1
|
Jiang Z, Sullivan PF, Li T, Zhao B, Wang X, Luo T, Huang S, Guan PY, Chen J, Yang Y, Stein JL, Li Y, Liu D, Sun L, Zhu H. The pivotal role of the X-chromosome in the genetic architecture of the human brain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.08.30.23294848. [PMID: 37693466 PMCID: PMC10491353 DOI: 10.1101/2023.08.30.23294848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Genes on the X-chromosome are extensively expressed in the human brain. However, little is known for the X-chromosome's impact on the brain anatomy, microstructure, and functional network. We examined 1,045 complex brain imaging traits from 38,529 participants in the UK Biobank. We unveiled potential autosome-X-chromosome interactions, while proposing an atlas outlining dosage compensation (DC) for brain imaging traits. Through extensive association studies, we identified 72 genome-wide significant trait-locus pairs (including 29 new associations) that share genetic architectures with brain-related disorders, notably schizophrenia. Furthermore, we discovered unique sex-specific associations and assessed variations in genetic effects between sexes. Our research offers critical insights into the X-chromosome's role in the human brain, underscoring its contribution to the differences observed in brain structure and functionality between sexes.
Collapse
|
2
|
Liu X, Dong L, Jiang Z, Song M, Yan P. Identifying the differentially expressed peripheral blood microRNAs in psychiatric disorders: a systematic review and meta-analysis. Front Psychiatry 2024; 15:1390366. [PMID: 38827444 PMCID: PMC11140110 DOI: 10.3389/fpsyt.2024.1390366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/25/2024] [Indexed: 06/04/2024] Open
Abstract
Background Evidence has suggested that microRNAs (miRNAs) may play an important role in the pathogenesis of psychiatric disorders (PDs), but the results remain inconclusive. We aimed to identify specific differentially expressed miRNAs and their overlapping miRNA expression profiles in schizophrenia (SZ), major depression disorder (MDD), and bipolar disorder (BD), the three major PDs. Methods The literatures up to September 30, 2023 related to peripheral blood miRNAs and PDs were searched and screened from multiple databases. The differences in miRNA levels between groups were illustrated by the standardized mean difference (SMD) and 95% confidence interval (95% CI). Results In total, 30 peripheral blood miRNAs were included in the meta-analysis, including 16 for SZ, 12 for MDD, and 2 for BD, each was reported in more than 3 independent studies. Compared with the control group, miR-181b-5p, miR-34a-5p, miR-195-5p, miR-30e-5p, miR-7-5p, miR-132-3p, miR-212-3p, miR-206, miR-92a-3p and miR-137-3p were upregulated in SZ, while miR-134-5p, miR-107 and miR-99b-5p were downregulated. In MDD, miR-124-3p, miR-132-3p, miR-139-5p, miR-182-5p, miR-221-3p, miR-34a-5p and miR-93-5p were upregulated, while miR-144-5p and miR-135a-5p were downregulated. However, we failed to identify statistically differentially expressed miRNAs in BD. Interestingly, miR-132-3p and miR-34a-5p were upregulated in both SZ and MDD. Conclusions Our study identified 13 differentially expressed miRNAs in SZ and 9 in MDD, among which miR-132-3p and miR-34a-5p were upregulated in both SZ and MDD by systematically analyzing qualified studies. These miRNAs may be used as potential biomarkers for the diagnosis of SZ and MDD in the future. Systematic Review Registration http://www.crd.york.ac.uk/PROSPERO, identifier CRD42023486982.
Collapse
Affiliation(s)
- Xiaoyan Liu
- Department of Psychiatry, Affiliated Mental Health Center & Hangzhou Seventh People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liying Dong
- Internal Medicine of Traditional Chinese Medicine, The 4th Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhaowei Jiang
- Internal Medicine of Traditional Chinese Medicine, The 4th Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Mingfen Song
- Molecular Biology Laboratory, Affiliated Mental Health Center & Hangzhou Seventh People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Pan Yan
- Molecular Biology Laboratory, Affiliated Mental Health Center & Hangzhou Seventh People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
3
|
Cosentino L, Zidda F, Dukal H, Witt SH, De Filippis B, Flor H. Low levels of Methyl-CpG binding protein 2 are accompanied by an increased vulnerability to the negative outcomes of stress exposure during childhood in healthy women. Transl Psychiatry 2022; 12:506. [PMID: 36481643 PMCID: PMC9731965 DOI: 10.1038/s41398-022-02259-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
Numerous mental illnesses arise following stressful events in vulnerable individuals, with females being generally more affected than males. Adverse childhood experiences are known to increase the risk of developing psychopathologies and DNA methylation was demonstrated to drive the long-lasting effects of early life stress and promote stress susceptibility. Methyl-CpG binding protein 2 (MECP2), an X-linked reader of the DNA methylome, is altered in many mental disorders of stress origin, suggesting MECP2 as a marker of stress susceptibility; previous works also suggest a link between MECP2 and early stress experiences. The present work explored whether a reduced expression of MECP2 is paralleled by an increased vulnerability to the negative outcomes of stress exposure during childhood. To this aim, blood MECP2 mRNA levels were analyzed in 63 people without history of mental disorders and traits pertaining to depressive and anxiety symptom clusters were assessed as proxies of the vulnerability to develop stress-related disorders; stress exposure during childhood was also evaluated. Using structural equation modeling, we demonstrate that reduced MECP2 expression is accompanied by symptoms of anxiety/depression in association with exposure to stress in early life, selectively in healthy women. These results suggest a gender-specific involvement of MECP2 in the maladaptive outcomes of childhood adversities, and shed new light on the complex biology underlying gender bias in stress susceptibility.
Collapse
Affiliation(s)
- Livia Cosentino
- grid.416651.10000 0000 9120 6856Center for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità, Roma, Italy ,grid.7700.00000 0001 2190 4373Institute of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Francesca Zidda
- grid.7700.00000 0001 2190 4373Institute of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Helene Dukal
- grid.7700.00000 0001 2190 4373Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Stephanie H. Witt
- grid.7700.00000 0001 2190 4373Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Bianca De Filippis
- Center for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità, Roma, Italy.
| | - Herta Flor
- Institute of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
| |
Collapse
|
4
|
Rodríguez-Urgellés E, Rodríguez-Navarro I, Ballasch I, Del Toro D, Del Castillo I, Brito V, Alberch J, Giralt A. Postnatal Foxp2 regulates early psychiatric-like phenotypes and associated molecular alterations in the R6/1 transgenic mouse model of Huntington's disease. Neurobiol Dis 2022; 173:105854. [PMID: 36029989 DOI: 10.1016/j.nbd.2022.105854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/11/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Huntington's Disease (HD) is a devastating disorder characterized by a triad of motor, psychiatric and cognitive manifestations. Psychiatric and emotional symptoms appear at early stages of the disease which are consistently described by patients and caregivers among the most disabling. Here, we show for the first time that Foxp2 is strongly associated with some psychiatric-like disturbances in the R6/1 mouse model of HD. First, 4-week-old (juvenile) R6/1 mice behavioral phenotype was characterized by an increased impulsive-like behavior and less aggressive-like behavior. In this line, we identified an early striatal downregulation of Foxp2 protein starting as soon as at postnatal day 15 that could explain such deficiencies. Interestingly, the rescue of striatal Foxp2 levels from postnatal stages completely reverted the impulsivity-phenotype and partially the social impairments concomitant with a rescue of dendritic spine pathology. A mass spectrometry study indicated that the rescue of spine loss was associated with an improvement of several altered proteins related with cytoskeleton dynamics. Finally, we reproduced and mimicked the impulsivity and social deficits in wild type mice by reducing their striatal Foxp2 expression from postnatal stages. Overall, these results imply that early postnatal reduction of Foxp2 might contribute to the appearance of some of the early psychiatric symptoms in HD.
Collapse
Affiliation(s)
- Ened Rodríguez-Urgellés
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Irene Rodríguez-Navarro
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Iván Ballasch
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Daniel Del Toro
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Ignacio Del Castillo
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Verónica Brito
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Jordi Alberch
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain; Production and Validation Center of Advanced Therapies (Creatio), Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain.
| | - Albert Giralt
- Departament de Biomedicina, Facultat de Medicina, Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain; Production and Validation Center of Advanced Therapies (Creatio), Faculty of Medicine and Health Science, University of Barcelona, 08036 Barcelona, Spain.
| |
Collapse
|
5
|
Tayel SI, Muharram NM, Fotoh DS, Elbarbary HS, Abd-Elhafiz HI, El-Masry EA, Taha AE, Soliman SE. Prognostic Impact of Genetic Variants of MECP2 and TIRAP on Clinical Outcomes of Systemic Lupus Erythematosus with and without Nephritis. Biomolecules 2021; 11:1378. [PMID: 34572591 PMCID: PMC8466489 DOI: 10.3390/biom11091378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/11/2021] [Accepted: 09/12/2021] [Indexed: 12/16/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune illness with a growing prevalence in many populations. Few studies have examined genetic predisposition to SLE, so we aimed to examine the clinical impact of the genetic polymorphisms MECP2 rs2734647and TIRAP rs8177374 on the outcomes and therapeutic precision of SLE with and without nephritis. This study included 110 SLE patients-divided into 63 with lupus nephritis (LN), and 47 without nephritis-and 100 controls. Laboratory measurements including CRP, ESR, ACR, CBC, anti-ds-DNA, vitamin A, C3, and C4 were carried out, along with genotyping of MECP2 rs2734647and TIRAP rs8177374 by real-time PCR and sequencing. Treg %, vitamin A, C3, and C4 were lower, whereas Th17 % was higher, in patients vs. controls (p < 0.001). The T allele of MECP2 rs2734647 was higher in LN than in non-nephritis and control subjects. Moreover, the T allele of TIRAP rs8177374 was higher in LN than in non-nephritis and control subjects. The MECP2 and TIRAP genes could play a role in predisposition to SLE, and can also predict disease progress to nephritis, helping to personalize medicine.
Collapse
Affiliation(s)
- Safaa I. Tayel
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Shebin el Kom 32511, Egypt; (N.M.M.); (S.E.S.)
- Medical Biochemistry Unit, College of Medicine, Al Baha University, Al Baha 65779, Saudi Arabia
| | - Nashwa M. Muharram
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Shebin el Kom 32511, Egypt; (N.M.M.); (S.E.S.)
- Medical Biochemistry Unit, College of Medicine, Al Baha University, Al Baha 65779, Saudi Arabia
| | - Dina S. Fotoh
- Physical Medicine, Rheumatology and Rehabilitation Department, Faculty of Medicine, Menoufia University, Shebin el Kom 32511, Egypt;
| | - Hany S. Elbarbary
- Renal Unit, Department of Internal Medicine, Faculty of Medicine, Menoufia University, Shebin el Kom 32511, Egypt;
- Renal Unit, Department of Internal Medicine, College of Medicine, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Huda I. Abd-Elhafiz
- Clinical Pharmacology Department, Faculty of Medicine, Menoufia University, Shebin el Kom 32511, Egypt;
| | - Eman A. El-Masry
- Microbiology and Immunology Unit, Department of Pathology, College of Medicine, Jouf University, Sakaka 72388, Saudi Arabia; (E.A.E.-M.); (A.E.T.)
- Medical Microbiology and Immunology Department, Faculty of Medicine, Menoufia University, Shebin el Kom 32511, Egypt
| | - Ahmed E. Taha
- Microbiology and Immunology Unit, Department of Pathology, College of Medicine, Jouf University, Sakaka 72388, Saudi Arabia; (E.A.E.-M.); (A.E.T.)
- Medical Microbiology and Immunology Department, Faculty of Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Shimaa E. Soliman
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Shebin el Kom 32511, Egypt; (N.M.M.); (S.E.S.)
