1
|
Davis KN, Qu PP, Ma S, Lin L, Plastini M, Dahl N, Plazzi G, Pizza F, O’Hara R, Wong WH, Hallmayer J, Mignot E, Zhang X, Urban AE. Mutations in human DNA methyltransferase DNMT1 induce specific genome-wide epigenomic and transcriptomic changes in neurodevelopment. Hum Mol Genet 2023; 32:3105-3120. [PMID: 37584462 PMCID: PMC10586194 DOI: 10.1093/hmg/ddad123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 08/17/2023] Open
Abstract
DNA methyltransferase type 1 (DNMT1) is a major enzyme involved in maintaining the methylation pattern after DNA replication. Mutations in DNMT1 have been associated with autosomal dominant cerebellar ataxia, deafness and narcolepsy (ADCA-DN). We used fibroblasts, induced pluripotent stem cells (iPSCs) and induced neurons (iNs) generated from patients with ADCA-DN and controls, to explore the epigenomic and transcriptomic effects of mutations in DNMT1. We show cell type-specific changes in gene expression and DNA methylation patterns. DNA methylation and gene expression changes were negatively correlated in iPSCs and iNs. In addition, we identified a group of genes associated with clinical phenotypes of ADCA-DN, including PDGFB and PRDM8 for cerebellar ataxia, psychosis and dementia and NR2F1 for deafness and optic atrophy. Furthermore, ZFP57, which is required to maintain gene imprinting through DNA methylation during early development, was hypomethylated in promoters and exhibited upregulated expression in patients with ADCA-DN in both iPSC and iNs. Our results provide insight into the functions of DNMT1 and the molecular changes associated with ADCA-DN, with potential implications for genes associated with related phenotypes.
Collapse
Affiliation(s)
- Kasey N Davis
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
| | - Ping-Ping Qu
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
| | - Shining Ma
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Ling Lin
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Center for Narcolepsy, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Melanie Plastini
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology Sciences for Life Laboratory, Uppsala University BMC, Uppsala 75122, Sweden
| | - Giuseppe Plazzi
- IRCCS—Istituto delle Scienze Neurologiche di Bologna, Bologna 40139, Italy
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Fabio Pizza
- IRCCS—Istituto delle Scienze Neurologiche di Bologna, Bologna 40139, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna 40126, Italy
| | - Ruth O’Hara
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Joachim Hallmayer
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Emmanuel Mignot
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Center for Narcolepsy, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Xianglong Zhang
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Department of Genetics, Stanford University School of Medicine, Palo Alto CA 94304, USA
| |
Collapse
|
2
|
Ibrahim MA, Yamasaki T, Furukawa K, Yamasaki K. Fragment-Based Drug Discovery for Trypanosoma brucei Glycosylphosphatidylinositol-Specific Phospholipase C through Biochemical and WaterLOGSY-NMR Methods. J Biochem 2022; 171:619-629. [PMID: 35191956 DOI: 10.1093/jb/mvac020] [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: 09/06/2021] [Accepted: 02/16/2022] [Indexed: 11/15/2022] Open
Abstract
Glycosylphosphatidylinositol-specific phospholipase C (GPI-PLC) of Trypanosoma brucei, the causative protozoan parasite of African trypanosomiasis, is a membrane-bound enzyme essential for antigenic variation, because it catalyses the release of the membrane-bound form of variable surface glycoproteins. Here, we performed a fragment-based drug discovery of TbGPI-PLC inhibitors using a combination of enzymatic inhibition assay and water-ligand observed via gradient spectroscopy (WaterLOGSY) NMR experiment. The TbGPI-PLC was cloned and over-expressed using an Escherichia coli expression system followed by purification using three-phase partitioning and gel filtration. Subsequently, the inhibitory activity of 873 fragment compounds against the recombinant TbGPI-PLC led to the identification of 66 primary hits. These primary hits were subjected to the WaterLOGSY NMR experiment where 10 fragment hits were confirmed to directly bind to the TbGPI-PLC. These included benzothiazole, chlorobenzene, imidazole, indole, pyrazol and quinolinone derivatives. Molecular docking simulation indicated that six of them share a common binding site, which corresponds to the catalytic pocket. The present study identified chemically diverse fragment hits that could directly bind and inhibit the TbGPI-PLC activity which constructed a framework for fragment optimisation or linking towards the design of novel drugs for African trypanosomiasis.
Collapse
Affiliation(s)
- Mohammed Auwal Ibrahim
- Biomedical Research Institute, and Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 3058566, Japan.,Department of Biochemistry, Ahmadu Bello University, Zaria, Kaduna 800001, Nigeria
| | - Tomoko Yamasaki
- Biomedical Research Institute, and Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 3058566, Japan
| | - Koji Furukawa
- Biomedical Research Institute, and Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 3058566, Japan
| | - Kazuhiko Yamasaki
- Biomedical Research Institute, and Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 3058566, Japan
| |
Collapse
|
3
|
Plante DT, Papale LA, Madrid A, Cook JD, Prairie ML, Alisch RS. PAX8/PAX8-AS1 DNA methylation levels are associated with objective sleep duration in persons with unexplained hypersomnolence using a deep phenotyping approach. Sleep 2021; 44:6305146. [PMID: 34145460 DOI: 10.1093/sleep/zsab108] [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] [Received: 06/15/2020] [Revised: 12/09/2020] [Indexed: 11/13/2022] Open
Abstract
STUDY OBJECTIVES Patients with unexplained hypersomnolence have significant impairment related to daytime sleepiness and excessive sleep duration, the biological bases of which are poorly understood. This investigation sought to examine relationships between objectively measured hypersomnolence phenotypes and epigenetic modification of candidate hypersomnolence genes to advance this line of inquiry. METHODS Twenty-eight unmedicated clinical patients with unexplained hypersomnolence were evaluated using overnight ad libitum polysomnography, multiple sleep latency testing, infrared pupillometry, and the psychomotor vigilance task. DNA methylation levels on CpG sites annotated to 11 a priori hypersomnolence candidate genes were assessed for statistical association with hypersomnolence measures using independent regression models with adjusted local index of significance (aLIS) P-value threshold of 0.05. RESULTS Nine CpG sites exhibited significant associations between DNA methylation levels and total sleep time measured using ad libitum polysomnography (aLIS p-value < .05). All nine differentially methylated CpG sites were annotated to the paired box 8 (PAX8) gene and its related antisense gene (PAX8-AS1). Among these nine differentially methylated positions was a cluster of five CpG sites located in the body of the PAX8 gene and promoter of PAX8-AS1. CONCLUSIONS This study demonstrates that PAX8/PAX8-AS1 DNA methylation levels are associated with total sleep time in persons with unexplained hypersomnolence. Given prior investigations that have implicated single nucleotide polymorphisms in PAX8/PAX8-AS1 with habitual sleep duration, further research that clarifies the role of DNA methylation levels on these genes in the phenotypic expression of total sleep time is warranted.
