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Sun Y, Li Y, Jiang X, Wu Q, Lin R, Chen H, Zhang M, Zeng T, Tian Y, Xu E, Zhang Y, Lu L. Genome-wide association study identified candidate genes for egg production traits in the Longyan Shan-ma duck. Poult Sci 2024; 103:104032. [PMID: 39003796 DOI: 10.1016/j.psj.2024.104032] [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: 04/23/2024] [Revised: 06/19/2024] [Accepted: 06/22/2024] [Indexed: 07/16/2024] Open
Abstract
Egg production is an important economic trait in layer ducks and understanding the genetics basis is important for their breeding. In this study, a genome-wide association study (GWAS) for egg production traits in 303 female Longyan Shan-ma ducks was performed based on a genotyping-by-sequencing strategy. Sixty-two single nucleotide polymorphisms (SNPs) associated with egg weight traits were identified (P < 9.48 × 10-5), including 8 SNPs at 5% linkage disequilibrium (LD)-based Bonferroni-corrected genome-wide significance level (P < 4.74 × 10-6). One hundred and nineteen SNPs were associated with egg number traits (P < 9.48 × 10-5), including 13 SNPs with 5% LD-based Bonferroni-corrected genome-wide significance (P < 4.74 × 10-6). These SNPs annotated 146 target genes which contained known candidate genes for egg production traits, such as prolactin and prolactin releasing hormone receptor. This study identified that these associated genes were significantly enriched in egg production-related pathways (P < 0.05), such as the oxytocin signaling, MAPK signaling, and calcium signaling pathways. It was notable that 18 genes were differentially expressed in ovarian tissues between higher and lower egg production in Shan-ma ducks. The identified potential candidate genes and pathways provide insight into the genetic basis underlying the egg production trait of layer ducks.
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Affiliation(s)
- Yanfa Sun
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Yan Li
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Xiaobing Jiang
- Fujian Provincial Animal Husbandry Headquarters, Fuzhou, Fujian 350003, P.R. China
| | - Qiong Wu
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Rulong Lin
- Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, 364031, P.R. China
| | - Hongping Chen
- Longyan Shan-ma Duck Original Breeding Farm, Agricultural Bureau of Xinluo District, Longyan, 364031, P.R. China
| | - Min Zhang
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Tao Zeng
- Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P.R. China
| | - Yong Tian
- Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P.R. China
| | - Enrong Xu
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Yeqiong Zhang
- College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, P.R. China
| | - Lizhi Lu
- Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P.R. China..
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2
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Bhatia A, Upadhyay AK, Sharma S. Screening and analysis of single nucleotide polymorphism in the 3'-UTR microRNA target regions and its implications for lung tumorigenesis. Pharmacogenomics 2024:1-16. [PMID: 38884942 DOI: 10.1080/14622416.2024.2355864] [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: 02/26/2024] [Accepted: 05/13/2024] [Indexed: 06/18/2024] Open
Abstract
Aim: The study aims to identify high-impact single nucleotide polymorphisms (SNPs) in miRNA target sites of genes associated with lung cancer. Materials & methods: Lung cancer genes were obtained from Uniprot KB. miRNA target site SNPs were mined from MirSNP, miRdSNP and TargetScan. SNPs were shortlisted based on binding impact, minor allele frequency and conservation. Gene expression was analyzed in genes with high-impact SNPs in healthy versus lung cancer tissue. Additionally, enrichment, pathway and network analyzes were performed. Results: 19 high-impact SNPs were identified in miRNA target sites of lung cancer-associated genes. These SNPs affect miRNA binding and gene expression. The genes are involved in key cancer related pathways. Conclusion: The identified high-impact miRNA target site SNPs and associated genes provide a starting point for case-control studies in lung cancer patients in different populations.
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Affiliation(s)
- Anmol Bhatia
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Bhadson Rd, Adarsh Nagar, Prem Nagar, Patiala, Punjab, India
| | - Atul Kumar Upadhyay
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Bhadson Rd, Adarsh Nagar, Prem Nagar, Patiala, Punjab, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Bhadson Rd, Adarsh Nagar, Prem Nagar, Patiala, Punjab, India
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3
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Kong Y, Cai Z, Chen S, Ye X, Liu Z. Small molecule probes as versatile energy acceptors: A breakthrough in photoelectrochemical sensing for sulfur dioxide recording in rat brain. Biosens Bioelectron 2024; 243:115760. [PMID: 37866324 DOI: 10.1016/j.bios.2023.115760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/05/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023]
Abstract
Microelectrode-based photoelectrochemical (PEC) sensing is a newly developed and promising analytical technique for in vivo analysis. However, the inadequate specificity in complex environment of living bodies restricted its further in vivo application. Herein, we utilized a small molecule probe as the energy acceptor to quench the photocurrent of CdTe quantum dots through energy transfer. The efficiency of energy transfer was modulated by the concentration of target SO2, resulting in changes in photocurrent. The chemical recognition reaction between small molecule probes and SO2 enhanced the specificity of PEC sensing, thus guaranteeing its in vivo applications. Furthermore, with the use of light addressing strategy, simultaneous detection in the multiple brain regions was implemented. The energy transfer based light addressable PEC microsensor achieved monitoring fluctuations of SO2 levels in multiple brain regions of rats with epilepsy.
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Affiliation(s)
- Yao Kong
- College of Health Science and Engineering, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan, 430062, China
| | - Zirui Cai
- College of Health Science and Engineering, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan, 430062, China
| | - Shizhen Chen
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Science, Wuhan, 430071, China
| | - Xiaoxue Ye
- College of Health Science and Engineering, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan, 430062, China.
| | - Zhihong Liu
- College of Health Science and Engineering, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, Hubei University, Wuhan, 430062, China
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4
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Kim S, Nam S. The causal relationship of colorectal cancer on schizophrenia: A Mendelian randomization study. Medicine (Baltimore) 2023; 102:e35517. [PMID: 37800808 PMCID: PMC10553116 DOI: 10.1097/md.0000000000035517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/14/2023] [Indexed: 10/07/2023] Open
Abstract
Comorbidities associated with psychiatric disorders often occur in patients with cancer. A causal effect of schizophrenia on cancer was observed using Mendelian randomization (MR) analysis. However, the causal effect of colorectal cancer on schizophrenia has not been studied using MR analysis. Therefore, we performed MR analysis to investigate the causal effects of colorectal cancer on schizophrenia. We performed "two-sample summary-data Mendelian randomization" using publicly available genome-wide association studies data to investigate the causal relationship between colorectal cancer (as exposure) and schizophrenia (as outcome). The inverse variance weighted method was used to calculate causal estimates. In 2 TSMR analyses, we reported that the odds ratios for schizophrenia per log odds increase in colorectal cancer risk were 6.48 (95% confidential interval [CI] of OR 1.75-24.03; P = .005) and 9.62 × 106 (95% CI of OR 1.13-8.22 × 1013; P = .048). Pleiotropic tests and sensitivity analysis demonstrated minimal horizontal pleiotropy and robustness of the causal relationship. We provide evidence for a causal relationship between the incidence of colorectal cancer and the development of schizophrenia through TSMR analysis.
