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Wan X, Xiao J, Tam SST, Cai M, Sugimura R, Wang Y, Wan X, Lin Z, Wu AR, Yang C. Integrating spatial and single-cell transcriptomics data using deep generative models with SpatialScope. Nat Commun 2023; 14:7848. [PMID: 38030617 PMCID: PMC10687049 DOI: 10.1038/s41467-023-43629-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
The rapid emergence of spatial transcriptomics (ST) technologies is revolutionizing our understanding of tissue spatial architecture and biology. Although current ST methods, whether based on next-generation sequencing (seq-based approaches) or fluorescence in situ hybridization (image-based approaches), offer valuable insights, they face limitations either in cellular resolution or transcriptome-wide profiling. To address these limitations, we present SpatialScope, a unified approach integrating scRNA-seq reference data and ST data using deep generative models. With innovation in model and algorithm designs, SpatialScope not only enhances seq-based ST data to achieve single-cell resolution, but also accurately infers transcriptome-wide expression levels for image-based ST data. We demonstrate SpatialScope's utility through simulation studies and real data analysis from both seq-based and image-based ST approaches. SpatialScope provides spatial characterization of tissue structures at transcriptome-wide single-cell resolution, facilitating downstream analysis, including detecting cellular communication through ligand-receptor interactions, localizing cellular subtypes, and identifying spatially differentially expressed genes.
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Affiliation(s)
- Xiaomeng Wan
- Department of Mathematics, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Jiashun Xiao
- Shenzhen Research Institute of Big Data, Shenzhen, 518172, China
| | - Sindy Sing Ting Tam
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
| | - Mingxuan Cai
- Department of Biostatistics, City University of Hong Kong, Hong Kong SAR, China
| | - Ryohichi Sugimura
- Li Ka Shing Faculty of Medicine, School of Biomedical Sciences, University of Hong Kong, Hong Kong SAR, China
| | - Yang Wang
- Department of Mathematics, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Data-Driven Fluid Mechanics and Engineering Applications, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Big Data Bio-Intelligence Lab, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Xiang Wan
- Shenzhen Research Institute of Big Data, Shenzhen, 518172, China
| | - Zhixiang Lin
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Angela Ruohao Wu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China.
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
- Center for Aging Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
| | - Can Yang
- Department of Mathematics, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
- Guangdong-Hong Kong-Macao Joint Laboratory for Data-Driven Fluid Mechanics and Engineering Applications, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
- Big Data Bio-Intelligence Lab, The Hong Kong University of Science and Technology, Hong Kong SAR, China.
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2
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Wang Y, Yu T, Chen J, Zhao R, Diao M, Mei P, He S, Qiu W, Ye G, Jiang L, Xiao H, Liao Y. Immune characteristics analysis and construction of a four-gene prognostic signature for lung adenocarcinoma based on estrogen reactivity. BMC Cancer 2023; 23:1047. [PMID: 37907850 PMCID: PMC10619241 DOI: 10.1186/s12885-023-11415-y] [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: 03/03/2023] [Accepted: 09/17/2023] [Indexed: 11/02/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is a common type of malignant tumor with poor prognosis and high mortality. In our previous studies, we found that estrogen is an important risk factor for LUAD, and different estrogen statuses can predict different prognoses. Therefore, in this study, we constructed a prognostic signature related to estrogen reactivity to determine the relationship between different estrogen reactivities and prognosis. We downloaded the LUAD dataset from The Cancer Genome Atlas (TCGA) database, calculated the estrogen reactivity of each sample, and divided them into a high-estrogen reactivity group and a low-estrogen reactivity group. The difference in overall survival between the groups was significant. We also analyzed the status of immune cell infiltration and immune checkpoint expression between the groups. We analyzed the differential gene expression between the groups and screened four key prognostic factors by the least absolute shrinkage and selection operator (LASSO) regression and univariable and multivariable Cox regression. Based on the four genes, a risk signature was established. To a certain extent, the receiver operating characteristic (ROC) curve showed the predictive ability of the risk signature, which was further verified using the GSE31210 dataset. We also determined the role of estrogen in LUAD using an orthotopic mouse model. Additionally, we developed a predictive nomogram combining the risk signature with other clinical characteristics. In conclusion, our four-gene prognostic signature based on estrogen reactivity had prognostic value and can provide new insights into the development of treatment strategies for LUAD.
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Affiliation(s)
- Yangwei Wang
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tong Yu
- Department of Rheumatology and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaping Chen
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rong Zhao
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mingxin Diao
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Peiyuan Mei
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shiwen He
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenlin Qiu
- Department of Rheumatology and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guanchao Ye
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lijuan Jiang
- Department of Rheumatology and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Han Xiao
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yongde Liao
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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3
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Marion-Poll L, Roussarie JP, Taing L, Dard-Dascot C, Servant N, Jaszczyszyn Y, Jordi E, Mulugeta E, Hervé D, Bourc’his D, Greengard P, Thermes C, Girault JA. DNA methylation and hydroxymethylation characterize the identity of D1 and D2 striatal projection neurons. Commun Biol 2022; 5:1321. [PMID: 36456703 PMCID: PMC9715678 DOI: 10.1038/s42003-022-04269-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
Neuronal DNA modifications differ from those in other cells, including methylation outside CpG context and abundant 5-hydroxymethylation whose relevance for neuronal identities are unclear. Striatal projection neurons expressing D1 or D2 dopamine receptors allow addressing this question, as they share many characteristics but differ in their gene expression profiles, connections, and functional roles. We compare translating mRNAs and DNA modifications in these two populations. DNA methylation differences occur predominantly in large genomic clusters including differentially expressed genes, potentially important for D1 and D2 neurons. Decreased gene body methylation is associated with higher gene expression. Hydroxymethylation differences are more scattered and affect transcription factor binding sites, which can influence gene expression. We also find a strong genome-wide hydroxymethylation asymmetry between the two DNA strands, particularly pronounced at expressed genes and retrotransposons. These results identify novel properties of neuronal DNA modifications and unveil epigenetic characteristics of striatal projection neurons heterogeneity.
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Affiliation(s)
- Lucile Marion-Poll
- grid.7429.80000000121866389INSERM UMR-S1270, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Faculty of Sciences and Engineering, Paris, 75005 France ,grid.462192.a0000 0004 0520 8345Institut du Fer à Moulin, Paris, 75005 France ,Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, 75005 France ,grid.8591.50000 0001 2322 4988Present Address: Department of Basic Neurosciences, Faculty of Medicine, University of Geneva, Geneva, 1211 Switzerland
| | - Jean-Pierre Roussarie
- grid.134907.80000 0001 2166 1519Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY 10065 USA ,grid.189504.10000 0004 1936 7558Present Address: Department of Anatomy & Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118 USA
| | - Lieng Taing
- grid.7429.80000000121866389INSERM UMR-S1270, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Faculty of Sciences and Engineering, Paris, 75005 France ,grid.462192.a0000 0004 0520 8345Institut du Fer à Moulin, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Present Address: UMR1166 Inserm and Sorbonne Université, Faculty of Medicine, Paris, 75013 France
| | - Cloelia Dard-Dascot
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198 France
| | - Nicolas Servant
- grid.440907.e0000 0004 1784 3645Institut Curie, INSERM U900, CBIO-Centre for Computational Biology, Mines Paris Tech, PSL-Research University, Paris, 75005 France
| | - Yan Jaszczyszyn
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198 France
| | - Emmanuelle Jordi
- grid.7429.80000000121866389INSERM UMR-S1270, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Faculty of Sciences and Engineering, Paris, 75005 France ,grid.462192.a0000 0004 0520 8345Institut du Fer à Moulin, Paris, 75005 France ,Present Address: Coave Therapeutics, Paris, 75014 France
| | - Eskeatnaf Mulugeta
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, 75005 France ,grid.5645.2000000040459992XPresent Address: Erasmus University Medical Center (Erasmus MC), Department of Cell Biology, Rotterdam, 3000 CA The Netherlands
| | - Denis Hervé
- grid.7429.80000000121866389INSERM UMR-S1270, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Faculty of Sciences and Engineering, Paris, 75005 France ,grid.462192.a0000 0004 0520 8345Institut du Fer à Moulin, Paris, 75005 France
| | - Déborah Bourc’his
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, 75005 France
| | - Paul Greengard
- grid.134907.80000 0001 2166 1519Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY 10065 USA
| | - Claude Thermes
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198 France
| | - Jean-Antoine Girault
- grid.7429.80000000121866389INSERM UMR-S1270, Paris, 75005 France ,grid.462844.80000 0001 2308 1657Sorbonne Université, Faculty of Sciences and Engineering, Paris, 75005 France ,grid.462192.a0000 0004 0520 8345Institut du Fer à Moulin, Paris, 75005 France
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Liu M, Zhang Q, Ma S. A tree-based gene-environment interaction analysis with rare features. Stat Anal Data Min 2022; 15:648-674. [PMID: 38046814 PMCID: PMC10691867 DOI: 10.1002/sam.11578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 02/14/2022] [Indexed: 01/20/2023]
Abstract
Gene-environment (G-E) interaction analysis plays a critical role in understanding and modeling complex diseases. Compared to main-effect-only analysis, it is more seriously challenged by higher dimensionality, weaker signals, and the unique "main effects, interactions" variable selection hierarchy. In joint G-E interaction analysis under which a large number of G factors are analysed in a single model, effort tailored to rare features (e.g., SNPs with low minor allele frequencies) has been limited. Existing investigations on rare features have been mostly focused on marginal analysis, where various data aggregation techniques have been developed, and hypothesis testings have been conducted to identify significant aggregated features. However, such techniques cannot be extended to joint G-E interaction analysis. In this study, building on a very recent tree-based data aggregation technique, which has been developed for main-effect-only analysis, we develop a new G-E interaction analysis approach tailored to rare features. The adopted data aggregation technique allows for more efficient information borrowing from neighboring rare features. Similar to some existing state-of-the-art ones, the proposed approach adopts penalization for variable selection, regularized estimation, and respect of the variable selection hierarchy. Simulation shows that it has more accurate identification of important interactions and main effects than several competing alternatives. In the analysis of NFBC1966 study, the proposed approach leads to findings different from the alternatives and with satisfactory prediction and stability performance.