Collapse
Affiliation(s)
| | | | - Andy Madrid
- Department of Neurological Surgery, Madison, WI.,Neuroscience Training Program, University of Wisconsin - Madison, Madison, WI
| | | | | | | |
Collapse
|
4
|
Ouyang H, Han F, Zhou ZC, Zhang J. Differences in clinical and genetic characteristics between early- and late-onset narcolepsy in a Han Chinese cohort. Neural Regen Res 2020; 15:1887-1893. [PMID: 32246636 PMCID: PMC7513989 DOI: 10.4103/1673-5374.280322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/05/2019] [Accepted: 12/31/2019] [Indexed: 01/16/2023] Open
Abstract
Early- and late-onset narcolepsy constitutes two distinct diagnostic subgroups. However, it is not clear whether symptomology and genetic risk factors differ between early- and late-onset narcoleptics. This study compared clinical data and single-nucleotide polymorphisms (SNPs) between early- and late-onset patients in a large cohort of 899 Han Chinese narcolepsy patients. Blood, cerebrospinal fluid, and clinical data were prospectively collected from patients, and patients were genotyped for 40 previously reported narcolepsy risk-conferring SNPs. Genetic risk scores (GRSs), associations of five different sets of SNPs (GRS1-GRS5) with early- and late-onset narcolepsy, were evaluated using logistic regression and receiver operating characteristic curves. Mean sleep latency was significantly shorter in early-onset cases than in late-onset cases. Symptom severity was greater among late-onset patients, with higher rates of sleep paralysis, hypnagogic hallucinations, health-related quality of life impairment, and concurrent presentation with four or more symptoms. Hypocretin levels did not differ significantly between early- and late-onset cases. Only rs3181077 (CCR1/CCR3) and rs9274477 (HLA-DQB1) were more prevalent among early-onset cases. Only GRS1 (26 SNPs; OR = 1.513, 95% CI: 0.893-2.585; P < 0.05) and GRS5 (6 SNPs; OR = 1.893, 95% CI: 1.204-2.993; P < 0.05) were associated with early-onset narcolepsy, with areas under the receiver operating characteristic curves of 0.731 and 0.732, respectively. Neither GRS1 nor GRS5 included SNPs in HLA regions. Our results indicate that symptomology and genetic risk factors differ between early- and late-onset narcolepsy. This protocol was approved by the Institutional Review Board (IRB) Panels on Medical Human Subjects at Peking University People's Hospital, China (approval No. Yuanlunshenlinyi 86) in October 2011.
Collapse
Affiliation(s)
- Hui Ouyang
- Department of Clinical Neurology, Peking University People's Hospital, Beijing, China
| | - Fang Han
- Department of Clinical Pulmonology, Peking University People's Hospital, Beijing, China
| | - Ze-Chen Zhou
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Jun Zhang
- Department of Clinical Neurology, Peking University People's Hospital, Beijing, China
| |
Collapse
|
5
|
Ouyang H, Wang S, Zheng Q, Zhang J. Constructing gene network for type 1 narcolepsy based on genome-wide association study and differential gene expression analysis (STROBE). Medicine (Baltimore) 2020; 99:e19985. [PMID: 32358372 PMCID: PMC7440059 DOI: 10.1097/md.0000000000019985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Although many genes that affect narcolepsy risk have been identified, the interactions among these genes are still unclear. Moreover, there is a lack of research on the construction of the genetic network of narcolepsy. To screen candidate genes related to the onset of narcolepsy type 1, the function and distribution of important genes related to narcolepsy type 1 were studied and a gene network was constructed to study the pathogenesis of narcolepsy type 1.A case-control study (observational study) of 1075 Chinese narcoleptic patients and 1997 controls was conducted. The gene-sequencing data was analyzed using genome-wide association analysis. The candidate genes related to narcolepsy were identified by differential gene expression analysis and literature research. Then, the 28 candidate genes were input into the KEGG database and 32 pathway data related to candidate genes were obtained. A gene network, with the pathways as links and the genes as nodes, was constructed. According to our results, TNF, MHC II, NFATC2, and CXCL8 were the top genes in the gene network.TNF, MHC II, NFATC2, and CXCL8 are closely related to narcolepsy type I and require further study. By analyzing the pathways of disease-related genes and the network of gene interaction, we can provide an outlinefor the study of specific mechanisms of and treatments for narcolepsy.
Collapse
Affiliation(s)
- Hui Ouyang
- Department of Clinical Neurology, Peking University, People's Hospital
| | - Shiying Wang
- Department of Epidemiology and Biostatistics, Peking University Health Science Center, Beijing, China
| | - Qiwen Zheng
- Department of Epidemiology and Biostatistics, Peking University Health Science Center, Beijing, China
| | - Jun Zhang
- Department of Clinical Neurology, Peking University, People's Hospital
| |
Collapse
|
6
|
Ouyang H, Zhou Z, Zheng Q, Zhang J. Analyzing Functional Pathways and constructing gene-gene network for Narcolepsy based on candidate genes. Int J Med Sci 2020; 17:1508-1514. [PMID: 32669953 PMCID: PMC7359385 DOI: 10.7150/ijms.41812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 05/15/2020] [Indexed: 12/02/2022] Open
Abstract
Aims: To investigate the interactions among narcolepsy-associated genes and reveal the pathways these genes involved through bioinformatics analyses. Methods: The study was performed with the following steps: 1) Selected the previously discovered narcolepsy risk genes through literature review, 2) pathway enrichment analysis, and construction of gene-gene and protein-protein interaction (PPI) networks for narcolepsy. Results: 1) GO analysis revealed the positive regulation of interferon-gamma production as the most enriched terms in biological process, and C-C chemokine receptor activity as the most enriched term in molecular function, 2) KEGG pathway enrichment analysis revealed selective enrichment of genes in cytokine-cytokine receptor interaction signaling pathways, and 3) five hub genes were identified (IFNAR1, IL10RB, DNMT1, TNFSF4 and NFATC2). Conclusion: The bioinformatics results provide new insights into the molecular pathogenesis of narcolepsy and the identification of potential therapeutic targets for narcolepsy treatment.
Collapse
Affiliation(s)
- Hui Ouyang
- Department of Neuromedicine, Peking University People's Hospital, Beijing, China
| | - Zechen Zhou
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Qiwen Zheng
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Jun Zhang
- Department of Neuromedicine, Peking University People's Hospital, Beijing, China
| |
Collapse
|
7
|
Andrade A, Brennecke A, Mallat S, Brown J, Gomez-Rivadeneira J, Czepiel N, Londrigan L. Genetic Associations between Voltage-Gated Calcium Channels and Psychiatric Disorders. Int J Mol Sci 2019; 20:E3537. [PMID: 31331039 PMCID: PMC6679227 DOI: 10.3390/ijms20143537] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/12/2019] [Accepted: 07/13/2019] [Indexed: 12/23/2022] Open
Abstract
Psychiatric disorders are mental, behavioral or emotional disorders. These conditions are prevalent, one in four adults suffer from any type of psychiatric disorders world-wide. It has always been observed that psychiatric disorders have a genetic component, however, new methods to sequence full genomes of large cohorts have identified with high precision genetic risk loci for these conditions. Psychiatric disorders include, but are not limited to, bipolar disorder, schizophrenia, autism spectrum disorder, anxiety disorders, major depressive disorder, and attention-deficit and hyperactivity disorder. Several risk loci for psychiatric disorders fall within genes that encode for voltage-gated calcium channels (CaVs). Calcium entering through CaVs is crucial for multiple neuronal processes. In this review, we will summarize recent findings that link CaVs and their auxiliary subunits to psychiatric disorders. First, we will provide a general overview of CaVs structure, classification, function, expression and pharmacology. Next, we will summarize tools to study risk loci associated with psychiatric disorders. We will examine functional studies of risk variations in CaV genes when available. Finally, we will review pharmacological evidence of the use of CaV modulators to treat psychiatric disorders. Our review will be of interest for those studying pathophysiological aspects of CaVs.