- Medical Biochemistry Unit, Department of Pathology, College of Medicine, Qassim University, Buraydah 51452, Saudi Arabia
| |
Collapse
|
6
|
Bodemer C, Diociaiuti A, Hadj-Rabia S, Robert MP, Desguerre I, Manière MC, de la Dure-Molla M, De Liso P, Federici M, Galeotti A, Fusco F, Fraitag S, Demily C, Taieb C, Valeria Ursini M, El Hachem M, Steffann J. Multidisciplinary consensus recommendations from a European network for the diagnosis and practical management of patients with incontinentia pigmenti. J Eur Acad Dermatol Venereol 2021; 34:1415-1424. [PMID: 32678511 DOI: 10.1111/jdv.16403] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 02/28/2020] [Accepted: 03/10/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Incontinentia pigmenti (IP) is a rare multisystemic X-linked dominant genetic disorder characterized by highly diagnostic skin lesions. The disease can be misdiagnosed in infants, and complications affecting the eyes and/or the brain can be severe. Our objective was to highlight the urgency of an appropriate diagnosis and management strategy, as soon as the first symptoms appear, and the need for a well-codified monitoring strategy for each child. METHODS An in-depth literature review using a large number of databases was conducted. The selection criteria for articles were literature review articles on the disease, case series and retrospective studies based on the disease, clinical studies (randomized or not) on treatment, articles discussing patient care and management (treatment, diagnosis, care pathways), and recommendations. The research period was from 2000 until 2018. A group of multidisciplinary experts in IP management was involved, issued from different healthcare providers of the European Network for Rare Skin Diseases (ERN-Skin). The final recommendations have been submitted to two patient representative associations and to a general practitioner and a neonatal specialist prior to their finalization. RESULTS AND CONCLUSION The diagnosis of IP must be promptly performed to detect potential extracutaneous manifestations, thus allowing the timely implementation of specific therapeutic and monitoring strategies. Eye involvement can be a therapeutic urgency, and central nervous system (CNS) involvement requires a very rigorous long-term follow-up. Assessments and patient support should take into account the possible co-occurrence of various symptoms (including motor, visual and cognitive symptoms).
Collapse
Affiliation(s)
- C Bodemer
- Department of Dermatology, Reference Centre for Genodermatoses (MAGEC) Necker Enfants Malades Hospital, Imagine Institute, FIMARAD, ERN-Skin, Paris Centre University, Paris, France
| | - A Diociaiuti
- Department of Dermatology, ERN-Skin, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - S Hadj-Rabia
- Department of Dermatology, Reference Centre for Genodermatoses (MAGEC) Necker Enfants Malades Hospital, Imagine Institute, FIMARAD, ERN-Skin, Paris Centre University, Paris, France
| | - M P Robert
- Department of Ophthalmology, Imagine Institute, Necker Enfants Malades Hospital, Paris Centre University France, Paris, France
| | - I Desguerre
- Department of Pediatric Neurology, Imagine Institute, Necker Enfants Malades Hospital, Paris Centre University France, Paris, France
| | - M-C Manière
- Department of Pediatric Odontology, Expert Centre (MAFACE), Strasbourg Hospital, Université de Chirurgie Dentaire, Strasbourg, France
| | - M de la Dure-Molla
- Expert Centre for Rare Face and Oral Cavity Malformations, Rothschild Cavity, Paris, France
| | - P De Liso
- Neurology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - M Federici
- Ophthalmology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - A Galeotti
- Dentistry Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - F Fusco
- Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', IGB-CNR, Naples, Italy
| | - S Fraitag
- Department of Pathology, Necker Enfants Malades Hospital, Paris, France
| | - C Demily
- Reference Centre Génopsy, CRMR Maladies Rares à Expression Psychiatrique, Centre Hospitalier Le Vinatier, Bron, France
| | - C Taieb
- National Network for Rare Diseases FIMARA, Necker Enfants Malades Hospital, Paris, France
| | - M Valeria Ursini
- Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', IGB-CNR, Naples, Italy
| | - M El Hachem
- Department of Dermatology, ERN-Skin, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - J Steffann
- Department of Genetics, Imagine Institute, Necker Enfants Malades Hospital, Paris Centre Université, Paris, France
| |
Collapse
|
7
|
Xiang B, Yang J, Zhang J, Yu M, Huang C, He W, Lei W, Chen J, Liu K. The role of genes affected by human evolution marker GNA13 in schizophrenia. Prog Neuropsychopharmacol Biol Psychiatry 2020; 98:109764. [PMID: 31676466 DOI: 10.1016/j.pnpbp.2019.109764] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/04/2019] [Accepted: 09/20/2019] [Indexed: 11/20/2022]
Abstract
Numerous variants associated with increased risk for SCZ have undergone positive selection and were associated with human brain development, but which brain regions and developmental stages were influenced by the positive selection for SCZ risk alleles are unclear. We analyzed SCZ using summary statistics from a genome-wide association study (GWAS) from the Psychiatric Genomics Consortium (PGC). Machine-learning scores were used to investigate two natural-selection scenarios: complete selection (loci where a selected allele has reached fixation) and incomplete selection (loci where a selected allele has not yet reached fixation). Based on the p value of single nucleotide polymorphisms (SNPs) with selection scores in the top 5%, we formed five subgroups: p < 0.0001, 0.001, 0.01, 0.05, or 0.1. We found that 48 and 29 genes (p < 0.0001) in complete and incomplete selection, respectively, were enrichedfor the transcriptionalco-expressionprofilein theprenatal dorsolateral prefrontal cortex (DFC), inferior parietal cortex (IPC), and ventrolateral prefrontal cortex (VFC). Core genes (GNA13, TBC1D19, and ZMYM4) involved in regulating early brain development were identified in these three brain regions. RNA sequencing for primary cortical neurons that were transfected Gna13 overexpressed lentivirus demonstrated that 135 gene expression levels changed in the Gna13 overexpressed groups compared with the controls. Gene-set analysis identified important associations among common variants of these 13 genes, which were associated with neurodevelopment and putamen volume [p = 0.031; family-wise error correction (FWEC)], SCZ (p = 0.022; FWEC). The study indicate that certain SCZ risk alleles were likely to undergo positive selection during human evolution due to their involvement in the development of prenatal DFC, IPC and VFC, and suggest that SCZ is related to abnormal neurodevelopment.
Collapse
Affiliation(s)
- Bo Xiang
- Department of Psychiatry, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China.
| | - Juanjuan Yang
- Department of cell Biology, School of Biology and Basic Medical, Soochow University, Suzhou, Jiangsu Province, China
| | - Jin Zhang
- Department of Psychiatry, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Minglan Yu
- Medical Laboratory Center, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Chaohua Huang
- Department of Psychiatry, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Wenying He
- Department of Psychiatry, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Wei Lei
- Department of Psychiatry, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Jing Chen
- Department of Psychiatry, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China
| | - Kezhi Liu
- Department of Psychiatry, Nuclear Medicine and Molecular Imaging Key Laboratory of Sichuan Province, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan Province, China.
| |
Collapse
|
8
|
Xiao X, Yu H, Li J, Wang L, Li L, Chang H, Zhang D, Yue W, Li M. Further evidence for the association between LRP8 and schizophrenia. Schizophr Res 2020; 215:499-505. [PMID: 28495490 DOI: 10.1016/j.schres.2017.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 04/25/2017] [Accepted: 05/01/2017] [Indexed: 11/25/2022]
Abstract
Previous studies (including genome-wide association study (GWAS) and candidate gene studies) have revealed the important roles of genetic risk factors in schizophrenia, and RELN has been identified as a risk gene for this illness. We recently found that the low-density lipoprotein receptor-related protein 8 (LRP8), a receptor of Reelin (the protein encoded by RELN), was significantly associated with schizophrenia and bipolar disorder in European populations. To further enhance our understanding of its role in the risk of psychiatric illnesses, we conducted meta-analyses of a higher density of single nucleotide polymorphisms (SNPs, N=173) in LRP8 to understand their associations with schizophrenia in much larger samples (39,400 cases and 50,357 controls) from populations of European, Chinese and African American ancestries. The significant risk SNPs then underwent further analyses to understand their correlations with bipolar disorder and anxiety disorders, as well as LRP8 expression. We observed that rs5177 in the 3' untranslated region (3'UTR) of LRP8 was associated with schizophrenia and other psychiatric disorders, and rs5177 was also associated with LRP8 mRNA expression. These data further support LRP8 as a schizophrenia susceptibility gene, and suggest that this variant is likely a risk locus in general populations.
Collapse
Affiliation(s)
- Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Hao Yu
- Peking University Sixth Hospital & Institute of Mental Health, Beijing, China; National Clinical Research Center for Mental Disorders & Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China; Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China; Department of Psychiatry, Jining Medical University, Jining, Shandong, China
| | - Jun Li
- Peking University Sixth Hospital & Institute of Mental Health, Beijing, China; National Clinical Research Center for Mental Disorders & Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China
| | - Lu Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Lingyi Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Hong Chang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Dai Zhang
- Peking University Sixth Hospital & Institute of Mental Health, Beijing, China; National Clinical Research Center for Mental Disorders & Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China
| | - Weihua Yue
- Peking University Sixth Hospital & Institute of Mental Health, Beijing, China; National Clinical Research Center for Mental Disorders & Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing, China.
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China.
| |
Collapse
|
9
|
Two Thalamic Regions Screened Using Laser Capture Microdissection with Whole Human Genome Microarray in Schizophrenia Postmortem Samples. SCHIZOPHRENIA RESEARCH AND TREATMENT 2020; 2020:5176834. [PMID: 32566292 PMCID: PMC7285254 DOI: 10.1155/2020/5176834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/25/2020] [Accepted: 04/02/2020] [Indexed: 12/23/2022]
Abstract
We used whole human genome microarray screening of highly enriched neuronal populations from two thalamic regions in postmortem samples from subjects with schizophrenia and controls to identify brain region-specific gene expression changes and possible transcriptional targets. The thalamic anterior nucleus is reciprocally connected to anterior cingulate, a schizophrenia-affected cortical region, and is also thought to be schizophrenia affected; the other thalamic region is not. Using two regions in the same subject to identify disease-relevant gene expression differences was novel and reduced intersubject heterogeneity of findings. We found gene expression differences related to miRNA-137 and other SZ-associated microRNAs, ELAVL1, BDNF, DISC-1, MECP2 and YWHAG associated findings, synapses, and receptors. Manual curation of our data may support transcription repression.
Collapse
|
10
|
Yin L, Chau CKL, Sham PC, So HC. Integrating Clinical Data and Imputed Transcriptome from GWAS to Uncover Complex Disease Subtypes: Applications in Psychiatry and Cardiology. Am J Hum Genet 2019; 105:1193-1212. [PMID: 31785786 PMCID: PMC6904812 DOI: 10.1016/j.ajhg.2019.10.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 10/22/2019] [Indexed: 12/19/2022] Open
Abstract
Classifying subjects into clinically and biologically homogeneous subgroups will facilitate the understanding of disease pathophysiology and development of targeted prevention and intervention strategies. Traditionally, disease subtyping is based on clinical characteristics alone, but subtypes identified by such an approach may not conform exactly to the underlying biological mechanisms. Very few studies have integrated genomic profiles (e.g., those from GWASs) with clinical symptoms for disease subtyping. Here we proposed an analytic framework capable of finding complex diseases subgroups by leveraging both GWAS-predicted gene expression levels and clinical data by a multi-view bicluster analysis. This approach connects SNPs to genes via their effects on expression, so the analysis is more biologically relevant and interpretable than a pure SNP-based analysis. Transcriptome of different tissues can also be readily modeled. We also proposed various evaluation metrics for assessing clustering performance. Our framework was able to subtype schizophrenia subjects into diverse subgroups with different prognosis and treatment response. We also applied the framework to the Northern Finland Birth Cohort (NFBC) 1966 dataset and identified high and low cardiometabolic risk subgroups in a gender-stratified analysis. The prediction strength by cross-validation was generally greater than 80%, suggesting good stability of the clustering model. Our results suggest a more data-driven and biologically informed approach to defining metabolic syndrome and subtyping psychiatric disorders. Moreover, we found that the genes "blindly" selected by the algorithm are significantly enriched for known susceptibility genes discovered in GWASs of schizophrenia or cardiovascular diseases. The proposed framework opens up an approach to subject stratification.
