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Hou W, Cai J, Shen P, Zhang S, Xiao S, You P, Tong Y, Li K, Qi Z, Luo H. Identification of FXYD6 as the novel biomarker for glioma based on differential expression and DNA methylation. Cancer Med 2023; 12:22170-22184. [PMID: 38093622 PMCID: PMC10757084 DOI: 10.1002/cam4.6752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/15/2023] [Accepted: 11/09/2023] [Indexed: 12/31/2023] Open
Abstract
OBJECTIVE As a single-transmembrane protein of the FXYD family, FXYD6 plays different roles under physiological and pathological status, especially in the nervous system. This study aims to identify FXYD6 as a biomarker for glioma, by analyzing its expression and methylation patterns. METHODS Using TCGA and GTEx datasets, we analyzed FXYD6 expression in various tissues, confirming its levels in normal brain and different glioma grades via immunoblotting and immunostaining. FXYD6 biological functions were explored through enrichment analysis, and tumor immune infiltration was assessed using ESTIMATE and TIMER algorithms. Pearson correlation analysis probed FXYD6 associations with biological function-related genes. A glioma detection model was developed using FXYD6 methylation data from TCGA and GEO. Consistently, a FXYD6 methylation-based prognostic model was constructed for glioma via LASSO Cox regression. RESULTS FXYD6 was observed to be downregulated in GBM and implicated in a range of cellular functions, including synapse formation, cell junctions, immune checkpoint, ferroptosis, EMT, and pyroptosis. Hypermethylation of specific FXYD6 CpG sites in gliomas was identified, which could be used to build a diagnostic model. Additionally, FXYD6 methylation-based prognostic model could serve as an independent factor as well. CONCLUSIONS FXYD6 is a promising biomarker for the diagnosis and prognosis of glioma, with its methylation-based prognostic model serving as an independent factor. This highlights its potential in clinical application for glioma management.
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Affiliation(s)
- Weiliang Hou
- Department of Neurosurgery, Huashan Hospital, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain ScienceFudan UniversityShanghaiChina
| | - Jing Cai
- Department of Neurosurgery, Huashan Hospital, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain ScienceFudan UniversityShanghaiChina
| | - Pei Shen
- Department of Oral Surgery, Shanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Shuo Zhang
- Shanghai QuietD Biotechnology Co., Ltd.ShanghaiChina
| | - Siyu Xiao
- Department of Rehabilitation, Gongan HospitalHubei University of Chinese MedicineWuhanHubei ProvinceChina
| | - Pu You
- Shanghai QuietD Biotechnology Co., Ltd.ShanghaiChina
| | - Yusheng Tong
- Department of Neurosurgery, Huashan Hospital, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain ScienceFudan UniversityShanghaiChina
| | - Kaicheng Li
- Shanghai QuietD Biotechnology Co., Ltd.ShanghaiChina
| | - Zengxin Qi
- Department of Neurosurgery, Huashan Hospital, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain ScienceFudan UniversityShanghaiChina
| | - Hao Luo
- Shanghai QuietD Biotechnology Co., Ltd.ShanghaiChina
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McFalls AJ, Imperio CG, Woodward E, Krikorian C, Stoltsfus B, Wronowski B, Grigson PS, Freeman WM, Vrana KE. An RNA-seq study of the mPFC of rats with different addiction phenotypes. Brain Res Bull 2022; 191:107-120. [DOI: 10.1016/j.brainresbull.2022.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/23/2022] [Accepted: 09/28/2022] [Indexed: 11/15/2022]
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Deficiency in FTSJ1 Affects Neuronal Plasticity in the Hippocampal Formation of Mice. BIOLOGY 2022; 11:biology11071011. [PMID: 36101392 PMCID: PMC9312013 DOI: 10.3390/biology11071011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Neuronal plasticity refers to the brain’s ability to adapt in response to activity-dependent changes. This process, among others, allows the brain to acquire memory or to compensate for a neurocognitive deficit. We analyzed adult FTSJ1-deficient mice in order to gain insight into the role of FTSJ1 in neuronal plasticity. These mice displayed alterations in the hippocampus (a brain structure that is involved in memory and learning, among other functions) e.g., in the form of changes in dendritic spines. Changes in dendritic spines are considered to represent a morphological hallmark of altered neuronal plasticity, and thus FTSJ1 deficiency might have a direct effect upon the capacity of the brain to adapt to plastic changes. Long-term potentiation (LTP) is an electrophysiological correlate of neuronal plasticity, and is related to learning and to processes attributed to memory. Here we show that LTP in FTSJ1-deficient mice is reduced, hinting at disturbed neuronal plasticity. These findings suggest that FTSJ1 deficiency has an impact on neuronal plasticity not only morphologically but also on the physiological level. Abstract The role of the tRNA methyltransferase FTSJ1 in the brain is largely unknown. We analyzed whether FTSJ1-deficient mice (KO) displayed altered neuronal plasticity. We explored open field behavior (10 KO mice (aged 22–25 weeks)) and 11 age-matched control littermates (WT) and examined mean layer thickness (7 KO; 6 WT) and dendritic spines (5 KO; 5 WT) in the hippocampal area CA1 and the dentate gyrus. Furthermore, long-term potentiation (LTP) within area CA1 was investigated (5 KO; 5 WT), and mass spectrometry (MS) using CA1 tissue (2 each) was performed. Compared to controls, KO mice showed a significant reduction in the mean thickness of apical CA1 layers. Dendritic spine densities were also altered in KO mice. Stable LTP could be induced in the CA1 area of KO mice and remained stable at for at least 1 h, although at a lower level as compared to WTs, while MS data indicated differential abundance of several proteins, which play a role in neuronal plasticity. FTSJ1 has an impact on neuronal plasticity in the murine hippocampal area CA1 at the morphological and physiological levels, which, in conjunction with comparable changes in other cortical areas, might accumulate in disturbed learning and memory functions.