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Affiliation(s)
- Mengque Liu
- School of Journalism and New Media, Xi’an Jiaotong Universit0y, Shanxi Xi’an, China
| | - Qingzhao Zhang
- Department of Statistics and Data Science, School of Economics, Wang Yanan Institute for Studies in Economics, and Fujian Key Lab of Statistics, Xiamen University, Fujian Xiamen, China
| | - Shuangge Ma
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
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5
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Li Z, Wang D, Liao H, Zhang S, Guo W, Chen L, Lu L, Huang T, Cai YD. Exploring the Genomic Patterns in Human and Mouse Cerebellums Via Single-Cell Sequencing and Machine Learning Method. Front Genet 2022; 13:857851. [PMID: 35309141 PMCID: PMC8930846 DOI: 10.3389/fgene.2022.857851] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/09/2022] [Indexed: 12/29/2022] Open
Abstract
In mammals, the cerebellum plays an important role in movement control. Cellular research reveals that the cerebellum involves a variety of sub-cell types, including Golgi, granule, interneuron, and unipolar brush cells. The functional characteristics of cerebellar cells exhibit considerable differences among diverse mammalian species, reflecting a potential development and evolution of nervous system. In this study, we aimed to recognize the transcriptional differences between human and mouse cerebellum in four cerebellar sub-cell types by using single-cell sequencing data and machine learning methods. A total of 321,387 single-cell sequencing data were used. The 321,387 cells included 4 cell types, i.e., Golgi (5,048, 1.57%), granule (250,307, 77.88%), interneuron (60,526, 18.83%), and unipolar brush (5,506, 1.72%) cells. Our results showed that by using gene expression profiles as features, the optimal classification model could achieve very high even perfect performance for Golgi, granule, interneuron, and unipolar brush cells, respectively, suggesting a remarkable difference between the genomic profiles of human and mouse. Furthermore, a group of related genes and rules contributing to the classification was identified, which might provide helpful information for deepening the understanding of cerebellar cell heterogeneity and evolution.
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Affiliation(s)
- ZhanDong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Deling Wang
- Department of Radiology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - HuiPing Liao
- Eye Institute of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - ShiQi Zhang
- Department of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Jiao Tong University School of Medicine (SJTUSM) & Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Lin Lu
- Department of Radiology, Columbia University Medical Center, New York, NY, United States
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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6
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Ulhaq ZS, Soraya GV, Garcia CP. Implication of the
LINGO2 gene in the predisposition to movement disorders. BRAIN SCIENCE ADVANCES 2021. [DOI: 10.26599/bsa.2021.9050018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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7
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Abstract
Essential tremor (ET) is one of the most common movement disorders, with a reported >60 million affected individuals worldwide. The definition and underlying pathophysiology of ET are contentious. Patients present primarily with motor features such as postural and action tremors, but may also have other non-motor features, including cognitive impairment and neuropsychiatric symptoms. Genetics account for most of the ET risk but environmental factors may also be involved. However, the variable penetrance and challenges in validating data make gene-environment analysis difficult. Structural changes in cerebellar Purkinje cells and neighbouring neuronal populations have been observed in post-mortem studies, and other studies have found GABAergic dysfunction and dysregulation of the cerebellar-thalamic-cortical circuitry. Commonly prescribed medications include propranolol and primidone. Deep brain stimulation and ultrasound thalamotomy are surgical options in patients with medically intractable ET. Further research in post-mortem studies, and animal and cell-based models may help identify new pathophysiological clues and therapeutic targets and, together with advances in omics and machine learning, may facilitate the development of precision medicine for patients with ET.
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Skuladottir AT, Bjornsdottir G, Nawaz MS, Petersen H, Rognvaldsson S, Moore KHS, Olafsson PI, Magnusson SH, Bjornsdottir A, Sveinsson OA, Sigurdardottir GR, Saevarsdottir S, Ivarsdottir EV, Stefansdottir L, Gunnarsson B, Muhlestein JB, Knowlton KU, Jones DA, Nadauld LD, Hartmann AM, Rujescu D, Strupp M, Walters GB, Thorgeirsson TE, Jonsdottir I, Holm H, Thorleifsson G, Gudbjartsson DF, Sulem P, Stefansson H, Stefansson K. A genome-wide meta-analysis uncovers six sequence variants conferring risk of vertigo. Commun Biol 2021; 4:1148. [PMID: 34620984 PMCID: PMC8497462 DOI: 10.1038/s42003-021-02673-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/09/2021] [Indexed: 11/17/2022] Open
Abstract
Vertigo is the leading symptom of vestibular disorders and a major risk factor for falls. In a genome-wide association study of vertigo (Ncases = 48,072, Ncontrols = 894,541), we uncovered an association with six common sequence variants in individuals of European ancestry, including missense variants in ZNF91, OTOG, OTOGL, and TECTA, and a cis-eQTL for ARMC9. The association of variants in ZNF91, OTOGL, and OTOP1 was driven by an association with benign paroxysmal positional vertigo. Using previous reports of sequence variants associating with age-related hearing impairment and motion sickness, we found eight additional variants that associate with vertigo. Although disorders of the auditory and the vestibular system may co-occur, none of the six genome-wide significant vertigo variants were associated with hearing loss and only one was associated with age-related hearing impairment. Our results uncovered sequence variants associating with vertigo in a genome-wide association study and implicated genes with known roles in inner ear development, maintenance, and disease.
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Affiliation(s)
| | | | - Muhammad Sulaman Nawaz
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Hannes Petersen
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Akureyri Hospital, Akureyri, Iceland
| | | | | | | | | | | | - Olafur A Sveinsson
- Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
| | | | - Saedis Saevarsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
| | | | | | | | - Joseph B Muhlestein
- Intermountain Medical Center, Intermountain Heart Institute, Salt Lake City, UT, USA
- University of Utah, School of Medicine, Salt Lake City, UT, USA
| | - Kirk U Knowlton
- Intermountain Medical Center, Intermountain Heart Institute, Salt Lake City, UT, USA
- University of Utah, School of Medicine, Salt Lake City, UT, USA
| | - David A Jones
- Precision Genomics, Intermountain Healthcare, Saint George, UT, USA
| | - Lincoln D Nadauld
- Precision Genomics, Intermountain Healthcare, Saint George, UT, USA
- Stanford University, School of Medicine, Stanford, CA, USA
| | - Annette M Hartmann
- Department of Psychiatry, Psychotherapy and Psychosomatics, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Dan Rujescu
- Department of Psychiatry, Psychotherapy and Psychosomatics, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Michael Strupp
- Department of Neurology and German Center for Vertigo and Balance Disorders, Ludwig Maximilians University, Munich, Germany
| | - G Bragi Walters
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Hilma Holm
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | | | | | | | | | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
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9
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Jiménez-Jiménez FJ, Alonso-Navarro H, García-Martín E, Álvarez I, Pastor P, Agúndez JAG. Genomic Markers for Essential Tremor. Pharmaceuticals (Basel) 2021; 14:ph14060516. [PMID: 34072005 PMCID: PMC8226734 DOI: 10.3390/ph14060516] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 12/13/2022] Open
Abstract
There are many reports suggesting an important role of genetic factors in the etiopathogenesis of essential tremor (ET), encouraging continuing the research for possible genetic markers. Linkage studies in families with ET have identified 4 genes/loci for familial ET, although the responsible gene(s) have not been identified. Genome-wide association studies (GWAS) described several variants in LINGO1, SLC1A2, STK32B, PPARGC1A, and CTNNA3, related with ET, but none of them have been confirmed in replication studies. In addition, the case-control association studies performed for candidate variants have not convincingly linked any gene with the risk for ET. Exome studies described the association of several genes with familial ET (FUS, HTRA2, TENM4, SORT1, SCN11A, NOTCH2NLC, NOS3, KCNS2, HAPLN4, USP46, CACNA1G, SLIT3, CCDC183, MMP10, and GPR151), but they were found only in singular families and, again, not found in other families or other populations, suggesting that some can be private polymorphisms. The search for responsible genes for ET is still ongoing.
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Affiliation(s)
- Félix Javier Jiménez-Jiménez
- Section of Neurology, Hospital Universitario del Sureste, E28500 Arganda del Rey, Spain;
- Correspondence: ; Tel.: +34-636-96-83-95; Fax: +34-913-28-07-04
| | | | - Elena García-Martín
- ARADyAL Instituto de Salud Carlos III, University Institute of Molecular Pathology Biomarkers, University of Extremadura, E10071 Caceres, Spain; (E.G.-M.); (J.A.G.A.)
| | - Ignacio Álvarez
- Movement Disorders Unit, Department of Neurology, University Hospital Mútua de Terrassa, Fundació Docencia i Recerça Mútua de Terrassa, E08221 Terrassa, Spain; (I.Á.); (P.P.)
| | - Pau Pastor
- Movement Disorders Unit, Department of Neurology, University Hospital Mútua de Terrassa, Fundació Docencia i Recerça Mútua de Terrassa, E08221 Terrassa, Spain; (I.Á.); (P.P.)
| | - José A. G. Agúndez
- ARADyAL Instituto de Salud Carlos III, University Institute of Molecular Pathology Biomarkers, University of Extremadura, E10071 Caceres, Spain; (E.G.-M.); (J.A.G.A.)
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10
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Mekić S, Gunn DA, Jacobs LC, Hijnen D, Ikram MA, Mayes AE, Nijsten T, Pardo LM. Genetic Susceptibility to Dry Skin in a General Middle-Aged to Elderly Population: A GWAS. J Invest Dermatol 2021; 141:2077-2079.e5. [PMID: 33640410 DOI: 10.1016/j.jid.2020.12.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/01/2022]
Affiliation(s)
- Selma Mekić
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - David A Gunn
- Unilever Research and Development, Colworth Science Park, Sharnbrook, United Kingdom
| | - Leonie C Jacobs
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - DirkJan Hijnen
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Andrew E Mayes
- Unilever Research and Development, Colworth Science Park, Sharnbrook, United Kingdom
| | - Tamar Nijsten
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Luba M Pardo
- Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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11
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Mathkar PP, Chen X, Sulovari A, Li D. Characterization of Hepatitis B Virus Integrations Identified in Hepatocellular Carcinoma Genomes. Viruses 2021; 13:v13020245. [PMID: 33557409 PMCID: PMC7915589 DOI: 10.3390/v13020245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 12/19/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality. Almost half of HCC cases are associated with hepatitis B virus (HBV) infections, which often lead to HBV sequence integrations in the human genome. Accurate identification of HBV integration sites at a single nucleotide resolution is critical for developing a better understanding of the cancer genome landscape and of the disease itself. Here, we performed further analyses and characterization of HBV integrations identified by our recently reported VIcaller platform in recurrent or known HCC genes (such as TERT, MLL4, and CCNE1) as well as non-recurrent cancer-related genes (such as CSMD2, NKD2, and RHOU). Our pathway enrichment analysis revealed multiple pathways involving the alcohol dehydrogenase 4 gene, such as the metabolism pathways of retinol, tyrosine, and fatty acid. Further analysis of the HBV integration sites revealed distinct patterns involving the integration upper breakpoints, integrated genome lengths, and integration allele fractions between tumor and normal tissues. Our analysis also implies that the VIcaller method has diagnostic potential through discovering novel clonal integrations in cancer-related genes. In conclusion, although VIcaller is a hypothesis free virome-wide approach, it can still be applied to accurately identify genome-wide integration events of a specific candidate virus and their integration allele fractions.
