicating a role for a potential multiple-hit CNV model for schizophrenia. In total, we report three 15q11.2 BP1-2 deletion individuals with schizophrenia, adding to a growing body of evidence that this CNV is involved in disease etiology.
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Affiliation(s)
- Danielle S Rudd
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa; Department of Psychiatry, University of Iowa, Iowa City, Iowa
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15
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De Rocker N, Vergult S, Koolen D, Jacobs E, Hoischen A, Zeesman S, Bang B, Béna F, Bockaert N, Bongers EM, de Ravel T, Devriendt K, Giglio S, Faivre L, Joss S, Maas S, Marle N, Novara F, Nowaczyk MJM, Peeters H, Polstra A, Roelens F, Rosenberg C, Thevenon J, Tümer Z, Vanhauwaert S, Varvagiannis K, Willaert A, Willemsen M, Willems M, Zuffardi O, Coucke P, Speleman F, Eichler EE, Kleefstra T, Menten B. Refinement of the critical 2p25.3 deletion region: the role of MYT1L in intellectual disability and obesity. Genet Med 2014; 17:460-6. [PMID: 25232846 DOI: 10.1038/gim.2014.124] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/07/2014] [Indexed: 01/04/2023] Open
Abstract
PURPOSE Submicroscopic deletions of chromosome band 2p25.3 are associated with intellectual disability and/or central obesity. Although MYT1L is believed to be a critical gene responsible for intellectual disability, so far no unequivocal data have confirmed this hypothesis. METHODS In this study we evaluated a cohort of 22 patients (15 sporadic patients and two families) with a 2p25.3 aberration to further refine the clinical phenotype and to delineate the role of MYT1L in intellectual disability and obesity. In addition, myt1l spatiotemporal expression in zebrafish embryos was analyzed by quantitative polymerase chain reaction and whole-mount in situ hybridization. RESULTS Complete MYT1L deletion, intragenic deletion, or duplication was observed in all sporadic patients, in addition to two patients with a de novo point mutation in MYT1L. The familial cases comprise a 6-Mb deletion in a father and his three children and a 5' MYT1L overlapping duplication in a father and his two children. Expression analysis in zebrafish embryos shows specific myt1l expression in the developing brain. CONCLUSION Our data strongly strengthen the hypothesis that MYT1L is the causal gene for the observed syndromal intellectual disability. Moreover, because 17 patients present with obesity/overweight, haploinsufficiency of MYT1L might predispose to weight problems with childhood onset.Genet Med 17 6, 460-466.
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Affiliation(s)
- Nina De Rocker
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - David Koolen
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Eva Jacobs
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Susan Zeesman
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Birgitte Bang
- Paediatric Department, Copenhagen University Hospital, Herlev, Denmark
| | - Frédérique Béna
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Nele Bockaert
- Center for Developmental Disorders, Ghent University Hospital, Ghent, Belgium
| | - Ernie M Bongers
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Thomy de Ravel
- Center for Human Genetics, Leuven University Hospitals, KU Leuven, Leuven, Belgium
| | - Koenraad Devriendt
- Center for Human Genetics, Leuven University Hospitals, KU Leuven, Leuven, Belgium
| | - Sabrina Giglio
- Medical Genetics Unit, Meyer Children's University Hospital, Florence, Italy
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Shelagh Joss
- West of Scotland Regional Genetics Service, NHS Greater Glasgow and Clyde, Southern General Hospital, Glasgow, UK
| | - Saskia Maas
- Department of Clinical Genetics, Academic Medical Center, UVA, Amsterdam, The Netherlands
| | - Nathalie Marle
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Francesca Novara
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Malgorzata J M Nowaczyk
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Hilde Peeters
- Center for Human Genetics, Leuven University Hospitals, KU Leuven, Leuven, Belgium
| | - Abeltje Polstra
- Department of Clinical Genetics, Academic Medical Center, UVA, Amsterdam, The Netherlands
| | - Filip Roelens
- Heilig Hart Ziekenhuis Roeselare-Menen, Roeselare, Belgium
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Julien Thevenon
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Zeynep Tümer
- Center for Applied Human Molecular Genetics, Kennedy Center, University of Copenhagen, Glostrup, Denmark
| | | | | | - Andy Willaert
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Marjolein Willemsen
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Marjolaine Willems
- Département de Génétique Clinique, CHRU de Montpellier, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Paul Coucke
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Evan E Eichler
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent, Belgium
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16
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Morris BJ, Pratt JA. Novel treatment strategies for schizophrenia from improved understanding of genetic risk. Clin Genet 2014; 86:401-11. [PMID: 25142969 DOI: 10.1111/cge.12485] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/15/2014] [Accepted: 08/16/2014] [Indexed: 01/19/2023]
Abstract
Recent years have seen significant advances in our understanding of the genetic basis of schizophrenia. In particular, genome-wide approaches have suggested the involvement of many common genetic variants of small effect, together with a few rare variants exerting relatively large effects. While unequivocal identification of the relevant genes has, for the most part, remained elusive, the genes revealed as potential candidates can in many cases be clustered into functionally related groups which are potentially open to therapeutic intervention. In this review, we summarise this information, focusing on the accumulating evidence that genetic dysfunction at glutamatergic synapses and post-synaptic signalling complexes contributes to the aetiology of the disease. In particular, there is converging support for involvement of post-synaptic JNK pathways in disease aetiology. An expansion of our neurobiological knowledge of the basis of schizophrenia is urgently needed, yet some promising novel pharmacological targets can already be discerned.