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Ma L, Chen H, Zhang Z, Liu L, Zhao Y, Li Y, Zhao Z, Chen H, Kang L. Association Study Between Polymorphic Loci in Cholesterol Metabolism Pathway and Gallstone in the Tibetan Population. Front Genet 2022; 13:902553. [PMID: 35651949 PMCID: PMC9149373 DOI: 10.3389/fgene.2022.902553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/13/2022] [Indexed: 12/02/2022] Open
Abstract
Background: The incidence of gallstones in the Tibetan population is increasing rapidly. Previous studies indicated that genetic variation located in the cholesterol metabolism pathway may be associated with the incidence of gallstones. Methods: By recruiting 132 Tibetan gallstone patients and 52 normal Tibetan controls, we performed next-generation sequencing for 508 genes in the cholesterol metabolism pathway. Additionally, by integrating the sequence data of 41 normal Tibetan subjects in the public database, we finally obtained 93 normal Tibetan controls. Single nucleotide polymorphisms (SNPs) calling were performed by using the GATK pipeline. The quality control criteria for SNPs were: missing rate <0.05; minor allele frequency (MAF) > 0.01; and p value >0.001 in the Hardy-Weinberg Equilibrium (HWE) test. To eliminate the influence of population heterogeneity, Principal Component Analysis (PCA) was carried out by using the smartpca software. Association analyses were performed by Plink software. Multiple tests were adjusted by the false discovery rate (FDR) method. Results: A total of 2,401 SNPs were obtained by analyzing 508 genes, and 2,011 SNPs left after quality control. After adjusting the eigen vectors, we found that 10 SNPs (SNV05997, rs80145081, rs80005560, rs79074685, rs748546375, rs201880593, rs142559357, rs750769471, rs869789 and rs4072341) were significantly associated with gallstone. Subsequently, by comparing the case group with our control group and the public database control group separately, we further found that the SNP rs869789 was consistently significantly associated with gallstone (p = 9.04 × 10–3 in cases vs. our controls and 5.73 × 10–3 in cases vs. public controls, respectively). Conclusion: By systematically analyzed SNPs in the cholesterol metabolism pathway, we identified one polymorphic locus rs869789 significantly associated with the pathogenesis of gallstone in the Tibetan population. This study will provide clue for further mechanism study of gallstone in the Tibetan population.
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Affiliation(s)
- Lifeng Ma
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Xianyang, China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Hui Chen
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Xianyang, China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Zhiying Zhang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Xianyang, China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Lijun Liu
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Xianyang, China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Yiduo Zhao
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Xianyang, China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Yansong Li
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Xianyang, China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Zhipeng Zhao
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Xianyang, China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
| | - Haitao Chen
- School of Public Health, Sun Yat-sen University, Shenzhen, China
| | - Longli Kang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, Xianyang, China.,Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, China
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Jiao S, Johnson K, Moreno C, Yano S, Holmgren M. Comparative description of the mRNA expression profile of Na + /K + -ATPase isoforms in adult mouse nervous system. J Comp Neurol 2021; 530:627-647. [PMID: 34415061 PMCID: PMC8716420 DOI: 10.1002/cne.25234] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/16/2021] [Accepted: 08/16/2021] [Indexed: 11/09/2022]
Abstract
Mutations in genes encoding Na+ /K+ -ATPase α1, α2, and α3 subunits cause a wide range of disabling neurological disorders, and dysfunction of Na+ /K+ -ATPase may contribute to neuronal injury in stroke and dementia. To better understand the pathogenesis of these diseases, it is important to determine the expression patterns of the different Na+ /K+ -ATPase subunits within the brain and among specific cell types. Using two available scRNA-Seq databases from the adult mouse nervous system, we examined the mRNA expression patterns of the different isoforms of the Na+ /K+ -ATPase α, β and Fxyd subunits at the single-cell level among brain regions and various neuronal populations. We subsequently identified specific types of neurons enriched with transcripts for α1 and α3 isoforms and elaborated how α3-expressing neuronal populations govern cerebellar neuronal circuits. We further analyzed the co-expression network for α1 and α3 isoforms, highlighting the genes that positively correlated with α1 and α3 expression. The top 10 genes for α1 were Chn2, Hpcal1, Nrgn, Neurod1, Selm, Kcnc1, Snrk, Snap25, Ckb and Ccndbp1 and for α3 were Sorcs3, Eml5, Neurod2, Ckb, Tbc1d4, Ptprz1, Pvrl1, Kirrel3, Pvalb, and Asic2.
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Affiliation(s)
- Song Jiao
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Kory Johnson
- Bioinformatics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Cristina Moreno
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Sho Yano
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Miguel Holmgren
- Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
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Yap JQ, Seflova J, Sweazey R, Artigas P, Robia SL. FXYD proteins and sodium pump regulatory mechanisms. J Gen Physiol 2021; 153:211866. [PMID: 33688925 PMCID: PMC7953255 DOI: 10.1085/jgp.202012633] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 02/03/2021] [Indexed: 12/12/2022] Open
Abstract
The sodium/potassium-ATPase (NKA) is the enzyme that establishes gradients of sodium and potassium across the plasma membrane. NKA activity is tightly regulated for different physiological contexts through interactions with single-span transmembrane peptides, the FXYD proteins. This diverse family of regulators has in common a domain containing a Phe-X-Tyr-Asp (FXYD) motif, two conserved glycines, and one serine residue. In humans, there are seven tissue-specific FXYD proteins that differentially modulate NKA kinetics as appropriate for each system, providing dynamic responsiveness to changing physiological conditions. Our understanding of how FXYD proteins contribute to homeostasis has benefitted from recent advances described in this review: biochemical and biophysical studies have provided insight into regulatory mechanisms, genetic models have uncovered remarkable complexity of FXYD function in integrated physiological systems, new posttranslational modifications have been identified, high-resolution structural studies have revealed new details of the regulatory interaction with NKA, and new clinical correlations have been uncovered. In this review, we address the structural determinants of diverse FXYD functions and the special roles of FXYDs in various physiological systems. We also discuss the possible roles of FXYDs in protein trafficking and regulation of non-NKA targets.
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Affiliation(s)
- John Q Yap
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL
| | - Jaroslava Seflova
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL
| | - Ryan Sweazey
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX
| | - Pablo Artigas
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX
| | - Seth L Robia
- Department of Cell and Molecular Physiology, Loyola University Chicago, Maywood, IL
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Luo H, Cai B, Pan J, Shi HX, Wang KK, Zhong YQ, Lu YJ, Bao L, Zhang X, Li KC. FXYD6 promotes thermal nociception by regulating TRPV1. Mol Pain 2021. [PMCID: PMC7887684 DOI: 10.1177/1744806921992249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
FXYD6, an unnecessary auxiliary subunit of Na+,K+-ATPase, is expressed in the nervous system. However, its functions remain largely unclear. In the present study, we find that FXYD6 is involved in the thermal nociception. FXYD6 was mainly expressed in small-diameter DRG neurons expressing transient receptor potential channel V1 (TRPV1). In the SNS-Cre/Fxyd6F/F mice, loss of FXYD6 in these sensory neurons impaired the behavioral responses to noxious heat stimulus and intraplantar injection of capsaicin. The capsaicin-induced and TRPV1-mediated currents were decreased in the FXYD6–deficient DRG neurons. Heterologous expression of FXYD6 could increase the TRPV1 capsaicin-sensitive currents in HEK293 cells. Furthermore, we found that the negatively charged PGDEE motif in C-terminal of FXYD6 is required for the FXYD6/TRPV1 interaction and FXYD6-mediated enhancement of TRPV1. Disrupting the FXYD6/TRPV1 interaction with the TAT-PGDEE peptide could elevate the threshold of thermal nociception. Therefore, FXYD6 maintains the thermal nociception via interacting with TRPV1 channel in nociceptors.
