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Barki M, Xue H. GABRB2, a key player in neuropsychiatric disorders and beyond. Gene 2022; 809:146021. [PMID: 34673206 DOI: 10.1016/j.gene.2021.146021] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 08/05/2021] [Accepted: 09/14/2021] [Indexed: 01/11/2023]
Abstract
The GABA receptors represent the main inhibitory system in the central nervous system that ensure synaptogenesis, neurogenesis, and the regulation of neuronal plasticity and learning. GABAA receptors are pentameric in structure and belong to the Cys-loop superfamily. The GABRB2 gene, located on chromosome 5q34, encodes the β2 subunit that combines with the α and γ subunits to form the major subtype of GABAA receptors, which account for 43% of all GABAA receptors in the mammalian brain. Each subunit probably consists of an extracellular N-terminal domain, four membrane-spanning segments, a large intracellular loop between TM3 and TM4, and an extracellular C-terminal domain. Alternative splicing of the RNA transcript of the GABRB2 gene gives rise at least to four long and short isoforms with dissimilar electrophysiological properties. Furthermore, GABRB2 is imprinted and subjected to epigenetic regulation and positive selection. It has been associated with schizophrenia first in Han Chinese, and subsequently validated in other populations. Gabrb2 knockout mice also exhibited schizophrenia-like behavior and neuroinflammation that were ameliorated by the antipsychotic drug risperidone. GABRB2 was also associated with other neuropsychiatric disorders including bipolar disorder, epilepsy, autism spectrum disorder, Alzheimer's disease, frontotemporal dementia, substance dependence, depression, internet gaming disorder, and premenstrual dysphoric disorder. Recently, it has been postulated that GABRB2 might be a potential marker for different cancer types. As GABRB2 has a pivotal role in the central nervous system and is increasingly recognized to contribute to human diseases, further understanding of its structure and function may expedite the generation of new therapeutic approaches.
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Affiliation(s)
- Manel Barki
- Center for Cancer Genomics, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Hong Xue
- Center for Cancer Genomics, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China; Division of Life Science and Applied Genomics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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2
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Xue H, Wu Z, Long X, Ullah A, Chen S, Mat WK, Sun P, Gao MZ, Wang JQ, Wang HJ, Li X, Sun WJ, Qiao MQ. Copy number variation profile-based genomic typing of premenstrual dysphoric disorder in Chinese. J Genet Genomics 2021; 48:1070-1080. [PMID: 34530168 DOI: 10.1016/j.jgg.2021.08.012] [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: 03/10/2021] [Revised: 08/13/2021] [Accepted: 08/13/2021] [Indexed: 11/16/2022]
Abstract
Premenstrual dysphoric disorder (PMDD) affects nearly 5% women of reproductive age. Symptomatic heterogeneity, together with largely unknown genetics, have greatly hindered its effective treatment. In the present study, analysis of genomic sequencing-based copy-number-variations (CNVs) called from 100-kb white blood cell DNA sequence windows by means of semi-supervised clustering led to the segregation of patient genomes into the D and V groups, which correlated with the depression and invasion clinical types respectively with 89.0% consistency. Application of diagnostic CNV features selected using the correlation-based machine-learning method enabled the classification of the CNVs obtained into the D group, V group, total-patient group and control group with an average accuracy of 83.0%. The power of the diagnostic CNV features was 0.98 on average, suggesting that these CNV features could be employed for the molecular diagnosis of the major clinical types of PMDD. This demonstrated concordnce between the CNV profiles and clinical types of PMDD supported the validity of symptom-based diagnosis of PMDD for differentiating between its two major clinical types, as well as the predominanly genetic nature of PMDD with a host of overlaps between multiple susceptibility genes/pathways and the diagnostic CNV features as indicators of involvement in PMDD etiology.
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Affiliation(s)
- Hong Xue
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China; Division of Life Science and Applied Genomics Center, Hong Kong University of Science and Technology, Hong Kong, China; School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, 210009, China; HKUST Shenzhen Research Institute, 9 Yuexing First Road, Nanshan, Shenzhen, China; Guangzhou HKUST Fok Ying Tung Research Institute, Science and Technology Building, Nansha Information Technology Park, Nansha, Guangzhou, 511458, China.
| | - Zhenggang Wu
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science and Technology, Hong Kong, China; School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, 210009, China; HKUST Shenzhen Research Institute, 9 Yuexing First Road, Nanshan, Shenzhen, China; Guangzhou HKUST Fok Ying Tung Research Institute, Science and Technology Building, Nansha Information Technology Park, Nansha, Guangzhou, 511458, China
| | - Xi Long
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science and Technology, Hong Kong, China; School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, 210009, China; HKUST Shenzhen Research Institute, 9 Yuexing First Road, Nanshan, Shenzhen, China; Guangzhou HKUST Fok Ying Tung Research Institute, Science and Technology Building, Nansha Information Technology Park, Nansha, Guangzhou, 511458, China
| | - Ata Ullah
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science and Technology, Hong Kong, China
| | - Si Chen
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science and Technology, Hong Kong, China
| | - Wai-Kin Mat
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science and Technology, Hong Kong, China
| | - Peng Sun
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China
| | - Ming-Zhou Gao
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China
| | - Jie-Qiong Wang
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China
| | - Hai-Jun Wang
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China
| | - Xia Li
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China
| | - Wen-Jun Sun
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China
| | - Ming-Qi Qiao
- Shandong University of Traditional Chinese Medicine, Jinan, Shandong, 250355, China.
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Long X, Xue H. Genetic-variant hotspots and hotspot clusters in the human genome facilitating adaptation while increasing instability. Hum Genomics 2021; 15:19. [PMID: 33741065 PMCID: PMC7976700 DOI: 10.1186/s40246-021-00318-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 03/04/2021] [Indexed: 12/25/2022] Open
Abstract
Background Genetic variants, underlining phenotypic diversity, are known to distribute unevenly in the human genome. A comprehensive understanding of the distributions of different genetic variants is important for insights into genetic functions and disorders. Methods Herein, a sliding-window scan of regional densities of eight kinds of germline genetic variants, including single-nucleotide-polymorphisms (SNPs) and four size-classes of copy-number-variations (CNVs) in the human genome has been performed. Results The study has identified 44,379 hotspots with high genetic-variant densities, and 1135 hotspot clusters comprising more than one type of hotspots, accounting for 3.1% and 0.2% of the genome respectively. The hotspots and clusters are found to co-localize with different functional genomic features, as exemplified by the associations of hotspots of middle-size CNVs with histone-modification sites, work with balancing and positive selections to meet the need for diversity in immune proteins, and facilitate the development of sensory-perception and neuroactive ligand-receptor interaction pathways in the function-sparse late-replicating genomic sequences. Genetic variants of different lengths co-localize with retrotransposons of different ages on a “long-with-young” and “short-with-all” basis. Hotspots and clusters are highly associated with tumor suppressor genes and oncogenes (p < 10−10), and enriched with somatic tumor CNVs and the trait- and disease-associated SNPs identified by genome-wise association studies, exceeding tenfold enrichment in clusters comprising SNPs and extra-long CNVs. Conclusions In conclusion, the genetic-variant hotspots and clusters represent two-edged swords that spearhead both positive and negative genomic changes. Their strong associations with complex traits and diseases also open up a potential “Common Disease-Hotspot Variant” approach to the missing heritability problem. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-021-00318-3.
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Affiliation(s)
- Xi Long
- Division of Life Science and Applied Genomics Centre, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,HKUST Shenzhen Research Institute, 9 Yuexing First Road, Nanshan, Shenzhen, China
| | - Hong Xue
- Division of Life Science and Applied Genomics Centre, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China. .,HKUST Shenzhen Research Institute, 9 Yuexing First Road, Nanshan, Shenzhen, China. .,Centre for Cancer Genomics, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China.
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Heidari Nia M, Sargazi S, Saravani R, Mirinejad S, Jahantigh D, Shakiba M. Relationship between GABRB2 gene polymorphisms and schizophrenia susceptibility: a case-control study and in silico analyses. Int J Neurosci 2020; 132:633-642. [PMID: 32988247 DOI: 10.1080/00207454.2020.1830087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PURPOSE Converging evidence has recently established the significance of γ-aminobutyric acid neurotransmitter (GABA) system in the development of schizophrenia (SCZ). We aimed to determine the association of two markers of the GABAA receptor β2 subunit gene (GABRB2), rs12187676 G/C and rs1816072 T/C, with the risk of SCZ in Iranian population. MATERIALS AND METHODS In this case-control study, 190 patients with SCZ and 200 healthy controls were recruited from December 2018 to February 2020. Genotyping was done using the Tetra-ARMS-PCR technique. In silico analyses were performed to determine the potential effects of the variants. RESULTS The C allele and genotypes of codominant CC vs.TT and CT vs.TT, dominant TT vs. TC + CC, recessive TT + TC vs. CC of rs1816072 polymorphism, as well as codominant CC vs. GG and recessive GG + GC vs. CC genetic models of rs12187676 polymorphism were significantly associated with SCZ susceptibility. Compared to the TC/GC model, we have found that the TC/CC combination significantly increased the risk of SCZ by 4.32 fold while the TT/GG combination conferred a protective role against SCZ. Haplotypes analysis indicated that GABRB2 polymorphisms are in weak linkage disequilibrium with each other (LD = 0.1). However, bioinformatics analyses predicted that these polymorphisms do not have significant effects on the secondary structure and the splicing of GABRB2-mRNA. CONCLUSIONS We found that intronic GABRB2 polymorphisms were associated with SCZ risk in a sample of the Iranian population. These findings provided proof of concept for the involvement of the GABAergic neurotransmission system in SCZ development. These observations should be validated across other ethnicities and clinical subtypes.
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Affiliation(s)
- Milad Heidari Nia
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Saman Sargazi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ramin Saravani
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Danial Jahantigh
- Department of Biology, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
| | - Mansoor Shakiba
- Department of Psychiatry, Zahedan University of Medical Sciences, Zahedan, Iran
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Ullah A, Long X, Mat WK, Hu T, Khan MI, Hui L, Zhang X, Sun P, Gao M, Wang J, Wang H, Li X, Sun W, Qiao M, Xue H. Highly Recurrent Copy Number Variations in GABRB2 Associated With Schizophrenia and Premenstrual Dysphoric Disorder. Front Psychiatry 2020; 11:572. [PMID: 32695026 PMCID: PMC7338560 DOI: 10.3389/fpsyt.2020.00572] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 06/03/2020] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVE Although single-nucleotide polymorphisms in GABRB2, the gene encoding for GABAA receptors β2 subunit, have been associated with schizophrenia (SCZ), it is unknown whether there is any association of copy number variations (CNVs) in this gene with either SCZ or premenstrual dysphoric disorder (PMDD). METHODS In this study, the occurrences of the recurrent CNVs esv2730987 in Intron 6 and nsv1177513 in Exon 11 of GABRB2 in Chinese and German SCZ, and Chinese PMDD patients were compared to controls of same ethnicity and gender by quantitative PCR (qPCR). RESULTS The results demonstrated that copy-number-gains were enriched in both SCZ and PMDD patients with significant odds ratios (OR). For combined-gender SCZ patients versus controls, about two-fold increases were observed in both ethnic groups at both esv2730987 (OR = 2.15, p = 5.32E-4 in Chinese group; OR = 2.79, p = 8.84E-3 in German group) and nsv1177513 (OR = 3.29, p = 1.28E-11 in Chinese group; OR = 2.44, p = 6.17E-5 in German group). The most significant copy-number-gains were observed in Chinese females at nsv1177513 (OR = 3.41), and German females at esv2730987 (OR=3.96). Copy-number-gains were also enriched in Chinese PMDD patients versus controls at esv2730987 (OR = 10.53, p = 4.34E-26) and nsv1177513 (OR = 2.39, p = 3.19E-5). CONCLUSION These findings established for the first time the association of highly recurrent CNVs with SCZ and PMDD, suggesting the presence of an overlapping genetic basis with shared biomarkers for these two common psychiatric disorders.