Collapse
Affiliation(s)
- Liangying Yin
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Carlos K L Chau
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Pak-Chung Sham
- Centre for Genomic Sciences, University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, University of Hong Kong, Hong Kong SAR, China; State Key Laboratory for Cognitive and Brain Sciences, University of Hong Kong, Hong Kong SAR, China
| | - Hon-Cheong So
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Kunming Zoology Institute of Zoology and The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K.L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Hong Kong SAR, China; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518000, China.
| |
Collapse
|
11
|
Prata DP, Costa-Neves B, Cosme G, Vassos E. Unravelling the genetic basis of schizophrenia and bipolar disorder with GWAS: A systematic review. J Psychiatr Res 2019; 114:178-207. [PMID: 31096178 DOI: 10.1016/j.jpsychires.2019.04.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 04/08/2019] [Accepted: 04/10/2019] [Indexed: 01/02/2023]
Abstract
OBJECTIVES To systematically review findings of GWAS in schizophrenia (SZ) and in bipolar disorder (BD); and to interpret findings, with a focus on identifying independent replications. METHOD PubMed search, selection and review of all independent GWAS in SZ or BD, published since March 2011, i.e. studies using non-overlapping samples within each article, between articles, and with those of the previous review (Li et al., 2012). RESULTS From the 22 GWAS included in this review, the genetic associations surviving standard GWAS-significance were for genetic markers in the regions of ACSL3/KCNE4, ADCY2, AMBRA1, ANK3, BRP44, DTL, FBLN1, HHAT, INTS7, LOC392301, LOC645434/NMBR, LOC729457, LRRFIP1, LSM1, MDM1, MHC, MIR2113/POU3F2, NDST3, NKAPL, ODZ4, PGBD1, RENBP, TRANK1, TSPAN18, TWIST2, UGT1A1/HJURP, WHSC1L1/FGFR1 and ZKSCAN4. All genes implicated across both reviews are discussed in terms of their function and implication in neuropsychiatry. CONCLUSION Taking all GWAS to date into account, AMBRA1, ANK3, ARNTL, CDH13, EFHD1 (albeit with different alleles), MHC, PLXNA2 and UGT1A1 have been implicated in either disorder in at least two reportedly non-overlapping samples. Additionally, evidence for a SZ/BD common genetic basis is most strongly supported by the implication of ANK3, NDST3, and PLXNA2.
Collapse
Affiliation(s)
- Diana P Prata
- Instituto de Biofísica e Engenharia Biomédica, Faculdade de Ciências, Universidade de Lisboa, Portugal; Centre for Neuroimaging Sciences, Institute of Psychiatry, Psychology & Neuroscience, King's College London, 16 De Crespigny Park, SE5 8AF, UK; Instituto Universitário de Lisboa (ISCTE-IUL), Centro de Investigação e Intervenção Social, Lisboa, Portugal.
| | - Bernardo Costa-Neves
- Lisbon Medical School, University of Lisbon, Av. Professor Egas Moniz, 1649-028, Lisbon, Portugal; Centro Hospitalar Psiquiátrico de Lisboa, Av. do Brasil, 53 1749-002, Lisbon, Portugal
| | - Gonçalo Cosme
- Instituto de Biofísica e Engenharia Biomédica, Faculdade de Ciências, Universidade de Lisboa, Portugal
| | - Evangelos Vassos
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, 16 De Crespigny Park, SE5 8AF, UK
| |
Collapse
|
12
|
Zuo XY, Feng QS, Sun J, Wei PP, Chin YM, Guo YM, Xia YF, Li B, Xia XJ, Jia WH, Liu JJ, Khoo ASB, Mushiroda T, Ng CC, Su WH, Zeng YX, Bei JX. X-chromosome association study reveals genetic susceptibility loci of nasopharyngeal carcinoma. Biol Sex Differ 2019; 10:13. [PMID: 30909962 PMCID: PMC6434801 DOI: 10.1186/s13293-019-0227-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 02/27/2019] [Indexed: 02/08/2023] Open
Abstract
Background The male predominance in the incidence of nasopharyngeal carcinoma (NPC) suggests the contribution of the X chromosome to the susceptibility of NPC. However, no X-linked susceptibility loci have been examined by genome-wide association studies (GWASs) for NPC by far. Methods To understand the contribution of the X chromosome in NPC susceptibility, we conducted an X chromosome-wide association analysis on 1615 NPC patients and 1025 healthy controls of Guangdong Chinese, followed by two validation analyses in Taiwan Chinese (n = 562) and Malaysian Chinese (n = 716). Results Firstly, the proportion of variance of X-linked loci over phenotypic variance was estimated in the discovery samples, which revealed that the phenotypic variance explained by X chromosome polymorphisms was estimated to be 12.63% (non-dosage compensation model) in males, as compared with 0.0001% in females. This suggested that the contribution of X chromosome to the genetic variance of NPC should not be neglected. Secondly, association analysis revealed that rs5927056 in DMD gene achieved X chromosome-wide association significance in the discovery sample (OR = 0.81, 95% CI 0.73–0.89, P = 1.49 × 10−5). Combined analysis revealed rs5927056 for DMD gene with suggestive significance (P = 9.44 × 10−5). Moreover, the female-specific association of rs5933886 in ARHGAP6 gene (OR = 0.62, 95%CI: 0.47–0.81, P = 4.37 × 10−4) was successfully replicated in Taiwan Chinese (P = 1.64 × 10−2). rs5933886 also showed nominally significant gender × SNP interaction in both Guangdong (P = 6.25 × 10−4) and Taiwan datasets (P = 2.99 × 10−2). Conclusion Our finding reveals new susceptibility loci at the X chromosome conferring risk of NPC and supports the value of including the X chromosome in large-scale association studies. Electronic supplementary material The online version of this article (10.1186/s13293-019-0227-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xiao-Yu Zuo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Qi-Sheng Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Jian Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Pan-Pan Wei
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Yoon-Ming Chin
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Yun-Miao Guo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Yun-Fei Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Bo Li
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China.,RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, People's Republic of China
| | - Xiao-Jun Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China
| | - Jian-Jun Liu
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore, 138672, Singapore
| | - Alan Soo-Beng Khoo
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, 50603, Kuala Lumpur, Malaysia
| | - Taisei Mushiroda
- Laboratory for International Alliance on Genomic Research, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Ching-Ching Ng
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Wen-Hui Su
- Department of Biomedical Sciences, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung Molecular Medicine Research Center, Chang Gung University, Taoyuan, 333, Taiwan. .,Department of Otolaryngology, Chang Gung Memorial Hospital, Linkou, Taoyuan, 333, Taiwan.
| | - Yi-Xin Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China.
| | - Jin-Xin Bei
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, People's Republic of China. .,Center for Precision Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.
| |
Collapse
|
13
|
Vadgama N, Pittman A, Simpson M, Nirmalananthan N, Murray R, Yoshikawa T, De Rijk P, Rees E, Kirov G, Hughes D, Fitzgerald T, Kristiansen M, Pearce K, Cerveira E, Zhu Q, Zhang C, Lee C, Hardy J, Nasir J. De novo single-nucleotide and copy number variation in discordant monozygotic twins reveals disease-related genes. Eur J Hum Genet 2019; 27:1121-1133. [PMID: 30886340 DOI: 10.1038/s41431-019-0376-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/18/2019] [Accepted: 03/01/2019] [Indexed: 01/11/2023] Open
Abstract
Recent studies have demonstrated genetic differences between monozygotic (MZ) twins. To test the hypothesis that early post-twinning mutational events associate with phenotypic discordance, we investigated a cohort of 13 twin pairs (n = 26) discordant for various clinical phenotypes using whole-exome sequencing and screened for copy number variation (CNV). We identified a de novo variant in PLCB1, a gene involved in the hydrolysis of lipid phosphorus in milk from dairy cows, associated with lactase non-persistence, and a variant in the mitochondrial complex I gene MT-ND5 associated with amyotrophic lateral sclerosis (ALS). We also found somatic variants in multiple genes (TMEM225B, KBTBD3, TUBGCP4, TFIP11) in another MZ twin pair discordant for ALS. Based on the assumption that discordance between twins could be explained by a common variant with variable penetrance or expressivity, we screened the twin samples for known pathogenic variants that are shared and identified a rare deletion overlapping ARHGAP11B, in the twin pair manifesting with either schizotypal personality disorder or schizophrenia. Parent-offspring trio analysis was implemented for two twin pairs to assess potential association of variants of parental origin with susceptibility to disease. We identified a de novo variant in RASD2 shared by 8-year-old male twins with a suspected diagnosis of autism spectrum disorder (ASD) manifesting as different traits. A de novo CNV duplication was also identified in these twins overlapping CD38, a gene previously implicated in ASD. In twins discordant for Tourette's syndrome, a paternally inherited stop loss variant was detected in AADAC, a known candidate gene for the disorder.
Collapse
Affiliation(s)
- Nirmal Vadgama
- Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Alan Pittman
- Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Michael Simpson
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | | | - Robin Murray
- Institute of Psychiatry, Psychology, and Neuroscience, King's College, London, UK
| | - Takeo Yoshikawa
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
| | - Peter De Rijk
- Applied Molecular Genomics Group, University of Antwerp, Antwerp, Belgium
| | - Elliott Rees
- Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - George Kirov
- Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Deborah Hughes
- Institute of Neurology, University College London, London, WC1N 3BG, UK
| | | | - Mark Kristiansen
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Kerra Pearce
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Eliza Cerveira
- Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Qihui Zhu
- Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Chengsheng Zhang
- Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Charles Lee
- Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - John Hardy
- Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Jamal Nasir
- Cell Biology and Genetics Research Centre, St. George's University of London, London, UK. .,Molecular Biosciences Research Group, University of Northampton, Northampton, NN1 5PH, UK.
| |
Collapse
|
14
|
Bache WK, DeLisi LE. The Sex Chromosome Hypothesis of Schizophrenia: Alive, Dead, or Forgotten? A Commentary and Review. MOLECULAR NEUROPSYCHIATRY 2018; 4:83-89. [PMID: 30397596 DOI: 10.1159/000491489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/22/2018] [Indexed: 12/14/2022]
Abstract
The X chromosome has long been an intriguing site for harboring genes that have importance in brain development and function. It has received the most attention for having specific genes underlying the X-linked inherited intellectual disabilities, but has also been associated with schizophrenia in a number of early studies. An X chromosome hypothesis for a genetic predisposition for schizophrenia initially came from the X chromosome anomaly population data showing an excess of schizophrenia in Klinefelter's (XXY) males and triple X (XXX) females. Crow and colleagues later expanded the X chromosome hypothesis to include the possibility of a locus on the Y chromosome and, specifically, genes on X that escaped inactivation and are X-Y homologous loci. Some new information about possible risk loci on these chromosomes has come from the current large genetic consortia genome-wide association studies, suggesting that perhaps this hypothesis needs to be revisited for some schizophrenias. The following commentary reviews the early and more recent literature supporting or refuting this dormant hypothesis and emphasizes the possible candidate genes still of interest that could be explored in further studies.