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Affiliation(s)
- Hao Luo
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Bing Cai
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Institute of Brain-Intelligence Science and Technology, Zhangjiang Laboratory, Shanghai, China
| | - Jing Pan
- Institute of Brain-Intelligence Science and Technology, Zhangjiang Laboratory, Shanghai, China
| | - Hai-Xiang Shi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Biology, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kai-Kai Wang
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yan-Qing Zhong
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ying-Jin Lu
- Institute of Brain-Intelligence Science and Technology, Zhangjiang Laboratory, Shanghai, China
| | - Lan Bao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Biology, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xu Zhang
- Institute of Neuroscience and State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Institute of Brain-Intelligence Science and Technology, Zhangjiang Laboratory, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research Center, Chinese Academy of Sciences/XuHui Central Hospital, Shanghai, China
| | - Kai-Cheng Li
- Institute of Brain-Intelligence Science and Technology, Zhangjiang Laboratory, Shanghai, China
- Shanghai Clinical Research Center, Chinese Academy of Sciences/XuHui Central Hospital, Shanghai, China
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Hormonal regulation of Na +-K +-ATPase from the evolutionary perspective. CURRENT TOPICS IN MEMBRANES 2019; 83:315-351. [PMID: 31196608 DOI: 10.1016/bs.ctm.2019.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Na+-K+-ATPase, an α/β heterodimer, is an ancient enzyme that maintains Na+ and K+ gradients, thus preserving cellular ion homeostasis. In multicellular organisms, this basic housekeeping function is integrated to fulfill the needs of specialized organs and preserve whole-body homeostasis. In vertebrates, Na+-K+-ATPase is essential for many fundamental physiological processes, such as nerve conduction, muscle contraction, nutrient absorption, and urine excretion. During vertebrate evolution, three key developments contributed to diversification and integration of Na+-K+-ATPase functions. Generation of novel α- and β-subunits led to formation of multiple Na+-K+-ATPase isoenyzmes with distinct functional characteristics. Development of a complex endocrine system enabled efficient coordination of diverse Na+-K+-ATPase functions. Emergence of FXYDs, small transmembrane proteins that regulate Na+-K+-ATPase, opened new ways to modulate its function. FXYDs are a vertebrate innovation and an important site of hormonal action, suggesting they played an especially prominent role in evolving interaction between Na+-K+-ATPase and the endocrine system in vertebrates.
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Cheng Z, Zhou H, Sherva R, Farrer LA, Kranzler HR, Gelernter J. Genome-wide Association Study Identifies a Regulatory Variant of RGMA Associated With Opioid Dependence in European Americans. Biol Psychiatry 2018; 84:762-770. [PMID: 29478698 PMCID: PMC6041180 DOI: 10.1016/j.biopsych.2017.12.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 12/22/2017] [Accepted: 12/30/2017] [Indexed: 01/07/2023]
Abstract
BACKGROUND Opioid dependence (OD) is at epidemic levels in the United States. Genetic studies can provide insight into its biology. METHODS We completed an OD genome-wide association study in 3058 opioid-exposed European Americans, 1290 of whom met criteria for a DSM-IV diagnosis of OD. Analysis used DSM-IV criterion count. RESULTS By meta-analysis of four cohorts, Yale-Penn 1 (n = 1388), Yale-Penn 2 (n = 996), Yale-Penn 3 (n = 98), and SAGE (Study of Addiction: Genetics and Environment) (n = 576), we identified a variant on chromosome 15, rs12442183, near RGMA, associated with OD (p = 1.3 × 10-8). The association was also genome-wide significant in Yale-Penn 1 taken individually and nominally significant in two of the other three samples. The finding was further supported in a meta-analysis of all available opioid-exposed African Americans (n = 2014 [1106 meeting DSM-IV OD criteria]; p = 3.0 × 10-3) from three cohorts; there was nominal significance in two of these samples. Thus, of seven subsamples examined in two populations, one was genome-wide significant, and four of six were nominally (or nearly) significant. RGMA encodes repulsive guidance molecule A, which is a central nervous system axon guidance protein. Risk allele rs12442183*T was correlated with higher expression of a specific RGMA transcript variant in frontal cortex (p = 2 × 10-3). After chronic morphine injection, the homologous mouse gene (Rgma) was upregulated in C57BL/6J striatum. Coexpression analysis of 1301 brain samples revealed that RGMA messenger RNA expression was associated with that of four genes implicated in other psychiatric disorders, including GRIN1. CONCLUSIONS This is the first study to demonstrate an association of RGMA with OD. It provides a new lead into our understanding of OD pathophysiology.
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Affiliation(s)
- Zhongshan Cheng
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Massachusetts; VA Connecticut Healthcare Center, West Haven, Massachusetts
| | - Hang Zhou
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Massachusetts; VA Connecticut Healthcare Center, West Haven, Massachusetts
| | - Richard Sherva
- Departments of Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics, Boston University School of Medicine and School Public Health, Boston, Massachusetts
| | - Lindsay A Farrer
- Departments of Neurology, Ophthalmology, Genetics & Genomics, Epidemiology, and Biostatistics, Boston University School of Medicine and School Public Health, Boston, Massachusetts
| | - Henry R Kranzler
- Center for Studies of Addiction, Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, Pennsylvania
| | - Joel Gelernter
- Division of Human Genetics, Department of Psychiatry, Yale University School of Medicine, New Haven, Massachusetts; Departments of Genetics and Neuroscience, Yale University School of Medicine, New Haven, Massachusetts; VA Connecticut Healthcare Center, West Haven, Massachusetts.