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Affiliation(s)
- Ata Ullah
- Applied Genomics Center and State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Division of Life Science, Hong Kong, Hong Kong
| | - Xi Long
- Applied Genomics Center and State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Division of Life Science, Hong Kong, Hong Kong
| | - Wai-Kin Mat
- Applied Genomics Center and State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Division of Life Science, Hong Kong, Hong Kong
| | - Taobo Hu
- Applied Genomics Center and State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Division of Life Science, Hong Kong, Hong Kong
| | - Muhammad Ismail Khan
- Applied Genomics Center and State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Division of Life Science, Hong Kong, Hong Kong
| | - Li Hui
- Suzhou Guangji Hospital, The Affiliated Guangji Hospital of Soochow University, Suzhou, China
| | - Xiangyang Zhang
- Institute of Psychology, Chinese Academy of Sciences, Beijing, China
| | - Peng Sun
- School of Basic Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Mingzhou Gao
- School of Basic Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jieqiong Wang
- School of Basic Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Haijun Wang
- School of Basic Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xia Li
- School of Basic Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Wenjun Sun
- School of Basic Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Mingqi Qiao
- School of Basic Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Hong Xue
- Applied Genomics Center and State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Division of Life Science, Hong Kong, Hong Kong
- School of Basic Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
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6
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The association of GABRB2 SNPs with cognitive function in schizophrenia. Eur Arch Psychiatry Clin Neurosci 2020; 270:443-449. [PMID: 30706170 DOI: 10.1007/s00406-019-00985-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 01/09/2019] [Indexed: 12/21/2022]
Abstract
Cognitive impairment is one of the core symptoms of schizophrenia. Multiple domains of cognition are affected in patients with schizophrenia, which has a major effect on the functional outcome. Recent studies indicate that SNPs in the gamma-aminobutyric acid type A receptor beta 2 subunit (GABRB2) gene are associated with the risk of schizophrenia, however, the effect of these SNPs on cognitive function in patients with schizophrenia has not been explored. In this study, we first performed a case-control analysis of three SNPs (rs187269 allele A vs. G, rs252944 allele C vs. G, and rs194072 allele A vs. G) in 100 patients and 90 controls, then conducted a meta-analysis and found the SNP rs194072 was associated with schizophrenia (OR = 0.86, P = 0.0119), and survived after Bonferroni correction. The haplotype analysis suggested that the haplotype ACA, comprising the three SNPs (rs187269, rs252944 and rs194072) was also significantly associated with schizophrenia (P = 0.049).Then, we performed an association analysis of three SNPs (rs187269, rs252944 and rs194072) in GABRB2 gene with cognitive performance in patients with first episode schizophrenia. We found that the allele G of rs187269 in the GABRB2 gene was significantly associated with better cognitive flexibility (P = 0.005), a major aspect of executive function, in patients with first episode schizophrenia. The haplotype ACA was significantly associated with cognitive flexibility in patients with schizophrenia (P = 0.023). Our study showed that SNPs in GABRB2 may have a significant effect on cognitive function in patients with schizophrenia, suggesting that modulating GABRB2 may have therapeutic potential to improve cognitive function of patients with schizophrenia.
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Gabrb2-knockout mice displayed schizophrenia-like and comorbid phenotypes with interneuron-astrocyte-microglia dysregulation. Transl Psychiatry 2018; 8:128. [PMID: 30013074 PMCID: PMC6048160 DOI: 10.1038/s41398-018-0176-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/30/2018] [Accepted: 06/04/2018] [Indexed: 12/05/2022] Open
Abstract
Intronic polymorphisms of the GABAA receptor β2 subunit gene (GABRB2) under adaptive evolution were associated with schizophrenia and reduced expression, especially of the long isoform which differs in electrophysiological properties from the short isoform. The present study was directed to examining the gene dosage effects of Gabrb2 in knockout mice of both heterozygous (HT) and homozygous (KO) genotypes with respect to possible schizophrenia-like and comorbid phenotypes. The KO mice, and HT mice to a lesser extent, were found to display prepulse inhibition (PPI) deficit, locomotor hyperactivity, stereotypy, sociability impairments, spatial-working and spatial-reference memory deficits, reduced depression and anxiety, and accelerated pentylenetetrazol (PTZ)-induced seizure. In addition, the KO mice were highly susceptible to audiogenic epilepsy. Some of the behavioral phenotypes showed evidence of imprinting, gender effect and amelioration by the antipsychotic risperidone, and the audiogenic epilepsy was inhibited by the antiepileptic diazepam. GABAergic parvalbumin (PV)-positive interneuron dystrophy, astrocyte dystrophy, and extensive microglia activation were observed in the frontotemporal corticolimbic regions, and reduction of newborn neurons was observed in the hippocampus by immunohistochemical staining. The neuroinflammation indicated by microglial activation was accompanied by elevated brain levels of oxidative stress marker malondialdehyde (MDA) and the pro-inflammatory cytokines tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6). These extensive schizophrenia-like and comorbid phenotypes brought about by Gabrb2 knockout, in conjunction with our previous findings on GABRB2 association with schizophrenia, support a pivotal role of GABRB2 in schizophrenia etiology.
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Zhang T, Li J, Yu H, Shi Y, Li Z, Wang L, Wang Z, Lu T, Wang L, Yue W, Zhang D. Meta-analysis of GABRB2 polymorphisms and the risk of schizophrenia combined with GWAS data of the Han Chinese population and psychiatric genomics consortium. PLoS One 2018; 13:e0198690. [PMID: 29894498 PMCID: PMC5997335 DOI: 10.1371/journal.pone.0198690] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 05/23/2018] [Indexed: 12/31/2022] Open
Abstract
Schizophrenia (SCZ) is a severe psychiatric disorder with evidence of a strong genetic component in the complex etiologies. Some studies indicated that gamma-aminobutyric acid (GABA)A receptor β2 subunit gene (GABRB2) was associated with SCZ. Other studies reported a negative association. Moreover, the results of two previous meta-analyses of GABRB2 with SCZ were inconsistent and the sample sizes were limited. Therefore, an updated meta-analysis combined with genome-wide association study (GWAS) data of the Han Chinese population and Psychiatric Genomics Consortium (PGC) was performed. Available case–control and family-based genetic data were extracted from association studies, and the GWAS data were included. The findings showed no association between six single-nucleotide polymorphisms of GABRB2 (rs6556547, rs1816071, rs1816072, rs194072, rs252944, and rs187269) and SCZ in a total of 51,491 patients and 74,667 controls. The ethnic subgroup analysis revealed no significant association in Asian populations. Since the PGC data of SCZ (SCZ-PGC, 2014) contained 3 studies of Asian populations (1866 patients and 3418 controls), only the data of European samples in SCZ-PGC were used for the meta-analysis of the Caucasian population in the present study. The result still showed no association in the Caucasian population. In conclusion, the present meta-analysis on combined data from GWASs of the Han Chinese population and PGC suggested that GABRB2 polymorphisms might not be associated with SCZ.
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Affiliation(s)
- Tian Zhang
- Peking University Sixth Hospital, Beijing, China
- Peking University Institute of Mental Health, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China
- National Clinical Research Center for Mental Disorders, (Peking University Sixth Hospital), Beijing, China
| | - Jun Li
- Peking University Sixth Hospital, Beijing, China
- Peking University Institute of Mental Health, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China
- National Clinical Research Center for Mental Disorders, (Peking University Sixth Hospital), Beijing, China
| | - Hao Yu
- Department of Psychiatry, Jining Medical University, Jining, Shandong, China
| | - Yongyong Shi
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
- Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, China
- Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Psychiatry, First Teaching Hospital of Xinjiang Medical University, Urumqi, China
- Changning Mental Health Center, Shanghai, China
| | - Zhiqiang Li
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
- Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, China
- Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Linyan Wang
- Peking University Sixth Hospital, Beijing, China
- Peking University Institute of Mental Health, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China
- National Clinical Research Center for Mental Disorders, (Peking University Sixth Hospital), Beijing, China
| | - Ziqi Wang
- Peking University Sixth Hospital, Beijing, China
- Peking University Institute of Mental Health, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China
- National Clinical Research Center for Mental Disorders, (Peking University Sixth Hospital), Beijing, China
| | - Tianlan Lu
- Peking University Sixth Hospital, Beijing, China
- Peking University Institute of Mental Health, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China
- National Clinical Research Center for Mental Disorders, (Peking University Sixth Hospital), Beijing, China
| | - Lifang Wang
- Peking University Sixth Hospital, Beijing, China
- Peking University Institute of Mental Health, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China
- National Clinical Research Center for Mental Disorders, (Peking University Sixth Hospital), Beijing, China
- * E-mail: (LW); (WY); (DZ)
| | - Weihua Yue
- Peking University Sixth Hospital, Beijing, China
- Peking University Institute of Mental Health, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China
- National Clinical Research Center for Mental Disorders, (Peking University Sixth Hospital), Beijing, China
- * E-mail: (LW); (WY); (DZ)
| | - Dai Zhang
- Peking University Sixth Hospital, Beijing, China
- Peking University Institute of Mental Health, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China
- National Clinical Research Center for Mental Disorders, (Peking University Sixth Hospital), Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
- * E-mail: (LW); (WY); (DZ)
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Ferri F, Nikolova YS, Perrucci MG, Costantini M, Ferretti A, Gatta V, Huang Z, Edden RAE, Yue Q, D’Aurora M, Sibille E, Stuppia L, Romani GL, Northoff G. A Neural "Tuning Curve" for Multisensory Experience and Cognitive-Perceptual Schizotypy. Schizophr Bull 2017; 43:801-813. [PMID: 28168302 PMCID: PMC5472158 DOI: 10.1093/schbul/sbw174] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Our coherent perception of external events is enabled by the integration of inputs from different senses occurring within a range of temporal offsets known as the temporal binding window (TBW), which varies from person to person. A relatively wide TBW may increase the likelihood that stimuli originating from different environmental events are erroneously integrated and abnormally large TBW has been found in psychiatric disorders characterized by unusual perceptual experiences. Despite strong evidence of inter-individual differences in TBW, both within clinical and nonclinical populations, the neurobiological underpinnings of this variability remain unclear. We adopted an integrated strategy linking TBW to temporal dynamics in functional magnetic resonance imaging (fMRI)-resting-state activity and cortical excitation/inhibition (E/I) balance. E/I balance was indexed by glutamate/Gamma-AminoButyric Acid (GABA) concentrations and common variation in glutamate and GABA genes in a healthy sample. Stronger resting-state long-range temporal correlations, indicated by larger power law exponent (PLE), in the auditory cortex, robustly predicted narrower audio-tactile TBW, which was in turn associated with lower cognitive-perceptual schizotypy. Furthermore, PLE was highest and TBW narrowest for individuals with intermediate levels of E/I balance, with shifts towards either extreme resulting in reduced multisensory temporal precision and increased schizotypy, effectively forming a neural "tuning curve" for multisensory experience and schizophrenia risk. Our findings shed light on the neurobiological underpinnings of multisensory integration and its potentially clinically relevant inter-individual variability.
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Affiliation(s)
- Francesca Ferri
- Department of Psychology, University of Essex, Colchester, UK;,Institute of Mental Health Research, Brain and Mind Research Centre, University of Ottawa, Ottawa, ON, Canada;,These authors contributed equally to the article
| | - Yuliya S. Nikolova
- Campbell Family Mental Health Research Institute of CAMH, Toronto, ON, Canada;,These authors contributed equally to the article
| | - Mauro Gianni Perrucci
- Department of Neuroscience, Imaging and Clinical Science, “G.d’Annunzio” University of Chieti, and ITAB—Institute for Advanced Biomedical Technologies, Chieti, Italy
| | - Marcello Costantini
- Department of Psychology, University of Essex, Colchester, UK;,Department of Neuroscience, Imaging and Clinical Science, “G.d’Annunzio” University of Chieti, and ITAB—Institute for Advanced Biomedical Technologies, Chieti, Italy
| | - Antonio Ferretti
- Department of Neuroscience, Imaging and Clinical Science, “G.d’Annunzio” University of Chieti, and ITAB—Institute for Advanced Biomedical Technologies, Chieti, Italy
| | - Valentina Gatta
- Department of Psychological, Humanities and Territorial Sciences, “G.d’Annunzio” University of Chieti, Chieti, Italy
| | - Zirui Huang
- Institute of Mental Health Research, Brain and Mind Research Centre, University of Ottawa, Ottawa, ON, Canada
| | - Richard A. E. Edden
- Russel H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University, Baltimore, MD;,F. M. Kirby Center for Functional Brain Imaging, Kennedy Krieger Institute, Baltimore, MD
| | - Qiang Yue
- Department of Radiology, West China Hospital of Sichuan University, Chengdu, China
| | - Marco D’Aurora
- Department of Psychological, Humanities and Territorial Sciences, “G.d’Annunzio” University of Chieti, Chieti, Italy
| | - Etienne Sibille
- Campbell Family Mental Health Research Institute of CAMH, Toronto, ON, Canada;,Departments of Psychiatry and of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Liborio Stuppia
- Department of Psychological, Humanities and Territorial Sciences, “G.d’Annunzio” University of Chieti, Chieti, Italy
| | - Gian Luca Romani
- Department of Neuroscience, Imaging and Clinical Science, “G.d’Annunzio” University of Chieti, and ITAB—Institute for Advanced Biomedical Technologies, Chieti, Italy
| | - Georg Northoff
- Institute of Mental Health Research, Brain and Mind Research Centre, University of Ottawa, Ottawa, ON, Canada
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10
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Balan S, Yamada K, Iwayama Y, Hashimoto T, Toyota T, Shimamoto C, Maekawa M, Takagai S, Wakuda T, Kameno Y, Kurita D, Yamada K, Kikuchi M, Hashimoto T, Kanahara N, Yoshikawa T. Comprehensive association analysis of 27 genes from the GABAergic system in Japanese individuals affected with schizophrenia. Schizophr Res 2017; 185:33-40. [PMID: 28073605 DOI: 10.1016/j.schres.2017.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/26/2016] [Accepted: 01/01/2017] [Indexed: 01/01/2023]
Abstract
Involvement of the gamma-aminobutyric acid (GABA)-ergic system in schizophrenia pathogenesis through disrupted neurodevelopment has been highlighted in numerous studies. However, the function of common genetic variants of this system in determining schizophrenia risk is unknown. We therefore tested the association of 375 tagged SNPs in genes derived from the GABAergic system, such as GABAA receptor subunit genes, and GABA related genes (glutamate decarboxylase genes, GABAergic-marker gene, genes involved in GABA receptor trafficking and scaffolding) in Japanese schizophrenia case-control samples (n=2926; 1415 cases and 1511 controls). We observed nominal association of SNPs in nine GABAA receptor subunit genes and the GPHN gene with schizophrenia, although none survived correction for study-wide multiple testing. Two SNPs located in the GABRA1 gene, rs4263535 (Pallele=0.002; uncorrected) and rs1157122 (Pallele=0.006; uncorrected) showed top hits, followed by rs723432 (Pallele=0.007; uncorrected) in the GPHN gene. All three were significantly associated with schizophrenia and survived gene-wide multiple testing. Haplotypes containing associated variants in GABRA1 but not GPHN were significantly associated with schizophrenia. To conclude, we provided substantiating genetic evidence for the involvement of the GABAergic system in schizophrenia susceptibility. These results warrant further investigations to replicate the association of GABRA1 and GPHN with schizophrenia and to discern the precise mechanisms of disease pathophysiology.