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Affiliation(s)
- Pranav P. Mathkar
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; (P.P.M.); (A.S.)
| | - Xun Chen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; (P.P.M.); (A.S.)
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto 606-8501, Japan
- Correspondence: (X.C.); (D.L.)
| | - Arvis Sulovari
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; (P.P.M.); (A.S.)
- Cajal Neuroscience Inc., Seattle, WA 98102, USA
| | - Dawei Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; (P.P.M.); (A.S.)
- Department of Biomedical Science, Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA
- Correspondence: (X.C.); (D.L.)
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12
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Bantle CM, French CT, Cummings JE, Sadasivan S, Tran K, Slayden RA, Smeyne RJ, Tjalkens RB. Manganese exposure in juvenile C57BL/6 mice increases glial inflammatory responses in the substantia nigra following infection with H1N1 influenza virus. PLoS One 2021; 16:e0245171. [PMID: 33493177 PMCID: PMC7833173 DOI: 10.1371/journal.pone.0245171] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/22/2020] [Indexed: 01/22/2023] Open
Abstract
Infection with Influenza A virus can lead to the development of encephalitis and subsequent neurological deficits ranging from headaches to neurodegeneration. Post-encephalitic parkinsonism has been reported in surviving patients of H1N1 infections, but not all cases of encephalitic H1N1 infection present with these neurological symptoms, suggesting that interactions with an environmental neurotoxin could promote more severe neurological damage. The heavy metal, manganese (Mn), is a potential interacting factor with H1N1 because excessive exposure early in life can induce long-lasting effects on neurological function through inflammatory activation of glial cells. In the current study, we used a two-hit model of neurotoxin-pathogen exposure to examine whether exposure to Mn during juvenile development would induce a more severe neuropathological response following infection with H1N1 in adulthood. To test this hypothesis, C57BL/6 mice were exposed to MnCl2 in drinking water (50 mg/kg/day) for 30 days from days 21–51 postnatal, then infected intranasally with H1N1 three weeks later. Analyses of dopaminergic neurons, microglia and astrocytes in basal ganglia indicated that although there was no significant loss of dopaminergic neurons within the substantia nigra pars compacta, there was more pronounced activation of microglia and astrocytes in animals sequentially exposed to Mn and H1N1, as well as altered patterns of histone acetylation. Whole transcriptome Next Generation Sequencing (RNASeq) analysis was performed on the substantia nigra and revealed unique patterns of gene expression in the dual-exposed group, including genes involved in antioxidant activation, mitophagy and neurodegeneration. Taken together, these results suggest that exposure to elevated levels of Mn during juvenile development could sensitize glial cells to more severe neuro-immune responses to influenza infection later in life through persistent epigenetic changes.
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Affiliation(s)
- Collin M. Bantle
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - C. Tenley French
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jason E. Cummings
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Shankar Sadasivan
- Department of Neuroscience, Vickie & Jack Farber Institute for Neuroscience, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Kevin Tran
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Richard A. Slayden
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Richard J. Smeyne
- Department of Neuroscience, Vickie & Jack Farber Institute for Neuroscience, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Ronald B. Tjalkens
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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Abstract
Highlights In the current review, we thoroughly reviewed 74 identified articles regarding genes and genetic loci that confer susceptibility to ET. Over 50 genes/genetic loci have been examined for possible association with ET, but consistent results failed to be reported raising the need for collaborative multiethnic studies. Background: Essential tremor (ET) is a common movement disorder, which is mainly characterized by bilateral tremor (postural and/or kinetic) in the upper limbs, with other parts of the body possibly involved. While the pathophysiology of ET is still unclear, there is accumulating evidence indicating that genetic variability may be heavily involved in ET pathogenesis. This review focuses on the role of genetic risk factors in ET susceptibility. Methods: The PubMed database was searched for articles written in English, for studies with humans with ET, controls without ET, and genetic variants. The terms “essential tremor” and “polymorphism” (as free words) were used during search. We also performed meta-analyses for the most examined genetic variants. Results: Seventy four articles concerning LINGO1, LINGO2, LINGO4, SLC1A2, STK32B, PPARGC1A, CTNNA3, DRD3, ALAD, VDR, HMOX1, HMOX2, LRRK1,LRRK2, GBA, SNCA, MAPT, FUS, CYPsIL17A, IL1B, NOS1, ADH1B, TREM2, RIT2, HNMT, MTHFR, PPP2R2B, GSTP1, PON1, GABA receptors and GABA transporter, HS1BP3, ADH2, hSKCa3 and CACNL1A4 genes, and ETM genetic loci were included in the current review. Results from meta-analyses revealed a marginal association for the STK32B rs10937625 and a marginal trend for association (in sensitivity analysis) for the LINGO1 rs9652490, with ET. Discussion: Quite a few variants have been examined for their possible association with ET. LINGO1 rs9652490 and STK32B rs10937625 appear to influence, to some extent, ET susceptibility. However, the conflicting results and the lack of replication for many candidate genes raise the need for collaborative multiethnic studies.
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14
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Abstract
Essential tremor (ET) is a neurological movement disorder characterised by bilateral limb kinetic/postural tremor, with or without tremor in other body parts including head, voice and lower limbs. Since no causative genes for ET have been identified, it is likely that the disorder occurs as a result of complex genetic factors interacting with various cellular and environmental factors that can result in abnormal function of circuitry involving the cerebello-thalamo-cortical pathway. Genetic analyses have uncovered at least 14 loci and 11 genes that are related to ET, as well as various risk or protective genetic factors. Limitations in ET genetic analyses include inconsistent disease definition, small sample size, varied ethnic backgrounds and many other factors that may contribute to paucity of relevant genetic data in ET. Genetic analyses, coupled with functional and animal studies, have led to better insights into possible pathogenic mechanisms underlying ET. These genetic studies may guide the future development of genetic testing and counselling, and specific, pathogenesis-targeted, therapeutic strategies.
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15
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Tarakad A, Jankovic J. Essential Tremor and Parkinson's Disease: Exploring the Relationship. Tremor Other Hyperkinet Mov (N Y) 2019; 8:589. [PMID: 30643667 PMCID: PMC6329774 DOI: 10.7916/d8md0gvr] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/04/2018] [Indexed: 12/31/2022] Open
Abstract
Background There is longstanding controversy surrounding the possible link between essential tremor (ET) and Parkinson's disease (PD). Inconsistent and unreliable diagnostic criteria may in part account for some of the difficulties in defining the relationship between these two common movement disorders. Methods References for this systematic review were identified using PubMed with the search terms "essential tremor" AND "Parkinson's disease" with articles published in English between 1960 and September 2018 included. Results In this review we provide evidence that some patients diagnosed with ET have an increased risk of developing PD years or decades after onset of action tremor. There are several still unresolved questions about the link between the two disorders including lack of verifiable diagnostic criteria for the two disorders and marked overlap in phenomenology. Here we review clinical, epidemiologic, imaging, pathologic, and genetic studies that address the ET-PD relationship. Several lines of evidence support the association between ET and PD, including overlapping motor and non-motor features, relatively high prevalence of rapid eye movement sleep behavior disorder (26-43%) in ET patients, increased prevalence of PD in patients with longstanding antecedent ET, increased prevalence of ET in family members of patients with PD, and the presence of Lewy bodies in the brains of some ET patients (15-24%). Discussion There is a substantial body of evidence supporting the association between ET and PD within at least a subset of patients, although the nature and possible pathogenic mechanisms of the relationship are not well understood.
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Affiliation(s)
- Arjun Tarakad
- Parkinson’s Disease Center and Movement Disorders Clinic, Baylor College of Medicine Houston, TX, USA
| | - Joseph Jankovic
- Parkinson’s Disease Center and Movement Disorders Clinic, Baylor College of Medicine Houston, TX, USA
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16
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Su T, Ren Q, Lu Y, Tai W, Zhu Y, Li Z, Wen J, Hu L, Zhang L, Ma J. A genetic variant in LINGO2 contributes to the risk of gestational diabetes mellitus in a Chinese population. J Cell Physiol 2018; 234:7012-7018. [PMID: 30426492 DOI: 10.1002/jcp.27454] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 08/29/2018] [Indexed: 11/06/2022]
Abstract
Genome-wide association studies (GWASs) showed that three single nucleotide polymorphisms (SNPs; rs10968576, rs1412239, and rs824248) in the leucine-rich repeat and Ig domain containing 2 (LINGO2) were associated with obesity or type 2 diabetes (T2D). We aimed to determine the influence of the LINGO2 variants on the gestational diabetes mellitus (GDM) risk. Thus, we performed a case-control study including 964 GDM cases and 1,021 controls to test the associations between the three LINGO2 variants (rs10968576, rs1412239, and rs824248) and susceptibility to GDM. Logistic regression analyses showed no significant association between LINGO2 variations (rs10968576 and rs1412239) and GDM susceptibility, but we observed that LINGO2 rs824248 A > T was significantly associated with an increased risk of GDM using the dominant model (TT/AT vs. AA: adjusted odds ratio [OR] = 1.26, 95% confidence interval [CI] = 1.05-1.51; p = 0.012) and the additive model (TT vs. AT vs. AA: adjusted OR = 1.16, 95% CI = 1.03-1.31; p = 0.016). In the additive model, a stronger risk effect of rs824248 was observed among obese women (prepregnancy body mass index [BMI] > 22 kg/m2 , adjusted OR = 1.34, 95% CI = 1.12-1.59) compared with that in lean women (prepregnancy BMI ≤ 22 kg/m2 , adjusted OR = 1.02 , 95% CI = 0.86-1.21; p = 0.029 for heterogeneity test). Further interactive analyses also detected a significant multiplicative interaction between rs824248 and prepregnancy BMI for the risk of GDM (p = 0.041). These findings indicate that LINGO2 rs824248 may serve as a susceptibility marker for GDM in Chinese females.