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Affiliation(s)
- Sungyeon Kim
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, Korea
| | - Seungyoon Nam
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, Korea
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon, Korea
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5
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Durán A, Priestman DA, Las Heras M, Rebolledo-Jaramillo B, Olguín V, Calderón JF, Zanlungo S, Gutiérrez J, Platt FM, Klein AD. A Mouse Systems Genetics Approach Reveals Common and Uncommon Genetic Modifiers of Hepatic Lysosomal Enzyme Activities and Glycosphingolipids. Int J Mol Sci 2023; 24:ijms24054915. [PMID: 36902345 PMCID: PMC10002577 DOI: 10.3390/ijms24054915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/07/2023] [Accepted: 02/15/2023] [Indexed: 03/08/2023] Open
Abstract
Identification of genetic modulators of lysosomal enzyme activities and glycosphingolipids (GSLs) may facilitate the development of therapeutics for diseases in which they participate, including Lysosomal Storage Disorders (LSDs). To this end, we used a systems genetics approach: we measured 11 hepatic lysosomal enzymes and many of their natural substrates (GSLs), followed by modifier gene mapping by GWAS and transcriptomics associations in a panel of inbred strains. Unexpectedly, most GSLs showed no association between their levels and the enzyme activity that catabolizes them. Genomic mapping identified 30 shared predicted modifier genes between the enzymes and GSLs, which are clustered in three pathways and are associated with other diseases. Surprisingly, they are regulated by ten common transcription factors, and their majority by miRNA-340p. In conclusion, we have identified novel regulators of GSL metabolism, which may serve as therapeutic targets for LSDs and may suggest the involvement of GSL metabolism in other pathologies.
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Affiliation(s)
- Anyelo Durán
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
| | | | - Macarena Las Heras
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
| | - Boris Rebolledo-Jaramillo
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
| | - Valeria Olguín
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
| | - Juan F. Calderón
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
- Research Center for the Development of Novel Therapeutic Alternatives for Alcohol Use Disorders, Santiago 7610658, Chile
| | - Silvana Zanlungo
- Department of Gastroenterology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8330033, Chile
| | - Jaime Gutiérrez
- Cellular Signaling and Differentiation Laboratory, School of Medical Technology, Health Sciences Faculty, Universidad San Sebastian, Santiago 7510602, Chile
| | - Frances M. Platt
- Department of Pharmacology, University of Oxford, Oxford OX1 3QT, UK
| | - Andrés D. Klein
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 7610658, Chile
- Correspondence:
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6
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Robins C, Liu Y, Fan W, Duong DM, Meigs J, Harerimana NV, Gerasimov ES, Dammer EB, Cutler DJ, Beach TG, Reiman EM, De Jager PL, Bennett DA, Lah JJ, Wingo AP, Levey AI, Seyfried NT, Wingo TS. Genetic control of the human brain proteome. Am J Hum Genet 2021; 108:400-410. [PMID: 33571421 PMCID: PMC8008492 DOI: 10.1016/j.ajhg.2021.01.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/19/2021] [Indexed: 12/30/2022] Open
Abstract
We generated an online brain pQTL resource for 7,376 proteins through the analysis of genetic and proteomic data derived from post-mortem samples of the dorsolateral prefrontal cortex of 330 older adults. The identified pQTLs tend to be non-synonymous variation, are over-represented among variants associated with brain diseases, and replicate well (77%) in an independent brain dataset. Comparison to a large study of brain eQTLs revealed that about 75% of pQTLs are also eQTLs. In contrast, about 40% of eQTLs were identified as pQTLs. These results are consistent with lower pQTL mapping power and greater evolutionary constraint on protein abundance. The latter is additionally supported by observations of pQTLs with large effects' tending to be rare, deleterious, and associated with proteins that have evidence for fewer protein-protein interactions. Mediation analyses using matched transcriptomic and proteomic data provided additional evidence that pQTL effects are often, but not always, mediated by mRNA. Specifically, we identified roughly 1.6 times more mRNA-mediated pQTLs than mRNA-independent pQTLs (550 versus 341). Our pQTL resource provides insight into the functional consequences of genetic variation in the human brain and a basis for novel investigations of genetics and disease.
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7
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Vidal-Domènech F, Riquelme G, Pinacho R, Rodriguez-Mias R, Vera A, Monje A, Ferrer I, Callado LF, Meana JJ, Villén J, Ramos B. Calcium-binding proteins are altered in the cerebellum in schizophrenia. PLoS One 2020; 15:e0230400. [PMID: 32639965 PMCID: PMC7343173 DOI: 10.1371/journal.pone.0230400] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 06/17/2020] [Indexed: 12/16/2022] Open
Abstract
Alterations in the cortico-cerebellar-thalamic-cortical circuit might underlie the diversity of symptoms in schizophrenia. However, molecular changes in cerebellar neuronal circuits, part of this network, have not yet been fully determined. Using LC-MS/MS, we screened altered candidates in pooled grey matter of cerebellum from schizophrenia subjects who committed suicide (n = 4) and healthy individuals (n = 4). Further validation by immunoblotting of three selected candidates was performed in two cohorts comprising schizophrenia (n = 20), non-schizophrenia suicide (n = 6) and healthy controls (n = 21). We found 99 significantly altered proteins, 31 of them previously reported in other brain areas by proteomic studies. Transport function was the most enriched category, while cell communication was the most prevalent function. For validation, we selected the vacuolar proton pump subunit 1 (VPP1), from transport, and two EF-hand calcium-binding proteins, calmodulin and parvalbumin, from cell communication. All candidates showed significant changes in schizophrenia (n = 7) compared to controls (n = 7). VPP1 was altered in the non-schizophrenia suicide group and increased levels of parvalbumin were linked to antipsychotics. Further validation in an independent cohort of non-suicidal chronic schizophrenia subjects (n = 13) and non-psychiatric controls (n = 14) showed that parvalbumin was increased, while calmodulin was decreased in schizophrenia. Our findings provide evidence of calcium-binding protein dysregulation in the cerebellum in schizophrenia, suggesting an impact on normal calcium-dependent synaptic functioning of cerebellar circuits. Our study also links VPP1 to suicide behaviours, suggesting a possible impairment in vesicle neurotransmitter refilling and release in these phenotypes.
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Affiliation(s)
- Francisco Vidal-Domènech
- Psiquiatria Molecular, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
- Dept. de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Gemma Riquelme
- Psiquiatria Molecular, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | - Raquel Pinacho
- Psiquiatria Molecular, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | - Ricard Rodriguez-Mias
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - América Vera
- Psiquiatria Molecular, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | - Alfonso Monje
- Parc Sanitari Sant Joan de Déu, Sant Boi de Llobregat, Spain
| | - Isidre Ferrer
- Departamento de Patologia y Terapeutica Experimental, Universidad de Barcelona, Senior consultant Servicio Anatomia Patológica, Hospital Universitario de Bellvitge-IDIBELL, CIBERNED, Hospital de Llobregat, Barcelona, Spain
| | - Luis F. Callado
- Department of Pharmacology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Salud Mental, Madrid, CIBERSAM, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - J. Javier Meana
- Department of Pharmacology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
- Centro de Investigación Biomédica en Red de Salud Mental, Madrid, CIBERSAM, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Judit Villén
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Belén Ramos
- Psiquiatria Molecular, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
- Dept. de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Parc Sanitari Sant Joan de Déu, Sant Boi de Llobregat, Spain
- Centro de Investigación Biomédica en Red de Salud Mental, Madrid, CIBERSAM, Spain
- * E-mail:
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8
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Komatsu H, Takeuchi H, Kikuchi Y, Ono C, Yu Z, Iizuka K, Takano Y, Kakuto Y, Funakoshi S, Ono T, Ito J, Kunii Y, Hino M, Nagaoka A, Iwasaki Y, Yamamori H, Yasuda Y, Fujimoto M, Azechi H, Kudo N, Hashimoto R, Yabe H, Yoshida M, Saito Y, Kakita A, Fuse N, Kawashima R, Taki Y, Tomita H. Ethnicity-Dependent Effects of Schizophrenia Risk Variants of the OLIG2 Gene on OLIG2 Transcription and White Matter Integrity. Schizophr Bull 2020; 46:1619-1628. [PMID: 32285113 PMCID: PMC7846078 DOI: 10.1093/schbul/sbaa049] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Previous studies have indicated associations between several OLIG2 gene single-nucleotide polymorphisms (SNPs) and susceptibility to schizophrenia among Caucasians. Consistent with these findings, postmortem brain and diffusion tensor imaging studies have indicated that the schizophrenia-risk-associated allele (A) in the OLIG2 SNP rs1059004 predicts lower OLIG2 gene expression in the dorsolateral prefrontal cortex (DLPFC) of schizophrenia patients and reduced white matter (WM) integrity of the corona radiata in normal brains among Caucasians. In an effort to replicate the association between this variant and WM integrity among healthy Japanese, we found that the number of A alleles was positively correlated with WM integrity in some fiber tracts, including the right posterior limb of the internal capsule, and with mean blood flow in a widespread area, including the inferior frontal operculum, orbital area, and triangular gyrus. Because the A allele affected WM integrity in opposite directions in Japanese and Caucasians, we investigated a possible association between the OLIG2 gene SNPs and the expression level of OLIG2 transcripts in postmortem DLPFCs. We evaluated rs1059004 and additional SNPs in the 5' upstream and 3' downstream regions of rs1059004 to cover the broader region of the OLIG2 gene. The 2 SNPs (rs1059004 and rs9653711) had opposite effects on OLIG2 gene expression in the DLPFC in Japanese and Caucasians. These findings suggest ethnicity-dependent opposite effects of OLIG2 gene SNPs on WM integrity and OLIG2 gene expression in the brain, which may partially explain the failures in replicating associations between genetic variants and psychiatric phenotypes among ethnicities.