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Affiliation(s)
- Shabeesh Balan
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama 351-0198, Japan
| | - Kazuo Yamada
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama 351-0198, Japan
| | - Yoshimi Iwayama
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama 351-0198, Japan
| | - Takanori Hashimoto
- Department of Psychiatry and Neurobiology, Kanazawa University Graduate School of Medicine, Kanazawa 920-8641, Japan
| | - Tomoko Toyota
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama 351-0198, Japan
| | - Chie Shimamoto
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama 351-0198, Japan
| | - Motoko Maekawa
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama 351-0198, Japan
| | - Shu Takagai
- Department of Psychiatry, Hamamatsu University School of Medicine, Shizuoka 431-3192, Japan
| | - Tomoyasu Wakuda
- Department of Psychiatry, Hamamatsu University School of Medicine, Shizuoka 431-3192, Japan
| | - Yosuke Kameno
- Department of Psychiatry, Hamamatsu University School of Medicine, Shizuoka 431-3192, Japan
| | - Daisuke Kurita
- Department of Psychiatry, Hamamatsu University School of Medicine, Shizuoka 431-3192, Japan
| | - Kohei Yamada
- Department of Psychiatry, Hamamatsu University School of Medicine, Shizuoka 431-3192, Japan
| | - Mitsuru Kikuchi
- Department of Psychiatry and Neurobiology, Kanazawa University Graduate School of Medicine, Kanazawa 920-8641, Japan
| | - Tasuku Hashimoto
- Department of Psychiatry, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | - Nobuhisa Kanahara
- Department of Psychiatry, Graduate School of Medicine, Chiba University, Chiba 260-8677, Japan
| | - Takeo Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama 351-0198, Japan.
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11
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Zong L, Zhou L, Hou Y, Zhang L, Jiang W, Zhang W, Wang L, Luo X, Wang S, Deng C, Peng Z, Li S, Hu J, Zhao H, Zhao C. Genetic and epigenetic regulation on the transcription of GABRB2: Genotype-dependent hydroxymethylation and methylation alterations in schizophrenia. J Psychiatr Res 2017; 88:9-17. [PMID: 28063323 DOI: 10.1016/j.jpsychires.2016.12.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/30/2016] [Accepted: 12/19/2016] [Indexed: 12/17/2022]
Abstract
To improve our understanding of the abnormalities and non-Mendelian inheritance characteristics of schizophrenia, this study examined DNA methylation (5mC) and hydroxymethylation (5hmC) in the schizophrenia-associated GABRB2 gene encoding the type A γ-aminobutyric acid receptor β2 subunit. DNAs from the peripheral white blood cells of 279 schizophrenic patients and 256 controls from the Chinese Han population were examined to reveal that the GABRB2 promoter P1-5mC level which was correlated with olanzapine administration, P2-5mC/5hmC level, and Alu-5mC level which was correlated with administration of ziprasidone or oxcarbazepine, were increased in schizophrenic patients. Significant correlations of the promoter 5mC/5hmC levels with the genotypes of single nucleotide polymorphisms (SNPs) were observed with SNPs rs72815526 (C/A) and rs3811997 (C/T). In schizophrenics, the heterozygous genotypes of rs72815526 (C/A) were correlated with increased 5hmC levels whereas the heterozygous genotypes of rs3811997 (C/T) were correlated with decreased 5mC levels. Moreover, the GABRB2 promoter with rs3811997(C/T) minor allele T or the methylation-disrupted type AG at -254 and -231 CCGG sites was observed to enhance the promoter activity in the luciferase reporter-transfected human embryonic kidney 293 cells. An elevated GABRB2 mRNA transcriptional level in human neuroblastoma IMR32 cells were accompanied by the decreased promoter 5hmC/5mC levels induced by 5-azacytidine or by increased histone H4 acetylation levels of the Alu-Yi6 region induced by valproic acid. These results reveal alterations in GABRB2 genotype-dependent methylation and hydroxymethylation in schizophrenia, which yielded transcriptional and translational alterations in the cultured cells, and help elucidate the genetic-epigenetic interactions influencing schizophrenia.
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Affiliation(s)
- Lu Zong
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China
| | - Lin Zhou
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China; Key Laboratory of Genetics and Birth Health of Hunan Province, Family Planning Institute of Hunan Province, Changsha, China
| | - Yu Hou
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China
| | - Lulu Zhang
- Department of Psychiatry, Guangzhou First People's Hospital, Guangzhou, Guangdong, China
| | - Wei Jiang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China
| | - Wenwei Zhang
- The Third People's Hospital of Zhongshan, Zhongshan, Guangdong, China
| | - Lijuan Wang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China
| | - Xia Luo
- Department of Psychiatry, Shenzhen Kangning Hospital & Shenzhen Mental Health Center, Shenzhen, China
| | - Shiqing Wang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China
| | - Cong Deng
- The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhizhen Peng
- The Third People's Hospital of Zhongshan, Zhongshan, Guangdong, China
| | - Shufen Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China
| | - Jiming Hu
- The Third People's Hospital of Zhongshan, Zhongshan, Guangdong, China
| | - Hu Zhao
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Cunyou Zhao
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China; Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China.
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12
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Chang CY, Chen YW, Wang TW, Lai WS. Akting up in the GABA hypothesis of schizophrenia: Akt1 deficiency modulates GABAergic functions and hippocampus-dependent functions. Sci Rep 2016; 6:33095. [PMID: 27615800 PMCID: PMC5018883 DOI: 10.1038/srep33095] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/19/2016] [Indexed: 12/29/2022] Open
Abstract
Accumulating evidence implies that both AKT1 and GABAA receptor (GABAAR) subunit genes are involved in schizophrenia pathogenesis. Activated Akt promotes GABAergic neuron differentiation and increases GABAAR expression on the plasma membrane. To elucidate the role of Akt1 in modulating GABAergic functions and schizophrenia-related cognitive deficits, a set of 6 in vitro and in vivo experiments was conducted. First, an Akt1/2 inhibitor was applied to evaluate its effect on GABAergic neuron-like cell formation from P19 cells. Inhibiting Akt resulted in a reduction in parvalbumin-positive neuron-like cells. In Akt1−/− and wild-type mice, seizures induced using pentylenetetrazol (a GABAAR antagonist) were measured, and GABAAR expression and GABAergic interneuron abundance in the brain were examined. Female Akt1−/− mice, but not male Akt1−/− mice, exhibited less pentylenetetrazol-induced convulsive activity than their corresponding wild-type controls. Reduced parvalbumin-positive interneuron abundance and GABAAR subunit expression, especially in the hippocampus, were also observed in female Akt1−/− mice compared to female wild-type mice. Neuromorphometric analyses revealed significantly reduced neurite complexity in hippocampal pyramidal neurons. Additionally, female Akt1−/− mice displayed increased hippocampal oscillation power and impaired spatial memory compared to female wild-type mice. Our findings suggest that Akt1 deficiency modulates GABAergic interneurons and GABAAR expression, contributing to hippocampus-dependent cognitive functional impairment.
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Affiliation(s)
- Chia-Yuan Chang
- Department of Psychology, National Taiwan University, Taipei, Taiwan
| | - Yi-Wen Chen
- Department of Psychology, National Taiwan University, Taipei, Taiwan
| | - Tsu-Wei Wang
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Wen-Sung Lai
- Department of Psychology, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Brain and Mind Sciences, National Taiwan University, Taipei, Taiwan.,Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan
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13
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Wang L, Jiang W, Lin Q, Zhang Y, Zhao C. DNA methylation regulatesgabrb2mRNA expression: developmental variations and disruptions inl-methionine-induced zebrafish with schizophrenia-like symptoms. GENES BRAIN AND BEHAVIOR 2016; 15:702-710. [DOI: 10.1111/gbb.12315] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 07/18/2016] [Accepted: 08/04/2016] [Indexed: 12/25/2022]
Affiliation(s)
- L. Wang
- Department of Medical Genetics, School of Basic Medical Sciences; Southern Medical University
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases
| | - W. Jiang
- Department of Medical Genetics, School of Basic Medical Sciences; Southern Medical University
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases
| | - Q. Lin
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Developmental Biology, Institute of Genetic Engineering, School of Basic Medical Sciences; Southern Medical University; Guangzhou China
| | - Y. Zhang
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Developmental Biology, Institute of Genetic Engineering, School of Basic Medical Sciences; Southern Medical University; Guangzhou China
| | - C. Zhao
- Department of Medical Genetics, School of Basic Medical Sciences; Southern Medical University
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases
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14
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Chekouo T, Stingo FC, Guindani M, Do KA. A Bayesian predictive model for imaging genetics with application to schizophrenia. Ann Appl Stat 2016. [DOI: 10.1214/16-aoas948] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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15
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Ng SK, Hu T, Long X, Chan CH, Tsang SY, Xue H. Feature co-localization landscape of the human genome. Sci Rep 2016; 6:20650. [PMID: 26854351 PMCID: PMC4745063 DOI: 10.1038/srep20650] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 01/07/2016] [Indexed: 12/11/2022] Open
Abstract
Although feature co-localizations could serve as useful guide-posts to genome architecture, a comprehensive and quantitative feature co-localization map of the human genome has been lacking. Herein we show that, in contrast to the conventional bipartite division of genomic sequences into genic and inter-genic regions, pairwise co-localizations of forty-two genomic features in the twenty-two autosomes based on 50-kb to 2,000-kb sequence windows indicate a tripartite zonal architecture comprising Genic zones enriched with gene-related features and Alu-elements; Proximal zones enriched with MIR- and L2-elements, transcription-factor-binding-sites (TFBSs), and conserved-indels (CIDs); and Distal zones enriched with L1-elements. Co-localizations between single-nucleotide-polymorphisms (SNPs) and copy-number-variations (CNVs) reveal a fraction of sequence windows displaying steeply enhanced levels of SNPs, CNVs and recombination rates that point to active adaptive evolution in such pathways as immune response, sensory perceptions, and cognition. The strongest positive co-localization observed between TFBSs and CIDs suggests a regulatory role of CIDs in cooperation with TFBSs. The positive co-localizations of cancer somatic CNVs (CNVT) with all Proximal zone and most Genic zone features, in contrast to the distinctly more restricted co-localizations exhibited by germline CNVs (CNVG), reveal disparate distributions of CNVTs and CNVGs indicative of dissimilarity in their underlying mechanisms.
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Affiliation(s)
- Siu-Kin Ng
- Division of Life Science, Applied Genomics Center and Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Taobo Hu
- Division of Life Science, Applied Genomics Center and Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Xi Long
- Division of Life Science, Applied Genomics Center and Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Cheuk-Hin Chan
- Division of Life Science, Applied Genomics Center and Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Shui-Ying Tsang
- Division of Life Science, Applied Genomics Center and Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
| | - Hong Xue
- Division of Life Science, Applied Genomics Center and Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong
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16
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Summaries of plenary, symposia, and oral sessions at the XXII World Congress of Psychiatric Genetics, Copenhagen, Denmark, 12-16 October 2014. Psychiatr Genet 2015; 26:1-47. [PMID: 26565519 DOI: 10.1097/ypg.0000000000000112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The XXII World Congress of Psychiatric Genetics, sponsored by the International Society of Psychiatric Genetics, took place in Copenhagen, Denmark, on 12-16 October 2014. A total of 883 participants gathered to discuss the latest findings in the field. The following report was written by student and postdoctoral attendees. Each was assigned one or more sessions as a rapporteur. This manuscript represents topics covered in most, but not all of the oral presentations during the conference, and contains some of the major notable new findings reported.