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Affiliation(s)
- Tong Su
- Department of Clinical Laboratory, People's Hospital of Rizhao, Rizhao, China
| | - Qingxia Ren
- Department of Clinical Laboratory, People's Hospital of Rizhao, Rizhao, China
| | - Yingying Lu
- Department of Clinical Laboratory, People's Hospital of Rizhao, Rizhao, China
| | - Wen Tai
- Nanjing Maternity and Child Health Care Institute, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Yuan Zhu
- Nanjing Maternity and Child Health Care Institute, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Zhengying Li
- Department of Neonatology, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, Wuxi, China
| | - Juan Wen
- Nanjing Maternity and Child Health Care Institute, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Lingmin Hu
- Department of Reproduction, The Affiliated Changzhou Maternity and Child Health Care Hospital of Nanjing Medical University, Changzhou, China
| | - Le Zhang
- Department of Neonatology, The Affiliated Wuxi Children's Hospital of Nanjing Medical University, Wuxi, China
| | - Jiehua Ma
- Nanjing Maternity and Child Health Care Institute, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
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17
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Jiang C, Lin WJ, Sadahiro M, Labonté B, Menard C, Pfau ML, Tamminga CA, Turecki G, Nestler EJ, Russo SJ, Salton SR. VGF function in depression and antidepressant efficacy. Mol Psychiatry 2018; 23:1632-1642. [PMID: 29158577 PMCID: PMC5962361 DOI: 10.1038/mp.2017.233] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 09/18/2017] [Accepted: 10/09/2017] [Indexed: 12/14/2022]
Abstract
Brain-derived neurotrophic factor (BDNF) is a critical effector of depression-like behaviors and antidepressant responses. Here, we show that VGF (non-acronymic), which is robustly regulated by BDNF/TrkB signaling, is downregulated in hippocampus (male/female) and upregulated in nucleus accumbens (NAc) (male) in depressed human subjects and in mice subjected to chronic social defeat stress (CSDS). Adeno-associated virus (AAV)-Cre-mediated Vgf ablation in floxed VGF mice, in dorsal hippocampus (dHc) or NAc, led to pro-depressant or antidepressant behaviors, respectively, while dHc- or NAc-AAV-VGF overexpression induced opposite outcomes. Mice with reduced VGF levels in the germ line (Vgf+/-) or in dHc (AAV-Cre-injected floxed mice) showed increased susceptibility to CSDS and impaired responses to ketamine treatment in the forced swim test. Floxed mice with conditional pan-neuronal (Synapsin-Cre) but not those with forebrain (αCaMKII-Cre) Vgf ablation displayed increased susceptibility to subthreshold social defeat stress, suggesting that neuronal VGF, expressed in part in inhibitory interneurons, regulates depression-like behavior. Acute antibody-mediated sequestration of VGF-derived C-terminal peptides AQEE-30 and TLQP-62 in dHc induced pro-depressant effects. Conversely, dHc TLQP-62 infusion had rapid antidepressant efficacy, which was reduced in BDNF floxed mice injected in dHc with AAV-Cre, and in NBQX- and rapamycin-pretreated wild-type mice, these compounds blocking α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor and mammalian target of rapamycin (mTOR) signaling, respectively. VGF is therefore a critical modulator of depression-like behaviors in dHc and NAc. In hippocampus, the antidepressant response to ketamine is associated with rapid VGF translation, is impaired by reduced VGF expression, and as previously reported, requires coincident, rapid BDNF translation and release.
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Affiliation(s)
- Cheng Jiang
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wei-Jye Lin
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Masato Sadahiro
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benoit Labonté
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Caroline Menard
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Madeline L. Pfau
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carol A. Tamminga
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75235, USA
| | - Gustavo Turecki
- Department of Psychiatry, McGill University, Montréal, Québec, Canada
| | - Eric J. Nestler
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Scott J. Russo
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stephen R. Salton
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA,Department of Geriatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA,Corresponding author: Dr. Stephen R. Salton, Department of Neuroscience, Box 1639, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York NY, 10029 USA Tel: 1-212-824-9308; Fax: 1-646-537-9583;
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18
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Iyer S, Acharya KR, Subramanian V. A comparative bioinformatic analysis of C9orf72. PeerJ 2018; 6:e4391. [PMID: 29479499 PMCID: PMC5822839 DOI: 10.7717/peerj.4391] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/29/2018] [Indexed: 12/12/2022] Open
Abstract
C9orf72 is associated with frontotemporal dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS), both of which are devastating neurodegenerative diseases. Findings suggest that an expanded hexanucleotide repeat in the non-coding region of the C9orf72 gene is the most common cause of familial FTD and ALS. Despite considerable efforts being made towards discerning the possible disease-causing mechanism/s of this repeat expansion mutation, the biological function of C9orf72 remains unclear. Here, we present the first comprehensive genomic study on C9orf72 gene. Analysis of the genomic level organization of C9orf72 across select species revealed architectural similarity of syntenic regions between human and mouse but a lack of conservation of the repeat-harboring intron 1 sequence. Information generated in this study provides a broad genomic perspective of C9orf72 which would form a basis for subsequent experimental approaches and facilitate future mechanistic and functional studies on this gene.
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Affiliation(s)
- Shalini Iyer
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - K Ravi Acharya
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Vasanta Subramanian
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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19
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Lo MT, Wang Y, Kauppi K, Sanyal N, Fan CC, Smeland OB, Schork A, Holland D, Hinds DA, Tung JY, Andreassen OA, Dale AM, Chen CH. Modeling prior information of common genetic variants improves gene discovery for neuroticism. Hum Mol Genet 2017; 26:4530-4539. [PMID: 28973307 PMCID: PMC5886256 DOI: 10.1093/hmg/ddx340] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/10/2017] [Accepted: 08/25/2017] [Indexed: 02/01/2023] Open
Abstract
Neuroticism reflects emotional instability, and is related to various mental and physical health issues. However, the majority of genetic variants associated with neuroticism remain unclear. Inconsistent genetic variants identified by different genome-wide association studies (GWAS) may be attributable to low statistical power. We proposed a novel framework to improve the power for gene discovery by incorporating prior information of single nucleotide polymorphisms (SNPs) and combining two relevant existing tools, relative enrichment score (RES) and conditional false discovery rate (FDR). Here, SNP's conditional FDR was estimated given its RES based on SNP prior information including linkage disequilibrium (LD)-weighted genic annotation scores, total LD scores and heterozygosity. A known significant locus in chromosome 8p was excluded before estimating FDR due to long-range LD structure. Only one significant LD-independent SNP was detected by analyses of unconditional FDR and traditional GWAS in the discovery sample (N = 59 225), and notably four additional SNPs by conditional FDR. Three of the five SNPs, all identified by conditional FDR, were replicated (P < 0.05) in an independent sample (N = 170 911). These three SNPs are located in intronic regions of CADM2, LINGO2 and EP300 which have been reported to be associated with autism, Parkinson's disease and schizophrenia, respectively. Our approach using a combination of RES and conditional FDR improved power of traditional GWAS for gene discovery providing a useful framework for the analysis of GWAS summary statistics by utilizing SNP prior information, and helping to elucidate the links between neuroticism and complex diseases from a genetic perspective.
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Affiliation(s)
- Min-Tzu Lo
- Department of Radiology, Center for Multimodal Imaging and Genetics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Yunpeng Wang
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo 0407, Norway
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92037, USA
| | - Karolina Kauppi
- Department of Radiology, Center for Multimodal Imaging and Genetics, University of California, San Diego, La Jolla, CA 92037, USA
- Department of Radiation Sciences, Umea University, Umea 90187, Sweden
| | - Nilotpal Sanyal
- Department of Radiology, Center for Multimodal Imaging and Genetics, University of California, San Diego, La Jolla, CA 92037, USA
| | - Chun-Chieh Fan
- Department of Radiology, Center for Multimodal Imaging and Genetics, University of California, San Diego, La Jolla, CA 92037, USA
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA
| | - Olav B Smeland
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo 0407, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo 0407, Norway
| | - Andrew Schork
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92037, USA
- Institute of Biological Psychiatry, Medical Health Center, Sct. Hans, Roskilde, 4000, Denmark
| | - Dominic Holland
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92037, USA
| | | | | | - Ole A Andreassen
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo 0407, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo 0407, Norway
| | - Anders M Dale
- Department of Radiology, Center for Multimodal Imaging and Genetics, University of California, San Diego, La Jolla, CA 92037, USA
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92037, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92037, USA
| | - Chi-Hua Chen
- Department of Radiology, Center for Multimodal Imaging and Genetics, University of California, San Diego, La Jolla, CA 92037, USA
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20
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Sulovari A, Liu Z, Zhu Z, Li D. Genome-wide meta-analysis of copy number variations with alcohol dependence. THE PHARMACOGENOMICS JOURNAL 2017; 18:398-405. [PMID: 28696413 DOI: 10.1038/tpj.2017.35] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/10/2017] [Accepted: 06/07/2017] [Indexed: 12/26/2022]
Abstract
Genetic association studies and meta-analyses of alcohol dependence (AD) have reported AD-associated single nucleotide polymorphisms (SNPs). These SNPs collectively account for a small portion of estimated heritability in AD. Recent genome-wide copy number variation (CNV) studies have identified CNVs associated with AD and substance dependence, suggesting that a portion of the missing heritability is explained by CNV. We applied PennCNV and QuantiSNP CNV calling algorithms to identify consensus CNVs in five AD cohorts of European and African origins. After rigorous quality control, genome-wide meta-analyses of CNVs were carried out in 3243 well-diagnosed AD cases and 2802 controls. We identified nine CNV regions, including a deletion in chromosome 5q21.3 with a suggestive association with AD (OR=2.15 (1.41-3.29) and P=3.8 × 10-4) and eight nominally significant CNV regions. All regions were replicated with consistent effect sizes across studies and populations. Pathway and gene-drug interaction enrichment analyses based on the resulting genes indicated the mitogen-activated protein kinase signaling pathway and the recombinant insulin and hyaluronidase drugs, which were relevant to AD biology or treatment. To our knowledge, this is the first genome-wide meta-analysis of CNVs with addiction. Further investigation of the AD-associated CNV regions will provide better understanding of the AD genetic mechanism.
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Affiliation(s)
- A Sulovari
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA
| | - Z Liu
- Spine Surgery, Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Z Zhu
- Spine Surgery, Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - D Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA.,Department of Computer Science, University of Vermont, Burlington, VT, USA.,Neuroscience, Behavior, and Health Initiative, University of Vermont, Burlington, VT, USA
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21
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Mizoguchi T, Minakuchi H, Ishisaka M, Tsuruma K, Shimazawa M, Hara H. Behavioral abnormalities with disruption of brain structure in mice overexpressing VGF. Sci Rep 2017; 7:4691. [PMID: 28680036 PMCID: PMC5498671 DOI: 10.1038/s41598-017-04132-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 05/10/2017] [Indexed: 01/01/2023] Open
Abstract
VGF nerve growth factor inducible (VGF) is a neuropeptide induced by nerve growth factor and brain-derived neurotrophic factor. This peptide is involved in synaptic plasticity, neurogenesis, and neurite growth in the brain. Patients with depression and bipolar disorder have lower-than-normal levels of VGF, whereas patients with schizophrenia and other cohorts of patients with depression have higher-than-normal levels. VGF knockout mice display behavioral abnormalities such as higher depressive behavior and memory dysfunction. However, it is unclear whether upregulation of VGF affects brain function. In the present study, we generated mice that overexpress VGF and investigated several behavioral phenotypes and the brain structure. These adult VGF-overexpressing mice showed (a) hyperactivity, working memory impairment, a higher depressive state, and lower sociality compared with wild-type mice; (b) lower brain weight without a change in body weight; (c) increased lateral ventricle volume compared with wild-type mice; and (d) striatal morphological defects. These results suggest that VGF may modulate a variety of behaviors and brain development. This transgenic mouse line may provide a useful model for research on mental illnesses.