Collapse
Affiliation(s)
- Arturo Andrade
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA.
| | - Ashton Brennecke
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Shayna Mallat
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Julian Brown
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| | | | - Natalie Czepiel
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Laura Londrigan
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| |
Collapse
|
8
|
Kara S, Pirela-Morillo GA, Gilliam CT, Wilson GD. Identification of novel susceptibility genes associated with seven autoimmune disorders using whole genome molecular interaction networks. J Autoimmun 2018; 97:48-58. [PMID: 30391024 DOI: 10.1016/j.jaut.2018.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/08/2018] [Accepted: 10/11/2018] [Indexed: 12/20/2022]
Abstract
Convergent evidence from multiple and independent genetics studies implicate a small number of genes that predispose individuals to multiple autoimmune disorders (AuD). These intersecting loci reinforced the hypothesis that disorders with overlapping etiology group into a cluster of closely related genes within a whole genome molecular interaction network. We tested the hypothesis that "biological network proximity" within a whole genome molecular interaction network can be used to inform the search for multigene inheritance. Using a set of nine previously published genome wide association studies (GWAS) of AuD genes, we generated AuD-specific molecular interaction networks to identify networks of associated genes. We show that all nine "seed genes" can be connected within a 35-member network via interactions with 26 connecting genes. We show that this network is more connected than expected by chance, and 13 of the connecting genes showed association with multiple AuD upon GWAS reanalysis. Furthermore, we report association of SNPs in five new genes (IL10RA, DGKA, GRB2, STAT5A, and NFATC2) which were not previously considered as AuD candidates, and show significant association in novel disease samples of Crohn's disease and systemic lupus erythematosus. Furthermore, we show that the connecting genes show no association in four non-AuD GWAS. Finally, we test the connecting genes in psoriasis GWAS, and show association to previously identified loci and report new loci. These findings support the hypothesis that molecular interaction networks can be used to inform the search for multigene disease etiology, especially for disorders with overlapping etiology.
Collapse
Affiliation(s)
- Sam Kara
- University of Chicago, Departments of Human Genetics, 920 East 58 th St., Chicago, IL 60637, USA; Radiation Oncology Department, Beaumont Health, 3811 W Thirteen Mile Road, Royal Oak, MI, 48073, USA
| | - Gerardo A Pirela-Morillo
- La Universidad del Zulia, Computer Science Department, Laboratories for Computational Models & Languages, and Bioinformatics, Edif. Grano de Oro, Planta Baja, Departamento de Computación, Ave. Universidad con Ave. 22, Maracaibo, 4002, Venezuela
| | - Conrad T Gilliam
- University of Chicago, Departments of Human Genetics, 920 East 58 th St., Chicago, IL 60637, USA
| | - George D Wilson
- Radiation Oncology Department, Beaumont Health, 3811 W Thirteen Mile Road, Royal Oak, MI, 48073, USA.
| |
Collapse
|
9
|
Tang J, Chen X, Cai B, Chen G. A logical relationship for schizophrenia, bipolar, and major depressive disorder. Part 4: Evidence from chromosome 4 high-density association screen. J Comp Neurol 2018; 527:392-405. [DOI: 10.1002/cne.24543] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Jian Tang
- Department of Radiology; Qianfo Hill Campus Hospital of Shandong University; Jinan 250061 Shandong People's Republic of China
| | - Xing Chen
- Department of Medical Genetics, Institute of Basic Medicine; Shandong Academy of Medical Sciences; Jinan Shandong People's Republic of China
| | - Bin Cai
- CapitalBio corporation, 18 Life Science Parkway, Changping District; Beijing People's Republic of China
| | - Gang Chen
- Department of Medical Genetics, Institute of Basic Medicine; Shandong Academy of Medical Sciences; Jinan Shandong People's Republic of China
| |
Collapse
|
10
|
Takeuchi H, Tomita H, Taki Y, Kikuchi Y, Ono C, Yu Z, Nouchi R, Yokoyama R, Kotozaki Y, Nakagawa S, Sekiguchi A, Iizuka K, Hanawa S, Araki T, Miyauchi CM, Sakaki K, Nozawa T, Ikeda S, Yokota S, Magistro D, Sassa Y, Kawashima R. A Common CACNA1C Gene Risk Variant has Sex-Dependent Effects on Behavioral Traits and Brain Functional Activity. Cereb Cortex 2018; 29:3211-3219. [DOI: 10.1093/cercor/bhy189] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 06/23/2018] [Indexed: 01/08/2023] Open
Abstract
Abstract
Genome-wide association studies have suggested that allelic variations in the CACNA1C gene confer susceptibility to schizophrenia and bipolar disorder only in women. Here we investigated the sex-specific effects of the CACNA1C variant rs1024582 on psychiatry-related traits, brain activity during tasks and rest, and brain volume in 1207 normal male and female subjects. After correcting for multiple comparisons, there were significant interaction effects between sex and the minor allele of this polymorphism on the hostile behavior subscale scores of the Coronary-Prone Type Scale mediated by higher scores in female carriers of the minor allele. Imaging analyses revealed significant interaction effects between sex and the minor allele on fractional amplitude of low-frequency fluctuations in the right dorsolateral prefrontal cortex and on brain activity during the 2-back task in areas of the right posterior cingulate cortex, right thalamus, and right hippocampus, which were all mediated by reduced activity in female carriers of the minor allele. Our results demonstrated that the rs1024582 risk variant of CACNA1C is associated with reduced activity in the frontolimbic regions at rest and during a working memory task as well as with greater hostility in females in the healthy population.
Collapse
Affiliation(s)
- Hikaru Takeuchi
- Division of Developmental Cognitive Neuroscience, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Hiroaki Tomita
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Yasuyuki Taki
- Division of Developmental Cognitive Neuroscience, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
- Division of Medical Neuroimaging Analysis, Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Radiology and Nuclear Medicine, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Yoshie Kikuchi
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Chiaki Ono
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Zhiqian Yu
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Rui Nouchi
- Creative Interdisciplinary Research Division, Frontier Research Institute for Interdisciplinary Science, Tohoku University, Sendai, Japan
- Human and Social Response Research Division, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
- Department of Advanced Brain Science, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | | | - Yuka Kotozaki
- Division of Clinical Research, Medical-Industry Translational Research Center, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Seishu Nakagawa
- Department of Human Brain Science, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
- Division of Psychiatry, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Atsushi Sekiguchi
- Division of Medical Neuroimaging Analysis, Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Behavioral Medicine, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Kunio Iizuka
- Department of Psychiatry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Sugiko Hanawa
- Department of Human Brain Science, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | | | - Carlos Makoto Miyauchi
- Department of Language Sciences, Graduate School of Humanities, Tokyo Metropolitan University, Tokyo, Japan
| | - Kohei Sakaki
- Department of Advanced Brain Science, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Takayuki Nozawa
- Collaborative Research Center for Happiness Co-Creation Society through Intelligent Communications, Tokyo Institute of Technology, Tokyo, Japan
| | - Shigeyuki Ikeda
- Department of Ubiquitous Sensing, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Susumu Yokota
- Division of Developmental Cognitive Neuroscience, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Daniele Magistro
- Department of Sport Science, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Yuko Sassa
- Division of Developmental Cognitive Neuroscience, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Ryuta Kawashima
- Division of Developmental Cognitive Neuroscience, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
- Department of Advanced Brain Science, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
- Department of Human Brain Science, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| |
Collapse
|
11
|
Chen X, Long F, Cai B, Chen X, Chen G. A novel relationship for schizophrenia, bipolar and major depressive disorder Part 3: Evidence from chromosome 3 high density association screen. J Comp Neurol 2017; 526:59-79. [PMID: 28856687 DOI: 10.1002/cne.24311] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 07/29/2017] [Accepted: 07/31/2017] [Indexed: 12/30/2022]
Abstract
Familial clustering of schizophrenia (SCZ), bipolar disorder (BPD), and major depressive disorder (MDD) was systematically reported (Aukes et al, Genet Med 2012, 14, 338-341) and convergent evidence from genetics, symptomatology, and psychopharmacology imply that there are intrinsic connections between these three major psychiatric disorders, for example, any two or even three of these disorders could co-exist in some families. A total of 60, 838 single-nucleotide polymorphisms (SNPs) on chromosome 3 were genotyped by Affymetrix Genome-Wide Human SNP array 6.0 on 119 SCZ, 253 BPD (type-I), 177 MDD patients and 1,000 controls. The population of Shandong province was formed in 14 century and believed that it belongs to homogenous population. Associated SNPs were systematically revealed and outstanding susceptibility genes (CADPS, GRM7,KALRN, LSAMP, NLGN1, PRICKLE2, ROBO2) were identified. Unexpectedly, flanking genes for the associated SNPs distinctive for BPD and/or MDD were replicated in an enlarged cohort of 986 SCZ patients. The evidence from this chromosome 3 analysis supports the notion that both of bipolar and MDD might be subtypes of schizophrenia rather than independent disease entity. Also, a similar finding was detected on chromosome 5, 6, 7, and 8 (Chen et al. Am J Transl Res 2017;9 (5):2473-2491; Curr Mol Med 2016;16(9):840-854; Behav Brain Res 2015;293:241-251; Mol Neurobiol 2016. doi: 10.1007/s12035-016-0102-1). Furthermore, PRICKLE2 play an important role in the pathogenesis of three major psychoses in this population.