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17
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Kim YS, Yang M, Mat WK, Tsang SY, Su Z, Jiang X, Ng SK, Liu S, Hu T, Pun F, Liao Y, Tang J, Chen X, Hao W, Xue H. GABRB2 Haplotype Association with Heroin Dependence in Chinese Population. PLoS One 2015; 10:e0142049. [PMID: 26561861 PMCID: PMC4643001 DOI: 10.1371/journal.pone.0142049] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 10/17/2015] [Indexed: 01/02/2023] Open
Abstract
Substance dependence is a frequently observed comorbid disorder in schizophrenia, but little is known about genetic factors possibly shared between the two psychotic disorders. GABRB2, a schizophrenia candidate gene coding for GABAA receptor β2 subunit, is examined for possible association with heroin dependence in Han Chinese population. Four single nucleotide polymorphisms (SNPs) in GABRB2, namely rs6556547 (S1), rs1816071 (S3), rs18016072 (S5), and rs187269 (S29), previously associated with schizophrenia, were examined for their association with heroin dependence. Two additional SNPs, rs10051667 (S31) and rs967771 (S32), previously associated with alcohol dependence and bipolar disorder respectively, were also analyzed. The six SNPs were genotyped by direct sequencing of PCR amplicons of target regions for 564 heroin dependent individuals and 498 controls of Han Chinese origin. Interestingly, it was found that recombination between the haplotypes of all-derived-allele (H1; OR = 1.00) and all-ancestral-allele (H2; OR = 0.74) at S5-S29 junction generated two recombinants H3 (OR = 8.51) and H4 (OR = 5.58), both conferring high susceptibility to heroin dependence. Additional recombination between H2 and H3 haplotypes at S1-S3 junction resulted in a risk-conferring haplotype H5 (OR = 1.94x109). In contrast, recombination between H1 and H2 haplotypes at S3-S5 junction rescued the risk-conferring effect of recombination at S5-S29 junction, giving rise to the protective haplotype H6 (OR = 0.68). Risk-conferring effects of S1-S3 and S5-S29 crossovers and protective effects of S3-S5 crossover were seen in both pure heroin dependent and multiple substance dependence subgroups. In conclusion, significant association was found with haplotypes of the S1-S29 segment in GABRB2 for heroin dependence in Han Chinese population. Local recombination was an important determining factor for switching haplotypes between risk-conferring and protective statuses. The present study provide evidence for the schizophrenia candidate gene GABRB2 to play a role in heroin dependence, but replication of these findings is required.
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Affiliation(s)
- Yung Su Kim
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Mei Yang
- Mental Health Institute, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Wai-Kin Mat
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Shui-Ying Tsang
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
- Center for Statistical Science, Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Zhonghua Su
- The Second Affiliated Hospital of Jining Medical College, Jining, Shandong, China
| | - Xianfei Jiang
- The Second Affiliated Hospital of Jining Medical College, Jining, Shandong, China
| | - Siu-Kin Ng
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Siyu Liu
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Taobo Hu
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Frank Pun
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
- Center for Statistical Science, Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Yanhui Liao
- Mental Health Institute, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Jinsong Tang
- Mental Health Institute, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Xiaogang Chen
- Mental Health Institute, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Wei Hao
- Mental Health Institute, the Second Xiangya Hospital of Central South University, Changsha, China
| | - Hong Xue
- Division of Life Science and Applied Genomics Center, Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
- Center for Statistical Science, Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
- State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
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18
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Bristow GC, Bostrom JA, Haroutunian V, Sodhi MS. Sex differences in GABAergic gene expression occur in the anterior cingulate cortex in schizophrenia. Schizophr Res 2015; 167:57-63. [PMID: 25660468 PMCID: PMC4524801 DOI: 10.1016/j.schres.2015.01.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 01/15/2015] [Accepted: 01/17/2015] [Indexed: 01/30/2023]
Abstract
GABAergic dysfunction has been strongly implicated in the pathophysiology of schizophrenia. In this study, we analyzed the expression levels of several GABAergic genes in the anterior cingulate cortex (ACC) of postmortem subjects with schizophrenia (n=21) and a comparison group of individuals without a history of psychiatric illness (n=18). Our analyses revealed a significant sex by diagnosis effect, along with significant differences in GABAergic gene expression based on medication status. Analyses revealed that in male groups, the expression of GABAergic genes was generally lower in schizophrenia cases compared to the controls, with significantly lower expression levels of GABA-Aα5, GABA-Aβ1, and GABA-Aε. In females, the expression of GABAergic genes was higher in the schizophrenia cases, with significantly higher expression of the GABA-Aβ1 and GAD67 genes. Analysis of the effect of medication in the schizophrenia subjects revealed significantly higher expression of GABA-Aα1-3, GABA-Aβ2, GABA-Aγ2, and GAD67 in the medicated group compared to the unmedicated group. These data show that sex differences in the expression of GABAergic genes occur in the ACC in schizophrenia. Therefore, our data support previous findings of GABAergic dysfunction in schizophrenia and emphasize the importance of considering sex in analyses of the pathophysiology of schizophrenia. Sex differences in the GABAergic regulation of ACC function may contribute to the differences observed in the symptoms of male and female patients with schizophrenia. In addition, our findings indicate that antipsychotic medications may alter GABAergic signaling in the ACC, supporting the potential of GABAergic targets for the development of novel antipsychotic medication.
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Affiliation(s)
- Greg C. Bristow
- Department of Pharmacy Practice and Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago IL 60607, USA.,Corresponding author: Dr. Greg Bristow, Department of Pharmacy Practice, University of Illinois at Chicago, 900 S. Ashland Ave., MC870, Chicago IL 60607-4067, USA. Tel: +1-312-996-1413, Fax: +1-312-413-9303,
| | - John A. Bostrom
- Department of Pharmacy Practice and Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago IL 60607, USA
| | - Vahram Haroutunian
- Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, USA
| | - Monsheel S. Sodhi
- Department of Pharmacy Practice and Center for Pharmaceutical Biotechnology, College of Pharmacy, University of Illinois at Chicago, Chicago IL 60607, USA.,Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA
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19
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Li S, Chen J, Guo J, Jing BY, Tsang SY, Xue H. Likelihood Ratio Test for Multi-Sample Mixture Model and Its Application to Genetic Imprinting. J Am Stat Assoc 2015. [DOI: 10.1080/01621459.2014.939272] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Yuan H, Low CM, Moody OA, Jenkins A, Traynelis SF. Ionotropic GABA and Glutamate Receptor Mutations and Human Neurologic Diseases. Mol Pharmacol 2015; 88:203-17. [PMID: 25904555 PMCID: PMC4468639 DOI: 10.1124/mol.115.097998] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/22/2015] [Indexed: 01/03/2023] Open
Abstract
The advent of whole exome/genome sequencing and the technology-driven reduction in the cost of next-generation sequencing as well as the introduction of diagnostic-targeted sequencing chips have resulted in an unprecedented volume of data directly linking patient genomic variability to disorders of the brain. This information has the potential to transform our understanding of neurologic disorders by improving diagnoses, illuminating the molecular heterogeneity underlying diseases, and identifying new targets for therapeutic treatment. There is a strong history of mutations in GABA receptor genes being involved in neurologic diseases, particularly the epilepsies. In addition, a substantial number of variants and mutations have been found in GABA receptor genes in patients with autism, schizophrenia, and addiction, suggesting potential links between the GABA receptors and these conditions. A new and unexpected outcome from sequencing efforts has been the surprising number of mutations found in glutamate receptor subunits, with the GRIN2A gene encoding the GluN2A N-methyl-d-aspartate receptor subunit being most often affected. These mutations are associated with multiple neurologic conditions, for which seizure disorders comprise the largest group. The GluN2A subunit appears to be a locus for epilepsy, which holds important therapeutic implications. Virtually all α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor mutations, most of which occur within GRIA3, are from patients with intellectual disabilities, suggesting a link to this condition. Similarly, the most common phenotype for kainate receptor variants is intellectual disability. Herein, we summarize the current understanding of disease-associated mutations in ionotropic GABA and glutamate receptor families, and discuss implications regarding the identification of human mutations and treatment of neurologic diseases.
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Affiliation(s)
- Hongjie Yuan
- Departments of Pharmacology (H.Y., A.J., S.F.T.) and Anesthesiology (O.A.M., A.J.), Emory University School of Medicine, Rollins Research Center, Atlanta, Georgia; and Departments of Pharmacology and Anaesthesia, Yong Loo Lin School of Medicine, National University of Singapore Graduate School for Integrative Sciences and Engineering, and Neurobiology/Ageing Programme, National University of Singapore, Singapore (C.-M.L.)
| | - Chian-Ming Low
- Departments of Pharmacology (H.Y., A.J., S.F.T.) and Anesthesiology (O.A.M., A.J.), Emory University School of Medicine, Rollins Research Center, Atlanta, Georgia; and Departments of Pharmacology and Anaesthesia, Yong Loo Lin School of Medicine, National University of Singapore Graduate School for Integrative Sciences and Engineering, and Neurobiology/Ageing Programme, National University of Singapore, Singapore (C.-M.L.)
| | - Olivia A Moody
- Departments of Pharmacology (H.Y., A.J., S.F.T.) and Anesthesiology (O.A.M., A.J.), Emory University School of Medicine, Rollins Research Center, Atlanta, Georgia; and Departments of Pharmacology and Anaesthesia, Yong Loo Lin School of Medicine, National University of Singapore Graduate School for Integrative Sciences and Engineering, and Neurobiology/Ageing Programme, National University of Singapore, Singapore (C.-M.L.)
| | - Andrew Jenkins
- Departments of Pharmacology (H.Y., A.J., S.F.T.) and Anesthesiology (O.A.M., A.J.), Emory University School of Medicine, Rollins Research Center, Atlanta, Georgia; and Departments of Pharmacology and Anaesthesia, Yong Loo Lin School of Medicine, National University of Singapore Graduate School for Integrative Sciences and Engineering, and Neurobiology/Ageing Programme, National University of Singapore, Singapore (C.-M.L.)
| | - Stephen F Traynelis
- Departments of Pharmacology (H.Y., A.J., S.F.T.) and Anesthesiology (O.A.M., A.J.), Emory University School of Medicine, Rollins Research Center, Atlanta, Georgia; and Departments of Pharmacology and Anaesthesia, Yong Loo Lin School of Medicine, National University of Singapore Graduate School for Integrative Sciences and Engineering, and Neurobiology/Ageing Programme, National University of Singapore, Singapore (C.-M.L.)
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Hénin J, Salari R, Murlidaran S, Brannigan G. A predicted binding site for cholesterol on the GABAA receptor. Biophys J 2014; 106:1938-49. [PMID: 24806926 DOI: 10.1016/j.bpj.2014.03.024] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 03/03/2014] [Accepted: 03/14/2014] [Indexed: 12/29/2022] Open
Abstract
Modulation of the GABA type A receptor (GABAAR) function by cholesterol and other steroids is documented at the functional level, yet its structural basis is largely unknown. Current data on structurally related modulators suggest that cholesterol binds to subunit interfaces between transmembrane domains of the GABAAR. We construct homology models of a human GABAAR based on the structure of the glutamate-gated chloride channel GluCl of Caenorhabditis elegans. The models show the possibility of previously unreported disulfide bridges linking the M1 and M3 transmembrane helices in the α and γ subunits. We discuss the biological relevance of such disulfide bridges. Using our models, we investigate cholesterol binding to intersubunit cavities of the GABAAR transmembrane domain. We find that very similar binding modes are predicted independently by three approaches: analogy with ivermectin in the GluCl crystal structure, automated docking by AutoDock, and spontaneous rebinding events in unbiased molecular dynamics simulations. Taken together, the models and atomistic simulations suggest a somewhat flexible binding mode, with several possible orientations. Finally, we explore the possibility that cholesterol promotes pore opening through a wedge mechanism.
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Affiliation(s)
- Jérôme Hénin
- Laboratoire de Biochimie Théorique, CNRS, IBPC, and Université Paris Diderot, Paris, France
| | - Reza Salari
- Department of Physics, Rutgers University-Camden, Camden, New Jersey; Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, New Jersey
| | - Sruthi Murlidaran
- Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, New Jersey
| | - Grace Brannigan
- Department of Physics, Rutgers University-Camden, Camden, New Jersey; Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, New Jersey.
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Salari R, Murlidaran S, Brannigan G. Pentameric Ligand-gated Ion Channels : Insights from Computation. MOLECULAR SIMULATION 2014; 40:821-829. [PMID: 25931676 PMCID: PMC4412168 DOI: 10.1080/08927022.2014.896462] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Pentameric ligand-gated ion channels (pLGICs) conduct upon the binding of an agonist and are fundamental to neurotransmission. New insights into the complex mechanisms underlying pLGIC gating, ion selectivity, and modulation have recently been gained via a series of crystal structures in prokaryotes and C .elegans, as well as computational studies relying on these structures. Here we review contributions from a variety of computational approaches, including normal mode analysis, automated docking, and fully atomistic molecular dynamics simulation. Examples from our own research, particularly concerning interactions with general anesthetics and lipids, are used to illustrate predictive results complementary to crystallographic studies.