Collapse
Affiliation(s)
- William K Bache
- VA Boston Healthcare System, Brockton, Massachusetts, USA.,Harvard South Shore Residency Program, Brockton, Massachusetts, USA
| | - Lynn E DeLisi
- VA Boston Healthcare System, Brockton, Massachusetts, USA.,Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
15
|
Yin L, Cheung EFC, Chen RYL, Wong EHM, Sham PC, So HC. Leveraging genome-wide association and clinical data in revealing schizophrenia subgroups. J Psychiatr Res 2018; 106:106-117. [PMID: 30312963 DOI: 10.1016/j.jpsychires.2018.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 09/13/2018] [Accepted: 09/18/2018] [Indexed: 02/04/2023]
Abstract
Schizophrenia (SCZ) has long been recognized as a highly heterogeneous disorder. Patients differed in their clinical manifestations, prognosis, and underlying pathophysiologies. Here we presented and applied a framework for finding subtypes of SCZ utilizing genome-wide association study (GWAS) and clinical data. We postulated that genetic information may help stratify patient into useful subgroups, and incorporation of other clinical information and cognitive profiles will further improve patient subtyping. We conducted cluster analysis in 387 Hong Kong Chinese with SCZ. First we performed 'single-view' clustering using genetic or clinical data alone, then proceeded to 'multi-view' clustering (MVC) accounting for both types of information. We validated clustering results by assessing subgroup differences in various outcomes. We found significant differences in outcomes including treatment response, disease course and symptom severity (Simes overall p-value using MVC = 1.64E-9). Overall speaking, we identified three subgroups with good, intermediate and poor prognosis respectively. MVC generally out-performed single-view methods. The analysis was repeated for different sets of input SNPs, and stratified analysis of male and female patients, and the results remained largely robust. We also found significant enrichment for SCZ loci among the SNPs selected by the cluster algorithm. Numerous selected genes (e.g. NRG1, ERBB4, NRXN1, ANK3) and pathways (e.g. neuregulin-ErbB4 and calcium signaling) were implicated in SCZ or related pathophysiological processes. This is first study to combine both genetic and clinical data for subtyping SCZ, and to employ genome-wide SNP data in cluster analysis of a complex disease. This work points to a new way of GWAS analysis of translational potential.
Collapse
Affiliation(s)
- Liangying Yin
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Eric Fuk-Chi Cheung
- Castle Peak Hospital, Hong Kong; Department of Psychiatry, University of Hong Kong, Hong Kong
| | | | | | - Pak-Chung Sham
- Department of Psychiatry, University of Hong Kong, Hong Kong; Centre for Genomic Sciences, University of Hong Kong, Hong Kong; State Key Laboratory for Cognitive and Brain Sciences, University of Hong Kong, Hong Kong
| | - Hon-Cheong So
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong; KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Kunming Zoology Institute of Zoology and the Chinese University of Hong Kong, China.
| |
Collapse
|
16
|
Liu J, Li M, Luo XJ, Su B. Systems-level analysis of risk genes reveals the modular nature of schizophrenia. Schizophr Res 2018; 201:261-269. [PMID: 29789256 DOI: 10.1016/j.schres.2018.05.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 05/10/2018] [Accepted: 05/12/2018] [Indexed: 12/31/2022]
Abstract
Schizophrenia (SCZ) is a complex mental disorder with high heritability. Genetic studies (especially recent genome-wide association studies) have identified many risk genes for schizophrenia. However, the physical interactions among the proteins encoded by schizophrenia risk genes remain elusive and it is not known whether the identified risk genes converge on common molecular networks or pathways. Here we systematically investigated the network characteristics of schizophrenia risk genes using the high-confidence protein-protein interactions (PPI) from the human interactome. We found that schizophrenia risk genes encode a densely interconnected PPI network (P = 4.15 × 10-31). Compared with the background genes, the schizophrenia risk genes in the interactome have significantly higher degree (P = 5.39 × 10-11), closeness centrality (P = 7.56 × 10-11), betweeness centrality (P = 1.29 × 10-11), clustering coefficient (P = 2.22 × 10-2), and shorter average shortest path length (P = 7.56 × 10-11). Based on the densely interconnected PPI network, we identified 48 hub genes and 4 modules formed by highly interconnected schizophrenia genes. We showed that the proteins encoded by schizophrenia hub genes have significantly more direct physical interactions. Gene ontology (GO) analysis revealed that cell adhesion, cell cycle, immune system response, and GABR-receptor complex categories were enriched in the modules formed by highly interconnected schizophrenia risk genes. Our study reveals that schizophrenia risk genes encode a densely interconnected molecular network and demonstrates the modular nature of schizophrenia.
Collapse
Affiliation(s)
- Jiewei Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
| |
Collapse
|
17
|
Like father like daughter: sex-specific parent-of-origin effects in the transmission of liability for psychotic symptoms to offspring. J Dev Orig Health Dis 2018; 10:100-107. [PMID: 30156170 DOI: 10.1017/s2040174418000612] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Children of parents with major mood and psychotic disorders are at increased risk of psychopathology, including psychotic symptoms. It has been suggested that the risk of psychosis may be more often transmitted from parent to opposite-sex offspring (e.g., from father to daughter) than to same-sex offspring (e.g., from father to son). To test whether sex-specific transmission extends to early manifestations of psychosis, we examined sex-specific contributions to psychotic symptoms among offspring of mothers and fathers with depression, bipolar disorder and schizophrenia. We assessed psychotic symptoms in 309 offspring (160 daughters and 149 sons) aged 8-24 years (mean=13.1, s.d.=4.3), of whom 113 had a mother with schizophrenia, bipolar disorder or major depression and 43 had a father with schizophrenia, bipolar disorder or major depression. In semi-structured interviews, 130 (42%) offspring had definite psychotic symptoms established and confirmed by psychiatrists on one or more assessments. We tested the effects of mental illness in parents on same-sex and opposite-sex offspring psychotic symptoms in mixed-effect logistic regression models. Psychotic symptoms were more prevalent among daughters of affected fathers and sons of affected mothers than among offspring of the same sex as their affected parent. Mental illness in the opposite-sex parent increased the odds of psychotic symptoms (odds ratio (OR)=2.65, 95% confidence interval (CI) 1.43-4.91, P=0.002), but mental illness in the same-sex parent did not have a significant effect on psychotic symptoms in offspring (OR=1.13, 95% CI 0.61-2.07, P=0.697). The opposite-sex-specific parent-of-origin effects may suggest X chromosome-linked genetic transmission or inherited chromosomal modifications in the etiology of psychotic symptoms.
Collapse
|
18
|
Genetic association and meta-analysis of a schizophrenia GWAS variant rs10489202 in East Asian populations. Transl Psychiatry 2018; 8:144. [PMID: 30087317 PMCID: PMC6081446 DOI: 10.1038/s41398-018-0211-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 03/16/2018] [Accepted: 04/04/2018] [Indexed: 12/14/2022] Open
Abstract
Previous genome-wide association studies (GWAS) suggest that rs10489202 in the intron of MPC2 (mitochondrial pyruvate carrier 2) is a risk locus for schizophrenia in Han Chinese populations. To validate this discovery, we conducted a replication analysis in an independent case-control sample of Han Chinese ancestry (437 cases and 2031 controls), followed by a meta-analytic investigation in multiple East Asian samples. In the replication analysis, rs10489202 showed marginal association with schizophrenia (two-tailed P = 0.071, OR = 1.192 for T allele); in the meta-analysis using a total of 14,340 cases and 20,349 controls from ten East Asian samples, rs10489202 was genome-wide significantly associated with schizophrenia (two-tailed P = 3.39 × 10-10, OR = 1.161 for T allele, under the fixed-effect model). We then performed an explorative investigation of the association between this SNP and bipolar disorder, as well as a major depressive disorder, and the schizophrenia-predisposing allele was associated with an increased risk of major depressive disorder in East Asians (two-tailed P = 2.49 × 10-2, OR = 1.103 for T allele). Furthermore, expression quantitative trait loci (eQTL) analysis in lymphoblastoid cell lines from East Asian donors (N = 85 subjects) revealed that rs10489202 was specifically and significantly associated with the expression of TIPRL gene (P = 5.67 × 10-4). Taken together, our data add further support for the genetic involvement of this genomic locus in the susceptibility to schizophrenia in East Asian populations, and also provide preliminary evidence for the underlying molecular mechanisms.
Collapse
|
19
|
Liu J, Su B. Integrated analysis supports ATXN1 as a schizophrenia risk gene. Schizophr Res 2018; 195:298-305. [PMID: 29055568 DOI: 10.1016/j.schres.2017.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 07/27/2017] [Accepted: 10/08/2017] [Indexed: 12/13/2022]
Abstract
Protein-protein interaction (PPI) is informative in identifying hidden disease risk genes that tend to interact with known risk genes usually working together in the same disease module. With the use of an integrated approach combining PPI information with pathway and expression analysis as well as genome-wide association study (GWAS), we intended to find new risk genes for schizophrenia (SCZ). We showed that ATXN1 was the only direct PPI partner of the know SCZ risk gene ZNF804A, and it also had direct PPIs with other 18 known SCZ risk genes. ATXN1 serves as one of the hub genes in the PPI network containing many known SCZ risk genes, and this network is significantly enriched for the MAPK signaling pathway. Further gene expression analysis indicated that ATXN1 is highly expressed in prefrontal cortex, and SCZ patients had significantly decreased expression compared with healthy controls. Finally, the published GWAS data supports an association of ATXN1 with SCZ as well as other psychiatric disorders though not reaching genome-wide significance. These convergent evidences support ATXN1 as a promising risk gene for SCZ, and the integrated approach serves as a useful tool for dissecting the genetic basis of psychiatric disorders.
Collapse
Affiliation(s)
- Jiewei Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, Yunnan, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China.
| |
Collapse
|
20
|
Zhang X, Yang J, Li Y, Ma X, Li R. Sex chromosome abnormalities and psychiatric diseases. Oncotarget 2018; 8:3969-3979. [PMID: 27992373 PMCID: PMC5354807 DOI: 10.18632/oncotarget.13962] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/07/2016] [Indexed: 12/02/2022] Open
Abstract
Excesses of sex chromosome abnormalities in patients with psychiatric diseases have recently been observed. It remains unclear whether sex chromosome abnormalities are related to sex differences in some psychiatric diseases. While studies showed evidence of susceptibility loci over many sex chromosomal regions related to various mental diseases, others demonstrated that the sex chromosome aneuploidies may be the key to exploring the pathogenesis of psychiatric disease. In this review, we will outline the current evidence on the interaction of sex chromosome abnormalities with schizophrenia, autism, ADHD and mood disorders.
Collapse
Affiliation(s)
- Xinzhu Zhang
- Beijing Institute for Brain Disorders, Capital Medical University, Beijing, China
| | - Jian Yang
- Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Beijing, China
| | - Yuhong Li
- Beijing Institute for Brain Disorders, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Beijing, China
| | - Xin Ma
- Beijing Institute for Brain Disorders, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Beijing, China
| | - Rena Li
- Beijing Institute for Brain Disorders, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Beijing, China.,Center for Hormone Advanced Science and Education, Roskamp Institute, Sarasota, FL, USA
| |
Collapse
|
21
|
Gui H, Li M, Sham PC, Baum L, Kwan P, Cherny SS. Genetic overlap between epilepsy and schizophrenia: Evidence from cross phenotype analysis in Hong Kong Chinese population. Am J Med Genet B Neuropsychiatr Genet 2018; 177:86-92. [PMID: 29150900 DOI: 10.1002/ajmg.b.32607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 10/06/2017] [Indexed: 01/05/2023]
Abstract
Epilepsy and schizophrenia are common and typical neurological or mental illness respectively, and sometimes they comorbid in the same patients, however the underlying genetic relationship between the two brain diseases is still not fully understood. To investigate the possible genetic contribution to their comorbidity, we performed polygenic risk score (PRS) analyses and genetic correlation estimation so as to identify the overall genetic overlap between the two diseases. The global schizophrenia PRS is strongly associated with schizophrenia phenotype in Hong Kong population (odds ratio = 1.7, p = 2.26E-16), and focal epilepsy PRS is moderately associated with epilepsy phenotype in Hong Kong population (odds ratio = 1.14, p = 0.013). However the disease-specific PRS can only predict its own well-matched phenotype but not the other ones (p > 0.05). This pattern is further supported by non-significant pairwise genetic correlation and insufficient statistical power for PRS association from the cross-phenotype analyses. Our study reveals there's limited shared genetic aetiology between schizophrenia and epilepsy, and thus supports a model of shared environmental factors to explain the comorbidity between the two phenotypes.