Collapse
Affiliation(s)
- Xing Chen
- Department of Medical Genetics, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Feng Long
- Department of Medical Genetics, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| | - Bin Cai
- CapitalBio corporation, Beijing, People's Republic of China
| | - Xiaohong Chen
- CapitalBio corporation, Beijing, People's Republic of China
| | - Gang Chen
- Department of Medical Genetics, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, Shandong, People's Republic of China
| |
Collapse
|
12
|
Kantojärvi K, Liuhanen J, Saarenpää-Heikkilä O, Satomaa AL, Kylliäinen A, Pölkki P, Jaatela J, Toivola A, Milani L, Himanen SL, Porkka-Heiskanen T, Paavonen J, Paunio T. Variants in calcium voltage-gated channel subunit Alpha1 C-gene (CACNA1C) are associated with sleep latency in infants. PLoS One 2017; 12:e0180652. [PMID: 28792954 PMCID: PMC5549883 DOI: 10.1371/journal.pone.0180652] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/19/2017] [Indexed: 12/12/2022] Open
Abstract
Genetic variants in CACNA1C (calcium voltage-gated channel subunit alpha1 C) are associated with bipolar disorder and schizophrenia where sleep disturbances are common. In an experimental model, Cacna1c has been found to modulate the electrophysiological architecture of sleep. There are strong genetic influences for consolidation of sleep in infancy, but only a few studies have thus far researched the genetic factors underlying the process. We hypothesized that genetic variants in CACNA1C affect the regulation of sleep in early development. Seven variants that were earlier associated (genome-wide significantly) with psychiatric disorders at CACNA1C were selected for analyses. The study sample consists of 1086 infants (520 girls and 566 boys) from the Finnish CHILD-SLEEP birth cohort (genotyped by Illumina Infinium PsychArray BeadChip). Sleep length, latency, and nightly awakenings were reported by the parents of the infants with a home-delivered questionnaire at 8 months of age. The genetic influence of CACNA1C variants on sleep in infants was examined by using PLINK software. Three of the examined CACNA1C variants, rs4765913, rs4765914, and rs2239063, were associated with sleep latency (permuted P<0.05). There was no significant association between studied variants and night awakenings or sleep duration. CACNA1C variants for psychiatric disorders were found to be associated with long sleep latency among 8-month-old infants. It remains to be clarified whether the findings refer to defective regulation of sleep, or to distractibility of sleep under external influences.
Collapse
Affiliation(s)
- Katri Kantojärvi
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Johanna Liuhanen
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | | | - Anna-Liisa Satomaa
- Department of Clinical Neurophysiology, Tampere University Hospital, Medical Imaging Centre and Hospital Pharmacy, Pirkanmaa Hospital District, Tampere, Finland
| | - Anneli Kylliäinen
- School of Social Sciences and Humanities/Psychology, University of Tampere, Tampere, Finland
| | - Pirjo Pölkki
- Department of Social Sciences, University of Eastern Finland, Kuopio, Finland
| | - Julia Jaatela
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Auli Toivola
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Lili Milani
- The Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Sari-Leena Himanen
- Department of Clinical Neurophysiology, Tampere University Hospital, Medical Imaging Centre and Hospital Pharmacy, Pirkanmaa Hospital District, Tampere, Finland
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | | | - Juulia Paavonen
- Child and Adolescent Mental Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Tiina Paunio
- Genomics and Biomarkers Unit, National Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| |
Collapse
|
13
|
Houghton KT, Forrest A, Awad A, Atkinson LZ, Stockton S, Harrison PJ, Geddes JR, Cipriani A. Biological rationale and potential clinical use of gabapentin and pregabalin in bipolar disorder, insomnia and anxiety: protocol for a systematic review and meta-analysis. BMJ Open 2017; 7:e013433. [PMID: 28348186 PMCID: PMC5372050 DOI: 10.1136/bmjopen-2016-013433] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
INTRODUCTION Gabapentin has been extensively prescribed off-label for psychiatric indications, with little established evidence of efficacy. Gabapentin and pregabalin, a very similar drug with the same mechanism of action, bind to a subunit of voltage-dependent calcium channels which are implicated in the aetiopathogenesis of bipolar disorder, anxiety and insomnia. This systematic review and meta-analysis aims to collect and critically appraise all the available evidence about the efficacy and tolerability of gabapentin and pregabalin in the treatment of bipolar disorder, insomnia and anxiety. METHODS AND ANALYSIS We will include all randomised controlled trials (RCTs) reported as double-blind and comparing gabapentin or pregabalin with placebo or any other active pharmacological treatment (any preparation, dose, frequency, route of delivery or setting) in patients with bipolar disorder, anxiety or insomnia. For consideration of adverse effects (tolerability), single-blind or open-label RCTs and non-randomised evidence will also be summarised. The main outcomes will be efficacy (measured as dichotomous and continuous outcome) and acceptability (proportion of patients who dropped out of the allocated treatment). Published and unpublished studies will be sought through relevant database searches, trial registries and websites; all reference selection and data extraction will be conducted by at least 2 independent reviewers. We will conduct a random-effects meta-analysis to synthesise all evidence for each outcome. Heterogeneity between studies will be investigated by the I2 statistic. Data from included studies will be entered into a funnel plot for investigation of small-study effects. No subgroup analysis will be undertaken, but we will carry out sensitivity analyses about combination treatment, psychiatric comorbidity, use of rescue medications and fixed versus random-effects model. ETHICS AND DISSEMINATION This review does not require ethical approval. This protocol has been registered on PROSPERO (CRD42016041802). The results of the systematic review will be disseminated via publication in a peer-reviewed journal.
Collapse
Affiliation(s)
- Kerensa T Houghton
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX3 7JX, UK
| | - Alexandra Forrest
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX3 7JX, UK
- Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford OX3 7JX, UK
| | - Amine Awad
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX3 7JX, UK
| | - Lauren Z Atkinson
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX3 7JX, UK
| | - Sarah Stockton
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX3 7JX, UK
| | - Paul J Harrison
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX3 7JX, UK
- Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford OX3 7JX, UK
| | - John R Geddes
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX3 7JX, UK
- Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford OX3 7JX, UK
| | - Andrea Cipriani
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford OX3 7JX, UK
- Oxford Health NHS Foundation Trust, Warneford Hospital, Oxford OX3 7JX, UK
| |
Collapse
|
14
|
Jawinski P, Sander C, Mauche N, Spada J, Huang J, Schmidt A, Häntzsch M, Burkhardt R, Scholz M, Hegerl U, Hensch T. Brain Arousal Regulation in Carriers of Bipolar Disorder Risk Alleles. Neuropsychobiology 2016; 72:65-73. [PMID: 26509803 DOI: 10.1159/000437438] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/06/2015] [Indexed: 11/19/2022]
Abstract
OBJECTIVES Recent genome-wide association studies identified a number of chromosomal risk loci for bipolar disorder (BD, 'manic-depressive illness'). According to the vigilance regulation model, the regulation of brain arousal (referred to as 'vigilance') when assessed via EEG is an emerging biomarker linked to the pathogenesis of manic and depressive episodes. On this basis, the present study aimed to assess whether carriers of BD risk alleles differ in brain arousal regulation. METHODS Healthy participants of the population-based Leipzig Health Care Study (LIFE) underwent a 20-min eyes-closed resting EEG paradigm. Brain arousal was assessed applying the computer-based Vigilance Algorithm Leipzig (VIGALL). The primary sample (n = 540) was genotyped for ten of the most reliable BD risk variants, of which two qualified for replication (n = 509). RESULTS Primary sample analyses revealed Bonferroni-adjusted significance for rs1006737 in CACNA1C (encoding a calcium channel subunit), with risk allele carriers exhibiting relatively steep brain arousal declines. Further, carriers of two risk alleles of rs472913 at 1p32.1 showed generally lower brain arousal levels for the duration of the resting paradigm. However, both associations failed replication. CONCLUSION Although our initial findings are in line with the vigilance regulation model and convincing in view of the previously reported notable role of ion channelopathies in BD, our results do not provide consistent evidence for a link between BD risk variants and brain arousal regulation. Several between-sample differences may account for this inconsistency. The molecular genetics of brain arousal regulation remain to be clarified.