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Missense variants in ATP1A3 and FXYD gene family are associated with childhood-onset schizophrenia. Mol Psychiatry 2018; 25:821-830. [PMID: 29895895 PMCID: PMC6291354 DOI: 10.1038/s41380-018-0103-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 05/07/2018] [Accepted: 05/14/2018] [Indexed: 11/09/2022]
Abstract
Childhood-onset schizophrenia (COS) is a rare and severe form of schizophrenia defined as onset before age of 13. Here we report on two unrelated cases diagnosed with both COS and alternating hemiplegia of childhood (AHC), and for whom two distinct pathogenic de novo variants were identified in the ATP1A3 gene. ATP1A3 encodes the α-subunit of a neuron-specific ATP-dependent transmembrane sodium-potassium pump. Using whole exome sequencing data derived from a cohort of 17 unrelated COS cases, we also examined ATP1A3 and all of its interactors known to be expressed in the brain to establish if variants could be identified. This led to the identification of a third case with a possibly damaging missense mutation in ATP1A3 and three others cases with predicted pathogenic missense variants in the FXYD gene family (FXYD1, FXYD6, and FXYD6-FXYD2 readthrough). FXYD genes encode proteins that modulate the ATP-dependant pump function. This report is the first to identify variants in the same pathway for COS. Our COS study illustrates the interest of stratifying a complex condition according to the age of onset for the identification of deleterious variants. Whereas ATP1A3 is a replicated gene in rare neuropediatric diseases, this gene has previously been linked with COS in only one case report. The association with rare variants in FXYD gene family is novel and highlights the interest of exploring these genes in COS as well as in pediatric neurodevelopmental disorders.
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Butler MG, McGuire AB, Masoud H, Manzardo AM. Currently recognized genes for schizophrenia: High-resolution chromosome ideogram representation. Am J Med Genet B Neuropsychiatr Genet 2016; 171B:181-202. [PMID: 26462458 PMCID: PMC6679920 DOI: 10.1002/ajmg.b.32391] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/02/2015] [Indexed: 11/09/2022]
Abstract
A large body of genetic data from schizophrenia-related research has identified an assortment of genes and disturbed pathways supporting involvement of complex genetic components for schizophrenia spectrum and other psychotic disorders. Advances in genetic technology and expanding studies with searchable genomic databases have led to multiple published reports, allowing us to compile a master list of known, clinically relevant, or susceptibility genes contributing to schizophrenia. We searched key words related to schizophrenia and genetics from peer-reviewed medical literature sources, authoritative public access psychiatric websites and genomic databases dedicated to gene discovery and characterization of schizophrenia. Our list of 560 genes were arranged in alphabetical order in tabular form with gene symbols placed on high-resolution human chromosome ideograms. Genome wide pathway analysis using GeneAnalytics was carried out on the resulting list of genes to assess the underlying genetic architecture for schizophrenia. Recognized genes of clinical relevance, susceptibility or causation impact a broad range of biological pathways and mechanisms including ion channels (e.g., CACNA1B, CACNA1C, CACNA1H), metabolism (e.g., CYP1A2, CYP2C19, CYP2D6), multiple targets of neurotransmitter pathways impacting dopamine, GABA, glutamate, and serotonin function, brain development (e.g., NRG1, RELN), signaling peptides (e.g., PIK3CA, PIK4CA) and immune function (e.g., HLA-DRB1, HLA-DQA1) and interleukins (e.g., IL1A, IL10, IL6). This summary will enable clinical and laboratory geneticists, genetic counselors, and other clinicians to access convenient pictorial images of the distribution and location of contributing genes to inform diagnosis and gene-based treatment as well as provide risk estimates for genetic counseling of families with affected relatives.
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Affiliation(s)
- Merlin G. Butler
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, Kansas,Department of Pediatrics, University of Kansas Medical Center, Kansas City, Kansas,Correspondence to: Merlin G. Butler, M.D., Ph.D., University of Kansas Medical Center, Department of Psychiatry and Behavioral Sciences, 3901 Rainbow Boulevard, MS 4015, Kansas City, KS 66160,
| | - Austen B. McGuire
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, Kansas
| | - Humaira Masoud
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, Kansas
| | - Ann M. Manzardo
- Department of Psychiatry and Behavioral Sciences, University of Kansas Medical Center, Kansas City, Kansas
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Chang S, Fang K, Zhang K, Wang J. Network-Based Analysis of Schizophrenia Genome-Wide Association Data to Detect the Joint Functional Association Signals. PLoS One 2015; 10:e0133404. [PMID: 26193471 PMCID: PMC4508050 DOI: 10.1371/journal.pone.0133404] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 06/26/2015] [Indexed: 12/31/2022] Open
Abstract
Schizophrenia is a common psychiatric disorder with high heritability and complex genetic architecture. Genome-wide association studies (GWAS) have identified several significant loci associated with schizophrenia. However, the explained heritability is still low. Growing evidence has shown schizophrenia is attributable to multiple genes with moderate effects. In-depth mining and integration of GWAS data is urgently expected to uncover disease-related gene combination patterns. Network-based analysis is a promising strategy to better interpret GWAS to identify disease-related network modules. We performed a network-based analysis on three independent schizophrenia GWASs by using a refined analysis framework, which included a more accurate gene P-value calculation, dynamic network module searching algorithm and detailed functional analysis for the obtained modules genes. The result generated 79 modules including 238 genes, which form a highly connected subnetwork with more statistical significance than expected by chance. The result validated several reported disease genes, such as MAD1L1, MCC, SDCCAG8, VAT1L, MAPK14, MYH9 and FXYD6, and also obtained several novel candidate genes and gene-gene interactions. Pathway enrichment analysis of the module genes suggested they were enriched in several neural and immune system related pathways/GO terms, such as neurotrophin signaling pathway, synaptosome, regulation of protein ubiquitination, and antigen processing and presentation. Further crosstalk analysis revealed these pathways/GO terms were cooperated with each other, and identified several important genes, which might play vital roles to connect these functions. Our network-based analysis of schizophrenia GWASs will facilitate the understanding of genetic mechanisms of schizophrenia.
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Affiliation(s)
- Suhua Chang
- Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
| | - Kechi Fang
- Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
| | - Kunlin Zhang
- Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
| | - Jing Wang
- Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
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13
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Rossier BC, Baker ME, Studer RA. Epithelial sodium transport and its control by aldosterone: the story of our internal environment revisited. Physiol Rev 2015; 95:297-340. [PMID: 25540145 DOI: 10.1152/physrev.00011.2014] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Transcription and translation require a high concentration of potassium across the entire tree of life. The conservation of a high intracellular potassium was an absolute requirement for the evolution of life on Earth. This was achieved by the interplay of P- and V-ATPases that can set up electrochemical gradients across the cell membrane, an energetically costly process requiring the synthesis of ATP by F-ATPases. In animals, the control of an extracellular compartment was achieved by the emergence of multicellular organisms able to produce tight epithelial barriers creating a stable extracellular milieu. Finally, the adaptation to a terrestrian environment was achieved by the evolution of distinct regulatory pathways allowing salt and water conservation. In this review we emphasize the critical and dual role of Na(+)-K(+)-ATPase in the control of the ionic composition of the extracellular fluid and the renin-angiotensin-aldosterone system (RAAS) in salt and water conservation in vertebrates. The action of aldosterone on transepithelial sodium transport by activation of the epithelial sodium channel (ENaC) at the apical membrane and that of Na(+)-K(+)-ATPase at the basolateral membrane may have evolved in lungfish before the emergence of tetrapods. Finally, we discuss the implication of RAAS in the origin of the present pandemia of hypertension and its associated cardiovascular diseases.