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Affiliation(s)
- Takahiro Mizoguchi
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Hiroko Minakuchi
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Mitsue Ishisaka
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Kazuhiro Tsuruma
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Masamitsu Shimazawa
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Hideaki Hara
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan.
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22
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Peng Q, Schork NJ, Wilhelmsen KC, Ehlers CL. Whole genome sequence association and ancestry-informed polygenic profile of EEG alpha in a Native American population. Am J Med Genet B Neuropsychiatr Genet 2017; 174:435-450. [PMID: 28436151 PMCID: PMC5435561 DOI: 10.1002/ajmg.b.32533] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 02/06/2017] [Indexed: 12/18/2022]
Abstract
EEG alpha activity is the dominant oscillation in most adult humans, is highly heritable, and has been associated with a number of cognitive functions. Two EEG phenotypes, low- and high-voltage alpha (LVA & HVA), have been demonstrated to have high heritabilities. They have different prevalence depending on a population's ancestral origins. In the present study we assessed the influence of ancestry admixture on EEG alpha power, and conducted a whole genome sequencing association analysis and an ancestry-informed polygenic study on those phenotypes in a Native American (NA) population that has a high prevalence of LVA. Seven common variants, in LD with each other upstream from gene ASIC2, reached genome-wide significance (p = 2 × 10-8 ) having a positive association with alpha voltage. They had lower minor allele frequencies in the NAs than in a global population sample. Overall correlations between lower degrees of NA (higher degree European) ancestry and HVA, and higher degrees of NA and LVA were also found. Additionally a rare-variant gene-based study identified gene TIA1 being negatively associated with LVA. Approximately 3% of SNPs exhibited a 15-fold enrichment that explained nearly half of the total SNP-heritability for EEG alpha. These regions showed the most significant anti-correlations between NA ancestry and alpha voltage, and were enriched for genes and pathways mediating cognitive functions. Our findings suggested that these regions likely harbor causal variants for HVA, and lacking of such variants could explain the high prevalence of LVA in this NA population, possibly illuminating the ancestral origin and genetic basis for EEG alpha.
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Affiliation(s)
- Qian Peng
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, California 92037 USA
- Department of Human Biology, J. Craig Venter Institute, La Jolla, California 92037 USA
| | - Nicholas J. Schork
- Department of Human Biology, J. Craig Venter Institute, La Jolla, California 92037 USA
| | - Kirk C. Wilhelmsen
- Department of Genetics and Neurology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 USA
| | - Cindy L. Ehlers
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, California 92037 USA
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23
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Ellis KL, Zhou Y, Rodriguez-Murillo L, Beshansky JR, Ainehsazan E, Selker HP, Huggins GS, Cupples LA, Peter I. Common variants associated with changes in levels of circulating free fatty acids after administration of glucose–insulin–potassium (GIK) therapy in the IMMEDIATE trial. THE PHARMACOGENOMICS JOURNAL 2015; 17:76-83. [DOI: 10.1038/tpj.2015.84] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/30/2015] [Accepted: 11/02/2015] [Indexed: 12/31/2022]
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24
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Role of long purine stretches in controlling the expression of genes associated with neurological disorders. Gene 2015; 572:175-83. [DOI: 10.1016/j.gene.2015.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 06/17/2015] [Accepted: 07/02/2015] [Indexed: 11/22/2022]
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25
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Hansel NN, Paré PD, Rafaels N, Sin DD, Sandford A, Daley D, Vergara C, Huang L, Elliott WM, Pascoe CD, Arsenault BA, Postma DS, Boezen HM, Bossé Y, van den Berge M, Hiemstra PS, Cho MH, Litonjua AA, Sparrow D, Ober C, Wise RA, Connett J, Neptune ER, Beaty TH, Ruczinski I, Mathias RA, Barnes KC. Genome-Wide Association Study Identification of Novel Loci Associated with Airway Responsiveness in Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol 2015; 53:226-34. [PMID: 25514360 DOI: 10.1165/rcmb.2014-0198oc] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Increased airway responsiveness is linked to lung function decline and mortality in subjects with chronic obstructive pulmonary disease (COPD); however, the genetic contribution to airway responsiveness remains largely unknown. A genome-wide association study (GWAS) was performed using the Illumina (San Diego, CA) Human660W-Quad BeadChip on European Americans with COPD from the Lung Health Study. Linear regression models with correlated meta-analyses, including data from baseline (n = 2,814) and Year 5 (n = 2,657), were used to test for common genetic variants associated with airway responsiveness. Genotypic imputation was performed using reference 1000 Genomes Project data. Expression quantitative trait loci (eQTL) analyses in lung tissues were assessed for the top 10 markers identified, and immunohistochemistry assays assessed protein staining for SGCD and MYH15. Four genes were identified within the top 10 associations with airway responsiveness. Markers on chromosome 9p21.2 flanked by LINGO2 met a predetermined threshold of genome-wide significance (P < 9.57 × 10(-8)). Markers on chromosomes 3q13.1 (flanked by MYH15), 5q33 (SGCD), and 6q21 (PDSS2) yielded suggestive evidence of association (9.57 × 10(-8) < P ≤ 4.6 × 10(-6)). Gene expression studies in lung tissue showed single nucleotide polymorphisms on chromosomes 5 and 3 to act as eQTL for SGCD (P = 2.57 × 10(-9)) and MYH15 (P = 1.62 × 10(-6)), respectively. Immunohistochemistry confirmed localization of SGCD protein to airway smooth muscle and vessels and MYH15 to airway epithelium, vascular endothelium, and inflammatory cells. We identified novel loci associated with airway responsiveness in a GWAS among smokers with COPD. Risk alleles on chromosomes 5 and 3 acted as eQTLs for SGCD and MYH15 messenger RNA, and these proteins were expressed in lung cells relevant to the development of airway responsiveness.
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Affiliation(s)
- Nadia N Hansel
- 1 Department of Medicine, School of Medicine; and.,Departments of 2 Environmental Health Sciences
| | - Peter D Paré
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | | | - Don D Sin
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | - Andrew Sandford
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | - Denise Daley
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | | | - Lili Huang
- 1 Department of Medicine, School of Medicine; and
| | - W Mark Elliott
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | - Chris D Pascoe
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | - Bryna A Arsenault
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | - Dirkje S Postma
- Departments of 4 Pulmonary Diseases and.,5 Groningen Research Institute for Asthma and COPD Research Institute, University Medical Center Groningen, Groningen; and
| | - H Marike Boezen
- 6 Epidemiology, and.,5 Groningen Research Institute for Asthma and COPD Research Institute, University Medical Center Groningen, Groningen; and
| | - Yohan Bossé
- 7 Department of Molecular Medicine, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec City, Québec, Canada
| | - Maarten van den Berge
- Departments of 4 Pulmonary Diseases and.,5 Groningen Research Institute for Asthma and COPD Research Institute, University Medical Center Groningen, Groningen; and
| | - Pieter S Hiemstra
- 8 Department of Pulmonology, Leiden University Medical Center, Leiden, the Netherlands
| | - Michael H Cho
- 9 Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Augusto A Litonjua
- 9 Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - David Sparrow
- 10 VA Normative Aging Study and Boston University School of Medicine, Boston, Massachusetts
| | - Carole Ober
- 11 Department of Human Genetics, University of Chicago, Chicago, Illinois
| | | | - John Connett
- 12 Division of Biostatistics, School of Public Health, University of Minnesota, St. Paul, Minnesota
| | | | | | - Ingo Ruczinski
- 14 Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | | | - Kathleen C Barnes
- 1 Department of Medicine, School of Medicine; and.,13 Epidemiology, and
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Chen Y, Cao B, Yang J, Wei Q, Ou RW, Zhao B, Song W, Guo X, Shang H. Analysis and meta-analysis of five polymorphisms of the LINGO1 and LINGO2 genes in Parkinson's disease and multiple system atrophy in a Chinese population. J Neurol 2015; 262:2478-83. [PMID: 26254004 DOI: 10.1007/s00415-015-7870-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/19/2015] [Accepted: 07/21/2015] [Indexed: 02/05/2023]
Abstract
Whether polymorphisms rs11856808 and rs9652490 of the Leucine-rich repeat and Ig domain containing, Nogo receptor-interacting protein-1 (LINGO1) gene, as well as rs10968280, rs13362909 and rs7033345 of the LINGO2 gene, increase the risk for Parkinson's disease (PD) is controversial. Considering the overlap of the clinical and pathological characteristics among PD and multiple system atrophy (MSA), we explored the associations between these five polymorphisms and PD and MSA in a Chinese population. A total of 1055 PD patients, 320 MSA patients, and 810 healthy controls (HCs) were genotyped for these five polymorphisms in LINGO1 and LINGO 2 using Sequenom iPLEX Assay technology. Moreover, after combining our results with available published data, a meta-analysis was conducted to investigate the associations between LINGO 1 rs11856808 and rs9652490 and the risk of PD. The frequency of the minor alleles "T" of LINGO1 rs11856808 was significantly lower in PD than that in HCs (p = 0.011, OR 0.89, 95 % CI 0.81-0.97), but not in MSA. Moreover, there were no significant differences in the minor allele frequency distributions of the other four polymorphisms between PD and HCs, and between MSA and HCs. The meta-analysis showed a lack of association of rs9652490 and PD, regardless of the genetic model or ethnic origin. However, the rs11856808 allele decreased the risk of PD in patients of Asian origin in a dominant genetic model. Our findings suggest that rs11856808 plays a protective role by decreasing the risk for PD, but not for MSA, in Asian population, the other four polymorphisms do not contribute to the risk for PD and MSA.
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Affiliation(s)
- YongPing Chen
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Bei Cao
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Jing Yang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - QianQian Wei
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Ru Wei Ou
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Bi Zhao
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Wei Song
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - XiaoYan Guo
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - HuiFang Shang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China.
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27
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Athanasiu L, Smorr LLH, Tesli M, Røssberg JI, Sønderby IE, Spigset O, Djurovic S, Andreassen OA. Genome-wide association study identifies common variants associated with pharmacokinetics of psychotropic drugs. J Psychopharmacol 2015; 29:884-91. [PMID: 25944848 DOI: 10.1177/0269881115584469] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Individual variation in pharmacokinetics of psychotropic drugs, particularly metabolism, is an important factor to consider in pharmacological treatment in psychiatry. A large proportion of this variance is still not accounted for, but evidence so far suggests the involvement of genetic factors. We performed a genome-wide association study (GWAS) with concentration dose ratio (CDR) as sub-phenotype to assess metabolism rate of psychotropic drugs in a homogenous Norwegian sample of 1334 individuals diagnosed with a severe mental disorder. The GWAS revealed one genome-wide significant marker (rs16935279, p-value=3.95×10(-10), pperm=7.5×10(-4)) located in an intronic region of the lncRNA LOC100505718. Carriers of the minor allele have a lower metabolism rate of antiepileptic drugs compared to major allele carriers. In addition, several nominally significant associations between single nucleotide polymorphisms (SNPs) and CDR for antipsychotic, antidepressant and antiepileptic drugs were disclosed. We consider standardised CDR to be a useful measure of the metabolism rate of a drug. The present findings indicate that common gene variants could affect the metabolism of psychotropic drugs. This warrants further investigations into the functional mechanisms involved as it may lead to identification of predictive markers as well as novel drug targets.