Collapse
Affiliation(s)
- Philippe Jawinski
- LIFE - Leipzig Research Centre for Civilization Diseases, Leipzig, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Scheinfeldt LB, Gharani N, Kasper RS, Schmidlen TJ, Gordon ES, Jarvis JP, Delaney S, Kronenthal CJ, Gerry NP, Christman MF. Using the Coriell Personalized Medicine Collaborative Data to conduct a genome-wide association study of sleep duration. Am J Med Genet B Neuropsychiatr Genet 2015; 168:697-705. [PMID: 26333835 PMCID: PMC5049662 DOI: 10.1002/ajmg.b.32362] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 07/31/2015] [Indexed: 11/08/2022]
Abstract
Sleep is critical to health and functionality, and several studies have investigated the inherited component of insomnia and other sleep disorders using genome-wide association studies (GWAS). However, genome-wide studies focused on sleep duration are less common. Here, we used data from participants in the Coriell Personalized Medicine Collaborative (CPMC) (n = 4,401) to examine putative associations between self-reported sleep duration, demographic and lifestyle variables, and genome-wide single nucleotide polymorphism (SNP) data to better understand genetic contributions to variation in sleep duration. We employed stepwise ordered logistic regression to select our model and retained the following predictive variables: age, gender, weight, physical activity, physical activity at work, smoking status, alcohol consumption, ethnicity, and ancestry (as measured by principal components analysis) in our association testing. Several of our strongest candidate genes were previously identified in GWAS related to sleep duration (TSHZ2, ABCC9, FBXO15) and narcolepsy (NFATC2, SALL4). In addition, we have identified novel candidate genes for involvement in sleep duration including SORCS1 and ELOVL2. Our results demonstrate that the self-reported data collected through the CPMC are robust, and our genome-wide association analysis has identified novel candidate genes involved in sleep duration. More generally, this study contributes to a better understanding of the complexity of human sleep.
Collapse
Affiliation(s)
| | - Neda Gharani
- Coriell Institute for Medical ResearchCamdenNew Jersey
| | | | | | | | | | - Susan Delaney
- Coriell Institute for Medical ResearchCamdenNew Jersey
| | | | | | | |
Collapse
|
16
|
Kumar D, Dedic N, Flachskamm C, Voulé S, Deussing JM, Kimura M. Cacna1c (Cav1.2) Modulates Electroencephalographic Rhythm and Rapid Eye Movement Sleep Recovery. Sleep 2015; 38:1371-80. [PMID: 25845695 DOI: 10.5665/sleep.4972] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/25/2015] [Indexed: 11/03/2022] Open
Abstract
STUDY OBJECTIVES The CACNA1C gene encodes the alpha 1C (α1C) subunit of the Cav1.2 voltage-dependent L-type calcium channel (LTCC). Some of the other voltage-dependent calcium channels, e.g., P-/Q-type, Cav2.1; N-type, Cav2.2; E-/R-type, Cav2.3; and T-type, Cav3.3 have been implicated in sleep modulation. However, the contribution of LTCCs to sleep remains largely unknown. Based on recent genome-wide association studies, CACNA1C emerged as one of potential candidate genes associated with both sleep and psychiatric disorders. Indeed, most patients with mental illnesses have sleep problems and vice versa. DESIGN To investigate an impact of Cav1.2 on sleep-wake behavior and electroencephalogram (EEG) activity, polysomnography was performed in heterozygous Cacna1c (HET) knockout mice and their wild-type (WT) littermates under baseline and challenging conditions (acute sleep deprivation and restraint stress). MEASUREMENTS AND RESULTS HET mice displayed significantly lower EEG spectral power than WT mice across high frequency ranges (beta to gamma) during wake and rapid eye movement (REM) sleep. Although HET mice spent slightly more time asleep in the dark period, daily amounts of sleep did not differ between the two genotypes. However, recovery sleep after exposure to both types of challenging stress conditions differed markedly; HET mice exhibited reduced REM sleep recovery responses compared to WT mice. CONCLUSIONS These results suggest the involvement of Cacna1c (Cav1.2) in fast electroencephalogram oscillations and REM sleep regulatory processes. Lower spectral gamma activity, slightly increased sleep demands, and altered REM sleep responses found in heterozygous Cacna1c knockout mice may rather resemble a sleep phenotype observed in schizophrenia patients.
Collapse
Affiliation(s)
| | - Nina Dedic
- Max Planck Institute of Psychiatry, Munich, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | | | | | | | | |
Collapse
|
17
|
Genome-wide analysis links NFATC2 with asparaginase hypersensitivity. Blood 2015; 126:69-75. [PMID: 25987655 DOI: 10.1182/blood-2015-02-628800] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/01/2015] [Indexed: 12/29/2022] Open
Abstract
Asparaginase is used to treat acute lymphoblastic leukemia (ALL); however, hypersensitivity reactions can lead to suboptimal asparaginase exposure. Our objective was to use a genome-wide approach to identify loci associated with asparaginase hypersensitivity in children with ALL enrolled on St. Jude Children's Research Hospital (SJCRH) protocols Total XIIIA (n = 154), Total XV (n = 498), and Total XVI (n = 271), or Children's Oncology Group protocols POG 9906 (n = 222) and AALL0232 (n = 2163). Germline DNA was genotyped using the Affymetrix 500K, Affymetrix 6.0, or the Illumina Exome BeadChip array. In multivariate logistic regression, the intronic rs6021191 variant in nuclear factor of activated T cells 2 (NFATC2) had the strongest association with hypersensitivity (P = 4.1 × 10(-8); odds ratio [OR] = 3.11). RNA-seq data available from 65 SJCRH ALL tumor samples and 52 Yoruba HapMap samples showed that samples carrying the rs6021191 variant had higher NFATC2 expression compared with noncarriers (P = 1.1 × 10(-3) and 0.03, respectively). The top ranked nonsynonymous polymorphism was rs17885382 in HLA-DRB1 (P = 3.2 × 10(-6); OR = 1.63), which is in near complete linkage disequilibrium with the HLA-DRB1*07:01 allele we previously observed in a candidate gene study. The strongest risk factors for asparaginase allergy are variants within genes regulating the immune response.
Collapse
|
18
|
Wang W, Lou J, Zhong R, Qi YQ, Shen N, Lu XZ, Wang YJ, Zhang Q, Zou L, Duan JY, Ke JT, Miao XP, Gong FQ. The roles of Ca2+/NFAT signaling genes in Kawasaki disease: single- and multiple-risk genetic variants. Sci Rep 2014; 4:5208. [PMID: 24903211 PMCID: PMC4047536 DOI: 10.1038/srep05208] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/20/2014] [Indexed: 12/17/2022] Open
Abstract
Ca2+/nuclear factor of activated T-cells (Ca2+/NFAT) signaling pathway may play a crucial role in Kawasaki disease (KD). We investigated 16 genetic variants, selected by bioinformatics analyses or previous studies, in 7 key genes involved in this pathway in a Chinese population. We observed a significantly or marginally increased KD risk associated with rs2720378 GC + CC genotypes (OR = 1.39, 95% CI = 1.07–1.80, P = 0.014) or rs2069762 AC + CC genotypes (OR = 1.28, 95% CI = 0.98–1.67, P = 0.066), compared with their wild type counterparts. In classification and regression tree analysis, individuals carrying the combined genotypes of rs2720378 GC or CC genotype, rs2069762 CA or CC genotype and rs1561876 AA genotype exhibited the highest KD risk (OR = 2.12, 95% CI = 1.46–3.07, P < 0.001), compared with the lowest risk carriers of rs2720378 GG genotype. Moreover, a significant dose effect was observed among these three variants (Ptrend < 0.001). In conclusion, this study implicates that single- and multiple-risk genetic variants in this pathway might contribute to KD susceptibility. Further studies on more comprehensive single nucleotide polymorphisms, different ethnicities and larger sample sizes are warranted, and the exact biological mechanisms need to be further clarified.