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Affiliation(s)
- Bernard C Rossier
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, Switzerland; Division of Nephrology-Hypertension, University of California San Diego, La Jolla, California; and Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Michael E Baker
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, Switzerland; Division of Nephrology-Hypertension, University of California San Diego, La Jolla, California; and Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
| | - Romain A Studer
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, Switzerland; Division of Nephrology-Hypertension, University of California San Diego, La Jolla, California; and Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom
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14
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Park HJ, Kang WS, Chung JH, Kim JW. Association between promoter polymorphism (rs10789970) in 5-hydroxytryptamine receptor 3B and poor concentration in schizophrenia. Psychiatry Res 2014; 219:235-7. [PMID: 24880582 DOI: 10.1016/j.psychres.2014.04.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 04/22/2014] [Accepted: 04/27/2014] [Indexed: 11/17/2022]
Affiliation(s)
- Hae Jeong Park
- Kohwang Medical Research Institute, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Won Sub Kang
- Department of Neuropsychiatry, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Joo-Ho Chung
- Kohwang Medical Research Institute, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Jong Woo Kim
- Department of Neuropsychiatry, School of Medicine, Kyung Hee University, Seoul, Republic of Korea.
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15
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Gong XM, Ding Y, Yu J, Yao Y, Marassi FM. Structure of the Na,K-ATPase regulatory protein FXYD2b in micelles: implications for membrane-water interfacial arginines. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:299-306. [PMID: 24794573 DOI: 10.1016/j.bbamem.2014.04.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/19/2014] [Accepted: 04/23/2014] [Indexed: 01/06/2023]
Abstract
FXYD2 is a membrane protein responsible for regulating the function of the Na,K-ATPase in mammalian kidney epithelial cells. Here we report the structure of FXYD2b, one of two splice variants of the protein, determined by NMR spectroscopy in detergent micelles. Solid-state NMR characterization of the protein embedded in phospholipid bilayers indicates that several arginine side chains may be involved in hydrogen bond interactions with the phospholipid polar head groups. The structure and the NMR data suggest that FXYD2b could regulate the Na,K-ATPase by modulating the effective membrane surface electrostatics near the ion binding sites of the pump.
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Affiliation(s)
- Xiao-Min Gong
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yi Ding
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jinghua Yu
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yong Yao
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Francesca M Marassi
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
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16
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FXYD6: a novel therapeutic target toward hepatocellular carcinoma. Protein Cell 2014; 5:532-43. [PMID: 24715268 PMCID: PMC4085285 DOI: 10.1007/s13238-014-0045-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 02/23/2014] [Indexed: 10/30/2022] Open
Abstract
FXYD6, FXYD domain containing ion transport regulator 6, has been reported to affect the activity of Na(+)/K(+)-ATPase and be associated with mental diseases. Here, we demonstrate that FXYD6 is up-regulated in hepatocellular carcinoma (HCC) and enhances the migration and proliferation of HCC cells. Up-regulation of FXYD6 not only positively correlates with the increase of Na(+)/K(+)-ATPase but also coordinates with the activation of its downstream Src-ERK signaling pathway. More importantly, blocking FXYD6 by its functional antibody significantly inhibits the growth potential of the xenografted HCC tumors in mice, indicating that FXYD6 represents a potential therapeutic target toward HCC. Altogether, our results establish a critical role of FXYD6 in HCC progression and suggest that the therapy targeting FXYD6 can benefit the clinical treatment toward HCC patients.
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17
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Lu X, Pan J, Li S, Shen S, Chi P, Lin H, Huang Y, Xu Z, Huang S. Establishment of a predictive genetic model for estimating chemotherapy sensitivity of colorectal cancer with synchronous liver metastasis. Cancer Biother Radiopharm 2013; 28:552-8. [PMID: 23721165 DOI: 10.1089/cbr.2012.1431] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE We examined the whole genome expression profile in advanced colorectal cancer (ACC) patients who had received FOLFOX4 chemotherapy to establish a genetic biomarker model predicting chemotherapy sensitivity. METHODS Eligible ACC patients were divided into two groups, based on postchemotherapy evaluation results: specifically, the sensitive group (experimental group) and the resistant group (control group). The genome expression profiles of colorectal cancer tissues were examined using DNA microarray analysis, and differential gene expression was identified using a significance analysis of the microarray. The probe signal log ratios were used to produce the area-under-the-curve, sensitivity, and specificity for candidate genes. Genes exhibiting differential expression and significant predictive power were used to simulate a genetic model for estimating chemotherapy sensitivity. RESULTS Totally, 30 ACC patients were eligible for the study, 13 assigned to the experimental group and 17 to the control group. In total, 30 genes showing significant differential expression were identified. Seven candidate genes (NKX2-3, FXYD6, TGFB1I1, ACTG2, ANPEP, HOXB8, and KLK11), which exhibited positive or negative correlations, were incorporated into a genetic model, with an overall accurate predication rate of 93.3%. CONCLUSIONS The predictive model involving the seven genes listed had high accuracy in estimating chemotherapy sensitivity to the FOLFOX4 regimen.
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Affiliation(s)
- Xingrong Lu
- Department of Colorectal Surgery, Union Hospital, Fujian Medical University, Fuzhou, China
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18
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García-Alonso L, Alonso R, Vidal E, Amadoz A, de María A, Minguez P, Medina I, Dopazo J. Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. Nucleic Acids Res 2012; 40:e158. [PMID: 22844098 PMCID: PMC3488210 DOI: 10.1093/nar/gks699] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Genomic experiments (e.g. differential gene expression, single-nucleotide polymorphism association) typically produce ranked list of genes. We present a simple but powerful approach which uses protein–protein interaction data to detect sub-networks within such ranked lists of genes or proteins. We performed an exhaustive study of network parameters that allowed us concluding that the average number of components and the average number of nodes per component are the parameters that best discriminate between real and random networks. A novel aspect that increases the efficiency of this strategy in finding sub-networks is that, in addition to direct connections, also connections mediated by intermediate nodes are considered to build up the sub-networks. The possibility of using of such intermediate nodes makes this approach more robust to noise. It also overcomes some limitations intrinsic to experimental designs based on differential expression, in which some nodes are invariant across conditions. The proposed approach can also be used for candidate disease-gene prioritization. Here, we demonstrate the usefulness of the approach by means of several case examples that include a differential expression analysis in Fanconi Anemia, a genome-wide association study of bipolar disorder and a genome-scale study of essentiality in cancer genes. An efficient and easy-to-use web interface (available at http://www.babelomics.org) based on HTML5 technologies is also provided to run the algorithm and represent the network.