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Affiliation(s)
- Lavinia Athanasiu
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Lisa-Lena H Smorr
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway Institute of Clinical Medicine, Oslo University, Oslo, Norway
| | - Martin Tesli
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway Institute of Clinical Medicine, Oslo University, Oslo, Norway
| | - Jan I Røssberg
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway Institute of Clinical Medicine, Oslo University, Oslo, Norway
| | - Ida E Sønderby
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Olav Spigset
- Department of Clinical Pharmacology, St Olav University Hospital, Trondheim, Norway Department of Laboratory Medicine, Children's and Women's Health, Norwegian University of Science and Technology, Trondheim, Norway
| | - Srdjan Djurovic
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ole A Andreassen
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
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28
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Chao YX, Ng EY, Tan L, Prakash KM, Au WL, Zhao Y, Tan EK. Lrrk2 R1628P variant is a risk factor for essential tremor. Sci Rep 2015; 5:9029. [PMID: 25761573 PMCID: PMC4356963 DOI: 10.1038/srep09029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/16/2015] [Indexed: 12/30/2022] Open
Abstract
Essential tremor (ET) and Parkinson's disease (PD) are two of the most common adult onset movement disorders with overlapping clinical features. PD patients with leucine-rich repeat kinase-2 (LRRK2) mutations may present initially with an ET phenotype. To address the possibility of a common genetic link between ET and PD, we examined the association between a common LRRK2 R1628P gene variant and ET. The LRRK2 R1628P was genotyped in ET cases and matched healthy controls. A total of 1277 subjects comprising of 450 ET cases and 827 controls were included. There were 40 heterozygote (GG to CG) variant out of 450 ET cases (genotypic frequency 8.9%) and 36 heterozygote variant (GG to CG, genotypic frequency 4.3%) and one homozygote variant (GG to CC) out of 827 controls. Subjects carrying the R1628P variant had a twofold increased risk of ET (p = 0.0035, OR = 2.20 and 95% confidence interval is 1.30–3.73). Using a case control methodology, we demonstrated an association between a known PD risk variant, LRRK2 R1628P, with ET. Subjects carrying the R1628P variant had twice the risk of developing ET. The sharing of a similar gene risk variant suggests a possible pathophysiologic link between PD and ET.
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Affiliation(s)
- Yin Xia Chao
- 1] Departments of Neurology, Singapore General Hospital [2] National Neuroscience Institute
| | - Ebonne Yulin Ng
- 1] Departments of Neurology, Singapore General Hospital [2] National Neuroscience Institute
| | | | | | | | - Yi Zhao
- Clinical Research, Singapore General Hospital
| | - Eng-King Tan
- 1] Departments of Neurology, Singapore General Hospital [2] Clinical Research, Singapore General Hospital [3] National Neuroscience Institute [4] Duke-NUS Graduate Medical School
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29
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Koufaris C, Papagregoriou G, Kousoulidou L, Moutafi M, Tauber M, Jouret B, Kieffer I, Deltas C, Tanteles GA, Anastasiadou V, Patsalis PC, Sismani C. Haploinsufficiency of the miR-873/miR-876 microRNA cluster is associated with craniofacial abnormalities. Gene 2015; 561:95-100. [PMID: 25680557 DOI: 10.1016/j.gene.2015.02.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 02/05/2015] [Accepted: 02/08/2015] [Indexed: 11/20/2022]
Abstract
MicroRNA haploinsufficiency has been associated with developmental defects in only a limited number of cases. Here we report a de novo genomic microdeletion that includes the LINGO2 gene as well as two microRNA genes, MIR873 and MIR876, in a patient with craniofacial abnormalities - in particular macrocephaly and hypertelorism - and learning difficulties. Subsequent analysis revealed that the microRNAs affected by this de novo microdeletion form a mammalian-lineage, neuronal tissue-enriched cluster. In addition, bioinformatic analysis and experimental data indicate that miR-873 is involved in the regulation of the Hedgehog signaling, an essential pathway involved in craniofacial patterning and differentiation. Collectively these observations are consistent with a role of the miR-873/miR-876 microRNA cluster in physiological cranial bone development and indicate that mutations affecting these microRNAs could be a rare cause of developmental defect in humans.
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Affiliation(s)
- Costas Koufaris
- Department of Cytogenetics and Genomics, The Cyprus institute of Neurology and Genetics, Cyprus
| | | | - Ludmila Kousoulidou
- Department of Cytogenetics and Genomics, The Cyprus institute of Neurology and Genetics, Cyprus
| | - Maria Moutafi
- Department of Cytogenetics and Genomics, The Cyprus institute of Neurology and Genetics, Cyprus
| | - Maithé Tauber
- Centre de référence du Syndrome de Prader-Willi, Unité d'endocrinologie, obésité, maladies osseuses, génétique et gynécologiqe médicale, Hôpital des enfants CHU Toulouse, France
| | - Béatrice Jouret
- Centre de référence du Syndrome de Prader-Willi, Unité d'endocrinologie, obésité, maladies osseuses, génétique et gynécologiqe médicale, Hôpital des enfants CHU Toulouse, France
| | - Isabelle Kieffer
- Unité d'endocrinologie, obésité, maladies osseuses, génétique et gynécologiqe médicale, Hôpital des enfants CHU Toulouse, France
| | | | - George A Tanteles
- Department of Clinical Genetics, The Cyprus Institute of Neurology and Genetics, Cyprus
| | | | - Philippos C Patsalis
- Translational Genetics Team, The Cyprus Institute of Neurology and Genetics, Cyprus
| | - Carolina Sismani
- Department of Cytogenetics and Genomics, The Cyprus institute of Neurology and Genetics, Cyprus.
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30
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Van Gerpen JA, Ross OA. Essential Tremor. Mov Disord 2015. [DOI: 10.1016/b978-0-12-405195-9.00036-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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31
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Oh ES, Kim JM, Kim YE, Yun JY, Kim JS, Kim SE, Lee SB, Lee JJ, Park JH, Kim TH, Kim KW, Jeon BS. The prevalence of essential tremor in elderly Koreans. J Korean Med Sci 2014; 29:1694-8. [PMID: 25469072 PMCID: PMC4248593 DOI: 10.3346/jkms.2014.29.12.1694] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 08/25/2014] [Indexed: 11/20/2022] Open
Abstract
Essential tremor (ET) is one of the most common movement disorders. The prevalence of ET varies substantially among studies. In Korea, there is no well-designed epidemiological study of the prevalence of ET. Thus, we investigated the prevalence of ET in a community in Korea. Standardized interviews and in-person neurological examinations were performed in a random sample of the elderly aged 65 yr or older. Next, movement specialists attempted to diagnose ET clinically. People who showed equivocal parkinsonian features underwent dopamine transporter imaging using [(123)I]-FP-CIT SPECT, to differentiate ET from parkinsonism. A total of 714 subjects participated in this population-based study. Twenty six of these subjects were diagnosed as having ET. The crude prevalence of ET was 3.64 per 100 persons. Age, gender, or education period were not different between the ET patients and the non-ET subjects. The prevalence of ET was slightly lower than those reported in previous studies. Further studies including more subjects are warranted.
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Affiliation(s)
- Eung Seok Oh
- Department of Neurology, Chungnam National University School of Medicine, Chungnam National University Hospital, Daejeon, Korea
| | - Jong-Min Kim
- Department of Neurology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Young Eun Kim
- Department of Neurology, Hallym University College of Medicine, Hallym University Sacred Heart Hospital, Anyang, Korea
| | - Ji Young Yun
- Department of Neurology, Ewha Womans University Mokdong Hospital, Seoul, Korea
| | - Ji Seon Kim
- Department of Neurology, Chungbuk National University School of Medicine, Chungbuk National University Hospital, Cheongju, Korea
| | - Sang Eun Kim
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Department of Brain and Cognitive Science, Seoul National University College of Natural Sciences, Seoul, Korea
| | - Seok Bum Lee
- Department of Psychiatry, Dankook University College of Medicine, Dankook University Hospital, Cheonan, Korea
| | - Jung Jae Lee
- Department of Psychiatry, Dankook University College of Medicine, Dankook University Hospital, Cheonan, Korea
| | - Joon Hyuk Park
- Department of Psychiatry, Jeju National Universtiy School of Medicine, Jeju National University Hospital, Jeju, Korea
| | - Tae Hui Kim
- Department of Psychiatry, Yonsei University Wonju Severance Christian Hospital, Wonju, Korea
| | - Ki Woong Kim
- Department of Psychiatry, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Department of Brain and Cognitive Science, Seoul National University College of Natural Sciences, Seoul, Korea
| | - Beom S. Jeon
- Department of Neurology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
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32
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Ulloa AE, Chen J, Vergara VM, Calhoun V, Liu J. Association between copy number variation losses and alcohol dependence across African American and European American ethnic groups. Alcohol Clin Exp Res 2014; 38:1266-74. [PMID: 24512105 PMCID: PMC3999255 DOI: 10.1111/acer.12364] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 12/21/2013] [Indexed: 11/30/2022]
Abstract
BACKGROUND Copy number variations (CNVs) are structural genetic mutations consisting of segmental gains or losses in DNA sequence. Although CNVs contribute substantially to genomic variation, few genetic and imaging studies report association of CNVs with alcohol dependence (AD). Our purpose is to find evidence of this association across ethnic populations and genders. This work is the first AD-CNV study across ethnic groups and the first to include the African American (AA) population. METHODS This study considers 2 CNV data sets, one for discovery (2,345 samples) and the other for validation (239 samples), both including subjects with AD and healthy controls of European and African ancestry. Our analysis assesses the association between AD and CNV losses across ethnic groups and gender by examining the effect of overall losses across the whole genome, collective losses within individual cytogenetic bands, and specific losses in CNV regions. RESULTS Results from the discovery data set showed an association between CNV losses within 16q12.2 and AD diagnosis (p = 4.53 × 10(-3) ). An overlapping CNV region from the validation data set exhibited the same direction of effect with respect to AD (p = 0.051). This CNV region affects the genes CES1p1 and CES1, which are members of the carboxylesterase (CES) family. The enzyme encoded by CES1 is a major liver enzyme that typically catalyzes the decomposition of ester into alcohol and carboxylic acid and is involved in drug or xenobiotics, fatty acid, and cholesterol metabolisms. In addition, the most significantly associated CNV region was located at 9p21.2 (p = 1.9 × 10(-3) ) in our discovery data set. Although not observed in the validation data set, probably due to small sample size, this result might hold potential connection to AD given its connection with neuronal death. In contrast, we did not find any association between AD and the overall total losses or the collective losses within individual cytogenetic bands. CONCLUSIONS Overall, our study provides evidence that the specific CNVs at 16q12.2 contribute to the development of alcoholism in AA and European American populations.