Collapse
Affiliation(s)
- Wei Wang
- 1] Children's Hospital, Zhejiang University School of Medicine, Hangzhou, PR China [2]
| | - Jiao Lou
- 1] Department of Epidemiology and Biostatistics and Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China [2]
| | - Rong Zhong
- Department of Epidemiology and Biostatistics and Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Yan-qi Qi
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou, PR China
| | - Na Shen
- Department of Epidemiology and Biostatistics and Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Xu-zai Lu
- Guangdong Women and Children Hospital, Guangzhou, PR China
| | - Yu-jia Wang
- Centre Hospitalier de l'Université de Montréal, CRCHUM-Hôpital Notre-Dame, Pavillion DeSève, Montreal, Canada
| | - Qing Zhang
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou, PR China
| | - Li Zou
- Department of Epidemiology and Biostatistics and Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Jia-yu Duan
- Department of Epidemiology and Biostatistics and Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Jun-tao Ke
- Department of Epidemiology and Biostatistics and Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Xiao-ping Miao
- Department of Epidemiology and Biostatistics and Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, PR China
| | - Fang-qi Gong
- Children's Hospital, Zhejiang University School of Medicine, Hangzhou, PR China
| |
Collapse
|
19
|
Najafi A, Masoudi-Nejad A, Imani Fooladi AA, Ghanei M, Nourani MR. Microarray gene expression analysis of the human airway in patients exposed to sulfur mustard. J Recept Signal Transduct Res 2014; 34:283-9. [PMID: 24823320 DOI: 10.3109/10799893.2014.896379] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
There is much data about the acute effects of sulfur mustard gas on humans, animals and cells. But less is known regarding the molecular basics of chronic complications in humans. Basically, mustard gas, as an alkylating agent, causes several chronic problems in the eyes, skin and more importantly in the pulmonary system which is the main cause of death. Although recent proteomic research has been carried out on bronchoalveolar lavage (BAL) and serum, but high-throughput transcriptomics have not yet been applied to chronic airway remodeling. This is the first cDNA-microarray report on the chronic human mustard lung disease, 25 years after exposure during the Iran-Iraq war. Microarray transcriptional profiling indicated that a total of 122 genes were significantly dysregulated in tissues located in the airway of patients. These genes are associated with the extracellular matrix components, apoptosis, stress response, inflammation and mucus secretion.
Collapse
Affiliation(s)
- Ali Najafi
- Chemical Injuries Research Center, Systems Biology Institute, Genomics Division, Baqiyatallah University of Medical Sciences , Tehran , Iran
| | | | | | | | | |
Collapse
|
20
|
Liedhegner ES, Vogt CD, Sem DS, Cunningham CW, Hillard CJ. Sterol carrier protein-2: binding protein for endocannabinoids. Mol Neurobiol 2014; 50:149-58. [PMID: 24510313 DOI: 10.1007/s12035-014-8651-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 01/23/2014] [Indexed: 12/13/2022]
Abstract
The endocannabinoid (eCB) system, consisting of eCB ligands and the type 1 cannabinoid receptor (CB1R), subserves retrograde, activity-dependent synaptic plasticity in the brain. eCB signaling occurs "on-demand," thus the processes regulating synthesis, mobilization and degradation of eCBs are also primary mechanisms for the regulation of CB1R activity. The eCBs, N-arachidonylethanolamine (AEA) and 2-arachidonoylglycerol (2-AG), are poorly soluble in water. We hypothesize that their aqueous solubility, and, therefore, their intracellular and transcellular distribution, are facilitated by protein binding. Using in silico docking studies, we have identified the nonspecific lipid binding protein, sterol carrier protein 2 (SCP-2), as a potential AEA binding protein. The docking studies predict that AEA and AM404 associate with SCP-2 at a putative cholesterol binding pocket with ∆G values of -3.6 and -4.6 kcal/mol, respectively. These values are considerably higher than cholesterol (-6.62 kcal/mol) but consistent with a favorable binding interaction. In support of the docking studies, SCP-2-mediated transfer of cholesterol in vitro is inhibited by micromolar concentrations of AEA; and heterologous expression of SCP-2 in HEK 293 cells increases time-related accumulation of AEA in a temperature-dependent fashion. These results suggest that SCP-2 facilitates cellular uptake of AEA. However, there is no effect of SCP-2 transfection on the cellular accumulation of AEA determined at equilibrium or the IC50 values for AEA, AM404 or 2-AG to inhibit steady state accumulation of radiolabelled AEA. We conclude that SCP-2 is a low affinity binding protein for AEA that can facilitate its cellular uptake but does not contribute significantly to intracellular sequestration of AEA.
Collapse
Affiliation(s)
- Elizabeth Sabens Liedhegner
- Neuroscience Research Center and Departments of Pharmacology and Toxicology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA
| | | | | | | | | |
Collapse
|
21
|
Howell WM. HLA and disease: guilt by association. Int J Immunogenet 2013; 41:1-12. [DOI: 10.1111/iji.12088] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/10/2013] [Indexed: 02/06/2023]
Affiliation(s)
- W. M. Howell
- Department of Histocompatibility and Immunogenetics; NHS Blood and Transplant; Newcastle upon Tyne UK
| |
Collapse
|
22
|
Parsons MJ, Lester KJ, Barclay NL, Nolan PM, Eley TC, Gregory AM. Replication of Genome-Wide Association Studies (GWAS) loci for sleep in the British G1219 cohort. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:431-8. [PMID: 23780892 DOI: 10.1002/ajmg.b.32106] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 09/26/2012] [Indexed: 12/30/2022]
Abstract
Sleep is a critical behavior shared by most higher animals. Sleep disturbances are comorbid with numerous psychiatric disorders, most notably symptoms of depression. Twin studies have suggested that genetic influences partially underlie the variation seen for numerous sleep-related traits across individuals. Recently, two Genome-Wide Association Studies (GWAS) conducted for sleep traits have revealed new candidate genes for sleep-related measures. We attempted to replicate the two most significant associations from these two studies, CACNA1C (a l-type calcium channel) with sleep latency and quality and ABCC9 (an ATP-sensitive potassium channel) with sleep duration, using the G1219 British population sample. We genotyped single-nucleotide polymorphisms (SNPs) for each of the two different sleep GWAS loci. Linear regression analyses were conducted to assess main effects of these SNPs on their corresponding sleep measures, as well as for depressive symptoms. We successfully replicated an association of a genetic variant in the CACNA1C gene (rs16929277) with sleep quality using an additive model of inheritance. A significant association of the ABCC9 gene (rs11046209) with sleep duration was seen only in a recessive models based upon a rare homozygous genotype (n = 2). There was also a significant association between a different ABCC9 gene variant (rs11046205) and depressive symptoms. These findings add further support for the involvement of calcium channels in the mechanisms regulating sleep function and suggest a possible role of the ABCC9 gene in depression.