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Affiliation(s)
- B J Morris
- Psychiatric Research Institute of Neuroscience in Glasgow (PsyRING), University of Glasgow, Glasgow, UK; Institute of Neuroscience and Psychology, School of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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17
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Keene KL, Chen WM, Chen F, Williams SR, Elkhatib SD, Hsu FC, Mychaleckyj JC, Doheny KF, Pugh EW, Ling H, Laurie CC, Gogarten SM, Madden EB, Worrall BB, Sale MM. Genetic Associations with Plasma B12, B6, and Folate Levels in an Ischemic Stroke Population from the Vitamin Intervention for Stroke Prevention (VISP) Trial. Front Public Health 2014; 2:112. [PMID: 25147783 PMCID: PMC4123605 DOI: 10.3389/fpubh.2014.00112] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 07/21/2014] [Indexed: 11/13/2022] Open
Abstract
Background: B vitamins play an important role in homocysteine metabolism, with vitamin deficiencies resulting in increased levels of homocysteine and increased risk for stroke. We performed a genome-wide association study (GWAS) in 2,100 stroke patients from the Vitamin Intervention for Stroke Prevention (VISP) trial, a clinical trial designed to determine whether the daily intake of high-dose folic acid, vitamins B6, and B12 reduce recurrent cerebral infarction. Methods: Extensive quality control (QC) measures resulted in a total of 737,081 SNPs for analysis. Genome-wide association analyses for baseline quantitative measures of folate, Vitamins B12, and B6 were completed using linear regression approaches, implemented in PLINK. Results: Six associations met or exceeded genome-wide significance (P ≤ 5 × 10−08). For baseline Vitamin B12, the strongest association was observed with a non-synonymous SNP (nsSNP) located in the CUBN gene (P = 1.76 × 10−13). Two additional CUBN intronic SNPs demonstrated strong associations with B12 (P = 2.92 × 10−10 and 4.11 × 10−10), while a second nsSNP, located in the TCN1 gene, also reached genome-wide significance (P = 5.14 × 10−11). For baseline measures of Vitamin B6, we identified genome-wide significant associations for SNPs at the ALPL locus (rs1697421; P = 7.06 × 10−10 and rs1780316; P = 2.25 × 10−08). In addition to the six genome-wide significant associations, nine SNPs (two for Vitamin B6, six for Vitamin B12, and one for folate measures) provided suggestive evidence for association (P ≤ 10−07). Conclusion: Our GWAS study has identified six genome-wide significant associations, nine suggestive associations, and successfully replicated 5 of 16 SNPs previously reported to be associated with measures of B vitamins. The six genome-wide significant associations are located in gene regions that have shown previous associations with measures of B vitamins; however, four of the nine suggestive associations represent novel finding and warrant further investigation in additional populations.