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Affiliation(s)
- Hiroshi Komatsu
- Department of Psychiatry, Miyagi Psychiatric Center, Natori, Japan,Department of Disaster Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan,To whom correspondence should be addressed; Department of Disaster Psychiatry, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aobaku, Sendai, 980-8573, Japan; Department of Psychiatry, Miyagi Psychiatric Center, Mubanchi, Tekurada, Natori, 981-1231, Japan; tel: +81-22-384-2236, fax: +81-22-384-9100, e-mail:
| | - Hikaru Takeuchi
- Division of Developmental Cognitive Neuroscience, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Yoshie Kikuchi
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Chiaki Ono
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Zhiqian Yu
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Kunio Iizuka
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yuji Takano
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yoshihisa Kakuto
- Department of Psychiatry, Miyagi Psychiatric Center, Natori, Japan
| | - Shunichi Funakoshi
- Department of Psychiatry, Miyagi Psychiatric Center, Natori, Japan,Department of Community Psychiatry, Tohoku University, Sendai, Japan
| | - Takashi Ono
- Department of Psychiatry, Miyagi Psychiatric Center, Natori, Japan
| | - Junko Ito
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yasuto Kunii
- Department of Neuropsychiatry, Fukushima Medical University School of Medicine, Fukushima, Japan,Department of Psychiatry, Aizu Medical Center Fukushima Medical University, Fukushima, Japan
| | - Mizuki Hino
- Department of Neuropsychiatry, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Atsuko Nagaoka
- Department of Neuropsychiatry, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Yasushi Iwasaki
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Nagakute, Japan
| | - Hidenaga Yamamori
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo, Japan,Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yuka Yasuda
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo, Japan,Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Michiko Fujimoto
- Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hirotsugu Azechi
- Molecular Research Center for Children’s Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan
| | - Noriko Kudo
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo, Japan,Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Ryota Hashimoto
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo, Japan,Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan,Molecular Research Center for Children’s Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan
| | - Hirooki Yabe
- Department of Neuropsychiatry, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Mari Yoshida
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Nagakute, Japan
| | - Yuko Saito
- Department of Pathology and Laboratory Medicine, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Ryuta Kawashima
- Division of Developmental Cognitive Neuroscience, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan,Smart Aging International Research Center, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Yasuyuki Taki
- Division of Developmental Cognitive Neuroscience, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Department of Nuclear Medicine and Radiology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Hiroaki Tomita
- Department of Disaster Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan,Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan,Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
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9
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Predicting novel genomic regions linked to genetic disorders using GWAS and chromosome conformation data - a case study of schizophrenia. Sci Rep 2019; 9:17940. [PMID: 31784692 PMCID: PMC6884554 DOI: 10.1038/s41598-019-54514-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies identified numerous loci harbouring single nucleotide polymorphisms (SNPs) associated with various human diseases, although the causal role of many of them remains unknown. In this paper, we postulate that co-location and shared biological function of novel genes with genes known to associate with a specific phenotype make them potential candidates linked to the same phenotype (“guilt-by-proxy”). We propose a novel network-based approach for predicting candidate genes/genomic regions utilising the knowledge of the 3D architecture of the human genome and GWAS data. As a case study we used a well-studied polygenic disorder ‒ schizophrenia ‒ for which we compiled a comprehensive dataset of SNPs. Our approach revealed 634 novel regions covering ~398 Mb of the human genome and harbouring ~9000 genes. Using various network measures and enrichment analysis, we identified subsets of genes and investigated the plausibility of these genes/regions having an association with schizophrenia using literature search and bioinformatics resources. We identified several genes/regions with previously reported associations with schizophrenia, thus providing proof-of-concept, as well as novel candidates with no prior known associations. This approach has the potential to identify novel genes/genomic regions linked to other polygenic disorders and provide means of aggregating genes/SNPs for further investigation.
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10
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A multimodal attempt to follow-up linkage regions using RNA expression, SNPs and CpG methylation in schizophrenia and bipolar disorder kindreds. Eur J Hum Genet 2019; 28:499-507. [PMID: 31695175 DOI: 10.1038/s41431-019-0526-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 08/20/2019] [Accepted: 09/27/2019] [Indexed: 11/09/2022] Open
Abstract
The complexity of schizophrenia (SZ) and bipolar disorder (BD) has slowed down progress in understanding their genetic roots. Alternative genomic approaches are needed to bypass these difficulties. We attempted a multimodal approach to follow-up on reported linkage findings in SZ and BD from the Eastern Quebec kindreds in chromosomes 3q21, 4p34, 6p22, 8p21, 8p11, 13q11-q14, 15q13, 16p12, and 18q21. First, in 498 subjects, we measured RNA expression (47 K Illumina chips) in SZ and BD patients that we compared with their non-affected relatives (NARs) to identify, for each chromosomal region, genes showing the most significant differences in expression. Second, we performed SNP genotyping (700 K Illumina chips) and cis-eQTN analysis. Third, we measured DNA methylation on genes with RNA expression differences or eQTNs. We found a significant overexpression of the gene ITGB5 at 3q25 in SZ and BD after multiple testing p value adjustment. SPCS3 gene at 4q34, and FZD3 gene at 8p21, contained significant eQTNs after multiple testing corrections, while ITGB5 provided suggestive results. Methylation in associated genes did not explain the expression differences between patients and NARs. Our multimodal approach involving RNA expression, dense SNP genotyping and eQTN analyses, restricted to chromosomal regions having shown linkage, lowered the multiple testing burden and allowed for a deeper examination of candidate genes in SZ or BD.