Collapse
|
23
|
Byrne EM, Gehrman PR, Medland SE, Nyholt DR, Heath AC, Madden PAF, Hickie IB, Van Duijn CM, Henders AK, Montgomery GW, Martin NG, Wray NR. A genome-wide association study of sleep habits and insomnia. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:439-51. [PMID: 23728906 PMCID: PMC4083458 DOI: 10.1002/ajmg.b.32168] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 04/11/2013] [Indexed: 01/15/2023]
Abstract
Several aspects of sleep behavior such as timing, duration and quality have been demonstrated to be heritable. To identify common variants that influence sleep traits in the population, we conducted a genome-wide association study of six sleep phenotypes assessed by questionnaire in a sample of 2,323 individuals from the Australian Twin Registry. Genotyping was performed on the Illumina 317, 370, and 610K arrays and the SNPs in common between platforms were used to impute non-genotyped SNPs. We tested for association with more than 2,000,000 common polymorphisms across the genome. While no SNPs reached the genome-wide significance threshold, we identified a number of associations in plausible candidate genes. Most notably, a group of SNPs in the third intron of the CACNA1C gene ranked as most significant in the analysis of sleep latency (P = 1.3 × 10⁻⁶). We attempted to replicate this association in an independent sample from the Chronogen Consortium (n = 2,034), but found no evidence of association (P = 0.73). We have identified several other suggestive associations that await replication in an independent sample. We did not replicate the results from previous genome-wide analyses of self-reported sleep phenotypes after correction for multiple testing.
Collapse
Affiliation(s)
- Enda M Byrne
- Queensland Institute of Medical Research, Brisbane, Queensland, Australia.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Gonzalez S, Xu C, Ramirez M, Zavala J, Armas R, Contreras SA, Contreras J, Dassori A, Leach RJ, Flores D, Jerez A, Raventós H, Ontiveros A, Nicolini H, Escamilla M. Suggestive evidence for association between L-type voltage-gated calcium channel (CACNA1C) gene haplotypes and bipolar disorder in Latinos: a family-based association study. Bipolar Disord 2013; 15:206-14. [PMID: 23437964 PMCID: PMC3781018 DOI: 10.1111/bdi.12041] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
OBJECTIVES Through recent genome-wide association studies (GWASs), several groups have reported significant association between variants in the calcium channel, voltage-dependent, L-type, alpha 1C subunit (CACNA1C) and bipolar disorder (BP) in European and European-American cohorts. We performed a family-based association study to determine whether CACNA1C is associated with BP in the Latino population. METHODS This study included 913 individuals from 215 Latino pedigrees recruited from the USA, Mexico, Guatemala, and Costa Rica. The Illumina GoldenGate Genotyping Assay was used to genotype 58 single-nucleotide polymorphisms (SNPs) that spanned a 602.9-kb region encompassing the CACNA1C gene including two SNPs (rs7297582 and rs1006737) previously shown to associate with BP. Individual SNP and haplotype association analyses were performed using Family-Based Association Test (version 2.0.3) and Haploview (version 4.2) software. RESULTS An eight-locus haplotype block that included these two markers showed significant association with BP (global marker permuted p = 0.0018) in the Latino population. For individual SNPs, this sample had insufficient power (10%) to detect associations with SNPs with minor effect (odds ratio = 1.15). CONCLUSIONS Although we were not able to replicate findings of association between individual CACNA1C SNPs rs7297582 and rs1006737 and BP, we were able to replicate the GWAS signal reported for CACNA1C through a haplotype analysis that encompassed these previously reported significant SNPs. These results provide additional evidence that CACNA1C is associated with BP and provides the first evidence that variations in this gene might play a role in the pathogenesis of this disorder in the Latino population.
Collapse
Affiliation(s)
- Suzanne Gonzalez
- Department of Psychiatry and Center of Excellence for Neurosciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX
| | - Chun Xu
- Department of Psychiatry and Center of Excellence for Neurosciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX
| | - Mercedes Ramirez
- Department of Psychiatry and Center of Excellence for Neurosciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX
| | - Juan Zavala
- Department of Psychiatry and Center of Excellence for Neurosciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX
| | - Regina Armas
- Langley Porter Psychiatric Institute, University of California at San Francisco, San Francisco, CA
| | - Salvador A Contreras
- Department of Psychiatry, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Javier Contreras
- Centro de Investigación en Biología Celular y Molecular y Escuela de Biologia, Universidad de Costa Rica, San Jose, Costa Rica
| | - Albana Dassori
- Department of Psychiatry, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA,South Texas Veterans Health Care System, San Antonio, TX
| | - Robin J Leach
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Deborah Flores
- Los Angeles Biomedical Research Center at Harbor, University of California Los Angeles Medical Center, Torrance, CA, USA
| | - Alvaro Jerez
- Centro Internacional de Trastornos Afectivos y de la Conducta Adictiva, Guatemala City, Guatemala
| | - Henriette Raventós
- Centro de Investigación en Biología Celular y Molecular y Escuela de Biologia, Universidad de Costa Rica, San Jose, Costa Rica
| | - Alfonso Ontiveros
- Instituto de Información e Investigación en Salud Mental AC, Monterrey, Nuevo Leon
| | - Humberto Nicolini
- Grupo de Estudios Médicos y Familiares Carracci, S.C., México, D.F., México
| | - Michael Escamilla
- Department of Psychiatry and Center of Excellence for Neurosciences, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX
| |
Collapse
|
25
|
Boraska V, Davis OSP, Cherkas LF, Helder SG, Harris J, Krug I, Pei-Chi Liao T, Treasure J, Ntalla I, Karhunen L, Keski-Rahkonen A, Christakopoulou D, Raevuori A, Shin SY, Dedoussis GV, Kaprio J, Soranzo N, Spector TD, Collier DA, Zeggini E. Genome-wide association analysis of eating disorder-related symptoms, behaviors, and personality traits. Am J Med Genet B Neuropsychiatr Genet 2012; 159B:803-11. [PMID: 22911880 PMCID: PMC3494378 DOI: 10.1002/ajmg.b.32087] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/11/2012] [Indexed: 12/18/2022]
Abstract
Eating disorders (EDs) are common, complex psychiatric disorders thought to be caused by both genetic and environmental factors. They share many symptoms, behaviors, and personality traits, which may have overlapping heritability. The aim of the present study is to perform a genome-wide association scan (GWAS) of six ED phenotypes comprising three symptom traits from the Eating Disorders Inventory 2 [Drive for Thinness (DT), Body Dissatisfaction (BD), and Bulimia], Weight Fluctuation symptom, Breakfast Skipping behavior and Childhood Obsessive-Compulsive Personality Disorder trait (CHIRP). Investigated traits were derived from standardized self-report questionnaires completed by the TwinsUK population-based cohort. We tested 283,744 directly typed SNPs across six phenotypes of interest in the TwinsUK discovery dataset and followed-up signals from various strata using a two-stage replication strategy in two independent cohorts of European ancestry. We meta-analyzed a total of 2,698 individuals for DT, 2,680 for BD, 2,789 (821 cases/1,968 controls) for Bulimia, 1,360 (633 cases/727 controls) for Childhood Obsessive-Compulsive Personality Disorder trait, 2,773 (761 cases/2,012 controls) for Breakfast Skipping, and 2,967 (798 cases/2,169 controls) for Weight Fluctuation symptom. In this GWAS analysis of six ED-related phenotypes, we detected association of eight genetic variants with P < 10(-5) . Genetic variants that showed suggestive evidence of association were previously associated with several psychiatric disorders and ED-related phenotypes. Our study indicates that larger-scale collaborative studies will be needed to achieve the necessary power to detect loci underlying ED-related traits.