Collapse
Affiliation(s)
- Hongsheng Gui
- Center for Genomic Sciences, The University of Hong Kong, Hong Kong, SAR, China.,Center for Health Policy and Health Research Service, Henry Ford Health System, Detroit, Michigan
| | - Miaoxin Li
- Department of Psychiatry, The University of Hong Kong, Hong Kong, SAR, China
| | - Pak C Sham
- Center for Genomic Sciences, The University of Hong Kong, Hong Kong, SAR, China.,Department of Psychiatry, The University of Hong Kong, Hong Kong, SAR, China.,The State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Larry Baum
- Department of Psychiatry, The University of Hong Kong, Hong Kong, SAR, China
| | | | - Patrick Kwan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, SAR, China.,Department of Neurology, Royal Melbourne Hospital, Melbourne, Australia
| | - Stacey S Cherny
- Center for Genomic Sciences, The University of Hong Kong, Hong Kong, SAR, China.,Department of Psychiatry, The University of Hong Kong, Hong Kong, SAR, China.,The State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, SAR, China
| |
Collapse
|
22
|
Yue W, Yu X, Zhang D. Progress in genome-wide association studies of schizophrenia in Han Chinese populations. NPJ SCHIZOPHRENIA 2017; 3:24. [PMID: 28798405 PMCID: PMC5552785 DOI: 10.1038/s41537-017-0029-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/29/2017] [Accepted: 05/03/2017] [Indexed: 01/01/2023]
Abstract
Since 2006, genome-wide association studies of schizophrenia have led to the identification of numerous novel risk loci for this disease. However, there remains a geographical imbalance in genome-wide association studies, which to date have primarily focused on Western populations. During the last 6 years, genome-wide association studies in Han Chinese populations have identified both the sharing of susceptible loci across ethnicities and genes unique to Han Chinese populations. Here, we review recent progress in genome-wide association studies of schizophrenia in Han Chinese populations. Researchers have identified and replicated the sharing of susceptible genes, such as within the major histocompatibility complex, microRNA 137 (MIR137), zinc finger protein 804A (ZNF804A), vaccinia related kinase 2 (VRK2), and arsenite methyltransferase (AS3MT), across both European and East Asian populations. Several copy number variations identified in European populations have also been validated in the Han Chinese, including duplications at 16p11.2, 15q11.2-13.1, 7q11.23, and VIPR2 and deletions at 22q11.2, 1q21.1-q21.2, and NRXN1. However, these studies have identified some potential confounding factors, such as genetic heterogeneity and the effects of natural selection on tetraspanin 18 (TSPAN18) or zinc finger protein 323 (ZNF323), which may explain the population differences in genome-wide association studies. In the future, genome-wide association studies in Han Chinese populations should include meta-analyzes or mega-analyses with enlarged sample sizes across populations, deep sequencing, precision medicine treatment, and functional exploration of the risk genes for schizophrenia.
Collapse
Affiliation(s)
- Weihua Yue
- Institute of Mental Health, the Sixth Hospital, Peking University, 100191, Beijing, China.
- Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders (Peking University), 100191, Beijing, China.
| | - Xin Yu
- Institute of Mental Health, the Sixth Hospital, Peking University, 100191, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders (Peking University), 100191, Beijing, China
| | - Dai Zhang
- Institute of Mental Health, the Sixth Hospital, Peking University, 100191, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders (Peking University), 100191, Beijing, China
- Peking-Tsinghua Joint Center for Life Sciences & PKU-IDG/McGovern Institute for Brain Research, Peking University, 100871, Beijing, China
| |
Collapse
|
23
|
Yu H, Yan H, Li J, Li Z, Zhang X, Ma Y, Mei L, Liu C, Cai L, Wang Q, Zhang F, Iwata N, Ikeda M, Wang L, Lu T, Li M, Xu H, Wu X, Liu B, Yang J, Li K, Lv L, Ma X, Wang C, Li L, Yang F, Jiang T, Shi Y, Li T, Zhang D, Yue W. Common variants on 2p16.1, 6p22.1 and 10q24.32 are associated with schizophrenia in Han Chinese population. Mol Psychiatry 2017; 22:954-960. [PMID: 27922604 DOI: 10.1038/mp.2016.212] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 09/15/2016] [Accepted: 10/14/2016] [Indexed: 02/05/2023]
Abstract
Many schizophrenia susceptibility loci have been identified through genome-wide association studies (GWASs) in European populations. However, until recently, schizophrenia GWASs in non-European populations were limited to small sample sizes and have yielded few loci associated with schizophrenia. To identify genetic risk variations for schizophrenia in the Han Chinese population, we performed a two-stage GWAS of schizophrenia comprising 4384 cases and 5770 controls, followed by independent replications of 13 single-nucleotide polymorphisms in an additional 4339 schizophrenia cases and 7043 controls of Han Chinese ancestry. Furthermore, we conducted additional analyses based on the results in the discovery stage. The combined analysis confirmed evidence of genome-wide significant associations in the Han Chinese population for three loci, at 2p16.1 (rs1051061, in an exon of VRK2, P=1.14 × 10-12, odds ratio (OR)=1.17), 6p22.1 (rs115070292 in an intron of GABBR1, P=4.96 × 10-10, OR=0.77) and 10q24.32 (rs10883795 in an intron of AS3MT, P=7.94 × 10-10, OR=0.87; rs10883765 at an intron of ARL3, P=3.06 × 10-9, OR=0.87). The polygenic risk score based on Psychiatric Genomics Consortium schizophrenia GWAS data modestly predicted case-control status in the Chinese population (Nagelkerke R2: 1.7% ~5.7%). Our pathway analysis suggested that neurological biological pathways such as GABAergic signaling, dopaminergic signaling, cell adhesion molecules and myelination pathways are involved in schizophrenia. These findings provide new insights into the pathogenesis of schizophrenia in the Han Chinese population. Further studies are needed to establish the biological context and potential clinical utility of these findings.
Collapse
Affiliation(s)
- H Yu
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
- Department of Biochemistry, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health &National Clinical Research Center for Mental Disorders (Peking University), Beijing, China
| | - H Yan
- Department of Biochemistry, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health &National Clinical Research Center for Mental Disorders (Peking University), Beijing, China
| | - J Li
- Department of Biochemistry, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health &National Clinical Research Center for Mental Disorders (Peking University), Beijing, China
| | - Z Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
- Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, China
- Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
| | - X Zhang
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Y Ma
- Department of Biochemistry, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health &National Clinical Research Center for Mental Disorders (Peking University), Beijing, China
| | - L Mei
- Department of Biochemistry, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health &National Clinical Research Center for Mental Disorders (Peking University), Beijing, China
| | - C Liu
- Department of Psychiatry, the University of Melbourne, Parkville, VIC, Australia
| | - L Cai
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Q Wang
- Mental Health Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy, Psychiatric laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - F Zhang
- Department of Clinical Psychology, Wuxi Mental Health Center of Nanjing Medical University, Wuxi, China
| | - N Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Aichi, Japan
| | - M Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Aichi, Japan
| | - L Wang
- Department of Biochemistry, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health &National Clinical Research Center for Mental Disorders (Peking University), Beijing, China
| | - T Lu
- Department of Biochemistry, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health &National Clinical Research Center for Mental Disorders (Peking University), Beijing, China
| | - M Li
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, the Second Military Medical University, Shanghai, China
| | - H Xu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, the Second Military Medical University, Shanghai, China
| | - X Wu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, the Second Military Medical University, Shanghai, China
| | - B Liu
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - J Yang
- Tianjin Anding Hospital, Tianjin, China
| | - K Li
- Hebei Mental Health Center, Baoding, Hebei, China
| | - L Lv
- The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - X Ma
- Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - C Wang
- Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - L Li
- The Second Xiangya Hospital of Central South University, Changsha, China
| | - F Yang
- Beijing HuiLongGuan Hospital, Peking University, Beijing, China
| | - T Jiang
- Brainnetome Center, Institute of Automation, Chinese Academy of Sciences, Beijing, China
- National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Y Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) and the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
- Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, China
- Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
| | - T Li
- Mental Health Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- State Key Laboratory of Biotherapy, Psychiatric laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - D Zhang
- Department of Biochemistry, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health &National Clinical Research Center for Mental Disorders (Peking University), Beijing, China
- Peking-Tsinghua Joint Center for Life Sciences/PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - W Yue
- Department of Biochemistry, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
- Key Laboratory of Mental Health, Ministry of Health &National Clinical Research Center for Mental Disorders (Peking University), Beijing, China
| |
Collapse
|
24
|
Chang H, Xiao X, Li M. The schizophrenia risk gene ZNF804A: clinical associations, biological mechanisms and neuronal functions. Mol Psychiatry 2017; 22:944-953. [PMID: 28289284 DOI: 10.1038/mp.2017.19] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 01/02/2017] [Accepted: 01/09/2017] [Indexed: 02/07/2023]
Abstract
ZNF804A (zinc-finger protein 804A) has been recognized as a schizophrenia risk gene across multiple world populations. Its intronic single-nucleotide polymorphism (SNP) rs1344706 is among one of the strongest susceptibility variants that have achieved genome-wide significance in genome-wide association studies (GWAS) for schizophrenia and has been widely and intensively studied. To elucidate the biological mechanisms underlying the genetic risk conferred by rs1344706, we retrospectively analyzed the progresses in brain gene expression quantitative trait loci (eQTL) analyses, ZNF804A-induced pathway alterations in neural cells and changes in synaptic phenotypes associated with ZNF804A expression. Based on these data, we hypothesize a potential biological mechanism for a genetic risk allele of ZNF804A in schizophrenia pathogenesis. We also review the efforts being made to characterize the affected intermediate phenotypes using neuroimaging and neuropsychological approaches. We then discuss additional common and rare ZNF804A variants in schizophrenia susceptibility and the potential genetic heterogeneity of these genomic loci between Europeans and Asians. This review for we believe the first time systematically presents the evidence for ZNF804A, describing its discovery and likely roles in brain development and schizophrenia pathogenesis. We believe that this work has summarized this information with a systemic and broad assessment of recent findings.
Collapse
Affiliation(s)
- H Chang
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China
| | - X Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China
| | - M Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of The Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China
| |
Collapse
|
25
|
Are genetic polymorphisms in the renin-angiotensin-aldosterone system associated with essential hypertension? Evidence from genome-wide association studies. J Hum Hypertens 2017; 31:695-698. [PMID: 28425437 DOI: 10.1038/jhh.2017.29] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 01/20/2017] [Accepted: 03/03/2017] [Indexed: 01/01/2023]
Abstract
In candidate gene era, dozens of single-nucleotide polymorphisms (SNPs) within renin-angiotensin-aldosterone system (RAAS) have been reported to be significantly associated with hypertension. However, the unbiased genome-wide association studies (GWAS) rarely identified the SNPs within RAAS were associated with hypertension or blood pressure (BP) traits. In order to figure out whether genetic polymorphisms of RAAS are really associated with hypertension, we systemically searched the GWAS Catalogue and identified all the known RAAS genes and relevant diseases/traits. After data processing, we found that polymorphisms within REN, AGT, ACE2, CYP11B2, ATP6AP2 and HSD11B2 were not associated with any disease or trait. SNPs within ACE, AGTR1, AGTR2, MAS1, RENBP and NR3C2 were associated with other diseases or traits, but showed no direct connection with hypertension. The only SNP associated with a BP trait, systolic BP was rs17367504. However, it is located in the intronic region of MTHFR near many plausible candidate genes, including CLCN6, NPPA, NPPB and AGTRAP. Therefore, the effect of RAAS polymorphisms may have been overestimated during the 'candidate gene era'. In the time of 'precision medicine', the power of RAAS variants needs to be reconsidered when evaluating one's susceptibility of hypertension.