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11
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Zhao XF, Kohen R, Parent R, Duan Y, Fisher GL, Korn MJ, Ji L, Wan G, Jin J, Püschel AW, Dolan DF, Parent JM, Corfas G, Murphy GG, Giger RJ. PlexinA2 Forward Signaling through Rap1 GTPases Regulates Dentate Gyrus Development and Schizophrenia-like Behaviors. Cell Rep 2019; 22:456-470. [PMID: 29320740 PMCID: PMC5788190 DOI: 10.1016/j.celrep.2017.12.044] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/30/2017] [Accepted: 12/12/2017] [Indexed: 01/20/2023] Open
Abstract
Dentate gyrus (DG) development requires specification of granule cell (GC) progenitors in the hippocampal neuroepithelium, as well as their proliferation and migration into the primordial DG. We identify the Plexin family members Plxna2 and Plxna4 as important regulators of DG development. Distribution of immature GCs is regulated by Sema5A signaling through PlxnA2 and requires a functional PlxnA2 GTPase-activating protein (GAP) domain and Rap1 small GTPases. In adult Plxna2−/− but not Plxna2-GAP-deficient mice, the dentate GC layer is severely malformed, neurogenesis is compromised, and mossy fibers form aberrant synaptic boutons within CA3. Behavioral studies with Plxna2−/− mice revealed deficits in associative learning, sociability, and sensorimotor gating—traits commonly observed in neuropsychiatric disorder. Remarkably, while morphological defects are minimal in Plxna2-GAP-deficient brains, defects in fear memory and sensorimotor gating persist. Since allelic variants of human PLXNA2 and RAP1 associate with schizophrenia, our studies identify a biochemical pathway important for brain development and mental health.
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Affiliation(s)
- Xiao-Feng Zhao
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rafi Kohen
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rachel Parent
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuntao Duan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Grace L Fisher
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew J Korn
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lingchao Ji
- Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Guoqiang Wan
- Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jing Jin
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität, 48149 Münster, Germany; Cells-in-Motion Cluster of Excellence, University of Münster, 48149 Münster, Germany
| | - Andreas W Püschel
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität, 48149 Münster, Germany; Cells-in-Motion Cluster of Excellence, University of Münster, 48149 Münster, Germany
| | - David F Dolan
- Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jack M Parent
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; VA Ann Arbor Healthcare System, Ann Arbor, MI 48105, USA; Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabriel Corfas
- Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI 48109, USA; Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Geoffrey G Murphy
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Roman J Giger
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA.
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12
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Kim S, Webster MJ. The Stanley Neuropathology Consortium Integrative Database (SNCID) for Psychiatric Disorders. Neurosci Bull 2018; 35:277-282. [PMID: 30484114 DOI: 10.1007/s12264-018-0314-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/17/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Sanghyeon Kim
- Stanley Brain Research Laboratory, Stanley Medical Research Institute, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Maree J Webster
- Stanley Brain Research Laboratory, Stanley Medical Research Institute, 9800 Medical Center Drive, Rockville, MD, 20850, USA.
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13
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Müller B, Boltze J, Czepezauer I, Hesse V, Wilcke A, Kirsten H. Dyslexia risk variant rs600753 is linked with dyslexia-specific differential allelic expression of DYX1C1. Genet Mol Biol 2018; 41:41-49. [PMID: 29473935 PMCID: PMC5901500 DOI: 10.1590/1678-4685-gmb-2017-0165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/28/2017] [Indexed: 11/22/2022] Open
Abstract
An increasing number of genetic variants involved in dyslexia development were
discovered during the last years, yet little is known about the molecular
functional mechanisms of these SNPs. In this study we investigated whether
dyslexia candidate SNPs have a direct, disease-specific effect on local
expression levels of the assumed target gene by using a differential allelic
expression assay. In total, 12 SNPs previously associated with dyslexia and
related phenotypes were suitable for analysis. Transcripts corresponding to four
SNPs were sufficiently expressed in 28 cell lines originating from controls and
a family affected by dyslexia. We observed a significant effect of rs600753 on
expression levels of DYX1C1 in forward and reverse sequencing
approaches. The expression level of the rs600753 risk allele was increased in
the respective seven cell lines from members of the dyslexia family which might
be due to a disturbed transcription factor binding sites. When considering our
results in the context of neuroanatomical dyslexia-specific findings, we
speculate that this mechanism may be part of the pathomechanisms underlying the
dyslexia-specific brain phenotype. Our results suggest that allele-specific
DYX1C1 expression levels depend on genetic variants of
rs600753 and contribute to dyslexia. However, these results are preliminary and
need replication.
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Affiliation(s)
- Bent Müller
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Johannes Boltze
- Fraunhofer Research Institution for Marine Biotechnology, Department of Medical Cell Technology, Lübeck, Germany.,Institute for Medical and Marine Biotechnology, University of Lübeck, Lübeck, Germany
| | - Ivonne Czepezauer
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Volker Hesse
- German Center for Growth, Development and Health Encouragement in Childhood and Adolescence, Berlin, Germany.,Charité-University Medicine Berlin, Institute for Experimental Paediatric Endocrinolgy, Berlin
| | | | - Arndt Wilcke
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Holger Kirsten
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany.,Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.,LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
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14
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Ramachandran S, Coffin SL, Tang TY, Jobaliya CD, Spengler RM, Davidson BL. Cis-acting single nucleotide polymorphisms alter MicroRNA-mediated regulation of human brain-expressed transcripts. Hum Mol Genet 2018; 25:4939-4950. [PMID: 28171541 PMCID: PMC5418741 DOI: 10.1093/hmg/ddw317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/06/2016] [Accepted: 09/12/2016] [Indexed: 12/11/2022] Open
Abstract
Substantial variability exists in the presentation of complex neurological disorders, and the study of single nucleotide polymorphisms (SNPs) has shed light on disease mechanisms and pathophysiological variability in some cases. However, the vast majority of disease-linked SNPs have unidentified pathophysiological relevance. Here, we tested the hypothesis that SNPs within the miRNA recognition element (MRE; the region of the target transcript to which the miRNA binds) can impart changes in the expression of those genes, either by enhancing or reducing transcript and protein levels. To test this, we cross-referenced 7,153 miRNA-MRE brain interactions with the SNP database (dbSNP) to identify candidates, and functionally assessed 24 SNPs located in the 3’UTR or the coding sequence (CDS) of targets. For over half of the candidates tested, SNPs either enhanced (4 genes) or disrupted (10 genes) miRNA binding and target regulation. Additionally, SNPs causing a shift from a common to rare codon within the CDS facilitated miRNA binding downstream of the SNP, dramatically repressing target gene expression. The biological activity of the SNPs on miRNA regulation was also confirmed in induced pluripotent stem cell (iPSC) lines. These studies strongly support the notion that SNPs in the 3’UTR or the coding sequence of disease-relevant genes may be important in disease pathogenesis and should be reconsidered as candidate modifiers.