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Affiliation(s)
- Reza Salari
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ
- Department of Physics, Rutgers University, Camden, NJ
| | - Sruthi Murlidaran
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ
- Department of Physics, Rutgers University, Camden, NJ
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Tsang SY, Zhong S, Mei L, Chen J, Ng SK, Pun FW, Zhao C, Jing B, Chark R, Guo J, Tan Y, Li L, Wang C, Chew SH, Xue H. Social cognitive role of schizophrenia candidate gene GABRB2. PLoS One 2013; 8:e62322. [PMID: 23638040 PMCID: PMC3634734 DOI: 10.1371/journal.pone.0062322] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 03/20/2013] [Indexed: 11/18/2022] Open
Abstract
The occurrence of positive selection in schizophrenia-associated GABRB2 suggests a broader impact of the gene product on population fitness. The present study considered the possibility of cognition-related GABRB2 involvement by examining the association of GABRB2 with psychosis and altruism, respectively representing psychiatric and psychological facets of social cognition. Four single nucleotide polymorphisms (SNPs) were genotyped for quantitative trait analyses and population-based association studies. Psychosis was measured by either the Positive and Negative Syndrome Scale (PANSS) or antipsychotics dosage, and altruism was based on a self-report altruism scale. The minor alleles of SNPs rs6556547, rs1816071 and rs187269 in GABRB2 were correlated with high PANSS score for positive symptoms in a Han Chinese schizophrenic cohort, whereas those of rs1816071 and rs1816072 were associated with high antipsychotics dosage in a US Caucasian schizophrenic cohort. Moreover, strongly significant GABRB2-disease associations were found among schizophrenics with severe psychosis based on high PANSS positive score, but no significant association was observed for schizophrenics with only mild psychosis. Interestingly, in addition to association with psychosis in schizophrenics, rs187269 was also associated with altruism in healthy Han Chinese. Furthermore, parallel to correlation with severe psychosis, its minor allele was correlated with high altruism scores. These findings revealed that GABRB2 is associated with psychosis, the core symptom and an endophenotype of schizophrenia. Importantly, the association was found across the breadth of the psychiatric (psychosis) to psychological (altruism) spectrum of social cognition suggesting GABRB2 involvement in human cognition.
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Affiliation(s)
- Shui Ying Tsang
- Division of Life Science and Applied Genomics Laboratory, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Songfa Zhong
- Department of Economics, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Department of Economics, National University of Singapore, Singapore, Rep. of Singapore
| | - Lingling Mei
- Division of Life Science and Applied Genomics Laboratory, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Jianhuan Chen
- Division of Life Science and Applied Genomics Laboratory, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Siu-Kin Ng
- Division of Life Science and Applied Genomics Laboratory, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Frank W. Pun
- Division of Life Science and Applied Genomics Laboratory, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Cunyou Zhao
- Division of Life Science and Applied Genomics Laboratory, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Bingyi Jing
- Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Department of Mathematics, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Robin Chark
- Department of Marketing, National University of Singapore, Singapore, Rep. of Singapore
| | - Jianhua Guo
- School of Mathematics and Statistics, Northeast Normal University, Changchun, China
| | - Yunlong Tan
- Beijing Huilongguan Hospital, Beijing, China
| | - Lijun Li
- Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - Chuanyue Wang
- Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - Soo Hong Chew
- Department of Economics, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Department of Economics, National University of Singapore, Singapore, Rep. of Singapore
| | - Hong Xue
- Division of Life Science and Applied Genomics Laboratory, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Center for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- * E-mail:
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Zhao C, Wang F, Pun FW, Mei L, Ren L, Yu Z, Ng SK, Chen J, Tsang SY, Xue H. Epigenetic regulation on GABRB2 isoforms expression: developmental variations and disruptions in psychotic disorders. Schizophr Res 2012; 134:260-6. [PMID: 22206711 DOI: 10.1016/j.schres.2011.11.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 11/18/2011] [Accepted: 11/28/2011] [Indexed: 11/28/2022]
Abstract
INTRODUCTION To improve the understanding of psychotic abnormalities and their non-Mendelian inheritance patterns, the epigenetic regulation of the psychotic disorder-associated GABRB2, gene for the type A γ-aminobutyric acid receptor β(2)-subunit, was investigated. METHODS Expression of GABRB2, and the epigenetic regulatory enzymes histone deacetylases (HDACs) and DNA methyltransferases (DNMTs) in mouse and postmortem human brains was analyzed using real-time PCR. RESULTS Results showed that expression of GABRB2 isoforms significantly increased over time in both mouse and human, especially for the long splicing isoform. In the brains of non-psychiatric controls (CON), a significant positive correlation of GABRB2 expression with age was observed in individuals with MM genotypes of the single nucleotide polymorphisms (SNPs) rs187269 and rs1816072. This was reversed to a significant negative correlation in schizophrenics (SCZ). A similar reversal was also displayed by bipolar disorder (BPD) patients. In parallel, a significant co-variation of HDAC1 with GABRB2 expression observed in CON remained significant in BPD but not in SCZ; comparably, a significant co-variation of HDAC2 with GABRB2 expression observed in CON became non-significant in both SCZ and BPD. Moreover, co-variations of DNMT1 and DNMT3B with GABRB2, not observable in CON, became significant in BPD. CONCLUSION These findings demonstrated that GABRB2 expression was under epigenetic regulation that varied with development, genotype and disease status, and these regulatory mechanisms were observably disrupted in SCZ and BPD. This study provided insight into the complex inheritance patterns of psychiatric disorders, and pointed to the involvement of epigenetic dysregulation in the disease process of major psychotic disorders.
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Affiliation(s)
- Cunyou Zhao
- Division of Life Science, Applied Genomics Center and Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
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Mei L, Ding X, Tsang SY, Pun FW, Ng SK, Yang J, Zhao C, Li D, Wan W, Yu CH, Tan TC, Poon WS, Leung GKK, Ng HK, Zhang L, Xue H. AluScan: a method for genome-wide scanning of sequence and structure variations in the human genome. BMC Genomics 2011; 12:564. [PMID: 22087792 PMCID: PMC3228862 DOI: 10.1186/1471-2164-12-564] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 11/17/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To complement next-generation sequencing technologies, there is a pressing need for efficient pre-sequencing capture methods with reduced costs and DNA requirement. The Alu family of short interspersed nucleotide elements is the most abundant type of transposable elements in the human genome and a recognized source of genome instability. With over one million Alu elements distributed throughout the genome, they are well positioned to facilitate genome-wide sequence amplification and capture of regions likely to harbor genetic variation hotspots of biological relevance. RESULTS Here we report on the use of inter-Alu PCR with an enhanced range of amplicons in conjunction with next-generation sequencing to generate an Alu-anchored scan, or 'AluScan', of DNA sequences between Alu transposons, where Alu consensus sequence-based 'H-type' PCR primers that elongate outward from the head of an Alu element are combined with 'T-type' primers elongating from the poly-A containing tail to achieve huge amplicon range. To illustrate the method, glioma DNA was compared with white blood cell control DNA of the same patient by means of AluScan. The over 10 Mb sequences obtained, derived from more than 8,000 genes spread over all the chromosomes, revealed a highly reproducible capture of genomic sequences enriched in genic sequences and cancer candidate gene regions. Requiring only sub-micrograms of sample DNA, the power of AluScan as a discovery tool for genetic variations was demonstrated by the identification of 357 instances of loss of heterozygosity, 341 somatic indels, 274 somatic SNVs, and seven potential somatic SNV hotspots between control and glioma DNA. CONCLUSIONS AluScan, implemented with just a small number of H-type and T-type inter-Alu PCR primers, provides an effective capture of a diversity of genome-wide sequences for analysis. The method, by enabling an examination of gene-enriched regions containing exons, introns, and intergenic sequences with modest capture and sequencing costs, computation workload and DNA sample requirement is particularly well suited for accelerating the discovery of somatic mutations, as well as analysis of disease-predisposing germline polymorphisms, by making possible the comparative genome-wide scanning of DNA sequences from large human cohorts.
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Affiliation(s)
- Lingling Mei
- Division of Life Science and Applied Genomics Centre, Hong Kong University of Science and Technology, 1 University Road, Clear Water Bay, Kowloon, Hong Kong, China.
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Greenwood TA, Lazzeroni LC, Murray SS, Cadenhead KS, Calkins ME, Dobie DJ, Green MF, Gur RE, Gur RC, Hardiman G, Kelsoe JR, Leonard S, Light GA, Nuechterlein KH, Olincy A, Radant AD, Schork NJ, Seidman LJ, Siever LJ, Silverman JM, Stone WS, Swerdlow NR, Tsuang DW, Tsuang MT, Turetsky BI, Freedman R, Braff DL. Analysis of 94 candidate genes and 12 endophenotypes for schizophrenia from the Consortium on the Genetics of Schizophrenia. Am J Psychiatry 2011; 168:930-46. [PMID: 21498463 PMCID: PMC3751972 DOI: 10.1176/appi.ajp.2011.10050723] [Citation(s) in RCA: 204] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE The authors used a custom array of 1,536 single-nucleotide polymorphisms (SNPs) to interrogate 94 functionally relevant candidate genes for schizophrenia and identify associations with 12 heritable neurophysiological and neurocognitive endophenotypes in data collected by the Consortium on the Genetics of Schizophrenia. METHOD Variance-component association analyses of 534 genotyped subjects from 130 families were conducted by using Merlin software. A novel bootstrap total significance test was also developed to overcome the limitations of existing genomic multiple testing methods and robustly demonstrate significant associations in the context of complex family data and possible population stratification effects. RESULTS Associations with endophenotypes were observed for 46 genes of potential functional significance, with three SNPs at p<10(-4), 27 SNPs at p<10(-3), and 147 SNPs at p<0.01. The bootstrap analyses confirmed that the 47 SNP-endophenotype combinations with the strongest evidence of association significantly exceeded that expected by chance alone, with 93% of these findings expected to be true. Many of the genes interact on a molecular level, and eight genes (e.g., NRG1 and ERBB4) displayed evidence for pleiotropy, revealing associations with four or more endophenotypes. The results collectively support a strong role for genes related to glutamate signaling in mediating schizophrenia susceptibility. CONCLUSIONS This study supports use of relevant endophenotypes and the bootstrap total significance test for identifying genetic variation underlying the etiology of schizophrenia. In addition, the observation of extensive pleiotropy for some genes and singular associations for others suggests alternative, independent pathways mediating pathogenesis in the "group of schizophrenias."
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Affiliation(s)
- Tiffany A Greenwood
- Department of Psychiatry, University of California at San Diego, La Jolla, CA 92093-0804, USA
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Kvajo M, McKellar H, Gogos JA. Avoiding mouse traps in schizophrenia genetics: lessons and promises from current and emerging mouse models. Neuroscience 2011; 211:136-64. [PMID: 21821099 DOI: 10.1016/j.neuroscience.2011.07.051] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 07/15/2011] [Accepted: 07/19/2011] [Indexed: 01/31/2023]
Abstract
Schizophrenia is one of the most common psychiatric disorders, but despite progress in identifying the genetic factors implicated in its development, the mechanisms underlying its etiology and pathogenesis remain poorly understood. Development of mouse models is critical for expanding our understanding of the causes of schizophrenia. However, translation of disease pathology into mouse models has proven to be challenging, primarily due to the complex genetic architecture of schizophrenia and the difficulties in the re-creation of susceptibility alleles in the mouse genome. In this review we highlight current research on models of major susceptibility loci and the information accrued from their analysis. We describe and compare the different approaches that are necessitated by diverse susceptibility alleles, and discuss their advantages and drawbacks. Finally, we discuss emerging mouse models, such as second-generation pathophysiology models based on innovative approaches that are facilitated by the information gathered from the current genetic mouse models.