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Affiliation(s)
- Keith L Keene
- Center for Public Health Genomics, University of Virginia , Charlottesville, VA , USA ; Department of Biology, Center for Health Disparities, East Carolina University , Greenville, NC , USA
| | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia , Charlottesville, VA , USA ; Department of Public Health Sciences, University of Virginia , Charlottesville, VA , USA
| | - Fang Chen
- Center for Public Health Genomics, University of Virginia , Charlottesville, VA , USA
| | - Stephen R Williams
- Center for Public Health Genomics, University of Virginia , Charlottesville, VA , USA
| | - Stacey D Elkhatib
- Center for Public Health Genomics, University of Virginia , Charlottesville, VA , USA
| | - Fang-Chi Hsu
- Department of Biostatistical Sciences, Wake Forest School of Medicine , Winston Salem, NC , USA
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia , Charlottesville, VA , USA ; Department of Public Health Sciences, University of Virginia , Charlottesville, VA , USA
| | - Kimberly F Doheny
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine , Baltimore, MD , USA
| | - Elizabeth W Pugh
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine , Baltimore, MD , USA
| | - Hua Ling
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine , Baltimore, MD , USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington , Seattle, WA , USA
| | | | - Ebony B Madden
- National Human Genome Research Institute, National Institutes of Health , Bethesda, MD , USA
| | - Bradford B Worrall
- Department of Public Health Sciences, University of Virginia , Charlottesville, VA , USA ; Department of Neurology, University of Virginia , Charlottesville, VA , USA
| | - Michele M Sale
- Center for Public Health Genomics, University of Virginia , Charlottesville, VA , USA ; Department of Public Health Sciences, University of Virginia , Charlottesville, VA , USA ; Department of Biochemistry & Molecular Genetics, University of Virginia , Charlottesville, VA , USA
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Kinoshita M, Numata S, Tajima A, Ohi K, Hashimoto R, Shimodera S, Imoto I, Takeda M, Ohmori T. Aberrant DNA methylation of blood in schizophrenia by adjusting for estimated cellular proportions. Neuromolecular Med 2014; 16:697-703. [PMID: 25052007 DOI: 10.1007/s12017-014-8319-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 07/08/2014] [Indexed: 01/14/2023]
Abstract
DNA methylation, which is the transference of a methyl group to the 5'-carbon position of the cytosine in a CpG dinucleotide, is one of the major mechanisms of epigenetic modifications. A number of studies have demonstrated altered DNA methylation of peripheral blood cells in schizophrenia (SCZ) in previous studies. However, most of these studies have been limited to the analysis of the CpG sites in CpG islands in gene promoter regions, and cell-type proportions of peripheral leukocytes, which may be one of the potential confounding factors for DNA methylation, have not been adjusted in these studies. In this study, we performed a genome-wide DNA methylation profiling of the peripheral leukocytes from patients with SCZ and from non-psychiatric controls (N = 105; 63 SCZ and 42 control subjects) using a quantitative high-resolution DNA methylation microarray which covered across the whole gene region (485,764 CpG dinucleotides). In the DNA methylation data analysis, we first estimated the cell-type proportions of each sample with a published algorithm. Next, we performed a surrogate variable analysis to identify potential confounding factors in our microarray data. Finally, we conducted a multiple linear regression analysis in consideration of these factors, including estimated cell-type proportions, and identified aberrant DNA methylation in SCZ at 2,552 CpG loci at a 5% false discovery rate correction. Our results suggest that altered DNA methylation may be involved in the pathophysiology of SCZ, and cell heterogeneity adjustments may be necessary for DNA methylation analysis.
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Affiliation(s)
- Makoto Kinoshita
- Department of Psychiatry, Course of Integrated Brain Sciences, Medical Informatics, Institute of Health Biosciences, The University of Tokushima Graduate School, 3-8-15, Kuramoto-cho, Tokushima, 770-8503, Japan,
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19
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Orchestration of neurodevelopmental programs by RBFOX1: implications for autism spectrum disorder. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2014; 113:251-67. [PMID: 24290388 DOI: 10.1016/b978-0-12-418700-9.00008-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Neurodevelopmental and neuropsychiatric disorders result from complex interactions between critical genetic factors and as-yet-unknown environmental components. To gain clinical insight, it is critical to develop a comprehensive understanding of these genetic components. RBFOX1, an RNA splicing factor, regulates expression of large genetic networks during early neuronal development, and haploinsufficiency causes severe neurodevelopmental phenotypes including autism spectrum disorder (ASD), intellectual disability, and epilepsy. Genomic testing in individuals and large patient cohorts has identified phenotypically similar cases possessing copy number variations in RBFOX1, implicating the gene as an important cause of neurodevelopmental disease. However, a significant proportion of the observed structural variation is inherited from phenotypically normal individuals, raising questions regarding overall pathogenicity of variation at the RBFOX1 locus. In this chapter, we discuss the molecular, cellular, and clinical evidence supporting the role of RBFOX1 in neurodevelopment and present a comprehensive model for the contribution of structural variation in RBFOX1 to ASD.