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Affiliation(s)
- Shyam Ramachandran
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Stephanie L Coffin
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, USA
| | - Tin-Yun Tang
- Howard Hughes Medical Institute Medical Research Fellow, Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Chintan D Jobaliya
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, USA.,Human Pluripotent Stem Cell Core, Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ryan M Spengler
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Beverly L Davidson
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, USA.,The Department of Pathology & Laboratory Medicine, The Children’s Hospital of Philadelphia and The University of Pennsylvania, Philadelphia, PA, USA
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15
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Zhao XF, Kohen R, Parent R, Duan Y, Fisher GL, Korn MJ, Ji L, Wan G, Jin J, Püschel AW, Dolan DF, Parent JM, Corfas G, Murphy GG, Giger RJ. PlexinA2 Forward Signaling through Rap1 GTPases Regulates Dentate Gyrus Development and Schizophrenia-like Behaviors. Cell Rep 2018. [PMID: 29320740 DOI: 10.1016/j.celrep.2017.12.044.plexina2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
Dentate gyrus (DG) development requires specification of granule cell (GC) progenitors in the hippocampal neuroepithelium, as well as their proliferation and migration into the primordial DG. We identify the Plexin family members Plxna2 and Plxna4 as important regulators of DG development. Distribution of immature GCs is regulated by Sema5A signaling through PlxnA2 and requires a functional PlxnA2 GTPase-activating protein (GAP) domain and Rap1 small GTPases. In adult Plxna2-/- but not Plxna2-GAP-deficient mice, the dentate GC layer is severely malformed, neurogenesis is compromised, and mossy fibers form aberrant synaptic boutons within CA3. Behavioral studies with Plxna2-/- mice revealed deficits in associative learning, sociability, and sensorimotor gating-traits commonly observed in neuropsychiatric disorder. Remarkably, while morphological defects are minimal in Plxna2-GAP-deficient brains, defects in fear memory and sensorimotor gating persist. Since allelic variants of human PLXNA2 and RAP1 associate with schizophrenia, our studies identify a biochemical pathway important for brain development and mental health.
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Affiliation(s)
- Xiao-Feng Zhao
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rafi Kohen
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rachel Parent
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuntao Duan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Grace L Fisher
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew J Korn
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lingchao Ji
- Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Guoqiang Wan
- Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jing Jin
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität, 48149 Münster, Germany; Cells-in-Motion Cluster of Excellence, University of Münster, 48149 Münster, Germany
| | - Andreas W Püschel
- Institut für Molekulare Zellbiologie, Westfälische Wilhelms-Universität, 48149 Münster, Germany; Cells-in-Motion Cluster of Excellence, University of Münster, 48149 Münster, Germany
| | - David F Dolan
- Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jack M Parent
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; VA Ann Arbor Healthcare System, Ann Arbor, MI 48105, USA; Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabriel Corfas
- Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI 48109, USA; Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Geoffrey G Murphy
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Roman J Giger
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA; Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA.
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16
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Müller B, Schaadt G, Boltze J, Emmrich F, Skeide MA, Neef NE, Kraft I, Brauer J, Friederici AD, Kirsten H, Wilcke A. ATP2C2 and DYX1C1 are putative modulators of dyslexia-related MMR. Brain Behav 2017; 7:e00851. [PMID: 29201552 PMCID: PMC5698869 DOI: 10.1002/brb3.851] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 08/23/2017] [Accepted: 09/01/2017] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Dyslexia is a specific learning disorder affecting reading and spelling abilities. Its prevalence is ~5% in German-speaking individuals. Although the etiology of dyslexia largely remains to be determined, comprehensive evidence supports deficient phonological processing as a major contributing factor. An important prerequisite for phonological processing is auditory discrimination and, thus, essential for acquiring reading and spelling skills. The event-related potential Mismatch Response (MMR) is an indicator for auditory discrimination capabilities with dyslexics showing an altered late component of MMR in response to auditory input. METHODS In this study, we comprehensively analyzed associations of dyslexia-specific late MMRs with genetic variants previously reported to be associated with dyslexia-related phenotypes in multiple studies comprising 25 independent single-nucleotide polymorphisms (SNPs) within 10 genes. RESULTS First, we demonstrated validity of these SNPs for dyslexia in our sample by showing that additional inclusion of a polygenic risk score improved prediction of impaired writing compared with a model that used MMR alone. Secondly, a multifactorial regression analysis was conducted to uncover the subset of the 25 SNPs that is associated with the dyslexia-specific late component of MMR. In total, four independent SNPs within DYX1C1 and ATP2C2 were found to be associated with MMR stronger than expected from multiple testing. To explore potential pathomechanisms, we annotated these variants with functional data including tissue-specific expression analysis and eQTLs. CONCLUSION Our findings corroborate the late component of MMR as a potential endophenotype for dyslexia and support tripartite relationships between dyslexia-related SNPs, the late component of MMR and dyslexia.
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Affiliation(s)
- Bent Müller
- Fraunhofer Institute for Cell Therapy and Immunology Leipzig Germany
| | - Gesa Schaadt
- Department of Neuropsychology Max Planck Institute for Human Cognitive and Brain Sciences Leipzig Germany.,Department of Psychology Humboldt-Universität zu Berlin Berlin Germany
| | - Johannes Boltze
- Fraunhofer Institute for Cell Therapy and Immunology Leipzig Germany.,Department of Medical Cell Technology Fraunhofer Research Institution for Marine Biotechnology Lübeck Germany.,Institute for Medical and Marine Biotechnology University of Lübeck Lübeck Germany
| | - Frank Emmrich
- Fraunhofer Institute for Cell Therapy and Immunology Leipzig Germany
| | | | - Michael A Skeide
- Department of Neuropsychology Max Planck Institute for Human Cognitive and Brain Sciences Leipzig Germany
| | - Nicole E Neef
- Department of Neuropsychology Max Planck Institute for Human Cognitive and Brain Sciences Leipzig Germany
| | - Indra Kraft
- Department of Neuropsychology Max Planck Institute for Human Cognitive and Brain Sciences Leipzig Germany
| | - Jens Brauer
- Department of Neuropsychology Max Planck Institute for Human Cognitive and Brain Sciences Leipzig Germany
| | - Angela D Friederici
- Department of Neuropsychology Max Planck Institute for Human Cognitive and Brain Sciences Leipzig Germany
| | - Holger Kirsten
- Fraunhofer Institute for Cell Therapy and Immunology Leipzig Germany.,Institute for Medical Informatics Statistics and Epidemiology University of Leipzig Leipzig Germany.,LIFE-Leipzig Research Center for Civilization Diseases University of Leipzig Leipzig Germany
| | - Arndt Wilcke
- Fraunhofer Institute for Cell Therapy and Immunology Leipzig Germany
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17
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Javidfar B, Park R, Kassim BS, Bicks LK, Akbarian S. The epigenomics of schizophrenia, in the mouse. Am J Med Genet B Neuropsychiatr Genet 2017; 174:631-640. [PMID: 28699694 PMCID: PMC5573750 DOI: 10.1002/ajmg.b.32566] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 05/04/2017] [Accepted: 06/12/2017] [Indexed: 01/02/2023]
Abstract
Large-scale consortia including the Psychiatric Genomics Consortium, the Common Minds Consortium, BrainSeq and PsychENCODE, and many other studies taken together provide increasingly detailed insights into the genetic and epigenetic risk architectures of schizophrenia (SCZ) and offer vast amounts of molecular information, but with largely unexplored therapeutic potential. Here we discuss how epigenomic studies in human brain could guide animal work to test the impact of disease-associated alterations in chromatin structure and function on cognition and behavior. For example, transcription factors such as MYOCYTE-SPECIFIC ENHANCER FACTOR 2C (MEF2C), or multiple regulators of the open chromatin mark, methyl-histone H3-lysine 4, are associated with the genetic risk architectures of common psychiatric disease and alterations in chromatin structure and function in diseased brain tissue. Importantly, these molecules also affect cognition and behavior in genetically engineered mice, including virus-mediated expression changes in prefrontal cortex (PFC) and other key nodes in the circuitry underlying psychosis. Therefore, preclinical and small laboratory animal work could target genomic sequences affected by chromatin alterations in SCZ. To this end, in vivo editing of enhancer and other regulatory non-coding DNA by RNA-guided nucleases including CRISPR-Cas, and designer transcription factors, could be expected to deliver pipelines for novel therapeutic approaches aimed at improving cognitive dysfunction and other core symptoms of SCZ.