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Affiliation(s)
- M Kvajo
- Department of Physiology and Cellular Biophysics, College of Physicians & Surgeons, Columbia University Medical Center, 630 West 168th Street, New York, NY 10032, USA
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Pun FW, Zhao C, Lo WS, Ng SK, Tsang SY, Nimgaonkar V, Chung WS, Ungvari GS, Xue H. Imprinting in the schizophrenia candidate gene GABRB2 encoding GABA(A) receptor β(2) subunit. Mol Psychiatry 2011; 16:557-68. [PMID: 20404824 DOI: 10.1038/mp.2010.47] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Schizophrenia is a complex genetic disorder, the inheritance pattern of which is likely complicated by epigenetic factors yet to be elucidated. In this study, transmission disequilibrium tests with family trios yielded significant differences between paternal and maternal transmissions of the disease-associated single-nucleotide polymorphism (SNP) rs6556547 and its haplotypes. The minor allele (T) of rs6556547 was paternally undertransmitted to male schizophrenic offsprings, and this parent-of-origin effect strongly suggested that GABRB2 is imprinted. 'Flipping' of allelic expression in heterozygotes of SNP rs2229944 (C/T) in GABRB2 or rs2290732 (G/A) in the neighboring GABRA1 was compatible with imprinting effects on gene expression. Clustering analysis of GABRB2 mRNA expressions suggested that imprinting brought about the observed two-tiered distribution of expression levels in controls with heterozygous genotype at the disease-associated SNP rs1816071 (A/G). The deficit of upper-tiered expressions accounted for the lowered expression levels in the schizophrenic heterozygotes. The occurrence of a two-tiered distribution furnished support for imprinting, and also pointed to the necessity of differentiating between two kinds of heterozygotes of different parental origins in disease association studies on GABRB2. Bisulfite sequencing revealed hypermethylation in the neighborhood of SNP rs1816071, and methylation differences between controls and schizophrenia patients. Notably, the two schizophrenia-associated SNPs rs6556547 and rs1816071 overlapped with a CpG dinucleotide, thereby opening the possibility that CpG methylation status of these sites could have an impact on the risk of schizophrenia. Thus multiple lines of evidence pointed to the occurrence of imprinting in the GABRB2 gene and its possible role in the development of schizophrenia.
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Affiliation(s)
- F W Pun
- Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
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Vinkers CH, Mirza NR, Olivier B, Kahn RS. The inhibitory GABA system as a therapeutic target for cognitive symptoms in schizophrenia: investigational agents in the pipeline. Expert Opin Investig Drugs 2011; 19:1217-33. [PMID: 20812877 DOI: 10.1517/13543784.2010.513382] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
IMPORTANCE OF THE FIELD Cognitive impairments associated with schizophrenia include neuropsychological deficits in attention, working memory, learning and executive function. Because these cognitive deficits precede the onset of psychosis, are present in non-affected relatives and constitute the best predictor of functional outcome, they are a cardinal clinical feature in schizophrenia. Currently, no effective treatment for the cognitive symptoms in schizophrenia exists. AREAS COVERED IN THIS REVIEW There is evidence that the inhibitory GABA system is affected in schizophrenia, suggesting that cognitive impairments associated with schizophrenia may be effectively treated by drugs that modulate the GABA(A) receptor. However, classical benzodiazepines produce cognitive impairments and are associated with numerous side effects. The recent development of compounds with selective efficacy for different α subunits at the benzodiazepine site of the GABA(A) receptor has renewed interest for the therapeutic potential of GABAergic drugs. WHAT THE READER WILL GAIN This review summarizes the involvement of the inhibitory GABA system in the cognitive abnormalities of schizophrenia and discusses putative (selective) GABAergic cognition-enhancing drugs for schizophrenia. TAKE HOME MESSAGE If cognitive abnormalities in schizophrenic individuals are the result of GABAergic dysfunction, selectively modulating the GABA system could comprise a promising therapeutic intervention for cognitive symptoms in schizophrenia.
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Affiliation(s)
- Christiaan H Vinkers
- Department of Psychiatry, University Medical Center Utrecht, Rudolf Magnus Institute of Neuroscience, Utrecht, The Netherlands
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Horváth S, Janka Z, Mirnics K. Analyzing schizophrenia by DNA microarrays. Biol Psychiatry 2011; 69:157-62. [PMID: 20801428 PMCID: PMC2994975 DOI: 10.1016/j.biopsych.2010.07.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 07/12/2010] [Accepted: 07/14/2010] [Indexed: 01/20/2023]
Abstract
To understand the pathological processes of schizophrenia, we must embrace the analysis of the diseased human brain: we will never be able to recapitulate the pathology of uniquely human disorders in an animal model. Based on the outcome of the transcriptome profiling experiments performed to date, it appears that schizophrenia is associated with a global gene expression disturbance across many cortical regions. In addition, transcriptome changes are present in multiple cell types, including specific subclasses of principal neurons, interneurons, and oligodendrocytes. Furthermore, transcripts related to synaptic transmission, energy metabolism, and inhibitory neurotransmission are routinely found underexpressed in the postmortem brain tissue of subjects with schizophrenia. To put these transcriptome data in biological context, we must make our data publicly available and report our findings in a proper, expanded Minimum Information About a Microarray Experiment format. Cell-type specific expression profiling and sequencing-based transcript assessments should be expanded, with particular attention to understanding splice-variant changes in various mental disorders. Deciphering the pathophysiology of mental disorders depends on integrating data from across many research fields and techniques. Leads from postmortem transcriptome profiling will be essential to generate model animals, perform tissue culture experiments, and develop or evaluate novel drugs to treat this devastating disorder.
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Affiliation(s)
- Szatmár Horváth
- Department of Psychiatry, Vanderbilt University, Nashville, TN 37232, USA,Department of Psychiatry, University of Szeged, 6725 Szeged, Hungary
| | - Zoltán Janka
- Department of Psychiatry, University of Szeged, 6725 Szeged, Hungary
| | - Károly Mirnics
- Department of Psychiatry, Vanderbilt University, Nashville, TN 37232, USA,Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, TN 37232, USA,Correspondence: Karoly Mirnics, Department of Psychiatry, Vanderbilt University, 8130A MRB III, 465 21st Avenue South, Nashville TN 37232, USA, , Office phone: 615-936-1074, http://mirnicslab.vanderbilt.edu/mirnicslab/
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Sela N, Mersch B, Hotz-Wagenblatt A, Ast G. Characteristics of transposable element exonization within human and mouse. PLoS One 2010; 5:e10907. [PMID: 20532223 PMCID: PMC2879366 DOI: 10.1371/journal.pone.0010907] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Accepted: 05/06/2010] [Indexed: 12/16/2022] Open
Abstract
Insertion of transposed elements within mammalian genes is thought to be an important contributor to mammalian evolution and speciation. Insertion of transposed elements into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization. Elucidation of the evolutionary constraints that have shaped fixation of transposed elements within human and mouse protein coding genes and subsequent exonization is important for understanding of how the exonization process has affected transcriptome and proteome complexities. Here we show that exonization of transposed elements is biased towards the beginning of the coding sequence in both human and mouse genes. Analysis of single nucleotide polymorphisms (SNPs) revealed that exonization of transposed elements can be population-specific, implying that exonizations may enhance divergence and lead to speciation. SNP density analysis revealed differences between Alu and other transposed elements. Finally, we identified cases of primate-specific Alu elements that depend on RNA editing for their exonization. These results shed light on TE fixation and the exonization process within human and mouse genes.
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Affiliation(s)
- Noa Sela
- Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Britta Mersch
- Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Agnes Hotz-Wagenblatt
- Department of Molecular Biophysics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- * E-mail: (GA); (AHW)
| | - Gil Ast
- Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (GA); (AHW)
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Bithell A, Hsu T, Kandanearatchi A, Landau S, Everall IP, Tsuang MT, Chana G, Williams BP. Expression of the Rap1 guanine nucleotide exchange factor, MR-GEF, is altered in individuals with bipolar disorder. PLoS One 2010; 5:e10392. [PMID: 20436929 PMCID: PMC2861006 DOI: 10.1371/journal.pone.0010392] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2009] [Accepted: 03/03/2010] [Indexed: 11/18/2022] Open
Abstract
In the rodent forebrain GABAergic neurons are generated from progenitor cells that express the transcription factors Dlx1 and Dlx2. The Rap-1 guanine nucleotide exchange factor, MR-GEF, is turned on by many of these developing GABAergic neurons. Expression of both Dlx1/2 and MR-GEF is retained in both adult mouse and human forebrain where, in human, decreased Dlx1 expression has been associated with psychosis. Using in situ hybridization studies we show that MR-GEF expression is significantly down-regulated in the forebrain of Dlx1/2 double mutant mice suggesting that MR-GEF and Dlx1/2 form part of a common signalling pathway during GABAergic neuronal development. We therefore compared MR-GEF expression by in situ hybridization in individuals with major psychiatric disorders (schizophrenia, bipolar disorder, major depression) and control individuals. We observed a significant positive correlation between layers II and IV of the dorso-lateral prefrontal cortex (DLPFC) in the percentage of MR-GEF expressing neurons in individuals with bipolar disorder, but not in individuals with schizophrenia, major depressive disorder or in controls. Since MR-GEF encodes a Rap1 GEF able to activate G-protein signalling, we suggest that changes in MR-GEF expression could potentially influence neurotransmission.
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Affiliation(s)
- Angela Bithell
- Department of Psychological Medicine, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Tony Hsu
- Center for Behavioral Genomics, Department of Psychiatry, University of California San Diego, San Diego, California, United States of America
| | - Apsara Kandanearatchi
- Department of Psychological Medicine, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Sabine Landau
- Department of Biostatistics and Computing, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Ian P. Everall
- Department of Psychological Medicine, Institute of Psychiatry, King's College London, London, United Kingdom
- Center for Behavioral Genomics, Department of Psychiatry, University of California San Diego, San Diego, California, United States of America
| | - Ming T. Tsuang
- Center for Behavioral Genomics, Department of Psychiatry, University of California San Diego, San Diego, California, United States of America
| | - Gursharan Chana
- Department of Psychological Medicine, Institute of Psychiatry, King's College London, London, United Kingdom
- Center for Behavioral Genomics, Department of Psychiatry, University of California San Diego, San Diego, California, United States of America
| | - Brenda P. Williams
- Department of Psychological Medicine, Institute of Psychiatry, King's College London, London, United Kingdom
- * E-mail:
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A recombination hotspot in a schizophrenia-associated region of GABRB2. PLoS One 2010; 5:e9547. [PMID: 20221451 PMCID: PMC2833194 DOI: 10.1371/journal.pone.0009547] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Accepted: 01/28/2010] [Indexed: 12/01/2022] Open
Abstract
Background Schizophrenia is a major disorder with complex genetic mechanisms. Earlier, population genetic studies revealed the occurrence of strong positive selection in the GABRB2 gene encoding the β2 subunit of GABAA receptors, within a segment of 3,551 bp harboring twenty-nine single nucleotide polymorphisms (SNPs) and containing schizophrenia-associated SNPs and haplotypes. Methodology/Principal Findings In the present study, the possible occurrence of recombination in this ‘S1–S29’ segment was assessed. The occurrence of hotspot recombination was indicated by high resolution recombination rate estimation, haplotype diversity, abundance of rare haplotypes, recurrent mutations and torsos in haplotype networks, and experimental haplotyping of somatic and sperm DNA. The sub-segment distribution of relative recombination strength, measured by the ratio of haplotype diversity (Hd) over mutation rate (θ), was indicative of a human specific Alu-Yi6 insertion serving as a central recombining sequence facilitating homologous recombination. Local anomalous DNA conformation attributable to the Alu-Yi6 element, as suggested by enhanced DNase I sensitivity and obstruction to DNA sequencing, could be a contributing factor of the increased sequence diversity. Linkage disequilibrium (LD) analysis yielded prominent low LD points that supported ongoing recombination. LD contrast revealed significant dissimilarity between control and schizophrenic cohorts. Among the large array of inferred haplotypes, H26 and H73 were identified to be protective, and H19 and H81 risk-conferring, toward the development of schizophrenia. Conclusions/Significance The co-occurrence of hotspot recombination and positive selection in the S1–S29 segment of GABRB2 has provided a plausible contribution to the molecular genetics mechanisms for schizophrenia. The present findings therefore suggest that genome regions characterized by the co-occurrence of positive selection and hotspot recombination, two interacting factors both affecting genetic diversity, merit close scrutiny with respect to the etiology of common complex disorders.
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Cherlyn SYT, Woon PS, Liu JJ, Ong WY, Tsai GC, Sim K. Genetic association studies of glutamate, GABA and related genes in schizophrenia and bipolar disorder: a decade of advance. Neurosci Biobehav Rev 2010; 34:958-77. [PMID: 20060416 DOI: 10.1016/j.neubiorev.2010.01.002] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Revised: 01/01/2010] [Accepted: 01/04/2010] [Indexed: 12/31/2022]
Abstract
Schizophrenia (SZ) and bipolar disorder (BD) are debilitating neurobehavioural disorders likely influenced by genetic and non-genetic factors and which can be seen as complex disorders of synaptic neurotransmission. The glutamatergic and GABAergic neurotransmission systems have been implicated in both diseases and we have reviewed extensive literature over a decade for evidence to support the association of glutamate and GABA genes in SZ and BD. Candidate-gene based population and family association studies have implicated some ionotrophic glutamate receptor genes (GRIN1, GRIN2A, GRIN2B and GRIK3), metabotropic glutamate receptor genes (such as GRM3), the G72/G30 locus and GABAergic genes (e.g. GAD1 and GABRB2) in both illnesses to varying degrees, but further replication studies are needed to validate these results. There is at present no consensus on specific single nucleotide polymorphisms or haplotypes associated with the particular candidate gene loci in these illnesses. The genetic architecture of glutamate systems in bipolar disorder need to be better studied in view of recent data suggesting an overlap in the genetic aetiology of SZ and BD. There is a pressing need to integrate research platforms in genomics, epistatic models, proteomics, metabolomics, neuroimaging technology and translational studies in order to allow a more integrated understanding of glutamate and GABAergic signalling processes and aberrations in SZ and BD as well as their relationships with clinical presentations and treatment progress over time.