Collapse
Affiliation(s)
- Vesna Boraska
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | - Oliver SP Davis
- MRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College LondonLondon, UK
| | - Lynn F Cherkas
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital CampusWestminster Bridge Road, London, UK
| | - Sietske G Helder
- MRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College LondonLondon, UK
| | - Juliette Harris
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital CampusWestminster Bridge Road, London, UK
| | - Isabel Krug
- MRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College LondonLondon, UK,School of Psychological Sciences, University of MelbourneMelbourne, Victoria, Australia
| | - Thomas Pei-Chi Liao
- MRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College LondonLondon, UK
| | - Janet Treasure
- Department Academic Psychiatry, King's College LondonLondon, UK
| | - Ioanna Ntalla
- Department of Dietetics and Nutrition, Harokopio University of AthensAthens, Greece
| | - Leila Karhunen
- Department of Clinical Nutrition, Institute of Public Health and Clinical Nutrition, University of Eastern FinlandKuopio, Finland
| | - Anna Keski-Rahkonen
- Department of Public Health, The Hjelt Institute, University of HelsinkiHelsinki, Finland
| | | | - Anu Raevuori
- Department of Public Health, The Hjelt Institute, University of HelsinkiHelsinki, Finland
| | - So-Youn Shin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusHinxton, Cambridge, UK
| | - George V Dedoussis
- Department of Dietetics and Nutrition, Harokopio University of AthensAthens, Greece
| | - Jaakko Kaprio
- Department of Public Health, The Hjelt Institute, University of HelsinkiHelsinki, Finland,Institute of Molecular Medicine, University of HelsinkiHelsinki, Finland,Unit for Child and Adolescent Mental Health, National Institute for Health and WelfareHelsinki, Finland
| | - Nicole Soranzo
- Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusHinxton, Cambridge, UK
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, St Thomas' Hospital CampusWestminster Bridge Road, London, UK
| | - David A Collier
- MRC Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College LondonLondon, UK
| | - Eleftheria Zeggini
- Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusHinxton, Cambridge, UK
| |
Collapse
|
26
|
Han F, Lin L, Li J, Dong SX, An P, Zhao L, Liu NY, Li QY, Yan H, Gao ZC, Faraco J, Strohl KP, Liu X, Miyadera H, Mignot E. HLA-DQ association and allele competition in Chinese narcolepsy. ACTA ACUST UNITED AC 2012; 80:328-35. [PMID: 22862152 DOI: 10.1111/j.1399-0039.2012.01948.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 07/09/2012] [Accepted: 07/16/2012] [Indexed: 12/17/2022]
Abstract
In Japanese, Koreans and Caucasians, narcolepsy/hypocretin deficiency is tightly associated with the DRB1*15:01-DQA1*01:02-DQB1*06:02 haplotype. Studies in African-Americans suggest a primary effect of DQB1*06:02, but this observation has been difficult to confirm in other populations because of high linkage disequilibrium between DRB1*15:01/3 and DQB1*06:02 in most populations. In this study, we studied human leucocyte antigen (HLA) class II in 202 Chinese narcolepsy patients (11% from South China) and found all patients to be DQB1*06:02 positive. Comparing cases with 103 unselected controls, and 110 and 79 controls selected for the presence of DQB1*06:02 and DRB1*15:01, we found that the presence of DQB1*06:02 and not DRB1*15:01 was associated with narcolepsy. In particular, Southern Chinese haplotypes such as the DRB1*15:01-DQA1*01:02-DQB1*06:01 and DRB1*15:01-DQA1*01:02-DQB1*05 were not associated with narcolepsy. As reported in Japanese, Koreans, African-Americans and Caucasians, additional protective effects of DQA1*01 (non-DQA1*01:02) and susceptibility effects of DQB1*03:01 were observed. These results illustrate the extraordinary conservation of HLA class II effects in narcolepsy across populations and show that DRB1*15:01 has no effect on narcolepsy susceptibility in the absence of DQB1*06:02. The results are also in line with a previously proposed 'HLA-DQ allelic competition model' that involves competition between non-DQA1*01:02, non-DQB1*06:02 'competent' (able to dimerize together) DQ1 alleles and the major DQα*01:02/ DQβ*06:02 narcolepsy heterodimer to reduce susceptibility.
Collapse
Affiliation(s)
- F Han
- Department of Pulmonary Medicine, Beijing University People's Hospital, Beijing, China.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Smoothed functional principal component analysis for testing association of the entire allelic spectrum of genetic variation. Eur J Hum Genet 2012; 21:217-24. [PMID: 22781089 DOI: 10.1038/ejhg.2012.141] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Fast and cheaper next-generation sequencing technologies will generate unprecedentedly massive and highly dimensional genetic variation data that allow nearly complete evaluation of genetic variation including both common and rare variants. There are two types of association tests: variant-by-variant test and group test. The variant-by-variant test is designed to test the association of common variants, while the group test is suitable to collectively test the association of multiple rare variants. We propose here a smoothed functional principal component analysis (SFPCA) statistic as a general approach for testing association of the entire allelic spectrum of genetic variation (both common and rare variants), which utilizes the merits of both variant-by-variant analysis and group tests. By intensive simulations, we demonstrate that the SFPCA statistic has the correct type 1 error rates and much higher power than the existing methods to detect association of (1) common variants, (2) rare variants, (3) both common and rare variants and (4) variants with opposite directions of effects. To further evaluate its performance, the SFPCA statistic is applied to ANGPTL4 sequence and six continuous phenotypes data from the Dallas Heart Study as an example for testing association of rare variants and a GWAS of schizophrenia data as an example for testing association of common variants. The results show that the SFPCA statistic has much smaller P-values than many existing statistics in both real data analysis examples.
Collapse
|
28
|
Partinen M, Saarenpää-Heikkilä O, Ilveskoski I, Hublin C, Linna M, Olsén P, Nokelainen P, Alén R, Wallden T, Espo M, Rusanen H, Olme J, Sätilä H, Arikka H, Kaipainen P, Julkunen I, Kirjavainen T. Increased incidence and clinical picture of childhood narcolepsy following the 2009 H1N1 pandemic vaccination campaign in Finland. PLoS One 2012; 7:e33723. [PMID: 22470463 PMCID: PMC3314680 DOI: 10.1371/journal.pone.0033723] [Citation(s) in RCA: 287] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 02/15/2012] [Indexed: 11/19/2022] Open
Abstract
Background Narcolepsy is a rare neurological sleep disorder especially in children who are younger than 10 years. In the beginning of 2010, an exceptionally large number of Finnish children suffered from an abrupt onset of excessive daytime sleepiness (EDS) and cataplexy. Therefore, we carried out a systematic analysis of the incidence of narcolepsy in Finland between the years 2002–2010. Methods All Finnish hospitals and sleep clinics were contacted to find out the incidence of narcolepsy in 2010. The national hospital discharge register from 2002 to 2009 was used as a reference. Findings Altogether 335 cases (all ages) of narcolepsy were diagnosed in Finland during 2002–2009 giving an annual incidence of 0.79 per 100 000 inhabitants (95% confidence interval 0.62–0.96). The average annual incidence among subjects under 17 years of age was 0.31 (0.12–0.51) per 100 000 inhabitants. In 2010, 54 children under age 17 were diagnosed with narcolepsy (5.3/100 000; 17-fold increase). Among adults ≥20 years of age the incidence rate in 2010 was 0.87/100 000, which equals that in 2002–2009. Thirty-four of the 54 children were HLA-typed, and they were all positive for narcolepsy risk allele DQB1*0602/DRB1*15. 50/54 children had received Pandemrix vaccination 0 to 242 days (median 42) before onset. All 50 had EDS with abnormal multiple sleep latency test (sleep latency <8 min and ≥2 sleep onset REM periods). The symptoms started abruptly. Forty-seven (94%) had cataplexy, which started at the same time or soon after the onset of EDS. Psychiatric symptoms were common. Otherwise the clinical picture was similar to that described in childhood narcolepsy. Interpretation A sudden increase in the incidence of abrupt childhood narcolepsy was observed in Finland in 2010. We consider it likely that Pandemrix vaccination contributed, perhaps together with other environmental factors, to this increase in genetically susceptible children.
Collapse
Affiliation(s)
- Markku Partinen
- Helsinki Sleep Clinic, Vitalmed Research Centre, Helsinki, Finland.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|