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Affiliation(s)
| | | | | | - Lucy K. Bicks
- Department of Psychiatry; Friedman Brain Institute; Icahn School of Medicine at Mount Sinai; New York New York
| | - Schahram Akbarian
- Department of Psychiatry; Friedman Brain Institute; Icahn School of Medicine at Mount Sinai; New York New York
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18
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Mirza N, Appleton R, Burn S, du Plessis D, Duncan R, Farah JO, Feenstra B, Hviid A, Josan V, Mohanraj R, Shukralla A, Sills GJ, Marson AG, Pirmohamed M. Genetic regulation of gene expression in the epileptic human hippocampus. Hum Mol Genet 2017; 26:1759-1769. [PMID: 28334860 PMCID: PMC5411756 DOI: 10.1093/hmg/ddx061] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/12/2016] [Accepted: 02/16/2017] [Indexed: 01/21/2023] Open
Abstract
Epilepsy is a serious and common neurological disorder. Expression quantitative loci (eQTL) analysis is a vital aid for the identification and interpretation of disease-risk loci. Many eQTLs operate in a tissue- and condition-specific manner. We have performed the first genome-wide cis-eQTL analysis of human hippocampal tissue to include not only normal (n = 22) but also epileptic (n = 22) samples. We demonstrate that disease-associated variants from an epilepsy GWAS meta-analysis and a febrile seizures (FS) GWAS are significantly more enriched with epilepsy-eQTLs than with normal hippocampal eQTLs from two larger independent published studies. In contrast, GWAS meta-analyses of two other brain diseases associated with hippocampal pathology (Alzheimer's disease and schizophrenia) are more enriched with normal hippocampal eQTLs than with epilepsy-eQTLs. These observations suggest that an eQTL analysis that includes disease-affected brain tissue is advantageous for detecting additional risk SNPs for the afflicting and closely related disorders, but not for distinct diseases affecting the same brain regions. We also show that epilepsy eQTLs are enriched within epilepsy-causing genes: an epilepsy cis-gene is significantly more likely to be a causal gene for a Mendelian epilepsy syndrome than to be a causal gene for another Mendelian disorder. Epilepsy cis-genes, compared to normal hippocampal cis-genes, are more enriched within epilepsy-causing genes. Hence, we utilize the epilepsy eQTL data for the functional interpretation of epilepsy disease-risk variants and, thereby, highlight novel potential causal genes for sporadic epilepsy. In conclusion, an epilepsy-eQTL analysis is superior to normal hippocampal tissue eQTL analyses for identifying the variants and genes underlying epilepsy.
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Affiliation(s)
- Nasir Mirza
- Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GL, UK
| | - Richard Appleton
- The Roald Dahl EEG Unit, Paediatric Neurosciences Foundation, Alder Hey Children's NHS Foundation Trust, Liverpool L12 2AP, UK
| | - Sasha Burn
- Department of Neurosurgery, Alder Hey Children's NHS Foundation Trust, Liverpool L12 2AP, UK
| | - Daniel du Plessis
- Department of Cellular Pathology, Salford Royal NHS Foundation Trust, Salford M6 8HD, UK
| | - Roderick Duncan
- Department of Neurology, Christchurch Hospital, Christchurch 8140, New Zealand
| | - Jibril Osman Farah
- Department of Neurosurgery, The Walton Centre NHS Foundation Trust, Liverpool L9 7LJ, UK
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Hviid
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Vivek Josan
- Department of Neurosurgery, Salford Royal NHS Foundation Trust, Salford M6 8HD, UK
| | - Rajiv Mohanraj
- Department of Neurology, Salford Royal NHS Foundation Trust, Salford M6 8HD, UK
| | - Arif Shukralla
- Department of Neurology, Salford Royal NHS Foundation Trust, Salford M6 8HD, UK
| | - Graeme J. Sills
- Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GL, UK
| | - Anthony G. Marson
- Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GL, UK
| | - Munir Pirmohamed
- Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GL, UK
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19
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Deng Y, Zhao J, Sakurai D, Sestak AL, Osadchiy V, Langefeld CD, Kaufman KM, Kelly JA, James JA, Petri MA, Bae SC, Alarcón-Riquelme ME, Alarcón GS, Anaya JM, Criswell LA, Freedman BI, Kamen DL, Gilkeson GS, Jacob CO, Merrill JT, Gaffney PM, Sivils KM, Niewold TB, Ramsey-Goldman R, Reveille JD, Scofield RH, Stevens AM, Boackle SA, Vilá LM, Sohn W, Lee S, Chang DM, Song YW, Vyse TJ, Harley JB, Brown EE, Edberg JC, Kimberly RP, Cantor RM, Hahn BH, Grossman JM, Tsao BP. Decreased SMG7 expression associates with lupus-risk variants and elevated antinuclear antibody production. Ann Rheum Dis 2016; 75:2007-2013. [PMID: 26783109 PMCID: PMC4949149 DOI: 10.1136/annrheumdis-2015-208441] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/14/2015] [Indexed: 02/03/2023]
Abstract
OBJECTIVES Following up the systemic lupus erythematosus (SLE) genome-wide association studies (GWAS) identification of NMNAT2 at rs2022013, we fine-mapped its 150 kb flanking regions containing NMNAT2 and SMG7 in a 15 292 case-control multi-ancestry population and tested functions of identified variants. METHODS We performed genotyping using custom array, imputation by IMPUTE 2.1.2 and allele specific functions using quantitative real-time PCR and luciferase reporter transfections. SLE peripheral blood mononuclear cells (PBMCs) were cultured with small interfering RNAs to measure antinuclear antibody (ANA) and cyto/chemokine levels in supernatants using ELISA. RESULTS We confirmed association at NMNAT2 in European American (EA) and Amerindian/Hispanic ancestries, and identified independent signal at SMG7 tagged by rs2702178 in EA only (p=2.4×10-8, OR=1.23 (95% CI 1.14 to 1.32)). In complete linkage disequilibrium with rs2702178, rs2275675 in the promoter region robustly associated with SMG7 mRNA levels in multiple expression quantitative trait locus (eQTL) datasets. Its risk allele was dose-dependently associated with decreased SMG7 mRNA levels in PBMCs of 86 patients with SLE and 119 controls (p=1.1×10-3 and 6.8×10-8, respectively) and conferred reduced transcription activity in transfected HEK-293 (human embryonic kidney cell line) and Raji cells (p=0.0035 and 0.0037, respectively). As a critical component in the nonsense-mediated mRNA decay pathway, SMG7 could regulate autoantigens including ribonucleoprotein (RNP) and Smith (Sm). We showed SMG7 mRNA levels in PBMCs correlated inversely with ANA titres of patients with SLE (r=-0.31, p=0.01), and SMG7 knockdown increased levels of ANA IgG and chemokine (C-C motif) ligand 19 in SLE PBMCs (p=2.0×10-5 and 2.0×10-4, respectively). CONCLUSION We confirmed NMNAT2 and identified independent SMG7 association with SLE. The inverse relationship between levels of the risk allele-associated SMG7 mRNAs and ANA suggested the novel contribution of mRNA surveillance pathway to SLE pathogenesis.