Collapse
|
26
|
Zhao D, Mokhtari R, Pedrosa E, Birnbaum R, Zheng D, Lachman HM. Transcriptome analysis of microglia in a mouse model of Rett syndrome: differential expression of genes associated with microglia/macrophage activation and cellular stress. Mol Autism 2017; 8:17. [PMID: 28367307 PMCID: PMC5372344 DOI: 10.1186/s13229-017-0134-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/17/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Rett syndrome (RTT) is a severe, neurodevelopmental disorder primarily affecting girls, characterized by progressive loss of cognitive, social, and motor skills after a relatively brief period of typical development. It is usually due to de novo loss of function mutations in the X-linked gene, MeCP2, which codes for the gene expression and chromatin regulator, methyl-CpG binding protein 2. Although the behavioral phenotype appears to be primarily due to neuronal Mecp2 deficiency in mice, other cell types, including astrocytes and oligodendrocytes, also appear to contribute to some aspects of the RTT phenotype. In addition, microglia may also play a role. However, the effect of Mecp2 deficiency in microglia on RTT pathogenesis is controversial. METHODS In the current study, we applied whole transcriptome analysis using RNA-seq to gain insight into molecular pathways in microglia that might be dysregulated during the transition, in female mice heterozygous for an Mecp2-null allele (Mecp2+/-; Het), from the pre-phenotypic (5 weeks) to the phenotypic phases (24 weeks). RESULTS We found a significant overlap in differentially expressed genes (DEGs) with genes involved in regulating the extracellular matrix, and those that are activated or inhibited when macrophages and microglia are stimulated towards the M1 and M2 activation states. However, the M1- and M2-associated genes were different in the 5- and 24-week samples. In addition, a substantial decrease in the expression of nine members of the heat shock protein (HSP) family was found in the 5-week samples, but not at 24 weeks. CONCLUSIONS These findings suggest that microglia from pre-phenotypic and phenotypic female mice are activated in a manner different from controls and that pre-phenotypic female mice may have alterations in their capacity to response to heat stress and other stressors that function through the HSP pathway.
Collapse
Affiliation(s)
- Dejian Zhao
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| | - Ryan Mokhtari
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| | - Rayna Birnbaum
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA.,Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA.,Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| | - Herbert M Lachman
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA.,Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA.,Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA.,Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| |
Collapse
|
27
|
Abstract
Schizophrenia (SZ) is a debilitating brain disorder with a complex genetic architecture. Genetic studies, especially recent genome-wide association studies (GWAS), have identified multiple variants (loci) conferring risk to SZ. However, how to efficiently extract meaningful biological information from bulk genetic findings of SZ remains a major challenge. There is a pressing need to integrate multiple layers of data from various sources, eg, genetic findings from GWAS, copy number variations (CNVs), association and linkage studies, gene expression, protein-protein interaction (PPI), co-expression, expression quantitative trait loci (eQTL), and Encyclopedia of DNA Elements (ENCODE) data, to provide a comprehensive resource to facilitate the translation of genetic findings into SZ molecular diagnosis and mechanism study. Here we developed the SZDB database (http://www.szdb.org/), a comprehensive resource for SZ research. SZ genetic data, gene expression data, network-based data, brain eQTL data, and SNP function annotation information were systematically extracted, curated and deposited in SZDB. In-depth analyses and systematic integration were performed to identify top prioritized SZ genes and enriched pathways. Multiple types of data from various layers of SZ research were systematically integrated and deposited in SZDB. In-depth data analyses and integration identified top prioritized SZ genes and enriched pathways. We further showed that genes implicated in SZ are highly co-expressed in human brain and proteins encoded by the prioritized SZ risk genes are significantly interacted. The user-friendly SZDB provides high-confidence candidate variants and genes for further functional characterization. More important, SZDB provides convenient online tools for data search and browse, data integration, and customized data analyses.
Collapse
Affiliation(s)
- Yong Wu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China;,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China;,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China;,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China,YGY and XJL are co-corresponding authors who jointly directed this work
| | - Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, China;,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China;,YGY and XJL are co-corresponding authors who jointly directed this work
| |
Collapse
|
28
|
Genetic association of rs1344706 in ZNF804A with bipolar disorder and schizophrenia susceptibility in Chinese populations. Sci Rep 2017; 7:41140. [PMID: 28120939 PMCID: PMC5264157 DOI: 10.1038/srep41140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/15/2016] [Indexed: 02/06/2023] Open
Abstract
Rs1344706 in the the zinc finger protein 804A (ZNF804A) gene has been identified to be associated with schizophrenia and bipolar disorder (BD) in Europeans. However, whether rs1344706 is associated with schizophrenia in Chinese populations remains inconclusive; furthermore, the association between rs1344706 and BD in Chinese populations has been rarely explored. To explore the association between rs1344706 and schizophrenia/BD in Chinese populations, we genotyped rs1344706 among 1128 Chinese subjects (537 patients with BD and 591 controls) and found that rs1344706 showed marginal allelic association with BD (P = 0.028) with T-allele being more prevalent in cases than that in controls (OR = 1.19, 95% CI 1.03–1.37). Meta-analysis of rs1344706 by pooling all available data showed that rs1344706 was significantly associated with BD (P = 0.001). Besides, positive association of rs1344706 with schizophrenia was observed in Northern Chinese (P = 0.005). Furthermore, ZNF804A is highly expressed in human and mouse brains, especially in prenatal stage.
Collapse
|
29
|
Gigek CO, Chen ES, Smith MAC. Methyl-CpG-Binding Protein (MBD) Family: Epigenomic Read-Outs Functions and Roles in Tumorigenesis and Psychiatric Diseases. J Cell Biochem 2016. [PMID: 26205787 DOI: 10.1002/jcb.25281] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetics is the study of the heritable changes on gene expression that are responsible for the regulation of development and that have an impact on several diseases. However, it is of equal importance to understand how epigenetic machinery works. DNA methylation is the most studied epigenetic mark and is generally associated with the regulation of gene expression through the repression of promoter activity and by affecting genome stability. Therefore, the ability of the cell to interpret correct methylation marks and/or the correct interpretation of methylation plays a role in many diseases. The major family of proteins that bind methylated DNA is the methyl-CpG binding domain proteins, or the MBDs. Here, we discuss the structure that makes these proteins a family, the main functions and interactions of all protein family members and their role in human disease such as psychiatric disorders and cancer.
Collapse
Affiliation(s)
- Carolina Oliveira Gigek
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (UNIFESP), Rua Botucatu, 740, Edifício Leitão da Cunha, 1, ° andar, CEP 04023-900, São Paulo, SP, Brazil.,Disciplina de Gastroenterologia Cirúrgica, Departamento de Cirurgia, Universidade Federal de São Paulo (UNIFESP), R. Napoleão de Barros, 715, 2º andar, CEP:04024-002, São Paulo, Brazil
| | - Elizabeth Suchi Chen
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (UNIFESP), Rua Botucatu, 740, Edifício Leitão da Cunha, 1, ° andar, CEP 04023-900, São Paulo, SP, Brazil
| | - Marilia Arruda Cardoso Smith
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (UNIFESP), Rua Botucatu, 740, Edifício Leitão da Cunha, 1, ° andar, CEP 04023-900, São Paulo, SP, Brazil
| |
Collapse
|
30
|
Guan F, Zhang T, Li L, Fu D, Lin H, Chen G, Chen T. Two-stage replication of previous genome-wide association studies of AS3MT-CNNM2-NT5C2 gene cluster region in a large schizophrenia case-control sample from Han Chinese population. Schizophr Res 2016; 176:125-130. [PMID: 27401531 DOI: 10.1016/j.schres.2016.07.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 06/29/2016] [Accepted: 07/04/2016] [Indexed: 12/28/2022]
Abstract
Schizophrenia is a devastating psychiatric condition with high heritability. Replicating the specific genetic variants that increase susceptibility to schizophrenia in different populations is critical to better understand schizophrenia. CNNM2 and NT5C2 are genes recently identified as susceptibility genes for schizophrenia in Europeans, but the exact mechanism by which these genes confer risk for schizophrenia remains unknown. In this study, we examined the potential for genetic susceptibility to schizophrenia of a three-gene cluster region, AS3MT-CNNM2-NT5C2. We implemented a two-stage strategy to conduct association analyses of the targeted regions with schizophrenia. A total of 8218 individuals were recruited, and 45 pre-selected single nucleotide polymorphisms (SNPs) were genotyped. Both single-marker and haplotype-based analyses were conducted in addition to imputation analysis to increase the coverage of our genetic markers. Two SNPs, rs11191419 (OR=1.24, P=7.28×10(-5)) and rs11191514 (OR=1.24, P=0.0003), with significant independent effects were identified. These results were supported by the data from both the discovery and validation stages. Further haplotype and imputation analyses also validated these results, and bioinformatics analyses indicated that CALHM1, which is located approximately 630kb away from CNNM2, might be a susceptible gene for schizophrenia. Our results provide further support that AS3MT, CNNM2 and CALHM1 are involved with the etiology and pathogenesis of schizophrenia, suggesting these genes are potential targets of interest for the improvement of disease management and the development of novel pharmacological strategies.
Collapse
Affiliation(s)
- Fanglin Guan
- Department of Forensic Psychiatry, School of Medicine & Forensics, Xi'an Jiaotong University, Xi'an, China; Key Laboratory of National Ministry of Health for Forensic Sciences, School of Medicine & Forensics, Xi'an Jiaotong University, Xi'an, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, China.
| | - Tianxiao Zhang
- Department of Psychiatry, School of Medicine, Washington University, Saint Louis, MO, USA.
| | - Lu Li
- Department of Forensic Psychiatry, School of Medicine & Forensics, Xi'an Jiaotong University, Xi'an, China; Key Laboratory of National Ministry of Health for Forensic Sciences, School of Medicine & Forensics, Xi'an Jiaotong University, Xi'an, China
| | - Dongke Fu
- Key Laboratory of National Ministry of Health for Forensic Sciences, School of Medicine & Forensics, Xi'an Jiaotong University, Xi'an, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, China
| | - Huali Lin
- Xi'an Mental Health Center, Xi'an, China
| | - Gang Chen
- Key Laboratory of National Ministry of Health for Forensic Sciences, School of Medicine & Forensics, Xi'an Jiaotong University, Xi'an, China
| | - Teng Chen
- Department of Forensic Psychiatry, School of Medicine & Forensics, Xi'an Jiaotong University, Xi'an, China; Key Laboratory of National Ministry of Health for Forensic Sciences, School of Medicine & Forensics, Xi'an Jiaotong University, Xi'an, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, China
| |
Collapse
|
31
|
Multivariate eQTL mapping uncovers functional variation on the X-chromosome associated with complex disease traits. Hum Genet 2016; 135:827-39. [PMID: 27155841 DOI: 10.1007/s00439-016-1674-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 04/24/2016] [Indexed: 10/21/2022]
Abstract
Very few studies have investigated the associations between genetic polymorphisms and gene expression on the X-chromosome. This is a major bottleneck when conducting functional follow-up studies of trait-associated variants, as those identified in genome-wide association studies (GWAS). We used a multivariate approach to test the association between individual single nucleotide polymorphisms (SNPs) and exon expression levels measured in 356 Epstein-Barr virus-transformed lymphoblastoid cell lines (LCLs) from the Geuvadis RNA sequencing project to identify SNPs associated with variation in gene expression on the X-chromosome, which we refer to as eSNPs. At an FDR of 5 %, we discovered 548 independent [linkage disequilibrium (LD) r (2) < 0.1] eSNPs on the X-chromosome. Of these, 35 were in LD (r (2) > 0.8) with previously published disease- or trait-associated variants identified through GWAS. One of the strongest eSNPs identified was rs35975601, which was associated with F8A1 expression (p value = 3 × 10(-20)) and was in LD with a type 1 diabetes risk variant. Additionally, we identified a number of genes for which eSNPs were in LD with multiple diseases or traits, including DNASE1L1 which was mapped to bilirubin levels, type 1 diabetes and schizophrenia. Our results also indicate that multivariate exon-level analysis provides a more powerful approach than univariate gene-level analysis, particularly when SNPs influence the expression of different exons with different magnitude and/or direction of effect. The associations identified in our study may provide new insights into the molecular process by which gene expression may contribute to trait variation or disease risk in humans.