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Affiliation(s)
| | - Jiayu Chen
- Electrical and Computer Engineering Department, University of New Mexico
- The Mind Research Network and Lovelace Biomedical and Environmental Research Institute
| | - Victor Manuel Vergara
- The Mind Research Network and Lovelace Biomedical and Environmental Research Institute
| | - Vince Calhoun
- Electrical and Computer Engineering Department, University of New Mexico
- The Mind Research Network and Lovelace Biomedical and Environmental Research Institute
| | - Jingyu Liu
- Electrical and Computer Engineering Department, University of New Mexico
- The Mind Research Network and Lovelace Biomedical and Environmental Research Institute
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33
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Delay C, Tremblay C, Brochu E, Paris-Robidas S, Emond V, Rajput AH, Rajput A, Calon F. Increased LINGO1 in the cerebellum of essential tremor patients. Mov Disord 2014; 29:1637-47. [PMID: 24531928 DOI: 10.1002/mds.25819] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 11/28/2013] [Accepted: 12/30/2013] [Indexed: 12/21/2022] Open
Abstract
Essential tremor (ET) is the most prevalent adult-onset movement disorder. Despite its health burden, no clear pathognomonic sign has been identified to date because of the rarity of clinicopathological studies. Moreover, treatment options are still scarce and have not significantly changed in the last 30 years, underscoring the urgent need to develop new treatment avenues. In the recent years, leucine-rich repeat (LRR) and immunoglobulin (Ig) domain-containing Nogo receptor-interacting proteins 1 and 2 (LINGO1 and LINGO2, respectively) have been increasingly regarded as possible ET modulators due to emerging genetic association studies linking LINGO with ET. We have investigated LINGO protein and messenger RNA (mRNA) expression in the cerebellum of patients with ET, patients with Parkinson's disease (PD), and a control group using Western immunoblotting and in situ hybridization. Protein levels of LINGO1, but not LINGO2, were significantly increased in the cerebellar cortex of ET patients compared with controls, particularly in individuals with longer disease duration. Compared with controls, LINGO1 protein levels were increased in the cerebellar white matter of PD and ET patients but, for the latter, only when disease duration exceeded 20 years. However, no alteration in LINGO1 mRNA was observed between groups in either the cerebellar cortex or the white matter. We observed alterations in LINGO expression in diseased brain that seemed to progress along with the disease, being initiated in the cerebellar cortex before reaching the white matter. Because LINGO up-regulation has been identified as a potential pathological response to ongoing neurodegenerative processes, the present data suggest that LINGO1 is a potential drug target for ET.
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Affiliation(s)
- Charlotte Delay
- Faculty of Pharmacy, Université Laval, Québec City, Québec, Canada; Centre de Recherche du Centre Hospitalier Universitaire de Québec, Neurosciences Axis, Québec City, Québec, Canada
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Hendrickson SL. A genome wide study of genetic adaptation to high altitude in feral Andean Horses of the páramo. BMC Evol Biol 2013; 13:273. [PMID: 24344830 PMCID: PMC3878729 DOI: 10.1186/1471-2148-13-273] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 12/03/2013] [Indexed: 12/25/2022] Open
Abstract
Background Life at high altitude results in physiological and metabolic challenges that put strong evolutionary pressure on performance due to oxidative stress, UV radiation and other factors dependent on the natural history of the species. To look for genes involved in altitude adaptation in a large herbivore, this study explored genome differentiation between a feral population of Andean horses introduced by the Spanish in the 1500s to the high Andes and their Iberian breed relatives. Results Using allelic genetic models and Fst analyses of ~50 K single nucleotide polymorphisms (SNPs) across the horse genome, 131 candidate genes for altitude adaptation were revealed (Bonferoni of p ≤ 2 × 10–7). Significant signals included the EPAS1 in the hypoxia-induction-pathway (HIF) that was previously discovered in human studies (p = 9.27 × 10-8); validating the approach and emphasizing the importance of this gene to hypoxia adaptation. Strong signals in the cytochrome P450 3A gene family (p = 1.5 ×10-8) indicate that other factors, such as highly endemic vegetation in altitude environments are also important in adaptation. Signals in tenuerin 2 (TENM2, p = 7.9 × 10-14) along with several other genes in the nervous system (gene categories representation p = 5.1 × 10-5) indicate the nervous system is important in altitude adaptation. Conclusions In this study of a large introduced herbivore, it becomes apparent that some gene pathways, such as the HIF pathway are universally important for high altitude adaptation in mammals, but several others may be selected upon based on the natural history of a species and the unique ecology of the altitude environment.
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Affiliation(s)
- Sher L Hendrickson
- Department of Biology, Shepherd University, Shepherdstown WV 25443, USA.
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Zhou J, Liu F, Zhang D, Chen B, Li Q, Zhou L, Lu LM, Tao L. Significance of MDM2-309 polymorphisms and induced corresponding plasma MDM2 levels in susceptibility to laryngeal squamous cell carcinoma. DNA Cell Biol 2013; 33:88-94. [PMID: 24325471 DOI: 10.1089/dna.2013.2220] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The tumor suppressor p53 plays a crucial role in maintaining genomic stability and tumor prevention. Murine double-minute 2 (MDM2) oncoprotein plays a pivotal role in regulating p53, and the single-nucleotide polymorphism (SNP) 309T/G SNP in the promoter region of Mdm2 has been shown to be associated with increased risk of cancer. We investigated the association between Mdm2-309 promoter polymorphism, plasma MDM2 levels, and risk of laryngeal squamous cell carcinoma (LSCC). In this case-control study, 146 patients with LSCC, 61 patients with vocal leukoplakia, and 212 healthy controls were genotyped for the Mdm2-309 T/G gene using pyrosequencing. Plasma MDM2 levels were also analyzed by enzyme-linked immunosorbent assay (ELISA). Patients with LSCC had a significantly lower frequency of GT at Mdm2-309 (odds ratio [OR]=0.50, p=0.02) than controls. The proportion of GT heterozygotes in advanced stage cases were less than that in the initial stage patients (OR: 0.36 vs. 0.63; p=0.007 and 0.16). The same result was found between cases with and without lymph node metastases (OR: 0.45 vs. 0.52; p=0.075 and 0.04). Moreover, the plasma Mdm2 concentrations of LSCC patients (343.36±14.8 pg/mL) were significantly higher than those in controls (255.76±8.2 pg/mL; p<0.01) and vocal leukoplakia patients (301.42±8.6 pg/mL; p<0.05). Patients in advanced stages and with lymph node metastasis had higher plasma MDM2 levels, while the GT genotypes (308.06±18.9 pg/mL; p=0.037) had lower MDM2 plasma levels than the TT genotypes (369.00±25.2 pg/mL). The Mdm2 SNP309 G allele is implicated as an important LSCC and a vocal leukoplakia protective factor in the Chinese Han Population, and the proportion of GT genotype was lower in advanced LSCC patients and lymph node metastasis patients. Moreover, Mdm2-309 GT genotype patients had a lower plasma MDM2 level than the TT genotypes.
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Affiliation(s)
- Jian Zhou
- 1 Department of Otolaryngology, Eye Ear Nose and Throat Hospital, Fudan University , Shanghai, China
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Jiménez-Jiménez FJ, Alonso-Navarro H, García-Martín E, Lorenzo-Betancor O, Pastor P, Agúndez JAG. Update on genetics of essential tremor. Acta Neurol Scand 2013; 128:359-71. [PMID: 23682623 DOI: 10.1111/ane.12148] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2013] [Indexed: 12/25/2022]
Abstract
Despite the research, few advances in the etiopathogenesis on essential tremor (ET) have been made to date. The high frequency of positive family history of ET and the observed high concordance rates in monozygotic compared with dizygotic twins support a major role of genetic factors in the development of ET. In addition, a possible role of environmental factors has been suggested in the etiology of ET (at least in non-familial forms). Although several gene variants in the LINGO1 gene may increase the risk of ET, to date no causative mutated genes have been identified. In this review, we summarize the studies performed on families with tremor, twin studies, linkage studies, case-control association studies, and exome sequencing in familial ET.