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Affiliation(s)
- Yun Deng
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jian Zhao
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Daisuke Sakurai
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Andrea L. Sestak
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Vadim Osadchiy
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Carl D. Langefeld
- Department of Biostatistical Sciences and Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Kenneth M. Kaufman
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Jennifer A. Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Judith A. James
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michelle A. Petri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Marta E. Alarcón-Riquelme
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Pfizer-Universidad de Granada-Junta de Andalucía Center for Genomics and Oncological Research, Granada, Spain
| | - Graciela S Alarcón
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA), Universidad del Rosario, Bogotá, Colombia
| | - Lindsey A. Criswell
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Barry I Freedman
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Diane L. Kamen
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC, USA
| | - Gary S. Gilkeson
- Division of Rheumatology, Medical University of South Carolina, Charleston, SC, USA
| | - Chaim O. Jacob
- Department of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Joan T Merrill
- Clinical Pharmacology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Patrick M. Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Kathy Moser Sivils
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Timothy B Niewold
- Division of Rheumatology and Department of Immunology, Mayo Clinic, Rochester, MN, USA
| | - Rosalind Ramsey-Goldman
- Division of Rheumatology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - John D Reveille
- Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - R Hal Scofield
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- US Department of Veterans Affairs Medical Center, Oklahoma City, OK, USA
| | - Anne M Stevens
- Division of Rheumatology, Department of Pediatrics, University of Washington, Seattle, WA, USA
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA, USA
| | - Susan A Boackle
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
- US Department of Veterans Affairs Medical Center, Denver, CO, USA
| | - Luis M Vilá
- Division of Rheumatology, Department of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Woong Sohn
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Seung Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | | | - Yeong Wook Song
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Medical Research Center, Seoul National University, Seoul, Korea
| | - Timothy J. Vyse
- Division of Genetics and Molecular Medicine and Immunology, King’s College London, London, UK
| | - John B. Harley
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Elizabeth E. Brown
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jeffrey C. Edberg
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert P. Kimberly
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rita M. Cantor
- Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Bevra H. Hahn
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jennifer M. Grossman
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Betty P. Tsao
- Division of Rheumatology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
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Joshi AD, Andersson C, Buch S, Stender S, Noordam R, Weng LC, Weeke PE, Auer PL, Boehm B, Chen C, Choi H, Curhan G, Denny JC, De Vivo I, Eicher JD, Ellinghaus D, Folsom AR, Fuchs C, Gala M, Haessler J, Hofman A, Hu F, Hunter DJ, Janssen HL, Kang JH, Kooperberg C, Kraft P, Kratzer W, Lieb W, Lutsey PL, Murad SD, Nordestgaard BG, Pasquale LR, Reiner AP, Ridker PM, Rimm E, Rose LM, Shaffer CM, Schafmayer C, Tamimi RM, Uitterlinden AG, Völker U, Völzke H, Wakabayashi Y, Wiggs JL, Zhu J, Roden DM, Stricker BH, Tang W, Teumer A, Hampe J, Tybjærg-Hansen A, Chasman DI, Chan AT, Johnson AD. Four Susceptibility Loci for Gallstone Disease Identified in a Meta-analysis of Genome-Wide Association Studies. Gastroenterology 2016; 151:351-363.e28. [PMID: 27094239 PMCID: PMC4959966 DOI: 10.1053/j.gastro.2016.04.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 01/01/2023]
Abstract
BACKGROUND & AIMS A genome-wide association study (GWAS) of 280 cases identified the hepatic cholesterol transporter ABCG8 as a locus associated with risk for gallstone disease, but findings have not been reported from any other GWAS of this phenotype. We performed a large-scale, meta-analysis of GWASs of individuals of European ancestry with available prior genotype data, to identify additional genetic risk factors for gallstone disease. METHODS We obtained per-allele odds ratio (OR) and standard error estimates using age- and sex-adjusted logistic regression models within each of the 10 discovery studies (8720 cases and 55,152 controls). We performed an inverse variance weighted, fixed-effects meta-analysis of study-specific estimates to identify single-nucleotide polymorphisms that were associated independently with gallstone disease. Associations were replicated in 6489 cases and 62,797 controls. RESULTS We observed independent associations for 2 single-nucleotide polymorphisms at the ABCG8 locus: rs11887534 (OR, 1.69; 95% confidence interval [CI], 1.54-1.86; P = 2.44 × 10(-60)) and rs4245791 (OR, 1.27; P = 1.90 × 10(-34)). We also identified and/or replicated associations for rs9843304 in TM4SF4 (OR, 1.12; 95% CI, 1.08-1.16; P = 6.09 × 10(-11)), rs2547231 in SULT2A1 (encodes a sulfoconjugation enzyme that acts on hydroxysteroids and cholesterol-derived sterol bile acids) (OR, 1.17; 95% CI, 1.12-1.21; P = 2.24 × 10(-10)), rs1260326 in glucokinase regulatory protein (OR, 1.12; 95% CI, 1.07-1.17; P = 2.55 × 10(-10)), and rs6471717 near CYP7A1 (encodes an enzyme that catalyzes conversion of cholesterol to primary bile acids) (OR, 1.11; 95% CI, 1.08-1.15; P = 8.84 × 10(-9)). Among individuals of African American and Hispanic American ancestry, rs11887534 and rs4245791 were associated positively with gallstone disease risk, whereas the association for the rs1260326 variant was inverse. CONCLUSIONS In this large-scale GWAS of gallstone disease, we identified 4 loci in genes that have putative functions in cholesterol metabolism and transport, and sulfonylation of bile acids or hydroxysteroids.
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Affiliation(s)
- Amit D. Joshi
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA,Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital Boston, MA,To whom correspondence should be addressed: Amit D. Joshi, MBBS, PhD, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA. Tel: +1 617 724 7558; Charlotte Andersson, MD, PhD, The Framingham Heart Study, 73 Mt Wayte Avenue, Framingham, Massachusetts 01702, USA. , Andrew T. Chan, MD, MPH, Massachusetts General Hospital and Harvard Medical School, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, GRJ-825C, Boston, Massachusetts 02114, USA. Tel:+1 617 724 0283; Fax: +1 617 726 3673; , Andrew D. Johnson, PhD, Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA, 01702, USA. Tel: +1 508 663 4082; Fax: +1 508 626 1262;
| | - Charlotte Andersson
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts.