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Affiliation(s)
- Luz García-Alonso
- Department of Bioinformatics, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
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19
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Schnell A, Sun X, Igo, Jr. R, Elston R. Some capabilities for model-based and model-free linkage analysis using the program package S.A.G.E. (Statistical Analysis for Genetic Epidemiology). Hum Hered 2011; 72:237-46. [PMID: 22189466 PMCID: PMC3726232 DOI: 10.1159/000331672] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
For both model-free and model-based linkage analysis the S.A.G.E. (Statistical Analysis for Genetic Epidemiology) program package has some unique capabilities in analyzing both continuous traits and binary traits with variable age of onset. Here we highlight model-based linkage analysis of a quantitative trait (plasma dopamine β hydroxylase) that is known to be largely determined by monogenic inheritance, using a prior segregation analysis to produce the best fitting model for the trait. For a binary trait with variable age of onset (schizophrenia), we illustrate how using age of onset information to obtain a quantitative susceptibility trait leads to more statistically significant linkage signals, suggesting better power.
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Affiliation(s)
| | | | | | - R.C. Elston
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, USA
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20
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Zhong N, Zhang R, Qiu C, Yan H, Valenzuela RK, Zhang H, Kang W, Lu S, Guo T, Ma J. A novel replicated association between FXYD6 gene and schizophrenia. Biochem Biophys Res Commun 2011; 405:118-21. [DOI: 10.1016/j.bbrc.2011.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Accepted: 01/02/2011] [Indexed: 12/27/2022]
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21
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Daneshpour MS, Alfadhli S, Houshmand M, Zeinali S, Hedayati M, Zarkesh M, Azizi F. Allele frequency distribution for D11S1304, D11S1998, and D11S934 and metabolic syndrome in TLGS. EUR J LIPID SCI TECH 2010. [DOI: 10.1002/ejlt.201000340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Maryam Sadat Daneshpour
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
- Obesity Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti university of Medical Science, Tehran, Iran
| | - Suad Alfadhli
- Faculty of Allied Health Sciences, Department of Medical Laboratory Sciences, Kuwait University, Kuwait
| | - Massoud Houshmand
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Sirous Zeinali
- Biotechnology Research Centre, Pasteur Institute of Iran, Teheran, Iran
| | - Mehdi Hedayati
- Obesity Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti university of Medical Science, Tehran, Iran
| | - Maryam Zarkesh
- Obesity Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti university of Medical Science, Tehran, Iran
| | - Fereidoun Azizi
- Obesity Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti university of Medical Science, Tehran, Iran
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22
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Iwata Y, Yamada K, Iwayama Y, Anitha A, Thanseem I, Toyota T, Hattori E, Ohnishi T, Maekawa M, Nakamura K, Suzuki K, Matsuzaki H, Tsuchiya KJ, Suda S, Sugihara G, Takebayashi K, Yamamoto S, Iwata K, Mori N, Yoshikawa T. Failure to confirm genetic association of the FXYD6 gene with schizophrenia: the Japanese population and meta-analysis. Am J Med Genet B Neuropsychiatr Genet 2010; 153B:1221-7. [PMID: 20468077 DOI: 10.1002/ajmg.b.31095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The FXYD domain-containing ion transport regulator 6 (FXYD6) gene encodes phosphohippolin that regulates cellular ion transport by altering the kinetic properties of Na,K-ATPase. Phosphohippolin is highly expressed in brain regions that are relevant to schizophrenia. The FXYD6 gene is located at chromosome 11q22-24, one of the most established linkage regions for schizophrenia. Therefore, it may be possible that genetic variants in FXYD6, including the regulatory genomic elements could cause abnormal function or expression of phosphohippolin and increase the genetic risk for schizophrenia. A previous study suggested that polymorphisms in FXYD6 are associated with schizophrenia in UK samples. However, conflicting results have been reported in the Japanese population. In this study, we aimed to test the prior genetic association findings using different samples from the ethnically homogeneous Japanese population (1,060 schizophrenic patients and 1,060 age- and sex-matched controls). From the FXYD6 gene, we examined six single nucleotide polymorphisms (rs11216573, rs555577, rs1815774, rs4938445, rs4938446, and rs497768), all of which were previously analyzed for association. We did not detect any significant allelic, genotypic or haplotypic association in our Japanese samples. Meta-analysis incorporating previous and the present studies also showed that the FXYD6 gene is not associated with schizophrenia. We conclude that the FXYD6 gene does not have a major influence on susceptibility to schizophrenia across populations.
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Affiliation(s)
- Yasuhide Iwata
- Department of Psychiatry and Neurology, Hamamatsu University School of Medicine, Shizuoka, Japan
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23
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Yi X, Liang Y, Huerta-Sanchez E, Jin X, Cuo ZXP, Pool JE, Xu X, Jiang H, Vinckenbosch N, Korneliussen TS, Zheng H, Liu T, He W, Li K, Luo R, Nie X, Wu H, Zhao M, Cao H, Zou J, Shan Y, Li S, Yang Q, Asan, Ni P, Tian G, Xu J, Liu X, Jiang T, Wu R, Zhou G, Tang M, Qin J, Wang T, Feng S, Li G, Huasang, Luosang J, Wang W, Chen F, Wang Y, Zheng X, Li Z, Bianba Z, Yang G, Wang X, Tang S, Gao G, Chen Y, Luo Z, Gusang L, Cao Z, Zhang Q, Ouyang W, Ren X, Liang H, Zheng H, Huang Y, Li J, Bolund L, Kristiansen K, Li Y, Zhang Y, Zhang X, Li R, Li S, Yang H, Nielsen R, Wang J, Wang J. Sequencing of 50 human exomes reveals adaptation to high altitude. Science 2010; 329:75-8. [PMID: 20595611 DOI: 10.1126/science.1190371] [Citation(s) in RCA: 1049] [Impact Index Per Article: 74.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92% of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPAS1 shows a 78% frequency difference between Tibetan and Han samples, representing the fastest allele frequency change observed at any human gene to date. This SNP's association with erythrocyte abundance supports the role of EPAS1 in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus in genetic adaptation to high altitude.