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Affiliation(s)
- F. J. Jiménez-Jiménez
- Section of Neurology; Hospital Universitario del Sureste; Arganda del Rey Madrid Spain
| | - H. Alonso-Navarro
- Section of Neurology; Hospital Universitario del Sureste; Arganda del Rey Madrid Spain
| | - E. García-Martín
- Department of Biochemistry and Molecular Biology; University of Extremadura; Cáceres Spain
- AMGenomics; Edificio Tajo, Avda. de la Universidad s/n; Cáceres Spain
| | - O. Lorenzo-Betancor
- Neurogenetics Laboratory; Division of Neurosciences; Center for Applied Medical Research (CIMA); University of Navarra; Pamplona Spain
- Department of Neurology; Clínica Universidad de Navarra; University of Navarra School of Medicine; Pamplona Spain
| | - P. Pastor
- Neurogenetics Laboratory; Division of Neurosciences; Center for Applied Medical Research (CIMA); University of Navarra; Pamplona Spain
- Department of Neurology; Clínica Universidad de Navarra; University of Navarra School of Medicine; Pamplona Spain
- CIBERNED; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas; Instituto de Salud Carlos III; Madrid Spain
| | - J. A. G. Agúndez
- AMGenomics; Edificio Tajo, Avda. de la Universidad s/n; Cáceres Spain
- Department of Pharmacology; University of Extremadura; Cáceres Spain
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Won S, Kwon MS, Mattheisen M, Park S, Park C, Kihara D, Cichon S, Ophoff R, Nöthen MM, Rietschel M, Baur M, Uitterlinden AG, Hofmann A, Lange C. Efficient Strategy for Detecting Gene × Gene Joint Action and Its Application in Schizophrenia. Genet Epidemiol 2013; 38:60-71. [DOI: 10.1002/gepi.21779] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 08/21/2013] [Accepted: 10/21/2013] [Indexed: 01/21/2023]
Affiliation(s)
- Sungho Won
- Department of Applied Statistics; Chung-Ang University; Seoul Korea
- Research Center for Data Science; Chung-Ang University; Seoul Korea
| | - Min-Seok Kwon
- Bioinformatics Program; Seoul National University; Seoul Korea
| | - Manuel Mattheisen
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life and Brain Center; University of Bonn; Bonn Germany
| | - Suyeon Park
- Department of Applied Statistics; Chung-Ang University; Seoul Korea
| | - Changsoon Park
- Department of Applied Statistics; Chung-Ang University; Seoul Korea
- Research Center for Data Science; Chung-Ang University; Seoul Korea
| | - Daisuke Kihara
- Department of Computer Sciences; Purdue University; West Lafayette Indiana United States of America
| | - Sven Cichon
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life and Brain Center; University of Bonn; Bonn Germany
- Institute of Neuroscience and Medicine (INM-1); Research Center Juelich; Juelich Germany
| | - Roel Ophoff
- Department of Medical Genetics, Rudolf Magnus Institute of Neuroscience; University Medical Center Utrecht; Utrecht The Netherlands
| | - Markus M. Nöthen
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life and Brain Center; University of Bonn; Bonn Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry; Central Institute of Mental Health, University of Mannheim; Mannheim Germany
| | - Max Baur
- Institute for Medical Biometry; Informatics, and Epidemiology, University of Bonn; Bonn Germany
- German Center for Neurodegenerative Diseases (DZNE); Bonn Germany
| | - Andre G. Uitterlinden
- Department of Internal Medicine; Genetics Laboratory; Eramsmus Medical Center Rotterdam; The Netherlands
- Department of Epidemiology, Erasmus University Medical Center; Rotterdam The Netherlands
| | - A. Hofmann
- Department of Epidemiology, Erasmus University Medical Center; Rotterdam The Netherlands
| | - Christoph Lange
- German Center for Neurodegenerative Diseases (DZNE); Bonn Germany
- Institute for Genomic Mathematics; University of Bonn; Bonn Germany
- Department of Biostatistics; Harvard School of Public Health; Boston Massachusetts United States of America
- Center for Genomic Medicine; Brigham and Women's Hospital; Boston Massachusetts United States of America
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Speakman JR. Functional analysis of seven genes linked to body mass index and adiposity by genome-wide association studies: a review. Hum Hered 2013; 75:57-79. [PMID: 24081222 DOI: 10.1159/000353585] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified a total of about 40 single nucleotide polymorphisms (SNPs) that show significant linkage to body mass index, a widely utilised surrogate measure of adiposity. However, only 8 of these associations have been confirmed by follow-up GWAS using more sophisticated measures of adiposity (computed tomography). Among these 8, there is a SNP close to the gene FTO which has been the subject of considerable work to diagnose its function. The remaining 7 SNPs are adjacent to, or within, the genes NEGR1, TMEM18, ETV5, FLJ35779, LINGO2, SH2B1 and GIPR, most of which are less well studied than FTO, particularly in the context of obesity. This article reviews the available data on the functions of these genes, including information gleaned from studies in humans and animal models. At present, we have virtually no information on the putative mechanism associating the genes FLJ35779 and LINGO2 to obesity. All of these genes are expressed in the brain, and for 2 of them (SH2B1 and GIPR), a direct link to the appetite regulation system is known. SH2B1 is an enhancer of intracellular signalling in the JAK-STAT pathway, and GIPR is the receptor for an appetite-linked hormone (GIP) produced by the alimentary tract. NEGR1, ETV5 and SH2B1 all have suggested roles in neurite outgrowth, and hence SNPs adjacent to these genes may affect development of the energy balance circuitry. Although the genes have central patterns of gene expression, implying a central neuronal connection to energy balance, for at least 4 of them (NEGR1, TMEM18, SH2B1 and GIPR), there are also significant peripheral functions related to adipose tissue biology. These functions may contribute to their effects on the obese phenotype.
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Affiliation(s)
- John R Speakman
- Key State Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, PR China; Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
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Testa CM. Key issues in essential tremor genetics research: Where are we now and how can we move forward? TREMOR AND OTHER HYPERKINETIC MOVEMENTS (NEW YORK, N.Y.) 2013; 3. [PMID: 23450143 PMCID: PMC3582856 DOI: 10.7916/d8q23z0z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 12/04/2012] [Indexed: 01/06/2023]
Abstract
Background Genetics research is an avenue towards understanding essential tremor (ET). Advances have been made in genetic linkage and association: there are three reported ET susceptibility loci, and mixed but growing data on risk associations. However, causal mutations have not been forthcoming. This disappointing lack of progress has opened productive discussions on challenges in ET and specifically ET genetics research, including fundamental assumptions in the field. Methods This article reviews the ET genetics literature, results to date, the open questions in ET genetics and the current challenges in addressing them. Results Several inherent ET features complicate genetic linkage and association studies: high potential phenocopy rates, inaccurate tremor self-reporting, and ET misdiagnoses are examples. Increasing use of direct examination data for subjects, family members, and controls is one current response. Smaller moves towards expanding ET phenotype research concepts into non-tremor features, clinically disputed ET subsets, and testing phenotype features instead of clinical diagnosis against genetic data are gradually occurring. The field has already moved to considering complex trait mechanisms requiring detection of combinations of rare genetic variants. Hypotheses may move further to consider novel mechanisms of inheritance, such as epigenetics. Discussion It is an exciting time in ET genetics as investigators start moving past assumptions underlying both phenotype and genetics experimental contributions, overcoming challenges to collaboration, and engaging the ET community. Multicenter collaborative efforts comprising rich longitudinal prospective phenotype data and neuropathologic analysis combined with the latest in genetics experimental design and technology will be the next wave in the field.
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Affiliation(s)
- Claudia M Testa
- Virginia Commonwealth University, Parkinson's and Movement Disorders Center, Richmond Virginia, USA
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Identification of rare recurrent copy number variants in high-risk autism families and their prevalence in a large ASD population. PLoS One 2013; 8:e52239. [PMID: 23341896 PMCID: PMC3544904 DOI: 10.1371/journal.pone.0052239] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 11/09/2012] [Indexed: 11/29/2022] Open
Abstract
Structural variation is thought to play a major etiological role in the development of autism spectrum disorders (ASDs), and numerous studies documenting the relevance of copy number variants (CNVs) in ASD have been published since 2006. To determine if large ASD families harbor high-impact CNVs that may have broader impact in the general ASD population, we used the Affymetrix genome-wide human SNP array 6.0 to identify 153 putative autism-specific CNVs present in 55 individuals with ASD from 9 multiplex ASD pedigrees. To evaluate the actual prevalence of these CNVs as well as 185 CNVs reportedly associated with ASD from published studies many of which are insufficiently powered, we designed a custom Illumina array and used it to interrogate these CNVs in 3,000 ASD cases and 6,000 controls. Additional single nucleotide variants (SNVs) on the array identified 25 CNVs that we did not detect in our family studies at the standard SNP array resolution. After molecular validation, our results demonstrated that 15 CNVs identified in high-risk ASD families also were found in two or more ASD cases with odds ratios greater than 2.0, strengthening their support as ASD risk variants. In addition, of the 25 CNVs identified using SNV probes on our custom array, 9 also had odds ratios greater than 2.0, suggesting that these CNVs also are ASD risk variants. Eighteen of the validated CNVs have not been reported previously in individuals with ASD and three have only been observed once. Finally, we confirmed the association of 31 of 185 published ASD-associated CNVs in our dataset with odds ratios greater than 2.0, suggesting they may be of clinical relevance in the evaluation of children with ASDs. Taken together, these data provide strong support for the existence and application of high-impact CNVs in the clinical genetic evaluation of children with ASD.
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Su FC, Chen CM, Chen YC, Wu YR. LINGO-2 polymorphism and the risk of Parkinson’s disease in Taiwan. Parkinsonism Relat Disord 2012; 18:609-11. [DOI: 10.1016/j.parkreldis.2011.11.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 10/30/2011] [Accepted: 11/08/2011] [Indexed: 11/30/2022]
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Liang H, Zheng W, Xu H, Lei J, Song Z, Jiang X, Zeng Z, Deng H. No evidence of association between the LINGO4 gene and essential tremor in Chinese Han patients. Parkinsonism Relat Disord 2011; 18:303-5. [PMID: 22104011 DOI: 10.1016/j.parkreldis.2011.10.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 10/01/2011] [Accepted: 10/28/2011] [Indexed: 12/17/2022]
Abstract
Essential tremor (ET) is shown an autosomal dominant mode of inheritance, with no disease-causing gene has been found. Genetic variations in the leucine-rich repeat and lg domain containing nogo receptor-interacting protein genes (LINGO1 and LINGO2) were reported to be associated with an increased risk of developing ET. To explore whether the LINGO4 gene (a homologous gene of the LINGO1 and the LINGO2 genes) plays a role in ET susceptibility, we performed genetic analysis of coding region of the LINGO4 gene in 100 patients with ET from Mainland China. Two nucleotide variants had been identified: (1) T > A transition (rs61746299), predicted to lead to the amino acid change Thr444Ser, and (2) C > T transition (rs1521179), located 12 bp downstream to the end of coding region. To evaluate whether these variants are related to ET susceptibility, we investigated a total of 150 Chinese Han ET patients (77 familial ET and 73 sporadic ET) and 300 sex, age and ethnicity matched normal controls. No significant differences in genotypic and allele distributions between patients and control subjects for rs61746299 and rs1521179 (p = 0.531 and p = 0.867 for genotypic distributions; p = 1.000 and p = 0.844 for allele distributions) were observed, suggesting variants in coding region of the LINGO4 gene may play litter or no role in the risk of ET susceptibility.
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Affiliation(s)
- Hui Liang
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
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Wo X, Han D, Sun H, Liu Y, Meng X, Bai J, Chen F, Yu Y, Jin Y, Fu S. MDM2 SNP309 contributes to tumor susceptibility: a meta-analysis. J Genet Genomics 2011; 38:341-50. [PMID: 21867960 DOI: 10.1016/j.jgg.2011.07.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 07/18/2011] [Accepted: 07/18/2011] [Indexed: 02/07/2023]
Abstract
The potentially functional polymorphism, SNP309, in the promoter region of MDM2 gene has been implicated in cancer risk, but individual published studies showed inconclusive results. To obtain a more precise estimate of the association between MDM2 SNP309 and risk of cancer, we performed a meta-analysis of 70 individual studies in 59 publications that included 26,160 cases with different types of tumors and 33,046 controls. Summary odds ratios (OR) and corresponding 95% confidence intervals (CIs) were estimated using fixed- and random-effects models when appropriate. Overall, the variant genotypes were associated with a significantly increased cancer risk for all cancer types in different genetic models (GG vs. TT: OR, 1.123; 95% CI, 1.056-1.193; GG/GT vs. TT: OR, 1.028; 95% CI, 1.006-1.050). In the stratified analyses, the increased risk remained for the studies of most types of cancers, Asian populations, and hospital- /population-based studies in different genetic models, whereas significantly decreased risk was found in prostate cancer (GG vs. TT: OR, 0.606; 95% CI, 0.407-0.903; GG/GT vs. TT: OR, 0.748; 95% CI, 0.579-0.968). In conclusion, the data of meta-analysis suggests that MDM2 SNP309 is a potential biomarker for cancer risk.
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Affiliation(s)
- Xiaoman Wo
- Laboratory of Medical Genetics, Harbin Medical University, China
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