Collapse
|
32
|
Huang L, Ohi K, Chang H, Yu H, Wu L, Yue W, Zhang D, Gao L, Li M. A comprehensive meta-analysis of ZNF804A SNPs in the risk of schizophrenia among Asian populations. Am J Med Genet B Neuropsychiatr Genet 2016; 171B:437-46. [PMID: 26866941 DOI: 10.1002/ajmg.b.32425] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/26/2016] [Indexed: 11/10/2022]
Abstract
Common variants in ZNF804A increased the risk of schizophrenia (and bipolar disorder), with low effect sizes in Europeans, which is in line with the polygenic nature of the illnesses, and implies that genetic analyses in small samples may not be sufficient to detect stable results. This notion is supported by the inconsistent replications of ZNF804A variations among individual small Asian samples, indicating the absence of definitive conclusions in this population. We collected psychiatric phenotypic and genetic data from Asian genome-wide association (GWA) and individual replication studies, which include up to 13,452 cases, 17,826 healthy controls, and 680 families, that is, the largest-scale study on ZNF804A in Asian populations to date. The European GWAS risk single nucleotide polymorphism (SNP) rs1344706 was nominally associated with schizophrenia in these Asian samples (one-tailed P = 4.26 × 10(-2) , odds ratio [OR] = 1.048), and the association was further strengthened when bipolar disorder data was also included (one-tailed P = 1.85 × 10(-2) , OR = 1.057). Besides, a non-synonymous SNP rs1366842 in the exon 4 of ZNF804A was also associated with schizophrenia (P = 9.96 × 10(-3) , OR = 1.095). We additionally analyzed other 163 SNPs covering ZNF804A region, but none of them showed any evidence of association. Though the two SNPs did not remain significant if we applied multiple corrections, our analysis should be interpreted as a primary replication study with in prior hypothesis, and rs1344706 and rs1366842 might confer a small but detectable risk of schizophrenia (and bipolar disorder) in Asians. Moreover, the current data suggest the necessity of replication analyses in a large enough scale samples.
Collapse
Affiliation(s)
- Liang Huang
- First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Kazutaka Ohi
- Department of Neuropsychiatry, Kanazawa Medical University, Ishikawa, Japan
| | - Hong Chang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Hao Yu
- Institute of Mental Health, Peking University, Beijing, China.,Ministry of Health Key Laboratory of Mental Health, Peking University, Beijing, China
| | - Lichuan Wu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Weihua Yue
- Institute of Mental Health, Peking University, Beijing, China.,Ministry of Health Key Laboratory of Mental Health, Peking University, Beijing, China
| | - Dai Zhang
- Institute of Mental Health, Peking University, Beijing, China.,Ministry of Health Key Laboratory of Mental Health, Peking University, Beijing, China
| | - Lei Gao
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Science, Shandong University of Technology, Zibo, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
| |
Collapse
|
33
|
Xiao X, Li M. Replication of Han Chinese GWAS loci for schizophrenia via meta-analysis of four independent samples. Schizophr Res 2016; 172:75-7. [PMID: 26899211 DOI: 10.1016/j.schres.2016.02.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 02/06/2016] [Accepted: 02/11/2016] [Indexed: 01/14/2023]
Abstract
Schizophrenia is a highly heritable psychiatric disorder with unclear aetiology. Recent genome-wide association studies (GWAS) in European populations have reported numerous susceptibility variants, while GWAS in East Asians also identified several risk loci but with fewer independent replications. Here we focus on nine single nucleotide polymorphisms (SNPs) which have shown genome-wide significant associations with schizophrenia in previous Han Chinese GWAS, and we tend to replicate the associations in four independent samples of East Asian origin including a total of 3977 cases and 5589 controls. The results showed that rs10489202 in MPC2 (BRP44) is significantly associated with schizophrenia in these East Asian replication samples (one-tailed P=5.75×10(-3), OR=1.12), and further meta-analysis after including previous GWAS data yielded a genome-wide significant association (two-tailed P=1.11×10(-10), OR=1.19), adding further support for the involvement of this locus in the genetic risk of schizophrenia, and future studies regarding the underlying molecular mechanisms of the risk association are necessary.
Collapse
Affiliation(s)
- Xiao Xiao
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States.
| | - Ming Li
- Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD, United States
| |
Collapse
|
34
|
Liu YL, Wang SC, Hwu HG, Fann CSJ, Yang UC, Yang WC, Hsu PC, Chang CC, Wen CC, Tsai-Wu JJ, Hwang TJ, Hsieh MH, Liu CC, Chien YL, Fang CP, Faraone SV, Tsuang MT, Chen WJ, Liu CM. Haplotypes of the D-Amino Acid Oxidase Gene Are Significantly Associated with Schizophrenia and Its Neurocognitive Deficits. PLoS One 2016; 11:e0150435. [PMID: 26986737 PMCID: PMC4795637 DOI: 10.1371/journal.pone.0150435] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/13/2016] [Indexed: 01/01/2023] Open
Abstract
D-amino acid oxidase (DAO) has been reported to be associated with schizophrenia. This study aimed to search for genetic variants associated with this gene. The genomic regions of all exons, highly conserved regions of introns, and promoters of this gene were sequenced. Potentially meaningful single-nucleotide polymorphisms (SNPs) obtained from direct sequencing were selected for genotyping in 600 controls and 912 patients with schizophrenia and in a replicated sample consisting of 388 patients with schizophrenia. Genetic associations were examined using single-locus and haplotype association analyses. In single-locus analyses, the frequency of the C allele of a novel SNP rs55944529 located at intron 8 was found to be significantly higher in the original large patient sample (p = 0.016). This allele was associated with a higher level of DAO mRNA expression in the Epstein-Barr virus-transformed lymphocytes. The haplotype distribution of a haplotype block composed of rs11114083-rs2070586-rs2070587-rs55944529 across intron 1 and intron 8 was significantly different between the patients and controls and the haplotype frequencies of AAGC were significantly higher in patients, in both the original (corrected p < 0.0001) and replicated samples (corrected p = 0.0003). The CGTC haplotype was specifically associated with the subgroup with deficits in sustained attention and executive function and the AAGC haplotype was associated with the subgroup without such deficits. The DAO gene was a susceptibility gene for schizophrenia and the genomic region between intron 1 and intron 8 may harbor functional genetic variants, which may influence the mRNA expression of DAO and neurocognitive functions in schizophrenia.
Collapse
Affiliation(s)
- Yu-Li Liu
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli 35053, Taiwan
- Department of Psychiatry, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10051, Taiwan
| | - Sheng-Chang Wang
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Hai-Gwo Hwu
- Department of Psychiatry, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10051, Taiwan
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | | | - Ueng-Cheng Yang
- Institute of Bioinformatics, National Yang-Ming University, Taipei 112, Taiwan
| | - Wei-Chih Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Pei-Chun Hsu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10051, Taiwan
| | - Chien-Ching Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Chun-Chiang Wen
- Department of Psychiatry, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10051, Taiwan
| | - Jyy-Jih Tsai-Wu
- Department of Medical Research, National Taiwan University Hospital, Taipei 10051, Taiwan
| | - Tzung-Jeng Hwang
- Department of Psychiatry, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10051, Taiwan
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Ming H. Hsieh
- Department of Psychiatry, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10051, Taiwan
| | - Chen-Chung Liu
- Department of Psychiatry, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10051, Taiwan
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Yi-Ling Chien
- Department of Psychiatry, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10051, Taiwan
| | - Chiu-Ping Fang
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Stephen V. Faraone
- Medical Genetics Research Center and Department of Psychiatry and Neuroscience & Physiology, SUNY Upstate Medical University, Syracuse, NY 13210, United States of America
| | - Ming T. Tsuang
- Harvard Institute of Psychiatric Epidemiology and Genetics, and Departments of Epidemiology and Psychiatry, Harvard University, Boston, Massachusetts, 02115, United States of America
- Institute of Behavioral Genomics, University of California San Diego, San Diego, California 92093, United States of America
| | - Wei J. Chen
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 10051, Taiwan
| | - Chih-Min Liu
- Department of Psychiatry, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10051, Taiwan
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
- * E-mail:
| |
Collapse
|
35
|
Kim LH, Park BL, Cheong HS, Namgoong S, Kim JO, Kim JH, Shin JG, Park CS, Kim BJ, Kim JW, Choi IG, Hwang J, Shin HD, Woo SI. Genome-wide association study with the risk of schizophrenia in a Korean population. Am J Med Genet B Neuropsychiatr Genet 2016; 171B:257-65. [PMID: 26531332 DOI: 10.1002/ajmg.b.32400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 10/23/2015] [Indexed: 11/10/2022]
Abstract
Schizophrenia is regarded as a multifactorial and polygenic brain disorder that is attributed to different combinations of genetic and environmental risk factors. Recently, several genome-wide association studies (GWASs) of schizophrenia have identified numerous risk factors, but the replication results remain controversial and ambiguous. To identify schizophrenia susceptibility loci in the Korean population, we performed a GWAS using the Illumina HumanOmni1-Quad V1.0 Microarray. We genotyped 1,140,419 single nucleotide polymorphisms (SNPs) in 350 Korea schizophrenia patients and 700 control subjects, and approximately 620,001 autosomal SNPs were passed our quality control. In the case-control analysis, the rs9607195 A>G on intergenic area 250 kb away from the ISX gene and the rs12738007 A>G on the intron of the MECR gene were the most strongly associated SNPs with the risk of schizophrenia (P = 6.2 × 10(-8) , OR = 0.50 and P = 3.7 × 10(-7) , OR = 2.39, respectively). In subsequent fine-mapping analysis, 6 SNPs of MECR were genotyped with 310 schizophrenia patients and 604 control subjects. The association of the MECR rs12738007, a top ranked-SNP in GWAS, was replicated (P = 1.5 × 10(-2) , OR = 1.53 in fine mapping analysis, P = 1.5 × 10(-6) , OR = 1.90 in combined analysis). The identification of putative schizophrenia susceptibility loci could provide new insights into genetic factors related with schizophrenia and clues for the development of diagnosis strategies.
Collapse
Affiliation(s)
- Lyoung Hyo Kim
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea.,Department of Life Science, Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Byung Lae Park
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea
| | - Suhg Namgoong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea.,Department of Life Science, Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Ji On Kim
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea
| | - Jeong-Hyun Kim
- Department of Life Science, Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Joong-Gon Shin
- Department of Life Science, Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Chul Soo Park
- Department of Psychiatry, College of Medicine, Gyeongsang National University, Gyeongsang Nam Do, Republic of Korea
| | - Bong-Jo Kim
- Department of Psychiatry, College of Medicine, Gyeongsang National University, Gyeongsang Nam Do, Republic of Korea
| | - Jae Won Kim
- Division of Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju-ro, Gyeongsang Nam Do, Republic of Korea
| | - Ihn-Geun Choi
- Department of Neuropsychiatry, Hallym University, Han-Gang Sacred Heart Hospital, Yeongdeungpo-gu, Seoul, Republic of Korea
| | - Jaeuk Hwang
- Department of Neuropsychiatry, Soonchunhyang University Hospital, Yongsan-gu, Seoul, Republic of Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., Mapo-gu, Seoul, Republic of Korea.,Department of Life Science, Sogang University, Mapo-gu, Seoul, Republic of Korea
| | - Sung-Il Woo
- Department of Neuropsychiatry, Soonchunhyang University Hospital, Yongsan-gu, Seoul, Republic of Korea
| |
Collapse
|
36
|
Liu C, Saffen D, Schulze TG, Burmeister M, Sham PC, Yao YG, Kuo PH, Chen C, An Y, Dai J, Yue W, Li MX, Xue H, Su B, Chen L, Shi Y, Qiao M, Liu T, Xia K, Chan RCK. Psychiatric genetics in China: achievements and challenges. Mol Psychiatry 2016; 21:4-9. [PMID: 26481319 PMCID: PMC4830695 DOI: 10.1038/mp.2015.95] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To coordinate research efforts in psychiatric genetics in China, a group of Chinese and foreign investigators have established an annual “Summit on Chinese Psychiatric Genetics” to present their latest research and discuss the current state and future directions of this field. To date, two Summits have been held, the first in Changsha in April, 2014, and the second in Kunming in April, 2015. The consensus of roundtable discussions held at these meetings is that psychiatric genetics in China is in need of new policies to promote collaborations aimed at creating a framework for genetic research appropriate for the Chinese population: relying solely on Caucasian population-based studies may result in missed opportunities to diagnose and treat psychiatric disorders. In addition, participants agree on the importance of promoting collaborations and data sharing in areas where China has especially strong resources, such as advanced facilities for non-human primate studies and traditional Chinese medicine: areas that may also provide overseas investigators with unique research opportunities. In this paper, we present an overview of the current state of psychiatric genetics research in China, with emphasis on genome-level studies, and describe challenges and opportunities for future advances, particularly at the dawn of “precision medicine.” Together, we call on administrative bodies, funding agencies, the research community, and the public at large for increased support for research on the genetic basis of psychiatric disorders in the Chinese population. In our opinion, increased public awareness and effective collaborative research hold the keys to the future of psychiatric genetics in China.