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Affiliation(s)
- Suat Ying Tan Cherlyn
- Institute of Mental Health/Woodbridge Hospital, 10 Buangkok View, Singapore 539747, Singapore
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GABRB2 in schizophrenia and bipolar disorder: disease association, gene expression and clinical correlations. Biochem Soc Trans 2010; 37:1415-8. [PMID: 19909288 DOI: 10.1042/bst0371415] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The SCZ (schizophrenia)-associated GABA(A) receptor (gamma-aminobutyric acid type A receptor) beta(2) subunit gene GABRB2 was recently associated with BPD (bipolar disorder). Although weaker than its association with SCZ, significant association of GABRB2 with BPD was found in both German and Chinese, especially for the haplotypes rs1816071-rs187269 and rs1816072-rs187269 for which the M-M variants showed higher frequency in disease than the control. Significant genotype-dependent reduction in GABRB2 expression was shown for BPD, but to a lesser extent than that for SCZ. Temporal effects on GABRB2 expression were observed. Moreover, for the homozygous major genotypes of rs1816071, rs1816072 and rs187269, expression increased with time in CON but decreased in SCZ and BPD. The genotypes of these three SNPs (single nucleotide polymorphisms) were further correlated with antipsychotics dosage in SCZ cohorts. The findings highlight the importance of GABRB2 in neuropsychiatric disease aetiology, with respect to haplotype association, as well as reduction of and temporal effects on gene expression in both SCZ and BPD, but to a lesser extent in the latter, supporting the suggestion that functional psychosis can be conceptualized as a continuous spectrum of clinical phenotypes rather than as distinct categories.
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Zai CC, Tiwari AK, King N, De Luca V, Mueller DJ, Shaikh S, Wong GWH, Meltzer HY, Lieberman JA, Kennedy JL. Association study of the gamma-aminobutyric acid type a receptor gamma2 subunit gene with schizophrenia. Schizophr Res 2009; 114:33-8. [PMID: 19682861 DOI: 10.1016/j.schres.2009.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Revised: 06/11/2009] [Accepted: 07/10/2009] [Indexed: 02/08/2023]
Abstract
Schizophrenia (SCZ) is a severe neuropsychiatric disorder with a strong genetic basis. We analyzed eight GABRG2 and one DRD5 tag single-nucleotide polymorphisms for association with SCZ in 109 small nuclear families and 229 independent SCZ case-control pairs. The marker rs183294 in the 5' region of GABRG2 was found to be associated with SCZ in both samples with the C allele over-represented in SCZ cases and over-transmitted in SCZ families (combined z=9.18; p<1 x 10(-3)). Taken together, the results of the present study suggest that GABRG2 may be involved in SCZ susceptibility, but further studies are required.
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Affiliation(s)
- Clement C Zai
- Neurogenetics Section, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
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Zhao C, Xu Z, Wang F, Chen J, Ng SK, Wong PW, Yu Z, Pun FW, Ren L, Lo WS, Tsang SY, Xue H. Alternative-splicing in the exon-10 region of GABA(A) receptor beta(2) subunit gene: relationships between novel isoforms and psychotic disorders. PLoS One 2009; 4:e6977. [PMID: 19763268 PMCID: PMC2741204 DOI: 10.1371/journal.pone.0006977] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2009] [Accepted: 08/06/2009] [Indexed: 11/18/2022] Open
Abstract
Background Non-coding single nucleotide polymorphisms (SNPs) in GABRB2, the gene for β2-subunit of gamma-aminobutyric acid type A (GABAA) receptor, have been associated with schizophrenia (SCZ) and quantitatively correlated to mRNA expression and alternative splicing. Methods and Findings Expression of the Exon 10 region of GABRB2 from minigene constructs revealed this region to be an “alternative splicing hotspot” that readily gave rise to differently spliced isoforms depending on intron sequences. This led to a search in human brain cDNA libraries, and the discovery of two novel isoforms, β2S1 and β2S2, bearing variations in the neighborhood of Exon-10. Quantitative real-time PCR analysis of postmortem brain samples showed increased β2S1 expression and decreased β2S2 expression in both SCZ and bipolar disorder (BPD) compared to controls. Disease-control differences were significantly correlated with SNP rs187269 in BPD males for both β2S1 and β2S2 expressions, and significantly correlated with SNPs rs2546620 and rs187269 in SCZ males for β2S2 expression. Moreover, site-directed mutagenesis indicated that Thr365, a potential phosphorylation site in Exon-10, played a key role in determining the time profile of the ATP-dependent electrophysiological current run-down. Conclusion This study therefore provided experimental evidence for the importance of non-coding sequences in the Exon-10 region in GABRB2 with respect to β2-subunit splicing diversity and the etiologies of SCZ and BPD.
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Affiliation(s)
- Cunyou Zhao
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Zhiwen Xu
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Feng Wang
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Jianhuan Chen
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Siu-Kin Ng
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Pak-Wing Wong
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Zhiliang Yu
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Frank W. Pun
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Lihuan Ren
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Wing-Sze Lo
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Shui-Ying Tsang
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
| | - Hong Xue
- Department of Biochemistry and Applied Genomics Center, Fok Ying Tung Graduate School, The Hong Kong University of Science & Technology, Clear Water Bay, Hong Kong, China
- * E-mail:
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Abstract
Understanding the evolutionary origins of behaviour is a central aim in the study of biology and may lead to insights into human disorders. Synaptic transmission is observed in a wide range of invertebrate and vertebrate organisms and underlies their behaviour. Proteomic studies of the molecular components of the highly complex mammalian postsynaptic machinery point to an ancestral molecular machinery in unicellular organisms--the protosynapse--that existed before the evolution of metazoans and neurons, and hence challenges existing views on the origins of the brain. The phylogeny of the molecular components of the synapse provides a new model for studying synapse diversity and complexity, and their implications for brain evolution.
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Shan Q, Zheng Y, Chen G, Zheng G, Lu J, Lv X. Tag-extension-based method for sensitive and specific genotyping of single nucleotide polymorphism on microarray. Clin Chim Acta 2009; 409:11-7. [PMID: 19654005 DOI: 10.1016/j.cca.2009.07.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 07/08/2009] [Accepted: 07/27/2009] [Indexed: 11/17/2022]
Abstract
BACKGROUND The obtainment of a large amount of single nucleotide polymorphism (SNP) information has emphasized a need for a sensitive, accurate and high-throughput strategy for SNP genotyping. We developed a reliable and potential microarray-based method to meet this demand. METHODS A tag extension strategy is described to identify SNPs. The strategy is based on a fluorescent nucleotide extension from an extending primer that is hybridized to a bi-functional linker, which acts as an allele-specific primer that hybridizes with a PCR-amplified target DNA immobilized on a 3-dimensional (3-D) polyacrylamide gel microarray, as well as an extending template with a specific tag itself hybridized with a universal extension primer. Multiple fluorescence-dNTPs are simultaneously incorporated into the tagged linker. RESULTS The method not only significantly enhanced the sensitivity, but also efficiently improved the specificity of SNP genotyping. 89 samples for 8025575C/G polymorphisms in gamma-aminobutyric acid A receptor, beta 3 (GABAB3) gene were accurately discriminated using this method. Sanger sequencing was performed to validate these results. CONCLUSION Our experiments successfully demonstrated that a tag-extension-based method on microarray could be used as a high-throughput and useful tool to obtain SNP information.
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Affiliation(s)
- Qun Shan
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science, Xuzhou Normal University, Xuzhou 221116, China
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Charych EI, Liu F, Moss SJ, Brandon NJ. GABA(A) receptors and their associated proteins: implications in the etiology and treatment of schizophrenia and related disorders. Neuropharmacology 2009; 57:481-95. [PMID: 19631671 DOI: 10.1016/j.neuropharm.2009.07.027] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 07/02/2009] [Accepted: 07/13/2009] [Indexed: 02/05/2023]
Abstract
Gamma-aminobutyric acid type A (GABA(A)) receptors play an important role in mediating fast synaptic inhibition in the brain. They are ubiquitously expressed in the CNS and also represent a major site of action for clinically relevant drugs. Recent technological advances have greatly clarified the molecular and cellular roles played by distinct GABA(A) receptor subunit classes and isoforms in normal brain function. At the same time, postmortem and genetic studies have linked neuropsychiatric disorders including schizophrenia and bipolar disorder with GABAergic neurotransmission and various specific GABA(A) receptor subunits, while evidence implicating GABA(A)R-associated proteins is beginning to emerge. In this review we discuss the mounting genetic, molecular, and cellular evidence pointing toward a role for GABA(A) receptor heterogeneity in both schizophrenia etiology and therapeutic development. Finally, we speculate on the relationship between schizophrenia-related disorders and selected GABA(A) receptor associated proteins, key regulators of GABA(A) receptor trafficking, targeting, clustering, and anchoring that often carry out these functions in a subtype-specific manner.
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Affiliation(s)
- Erik I Charych
- Wyeth Research, Neuroscience Discovery, Princeton NJ 08852, USA.
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Kerner B, Jasinska AJ, DeYoung J, Almonte M, Choi OW, Freimer NB. Polymorphisms in the GRIA1 gene region in psychotic bipolar disorder. Am J Med Genet B Neuropsychiatr Genet 2009; 150B:24-32. [PMID: 18484081 PMCID: PMC4130207 DOI: 10.1002/ajmg.b.30780] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We reported previously a significant linkage signal between psychotic bipolar disorder (BP) and microsatellite markers on chromosome 5q31-34 in the National Institute of Mental Health Bipolar Genetics Initiative (NIMH-BPGI) data set, Wave 1. In an attempt to fine-map this linkage signal we genotyped 1,134 single nucleotide polymorphisms (SNPs) under the linkage peak in 23 informative families (131 individuals) with evidence of linkage. We tested family based association in the presence of linkage with the computer software package FBAT. The most significant association in these families was with a SNP in the second intron of GRIA1 (alpha-amino-3-hydroxy-5-methyl-4-isoxazole proprionic acid (AMPA) subunit 1 receptor gene) (rs490922, Z-score = 3.3, P = 0.001). The analysis of 37 additional families with psychotic BP from NIMH-BPGI data sets, Waves 2, 3, and 4 revealed a signal at a SNP in intron 5 of the GRIA1 gene (rs4385264, Z-score = 3.2, P-value = 0.002). A combined analysis of all 60 families continued to support evidence for association of GRIA1 with psychotic BP; however, individual SNPs could not be replicated across datasets. The AMPA1 receptor has been shown to influence cognitive function, such as working memory and reward learning. Our findings suggest that variations in this receptor may contribute to the pathophysiology of BP with psychotic features in some families.
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Affiliation(s)
- Berit Kerner
- Center for Neurobehavioral Genetics, Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California at Los Angeles, 90095-1761, USA.
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Pan Z, Li Y, Shan Q, Hong X, Zhou D, Zhang M, Chen P, Xiao P, Lu Z. Fabrication of 3-D gel microarrays directly with raw polymerase chain reaction products by heat-directed polymerization. Electrophoresis 2008; 29:2424-36. [DOI: 10.1002/elps.200700570] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Agrawal A, Pergadia ML, Saccone SF, Hinrichs AL, Lessov-Schlaggar CN, Saccone NL, Neuman RJ, Breslau N, Johnson E, Hatsukami D, Montgomery GW, Heath AC, Martin NG, Goate AM, Rice JP, Bierut LJ, Madden PAF. Gamma-aminobutyric acid receptor genes and nicotine dependence: evidence for association from a case-control study. Addiction 2008; 103:1027-38. [PMID: 18482426 DOI: 10.1111/j.1360-0443.2008.02236.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS The gamma-aminobutyric acid receptor A (GABRA) gene clusters on chromosomes 4 and 5 have been examined previously for their association with alcohol and drug dependence phenotypes. Compelling evidence suggests that GABRA2 is associated with alcohol and drug dependence. However, no study has investigated whether genes in the GABA(A) gene clusters are associated with nicotine dependence, an important phenotype with a high correlation to persistent smoking, the single most preventable cause of mortality world-wide. DESIGN Using data on 1050 nicotine-dependent cases and 879 non-dependent smoking controls, we used logistic regression to examine the association between single nucleotide polymorphisms (SNPs) in 13 genes in the GABA(A) receptor system as well as GABBR2 (a GABA(B) gene). FINDINGS We found evidence for association between four SNPs in GABRA4, two SNPs in GABRA2 and one SNP in GABRE with nicotine dependence. These included a synonymous polymorphism in GABRA2 (rs279858), lying in a highly conserved region, which has been shown previously to be associated with alcohol and drug dependence. A non-synonymous polymorphism (rs16859834/rs2229940) in GABRA4, also highly conserved, was associated at P-value of 0.03. Significant haplotypes associated with nicotine dependence were found for GABRA2. No evidence for epistatic interactions were noted. Our study did not find evidence for an association between GABBR2 gene and nicotine dependence. CONCLUSIONS Given the potential role of compounds that enhance GABAergic neurotransmission in smoking cessation research, these findings have enormous potential for informing the wider field of addiction research.