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Affiliation(s)
- Xin Yi
- BGI-Shenzhen, Shenzhen 518083, China
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Zhang J, Che R, Li X, Tang W, Zhao Q, Tang R, Wang Y, Zhang Z, Ji J, Yang F, Shi Y, Ji W, Zhou G, Feng G, He L, He G. No association between the FXYD6 gene and schizophrenia in the Chinese Han population. J Psychiatr Res 2010; 44:409-12. [PMID: 20149392 DOI: 10.1016/j.jpsychires.2009.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Revised: 10/18/2009] [Accepted: 10/19/2009] [Indexed: 11/15/2022]
Abstract
Choudhury et al. identified FXYD6 as a susceptible gene for schizophrenia in the London and Aberdeen populations. We genotyped D11S1998 and 8 SNPs (rs869789, rs11216567, rs10790212, rs876797, rs4938445, rs497768, rs11216598, rs11605223) in a Chinese sample consisting of 1514 schizophrenia patients and 1514 healthy controls. We also compared the expression levels of FXYD6 in lymphocytes in 86 schizophrenia patients and 94 controls. No association was detected either in D11S1998 or the 8 SNPs. No difference was found in expression level between patients and controls. Our study suggests that FXYD6 does not play a role in schizophrenia in the Chinese Han population.
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Affiliation(s)
- Jing Zhang
- Bio-X Center, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, PR China
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Hutz JE, Kraja AT, McLeod HL, Province MA. CANDID: a flexible method for prioritizing candidate genes for complex human traits. Genet Epidemiol 2009; 32:779-90. [PMID: 18613097 DOI: 10.1002/gepi.20346] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Genomewide studies and localized candidate gene approaches have become everyday study designs for identifying polymorphisms in genes that influence complex human traits. Yet, in general, the number of significant findings and the need to focus on smaller regions require a prioritization of genes for further study. Some candidate gene identification algorithms have been proposed in recent years to attempt to streamline this prioritization, but many suffer from limitations imposed by the source data or are difficult to use and understand. CANDID is a prioritization algorithm designed to produce impartial, accurate rankings of candidate genes that influence complex human traits. CANDID can use information from publications, protein domain descriptions, cross-species conservation measures, gene expression profiles and protein-protein interactions in its analysis. Additionally, users may supplement these data sources with results from linkage, association and other studies. CANDID was tested on well-known complex trait genes using data from the Online Mendelian Inheritance in Man database. Additionally, CANDID was evaluated in a modeled gene discovery environment, where it ranked genes whose trait associations were published after CANDID's databases were compiled. In all settings, CANDID exhibited high sensitivity and specificity, indicating an improvement upon previously published algorithms. Its accuracy and ease of use make CANDID a highly useful tool in study design and analysis for complex human traits.
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Affiliation(s)
- Janna E Hutz
- Division of Statistical Genomics, Washington University School of Medicine, Saint Louis, Missouri, USA.
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26
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Zhang F, Xu Y, Liu P, Fan H, Huang X, Sun G, Song Y, Sham PC. Association analyses of the interaction between the ADSS and ATM genes with schizophrenia in a Chinese population. BMC MEDICAL GENETICS 2008; 9:119. [PMID: 19115993 PMCID: PMC2654671 DOI: 10.1186/1471-2350-9-119] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2008] [Accepted: 12/30/2008] [Indexed: 02/04/2023]
Abstract
BACKGROUND The blood-derived RNA levels of the adenylosuccinate synthase (ADSS) and ataxia telangiectasia mutated (ATM) genes were found to be down- and up-regulated, respectively, in schizophrenics compared with controls, and ADSS and ATM were among eight biomarker genes to discriminate schizophrenics from normal controls. ADSS catalyzes the first committed step of AMP synthesis, while ATM kinase serves as a key signal transducer in the DNA double-strand breaks response pathway. It remains unclear whether these changes result from mutations or polymorphisms in the two genes. METHODS Six SNPs in the ADSS gene and three SNPs in the ATM gene in a Chinese population of 488 schizophrenics and 516 controls were genotyped to examine their association with schizophrenia (SZ). Genotyping was performed using the Sequenom platform. RESULTS There was no significant difference in the genotype, allele, or haplotype distributions of the nine SNPs between cases and controls. Using the Multifactor Dimensionality Reduction (MDR) method, we found that the interactions among rs3102460 in the ADSS gene and rs227061 and rs664143 in the ATM gene revealed a significant association with SZ. This model held a maximum testing accuracy of 60.4% and a maximum cross-validation consistency of 10 out of 10. CONCLUSION These findings suggest that the combined effects of the polymorphisms in the ADSS and ATM genes may confer susceptibility to the development of SZ in a Chinese population.
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Affiliation(s)
- Fuquan Zhang
- Institute of Neurological disorders, Tsinghua University, Department of Psychiatry, Yuquan Hospital, Tsinghua University, Bejing, 100049, PR China.
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27
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5-HT1A gene variants and psychiatric disorders: a review of current literature and selection of SNPs for future studies. Int J Neuropsychopharmacol 2008; 11:701-21. [PMID: 18047755 DOI: 10.1017/s1461145707008218] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
5-HT1A receptors are key components of the serotonin system, acting both pre- and post- synaptically in different brain areas. There is a growing amount of evidence showing the importance of 5-HT1A in different psychiatric disorders, from mood to anxiety disorders, moving through suicidal behaviour and psychotic disorders. Findings in the literature are not consistent with any definite 5-HT1A influence in psychiatric disorders. 5-HT1A gene variants have been reported to play some role in mood disorders, anxiety disorders and psychotic disorders. Again, the literature findings are not unequivocal. Concerning response to treatment, the C(-1019)G variant seems to be of primary interest in antidepressant response: C allele carriers generally show a better response to treatment, especially in Caucasian samples. Together with the C(-1019)G (rs6295) variant, the Ile28Val (rs1799921), Arg219Leu (rs1800044) and Gly22Ser (rs1799920) variants have been investigated in possible associations with psychiatric disorders, also with no definitive results. This lack of consistency can be also due to an incomplete gene investigation. To make progress on this point, a list of validated single nucleotide polymorphisms (SNPs) covering the whole gene is proposed for further investigations.