Collapse
Affiliation(s)
- Chunyu Liu
- State Key Laboratory of Medical Genetics of China, Central South University, Changsha, China
- Department of Psychiatry, University of Illinois at Chicago, Chicago, United States of America
| | - David Saffen
- Depatement of Cellular and Genetic Medicine, Fudan University, Shanghai, China
| | - Thomas G Schulze
- Department of Psychiatry and Psychotherapy, University Medical Center, Georg-August-Universität, Göttingen, Germany
- Institute of Psychiatric Phenomics and Genomics, Ludwig Maximilians-University, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health Mannheim, University Medical Center Mannheim, University of Heidelberg, Mannheim, Germany
| | - Margit Burmeister
- Molecular and Behavioral Neuroscience Institute, Departments of Psychiatry, Human Genetics and Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Pak Chung Sham
- Department of Psychiatry, University of Hong Kong, Pokfulam, Hong Kong
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, China
| | - Po-Hsiu Kuo
- Department of Public Health and Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Chao Chen
- State Key Laboratory of Medical Genetics of China, Central South University, Changsha, China
| | - Yu An
- Institute of Biomedical Sciences and MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China
| | - Jiapei Dai
- Wuhan Institute for Neuroscience and Neuroengineering, South-Central University for Nationalities, Wuhan, China
| | - Weihua Yue
- Key Laboratory of Mental Health, Ministry of Health, Institute of Mental Health, The Sixth Hospital, Peking University, Beijing, China
| | - Miao Xin Li
- Department of Psychiatry, University of Hong Kong, Pokfulam, Hong Kong
| | - Hong Xue
- Division of Life Science and Applied Genomics Center, The Hong Kong University of Science & Technology, Hong Kong, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology and Kunming Primate Research Centre, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Li Chen
- Depatement of Cellular and Genetic Medicine, Fudan University, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Mingqi Qiao
- Institute of Traditional Chinese Medicine theory, School of Basic Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250014, China
| | - Tiebang Liu
- Shenzhen Kang Ning Hospital, No.1080, Cuizhu Street, Luohu District, Shenzhen, Guangdong, 518020, China
| | - Kun Xia
- State Key Laboratory of Medical Genetics of China, Central South University, Changsha, China
- School of Life Sciences, Central South University, Changsha, China
| | - Raymond C K Chan
- Neuropsychology and Applied Cognitive Neuroscience Laboratory, Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences
| |
Collapse
|
37
|
Zhang J, Zhang L, Zhang Y, Yang J, Guo M, Sun L, Pan HF, Hirankarn N, Ying D, Zeng S, Lee TL, Lau CS, Chan TM, Leung AMH, Mok CC, Wong SN, Lee KW, Ho MHK, Lee PPW, Chung BHY, Chong CY, Wong RWS, Mok MY, Wong WHS, Tong KL, Tse NKC, Li XP, Avihingsanon Y, Rianthavorn P, Deekajorndej T, Suphapeetiporn K, Shotelersuk V, Ying SKY, Fung SKS, Lai WM, Garcia-Barceló MM, Cherny SS, Sham PC, Cui Y, Yang S, Ye DQ, Zhang XJ, Lau YL, Yang W. Gene-Based Meta-Analysis of Genome-Wide Association Study Data Identifies Independent Single-Nucleotide Polymorphisms inANXA6as Being Associated With Systemic Lupus Erythematosus in Asian Populations. Arthritis Rheumatol 2015. [PMID: 26202167 DOI: 10.1002/art.39275] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jing Zhang
- Queen Mary Hospital and The University of Hong Kong, Hong Kong, China, and Eye and ENT Hospital of Fudan University; Shanghai China
| | - Lu Zhang
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Yan Zhang
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Jing Yang
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Mengbiao Guo
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | | | | | - Dingge Ying
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Shuai Zeng
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Tsz Leung Lee
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Chak Sing Lau
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Tak Mao Chan
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | - Chi Chiu Mok
- Tuen Mun Hospital, Tuen Mun, New Territories; Hong Kong China
| | - Sik Nin Wong
- Tuen Mun Hospital, Tuen Mun, New Territories; Hong Kong China
| | - Ka Wing Lee
- Pamela Youde Nethersole Eastern Hospital; Hong Kong China
| | - Marco Hok Kung Ho
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | | | - Chun Yin Chong
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | - Mo Yin Mok
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Stacey S. Cherny
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Pak Chung Sham
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Yong Cui
- Anhui Medical University; China Hefei China
| | - Sen Yang
- Anhui Medical University; China Hefei China
| | | | | | - Yu Lung Lau
- Queen Mary Hospital and The University of Hong Kong, Hong Kong, China, and The University of Hong Kong-Shenzhen Hospital; Shenzhen China
| | - Wanling Yang
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| |
Collapse
|
38
|
FAPI: Fast and accurate P-value Imputation for genome-wide association study. Eur J Hum Genet 2015; 24:761-6. [PMID: 26306642 DOI: 10.1038/ejhg.2015.190] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 06/08/2015] [Accepted: 07/03/2015] [Indexed: 11/08/2022] Open
Abstract
Imputing individual-level genotypes (or genotype imputation) is now a standard procedure in genome-wide association studies (GWAS) to examine disease associations at untyped common genetic variants. Meta-analysis of publicly available GWAS summary statistics can allow more disease-associated loci to be discovered, but these data are usually provided for various variant sets. Thus imputing these summary statistics of different variant sets into a common reference panel for meta-analyses is impossible using traditional genotype imputation methods. Here we develop a fast and accurate P-value imputation (FAPI) method that utilizes summary statistics of common variants only. Its computational cost is linear with the number of untyped variants and has similar accuracy compared with IMPUTE2 with prephasing, one of the leading methods in genotype imputation. In addition, based on the FAPI idea, we develop a metric to detect abnormal association at a variant and showed that it had a significantly greater power compared with LD-PAC, a method that quantifies the evidence of spurious associations based on likelihood ratio. Our method is implemented in a user-friendly software tool, which is available at http://statgenpro.psychiatry.hku.hk/fapi.
Collapse
|
39
|
Tantra M, Hammer C, Kästner A, Dahm L, Begemann M, Bodda C, Hammerschmidt K, Giegling I, Stepniak B, Castillo Venzor A, Konte B, Erbaba B, Hartmann A, Tarami A, Schulz-Schaeffer W, Rujescu D, Mannan AU, Ehrenreich H. Mild expression differences of MECP2 influencing aggressive social behavior. EMBO Mol Med 2014; 6:662-84. [PMID: 24648499 PMCID: PMC4023888 DOI: 10.1002/emmm.201303744] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The X-chromosomal MECP2/Mecp2 gene encodes methyl-CpG-binding protein 2, a transcriptional activator and repressor regulating many other genes. We discovered in male FVB/N mice that mild (∼50%) transgenic overexpression of Mecp2 enhances aggression. Surprisingly, when the same transgene was expressed in C57BL/6N mice, transgenics showed reduced aggression and social interaction. This suggests that Mecp2 modulates aggressive social behavior. To test this hypothesis in humans, we performed a phenotype-based genetic association study (PGAS) in >1000 schizophrenic individuals. We found MECP2 SNPs rs2239464 (G/A) and rs2734647 (C/T; 3′UTR) associated with aggression, with the G and C carriers, respectively, being more aggressive. This finding was replicated in an independent schizophrenia cohort. Allele-specific MECP2mRNA expression differs in peripheral blood mononuclear cells by ∼50% (rs2734647: C > T). Notably, the brain-expressed, species-conserved miR-511 binds to MECP2 3′UTR only in T carriers, thereby suppressing gene expression. To conclude, subtle MECP2/Mecp2 expression alterations impact aggression. While the mouse data provides evidence of an interaction between genetic background and mild Mecp2 overexpression, the human data convey means by which genetic variation affects MECP2 expression and behavior.
Collapse
Affiliation(s)
- Martesa Tantra
- Clinical Neuroscience, Max Planck Institute of Experimental Medicine, Göttingen, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Morris BJ, Pratt JA. Novel treatment strategies for schizophrenia from improved understanding of genetic risk. Clin Genet 2014; 86:401-11. [PMID: 25142969 DOI: 10.1111/cge.12485] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/15/2014] [Accepted: 08/16/2014] [Indexed: 01/19/2023]
Abstract
Recent years have seen significant advances in our understanding of the genetic basis of schizophrenia. In particular, genome-wide approaches have suggested the involvement of many common genetic variants of small effect, together with a few rare variants exerting relatively large effects. While unequivocal identification of the relevant genes has, for the most part, remained elusive, the genes revealed as potential candidates can in many cases be clustered into functionally related groups which are potentially open to therapeutic intervention. In this review, we summarise this information, focusing on the accumulating evidence that genetic dysfunction at glutamatergic synapses and post-synaptic signalling complexes contributes to the aetiology of the disease. In particular, there is converging support for involvement of post-synaptic JNK pathways in disease aetiology. An expansion of our neurobiological knowledge of the basis of schizophrenia is urgently needed, yet some promising novel pharmacological targets can already be discerned.
Collapse
Affiliation(s)
- B J Morris
- Psychiatric Research Institute of Neuroscience in Glasgow (PsyRING), University of Glasgow, Glasgow, UK; Institute of Neuroscience and Psychology, School of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | |
Collapse
|
41
|
Prenatal maternal immune activation causes epigenetic differences in adolescent mouse brain. Transl Psychiatry 2014; 4:e434. [PMID: 25180573 PMCID: PMC4203009 DOI: 10.1038/tp.2014.80] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 07/02/2014] [Accepted: 07/14/2014] [Indexed: 12/17/2022] Open
Abstract
Epigenetic processes such as DNA methylation have been implicated in the pathophysiology of neurodevelopmental disorders including schizophrenia and autism. Epigenetic changes can be induced by environmental exposures such as inflammation. Here we tested the hypothesis that prenatal inflammation, a recognized risk factor for schizophrenia and related neurodevelopmental conditions, alters DNA methylation in key brain regions linked to schizophrenia, namely the dopamine rich striatum and endocrine regulatory centre, the hypothalamus. DNA methylation across highly repetitive elements (long interspersed element 1 (LINE1) and intracisternal A-particles (IAPs)) were used to proxy global DNA methylation. We also investigated the Mecp2 gene because it regulates transcription of LINE1 and has a known association with neurodevelopmental disorders. Brain tissue was harvested from 6 week old offspring of mice exposed to the viral analog PolyI:C or saline on gestation day 9. We used Sequenom EpiTYPER assay to quantitatively analyze differences in DNA methylation at IAPs, LINE1 elements and the promoter region of Mecp2. In the hypothalamus, prenatal exposure to PolyI:C caused significant global DNA hypomethylation (t=2.44, P=0.019, PolyI:C mean 69.67%, saline mean 70.19%), especially in females, and significant hypomethylation of the promoter region of Mecp2, (t=3.32, P=0.002; PolyI:C mean 26.57%, saline mean 34.63%). IAP methylation was unaltered. DNA methylation in the striatum was not significantly altered. This study provides the first experimental evidence that exposure to inflammation during prenatal life is associated with epigenetic changes, including Mecp2 promoter hypomethylation. This suggests that environmental and genetic risk factors associated with neurodevelopmental disorders may act upon similar pathways. This is important because epigenetic changes are potentially modifiable and their investigation may open new avenues for treatment.
Collapse
|