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20
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Copy number variation distribution in six monozygotic twin pairs discordant for schizophrenia. Twin Res Hum Genet 2014; 17:108-20. [PMID: 24556202 DOI: 10.1017/thg.2014.6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have evaluated copy number variants (CNVs) in six monozygotic twin pairs discordant for schizophrenia. The data from Affymetrix® Human SNP 6.0 arrays™ were analyzed using Affymetrix® Genotyping Console™, Partek® Genomics Suite™, PennCNV, and Golden Helix SVS™. This yielded both program-specific and overlapping results. Only CNVs called by Affymetrix Genotyping Console, Partek Genomics Suite, and PennCNV were used in further analysis. This analysis included an assessment of calls in each of the six twin pairs towards identification of unique CNVs in affected and unaffected co-twins. Real time polymerase chain reaction (PCR) experiments confirmed one CNV loss at 7q11.21 that was found in the affected patient but not in the unaffected twin. The results identified CNVs and genes that were previously implicated in mental abnormalities in four of the six twin pairs. It included PYY (twin pairs 1 and 5), EPHA3 (twin pair 3), KIAA1211L (twin pair 4), and GPR139 (twin pair 5). They represent likely candidate genes and CNVs for the discordance of four of the six monozygotic twin pairs for this heterogeneous neurodevelopmental disorder. An explanation for these differences is ontogenetic de novo events that differentiate in the monozygotic twins during development.
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Melka MG, Castellani CA, Laufer BI, Rajakumar RN, O'Reilly R, Singh SM. Olanzapine induced DNA methylation changes support the dopamine hypothesis of psychosis. J Mol Psychiatry 2013; 1:19. [PMID: 25408910 PMCID: PMC4223857 DOI: 10.1186/2049-9256-1-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/16/2013] [Indexed: 01/06/2023] Open
Abstract
Background The dopamine (DA) hypothesis of schizophrenia proposes the mental illness is caused by excessive transmission of dopamine in selected brain regions. Multiple lines of evidence, including blockage of dopamine receptors by antipsychotic drugs that are used to treat schizophrenia, support the hypothesis. However, the dopamine D2 receptor (DRD2) blockade cannot explain some important aspects of the therapeutic effect of antipsychotic drugs. In this study, we hypothesized that antipsychotic drugs could affect the transcription of genes in the DA pathway by altering their epigenetic profile. Methods To test this hypothesis, we examined the effect of olanzapine, a commonly used atypical antipsychotic drug, on the DNA methylation status of genes from DA neurotransmission in the brain and liver of rats. Genomic DNA isolated from hippocampus, cerebellum, and liver of olanzapine treated (n = 2) and control (n = 2) rats were analyzed using rat specific methylation arrays. Results Our results show that olanzapine causes methylation changes in genes encoding for DA receptors (dopamine D1 receptor, dopamine D2 receptor and dopamine D5 receptor), a DA transporter (solute carrier family 18 member 2), a DA synthesis (differential display clone 8), and a DA metabolism (catechol-O-methyltransferase). We assessed a total of 40 genes in the DA pathway and found 19 to be differentially methylated between olanzapine treated and control rats. Most (17/19) genes showed an increase in methylation, in their promoter regions with in silico analysis strongly indicating a functional potential to suppress transcription in the brain. Conclusion Our results suggest that chronic olanzapine may reduce DA activity by altering gene methylation. It may also explain the delayed therapeutic effect of antipsychotics, which occurs despite rapid dopamine blockade. Furthermore, given the common nature of epigenetic variation, this lends insight into the differential therapeutic response of psychotic patients who display adequate blockage of dopamine receptors.
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Affiliation(s)
- Melkaye G Melka
- Department of Biology, Molecular Genetics Unit, Western Science Centre, The University of Western Ontario, London, Ontario N6A 5B7 Canada
| | - Christina A Castellani
- Department of Biology, Molecular Genetics Unit, Western Science Centre, The University of Western Ontario, London, Ontario N6A 5B7 Canada
| | - Benjamin I Laufer
- Department of Biology, Molecular Genetics Unit, Western Science Centre, The University of Western Ontario, London, Ontario N6A 5B7 Canada
| | - Raj N Rajakumar
- Department of Psychiatry, The University of Western Ontario, London, Ontario N6A 5B7 Canada
| | - Richard O'Reilly
- Department of Psychiatry, The University of Western Ontario, London, Ontario N6A 5B7 Canada
| | - Shiva M Singh
- Department of Biology, Molecular Genetics Unit, Western Science Centre, The University of Western Ontario, London, Ontario N6A 5B7 Canada
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