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Affiliation(s)
- Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63110, USA.
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Windemuth A, Calhoun VD, Pearlson GD, Kocherla M, Jagannathan K, Ruaño G. Physiogenomic analysis of localized FMRI brain activity in schizophrenia. Ann Biomed Eng 2008; 36:877-88. [PMID: 18330705 DOI: 10.1007/s10439-008-9475-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Accepted: 02/15/2008] [Indexed: 11/29/2022]
Abstract
The search for genetic factors associated with disease is complicated by the complexity of the biological pathways linking genotype and phenotype. This analytical complexity is particularly concerning in diseases historically lacking reliable diagnostic biological markers, such as schizophrenia and other mental disorders. We investigate the use of functional magnetic resonance imaging (fMRI) as an intermediate phenotype (endophenotype) to identify physiogenomic associations to schizophrenia. We screened 99 subjects, 30 subjects diagnosed with schizophrenia, 13 unaffected relatives of schizophrenia patients, and 56 unrelated controls, for gene polymorphisms associated with fMRI activation patterns at two locations in temporal and frontal lobes previously implied in schizophrenia. A total of 22 single nucleotide polymorphisms (SNPs) in 15 genes from the dopamine and serotonin neurotransmission pathways were genotyped in all subjects. We identified three SNPs in genes that are significantly associated with fMRI activity. SNPs of the dopamine beta-hydroxylase (DBH) gene and of the dopamine receptor D4 (DRD4) were associated with activity in the temporal and frontal lobes, respectively. One SNP of serotonin-3A receptor (HTR3A) was associated with temporal lobe activity. The results of this study support the physiogenomic analysis of neuroimaging data to discover associations between genotype and disease-related phenotypes.
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Marino MJ, Knutsen LJS, Williams M. Emerging Opportunities for Antipsychotic Drug Discovery in the Postgenomic Era. J Med Chem 2008; 51:1077-107. [PMID: 18198826 DOI: 10.1021/jm701094q] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Michael J. Marino
- Worldwide Discovery Research, Cephalon, Inc., 145 Brandywine Parkway, West Chester, Pennsylvania 19380
| | - Lars J. S. Knutsen
- Worldwide Discovery Research, Cephalon, Inc., 145 Brandywine Parkway, West Chester, Pennsylvania 19380
| | - Michael Williams
- Worldwide Discovery Research, Cephalon, Inc., 145 Brandywine Parkway, West Chester, Pennsylvania 19380
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46
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The role of cortical inhibition in the pathophysiology and treatment of schizophrenia. ACTA ACUST UNITED AC 2007; 56:427-42. [DOI: 10.1016/j.brainresrev.2007.09.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Revised: 08/27/2007] [Accepted: 09/17/2007] [Indexed: 11/18/2022]
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Zhao X, Qin S, Shi Y, Zhang A, Zhang J, Bian L, Wan C, Feng G, Gu N, Zhang G, He G, He L. Systematic study of association of four GABAergic genes: glutamic acid decarboxylase 1 gene, glutamic acid decarboxylase 2 gene, GABA(B) receptor 1 gene and GABA(A) receptor subunit beta2 gene, with schizophrenia using a universal DNA microarray. Schizophr Res 2007; 93:374-84. [PMID: 17412563 DOI: 10.1016/j.schres.2007.02.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2006] [Revised: 02/28/2007] [Accepted: 02/28/2007] [Indexed: 11/16/2022]
Abstract
Several studies have suggested the dysfunction of the GABAergic system as a risk factor in the pathogenesis of schizophrenia. In the present study, case-control association analysis was conducted in four GABAergic genes: two glutamic acid decarboxylase genes (GAD1 and GAD2), a GABA(A) receptor subunit beta2 gene (GABRB2) and a GABA(B) receptor 1 gene (GABBR1). Using a universal DNA microarray procedure we genotyped a total of 20 SNPs on the above four genes in a study involving 292 patients and 286 controls of Chinese descent. Statistically significant differences were observed in the allelic frequencies of the rs187269C/T polymorphism in the GABRB2 gene (P=0.0450, chi(2)=12.40, OR=1.65) and the -292A/C polymorphism in the GAD1 gene (P=0.0450, chi(2)=14.64 OR=1.77). In addition, using an electrophoretic mobility shift assay (EMSA), we discovered differences in the U251 nuclear protein binding to oligonucleotides representing the -292 SNP on the GAD1 gene, which suggests that the -292C allele has reduced transcription factor binding efficiency compared with the 292A allele. Using the multifactor-dimensionality reduction method (MDR), we found that the interactions among the rs187269C/T polymorphism in the GABRB2 gene, the -243A/G polymorphism in the GAD2 gene and the 27379C/T and 661C/T polymorphisms in the GAD1 gene revealed a significant association with schizophrenia (P<0.001). These findings suggest that the GABRB2 and GAD1 genes alone and the combined effects of the polymorphisms in the four GABAergic system genes may confer susceptibility to the development of schizophrenia in the Chinese population.
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Affiliation(s)
- Xu Zhao
- Bio-X Life Science Research Center, Shanghai Jiao Tong University, Hao Ran Building, Shanghai 200030, China
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Lo WS, Xu Z, Yu Z, Pun FW, Ng SK, Chen J, Tong KL, Zhao C, Xu X, Tsang SY, Harano M, Stöber G, Nimgaonkar VL, Xue H. Positive selection within the Schizophrenia-associated GABA(A) receptor beta(2) gene. PLoS One 2007; 2:e462. [PMID: 17520021 PMCID: PMC1866178 DOI: 10.1371/journal.pone.0000462] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Accepted: 04/24/2007] [Indexed: 01/08/2023] Open
Abstract
The gamma-aminobutyric acid type-A (GABAA) receptor plays a major role in inhibitory neurotransmissions. Intronic SNPs and haplotypes in GABRB2, the gene for GABAA receptor β2 subunit, are associated with schizophrenia and correlated with the expression of two alternatively spliced β2 isoforms. In the present study, using chimpanzee as an ancestral reference, high frequencies were observed for the derived (D) alleles of the four SNPs rs6556547, rs187269, rs1816071 and rs1816072 in GABRB2, suggesting the occurrence of positive selection for these derived alleles. Coalescence-based simulation showed that the population frequency spectra and the frequencies of H56, the haplotype having all four D alleles, significantly deviated from neutral-evolution expectation in various demographic models. Haplotypes containing the derived allele of rs1816072 displayed significantly less diversity compared to haplotypes containing its ancestral allele, further supporting positive selection. The variations in DD-genotype frequencies in five human populations provided a snapshot of the evolutionary history, which suggested that the positive selections of the D alleles are recent and likely ongoing. The divergence between the DD-genotype profiles of schizophrenic and control samples pointed to the schizophrenia-relevance of positive selections, with the schizophrenic samples showing weakened selections compared to the controls. These DD-genotypes were previously found to increase the expression of β2, especially its long isoform. Electrophysiological analysis showed that this long β2 isoform favored by the positive selections is more sensitive than the short isoform to the inhibition of GABAA receptor function by energy depletion. These findings represent the first demonstration of positive selection in a schizophrenia-associated gene.
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Affiliation(s)
- Wing-Sze Lo
- Department of Biochemistry, Applied Genomics Laboratory and HKH Bioinformatics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Zhiwen Xu
- Department of Biochemistry, Applied Genomics Laboratory and HKH Bioinformatics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Zhiliang Yu
- Graduate program of Atmospheric, Marine, and Coastal Environment, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Frank W. Pun
- Department of Biochemistry, Applied Genomics Laboratory and HKH Bioinformatics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Siu-Kin Ng
- Graduate Program of Bioengineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Jianhuan Chen
- Department of Biochemistry, Applied Genomics Laboratory and HKH Bioinformatics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Ka-Lok Tong
- Department of Biochemistry, Applied Genomics Laboratory and HKH Bioinformatics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Cunyou Zhao
- Graduate Program of Bioengineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Xiaojing Xu
- Graduate Program of Bioengineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Shui-Ying Tsang
- Department of Biochemistry, Applied Genomics Laboratory and HKH Bioinformatics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Mutsuo Harano
- Department of Neuropsychiatry, Kurume University School of Medicine, Fukuka, Japan
| | - Gerald Stöber
- Department of Psychiatry and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Vishwajit L. Nimgaonkar
- Departments of Psychiatry and Human Genetics, University of Pittsburgh School of Medicine, and Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Hong Xue
- Department of Biochemistry, Applied Genomics Laboratory and HKH Bioinformatics Center, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- * To whom correspondence should be addressed. E-mail:
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Lo WS, Harano M, Gawlik M, Yu Z, Chen J, Pun FW, Tong KL, Zhao C, Ng SK, Tsang SY, Uchimura N, Stober G, Xue H. GABRB2 association with schizophrenia: commonalities and differences between ethnic groups and clinical subtypes. Biol Psychiatry 2007; 61:653-60. [PMID: 16950232 DOI: 10.1016/j.biopsych.2006.05.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Revised: 05/03/2006] [Accepted: 05/09/2006] [Indexed: 11/29/2022]
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) and haplotypes in intron 8 of type A gamma-aminobutyric acid (GABA(A)) receptor beta2 subunit gene (GABRB2) were initially found to be associated with schizophrenia in Chinese. This finding was subjected to cross-validation in this study with Japanese (JP) and German Caucasian (GE) subjects. METHODS Single nucleotide polymorphisms discovery and genotyping were carried out through resequencing of a 1839 base pair (bp) region in GABRB2. Tagging SNPs (tSNPs) were selected based on linkage disequilibrium (LD), combinations of which were analyzed with Bonferroni correction and permutation for disease association. Random resampling was applied to generate size- and gender-balanced cases and control subjects. RESULTS Out of the 17 SNPs (9.2/kilobase [kb]) revealed, 6 were population-specific. Population variations in LD were observable, and at least two low LD points were identified in both populations. Although disease association at single SNP level was only shown in GE, strong association was demonstrated in both JP (p = .0002 - .0191) and GE (p = .0033 - .0410) subjects, centering on haplotypes containing rs1816072 and rs1816071. Among different clinical subtypes, the most significant association was exhibited by systematic schizophrenia. CONCLUSIONS Cross-population validation of GABRB2 association with schizophrenia has been obtained with JP and GE subjects, with the genotype-disease correlations being strongest in systematic schizophrenia, the most severe subtype of the disease.
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Affiliation(s)
- Wing-Sze Lo
- Department of Biochemistry and Applied Genomics Laboratory, Hong Kong University of Science and Technology, Hong Kong, China
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Jamra RA, Becker T, Klopp N, Dahdouh F, Schulze TG, Gross M, Deschner M, Schmäl C, Illig T, Rietschel M, Propping P, Cichon S, Nöthen MM, Schumacher J. No evidence for an association between variants at the γ-amino-n-butyric acid type A receptor β2 locus and schizophrenia. Psychiatr Genet 2007; 17:43-5. [PMID: 17167345 DOI: 10.1097/ypg.0b013e32801118cd] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The alpha1/beta2/gamma2-containing heteropentamer is the most abundant gamma-amino-n-butyric acid type A receptor subtype in mammalian brains and the corresponding genes, the GABRA1, GABRB2, and GABRG2 genes, are located in chromosomal region 5q34 that several genome wide scans have implicated as a susceptibility region for schizophrenia. Given this positional and functional evidence, Lo et al. (Mol Psychiatry 2004; 9: 603-608) performed systematic linkage disequilibrium mapping of the GABAAR gene cluster on 5q34 in 130 schizophrenic patients and 170 controls, all of Chinese Han origin. In the single locus and haplotype analyses, single nucleotide polymorphisms in the GABRB2 gene showed highly significant association. The estimated effect caused by GABRB2 varied between odds ratios of 2.27 and 5.12. In order to re-examine their findings, we analyzed the most significantly associated single nucleotide polymorphism in the GABRB2 gene in a sample of 367 patients with schizophrenia and 360 controls, all of German descent. Our sample had a sufficient power to detect the effects described. Neither single marker nor haplotype analysis revealed a significant association with the disease status. Thus, our results do not support the hypothesis that genetic variation at the GABRB2 locus plays a major role in schizophrenic patients of European descent and that such variation would explain the previously observed linkage findings at this chromosomal region.
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Affiliation(s)
- Rami Abou Jamra
- Institute of Human Genetics, Department of Psychiatry, Life & Brain Center, University of Bonn, Bonn, Germany.
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