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28
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A genetic association study of the FXYD domain containing ion transport regulator 6 (FXYD6) gene, encoding phosphohippolin, in susceptibility to schizophrenia in a Japanese population. Neurosci Lett 2008; 438:70-5. [PMID: 18455306 DOI: 10.1016/j.neulet.2008.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2008] [Revised: 03/31/2008] [Accepted: 04/04/2008] [Indexed: 11/23/2022]
Abstract
The FXYD domain containing ion transport regulator 6 (FXYD6) gene is located within a region of chromosome 11 (11q23.3) that has been shown by a number of genome scans to be one of the most well-established linkages to schizophrenia. FXYD6 encodes the protein phosphohippolin, which is primarily expressed in the brain. Phosphohippolin modulates the kinetic activity of Na,K-ATPase and has long-term physiological importance in maintaining cation homeostasis. A recent study reported that FXYD6 was associated with schizophrenia in the United Kingdom samples. Applying the gene-based association concept, we carried out an association study regarding FXYD6 and schizophrenia in a Japanese population, with a sample consisting of 2026 subjects (906 schizophrenics and 1120 controls). After linkage disequilibrium analysis, 23 single nucleotide polymorphisms (SNPs) were genotyped using 5'-exonuclease allelic discrimination assay. We found a significant association of two SNPs (rs11216573; genotypic P value: 0.022 and rs555577; genotypic P value: 0.026, allelic P value: 0.011, uncorrected). Nominal P values did not survive correction for multiple testing (rs11216573; genotypic P value: 0.47 and rs555577; genotypic P value: 0.55, allelic P value: 0.24, after SNPSpD correction). No association was observed between schizophrenia patients and controls in allelic, genotypic and haplotypic analyses. Our findings suggest that FXYD6 is unlikely to be related to the development of schizophrenia in a Japanese population.
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Datta SR, McQuillin A, Puri V, Choudhury K, Thirumalai S, Lawrence J, Pimm J, Bass N, Lamb G, Moorey H, Morgan J, Punukollu B, Kandasami G, Kirwin S, Sule A, Quested D, Curtis D, Gurling HMD. Failure to confirm allelic and haplotypic association between markers at the chromosome 6p22.3 dystrobrevin-binding protein 1 (DTNBP1) locus and schizophrenia. Behav Brain Funct 2007; 3:50. [PMID: 17888175 PMCID: PMC2093937 DOI: 10.1186/1744-9081-3-50] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Accepted: 09/23/2007] [Indexed: 11/22/2022] Open
Abstract
Background Previous linkage and association studies may have implicated the Dystrobrevin-binding protein 1 (DTNBP1) gene locus or a gene in linkage disequilibrium with DTNBP1 on chromosome 6p22.3 in genetic susceptibility to schizophrenia. Methods We used the case control design to test for of allelic and haplotypic association with schizophrenia in a sample of four hundred and fifty research subjects with schizophrenia and four hundred and fifty ancestrally matched supernormal controls. We genotyped the SNP markers previously found to be significantly associated with schizophrenia in the original study and also other markers found to be positive in subsequent studies. Results We could find no evidence of allelic, genotypic or haplotypic association with schizophrenia in our UK sample. Conclusion The results suggest that the DTNBP1 gene contribution to schizophrenia must be rare or absent in our sample. The discrepant allelic association results in previous studies of association between DTNBP1 and schizophrenia could be due population admixture. However, even positive studies of European populations do not show any consistent DTNBP1 alleles or haplotypes associated with schizophrenia. Further research is needed to resolve these issues. The possible confounding of linkage with association in family samples already showing linkage at 6p22.3 might be revealed by testing genes closely linked to DTNBP1 for allelic association and by restricting family based tests of association to only one case per family.
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Affiliation(s)
- Susmita R Datta
- Molecular Psychiatry Laboratory, Department of Mental Health Sciences, University College London Medical School, Windeyer Institute of Medical Sciences, 46 Cleveland Street, London, W1T 4JF, UK
| | - Andrew McQuillin
- Molecular Psychiatry Laboratory, Department of Mental Health Sciences, University College London Medical School, Windeyer Institute of Medical Sciences, 46 Cleveland Street, London, W1T 4JF, UK
| | - Vinay Puri
- Molecular Psychiatry Laboratory, Department of Mental Health Sciences, University College London Medical School, Windeyer Institute of Medical Sciences, 46 Cleveland Street, London, W1T 4JF, UK
| | - Khalid Choudhury
- Molecular Psychiatry Laboratory, Department of Mental Health Sciences, University College London Medical School, Windeyer Institute of Medical Sciences, 46 Cleveland Street, London, W1T 4JF, UK
| | | | - Jacob Lawrence
- Molecular Psychiatry Laboratory, Department of Mental Health Sciences, University College London Medical School, Windeyer Institute of Medical Sciences, 46 Cleveland Street, London, W1T 4JF, UK
| | - Jonathan Pimm
- Molecular Psychiatry Laboratory, Department of Mental Health Sciences, University College London Medical School, Windeyer Institute of Medical Sciences, 46 Cleveland Street, London, W1T 4JF, UK
| | - Nicholas Bass
- Molecular Psychiatry Laboratory, Department of Mental Health Sciences, University College London Medical School, Windeyer Institute of Medical Sciences, 46 Cleveland Street, London, W1T 4JF, UK
| | - Graham Lamb
- Camden and Islington Mental Health and Social Care Trust, St Pancras Hospital, London, NW1 0PE, UK
| | - Helen Moorey
- Camden and Islington Mental Health and Social Care Trust, St Pancras Hospital, London, NW1 0PE, UK
| | - Jenny Morgan
- Hampshire Partnership NHS Trust, Mulfords Hill Centre, Tadley, Hampshire, RG26 3HX, UK
| | - Bhaskar Punukollu
- West London Mental Health Trust, Hammersmith & Fulham Mental Health Unit and St Bernard's Hospital, London, W6 8RF, UK
| | - Gomathinayagam Kandasami
- Mersey Care NHS Trust, University Hospital Aintree, Longmoor Lane, Aintree, Liverpool, L9 7AD, UK
| | - Simon Kirwin
- Molecular Psychiatry Laboratory, Department of Mental Health Sciences, University College London Medical School, Windeyer Institute of Medical Sciences, 46 Cleveland Street, London, W1T 4JF, UK
| | - Akeem Sule
- Department of Psychiatry, University of Oxford, Warneford Hospital, Headington, Oxford, UK
| | - Digby Quested
- West London Mental Health Trust, Hammersmith & Fulham Mental Health Unit and St Bernard's Hospital, London, W6 8RF, UK
- Department of Psychiatry, University of Oxford, Warneford Hospital, Headington, Oxford, UK
| | - David Curtis
- Queen Mary College, University of London and East London and City Mental Health Trust, Royal London Hospital, Whitechapel, London, E1 1BB, UK
| | - Hugh MD Gurling
- Molecular Psychiatry Laboratory, Department of Mental Health Sciences, University College London Medical School, Windeyer Institute of Medical Sciences, 46 Cleveland Street, London, W1T 4JF, UK
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