| | - Stephan Buch
- Medical Department 1, University Hospital Dresden, TU Dresden, Dresden Germany
| | - Stefan Stender
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen, Denmark
| | - Raymond Noordam
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Lu-Chen Weng
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, MN
| | - Peter E. Weeke
- Department of Medicine, Vanderbilt University, Nashville, TN,Department of Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Denmark
| | - Paul L. Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin, Milwaukee,Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Bernhard Boehm
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Constance Chen
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA
| | - Hyon Choi
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA
| | - Gary Curhan
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Renal Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Joshua C. Denny
- Department of Medicine, Vanderbilt University, Nashville, TN,Department of Biomedical Informatics, Vanderbilt University, Nashville, TN
| | - Immaculata De Vivo
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - John D. Eicher
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA,Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Framingham, MA
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Aaron R. Folsom
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, MN
| | - Charles Fuchs
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Manish Gala
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Frank Hu
- Department of Epidemiology, Harvard School of Public Health, Boston, MA,Department of Nutrition, Harvard School of Public Health, Boston, MA
| | - David J. Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA,Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - Harry L.A. Janssen
- Department of Gastroenterology and Hepatology, Erasmus MC, Rotterdam, the Netherlands,Toronto Centre for Liver Disease, Toronto Western and General Hospital, University Health Network, Toronto, Canada
| | - Jae H. Kang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA,Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - Wolfgang Kratzer
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian Albrechts Universität Kiel, Niemannsweg 11, Kiel, Germany
| | - Pamela L. Lutsey
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, MN
| | - Sarwa Darwish Murad
- Department of Gastroenterology and Hepatology, Erasmus MC, Rotterdam, the Netherlands
| | - Børge G. Nordestgaard
- The Copenhagen General Population Study and,Department of Clinical Biochemistry, Herlev Hospital, Herlev Denmark,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Louis R. Pasquale
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA
| | - Alex P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Paul M Ridker
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Eric Rimm
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Department of Epidemiology, Harvard School of Public Health, Boston, MA,Department of Nutrition, Harvard School of Public Health, Boston, MA
| | - Lynda M. Rose
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | | | - Clemens Schafmayer
- Department of General, Abdominal, Thoracic and Transplantation Surgery, University of Kiel, Kiel, Germany
| | - Rulla M. Tamimi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany,German Center for Cardiovascular Research, Partner Site Greifswald,German Center for Diabetes Research, Site Greifswald
| | - Yoshiyuki Wakabayashi
- The National Heart, Lung, and Blood Institute, DNA Sequencing Core Laboratory, Bethesda, MD
| | - Janey L. Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA
| | - Jun Zhu
- The National Heart, Lung, and Blood Institute, DNA Sequencing Core Laboratory, Bethesda, MD
| | - Dan M. Roden
- Department of Medicine, Vanderbilt University, Nashville, TN
| | - Bruno H. Stricker
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Weihong Tang
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, MN
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, TU Dresden, Dresden Germany
| | - Anne Tybjærg-Hansen
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen, Denmark,Department of Clinical Biochemistry, Herlev Hospital, Herlev Denmark
| | - Daniel I. Chasman
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Andrew T. Chan
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital Boston, MA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,To whom correspondence should be addressed: Amit D. Joshi, MBBS, PhD, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA. Tel: +1 617 724 7558; Charlotte Andersson, MD, PhD, The Framingham Heart Study, 73 Mt Wayte Avenue, Framingham, Massachusetts 01702, USA. , Andrew T. Chan, MD, MPH, Massachusetts General Hospital and Harvard Medical School, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, GRJ-825C, Boston, Massachusetts 02114, USA. Tel:+1 617 724 0283; Fax: +1 617 726 3673; , Andrew D. Johnson, PhD, Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA, 01702, USA. Tel: +1 508 663 4082; Fax: +1 508 626 1262;
| | - Andrew D. Johnson
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA,Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Framingham, MA,To whom correspondence should be addressed: Amit D. Joshi, MBBS, PhD, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA. Tel: +1 617 724 7558; Charlotte Andersson, MD, PhD, The Framingham Heart Study, 73 Mt Wayte Avenue, Framingham, Massachusetts 01702, USA. , Andrew T. Chan, MD, MPH, Massachusetts General Hospital and Harvard Medical School, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, GRJ-825C, Boston, Massachusetts 02114, USA. Tel:+1 617 724 0283; Fax: +1 617 726 3673; , Andrew D. Johnson, PhD, Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA, 01702, USA. Tel: +1 508 663 4082; Fax: +1 508 626 1262;
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John J, Bhatia T, Kukshal P, Chandna P, Nimgaonkar VL, Deshpande SN, Thelma BK. Association study of MiRSNPs with schizophrenia, tardive dyskinesia and cognition. Schizophr Res 2016; 174:29-34. [PMID: 27106592 PMCID: PMC5487370 DOI: 10.1016/j.schres.2016.03.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 03/22/2016] [Accepted: 03/24/2016] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) bind to 3'UTRs of genes and negatively regulate their expression. With ~50% of miRNAs expressing in the brain, they play an important role in neuronal development, plasticity, cognition and neurological disorders. Conserved miRNA targets are present in >60% genes in humans and are under evolutionary pressure to maintain pairing with miRNA. However, such binding may be affected by genetic variant(s) in the target sites (MiRSNPs), thereby altering gene expression. Differential expression of a large number of genes in postmortem brains of schizophrenia (SZ) patients compared to controls has been documented. Thus studying the role of MiRSNPs which are underinvestigated in SZ becomes attractive. We systematically selected 35 MiRSNPs with predicted functional relevance in 3'UTRs of genes shown previously to be associated with SZ, genotyped and tested their association with disease, using independent discovery and replication samples (total n=1017 cases; n=1073 controls). We also explored genetic associations with two sets of quantitative traits, namely tardive dyskinesia (TD) and cognitive functions disrupted in SZ in subsets of the study cohort. In the primary analysis, a significant association of MiRSNP rs7430 at PPP3CC was observed with SZ in the discovery and the replication samples [discovery: P=0.01; OR (95% CI) 1.24 (1.04-1.48); replication: P=0.03; OR (95% CI) 1.20 (1.02-1.43)]. In the exploratory analyses, five SNPs were nominally associated with TD (P values 0.04-0.004). Separately, 12 SNPs were associated with one or more of the eight cognitive domains (P values 0.05-0.003). These associations, particularly the SNP at PPP3CC merit further investigations.
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Affiliation(s)
- Jibin John
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Triptish Bhatia
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi 110 001, India
| | - Prachi Kukshal
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Puneet Chandna
- AceProbe Technologies (India) Pvt. Ltd., New Delhi, India
| | - Vishwajit L Nimgaonkar
- Department of Psychiatry, Western Psychiatric Institute and Clinic, University of Pittsburgh School of Medicine, 3811 O'Hara Street, Pittsburgh, PA 15213, USA
| | - Smita N Deshpande
- Department of Psychiatry, PGIMER-Dr. RML Hospital, New Delhi 110 001, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India.
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22
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Müller B, Wilcke A, Czepezauer I, Ahnert P, Boltze J, Kirsten H. Association, characterisation and meta-analysis of SNPs linked to general reading ability in a German dyslexia case-control cohort. Sci Rep 2016; 6:27901. [PMID: 27312598 PMCID: PMC4911550 DOI: 10.1038/srep27901] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 05/26/2016] [Indexed: 12/25/2022] Open
Abstract
Dyslexia is a severe disorder in the acquisition of reading and writing. Several studies investigated the role of genetics for reading, writing and spelling ability in the general population. However, many of the identified SNPs were not analysed in case-control cohorts. Here, we investigated SNPs previously linked to reading or spelling ability in the general population in a German case-control cohort. Furthermore, we characterised these SNPs for functional relevance with in silico methods and meta-analysed them with previous studies. A total of 16 SNPs within five genes were included. The total number of risk alleles was higher in cases than in controls. Three SNPs were nominally associated with dyslexia: rs7765678 within DCDC2, and rs2038137 and rs6935076 within KIAA0319. The relevance of rs2038137 and rs6935076 was further supported by the meta-analysis. Functional profiling included analysis of tissue-specific expression, annotations for regulatory elements and effects on gene expression levels (eQTLs). Thereby, we found molecular mechanistical implications for 13 of all 16 included SNPs. SNPs associated in our cohort showed stronger gene-specific eQTL effects than non-associated SNPs. In summary, our results validate SNPs previously linked to reading and spelling in the general population in dyslexics and provide insights into their putative molecular pathomechanisms.
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Affiliation(s)
- Bent Müller
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Arndt Wilcke
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany.,Translational Centre for Regenerative Medicine (TRM), Leipzig, Germany
| | - Ivonne Czepezauer
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Peter Ahnert
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.,LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Johannes Boltze
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany.,Fraunhofer Research Institution for Marine Biotechnology, Department of Medical Cell Technology, Lübeck, Germany.,Institute for Medical and Marine Biotechnology, University of Lübeck, Lübeck, Germany
| | - Holger Kirsten
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany.,Translational Centre for Regenerative Medicine (TRM), Leipzig, Germany.,Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.,LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
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Kim S, Hwang Y, Webster MJ, Lee D. Differential activation of immune/inflammatory response-related co-expression modules in the hippocampus across the major psychiatric disorders. Mol Psychiatry 2016; 21:376-85. [PMID: 26077692 DOI: 10.1038/mp.2015.79] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 04/13/2015] [Accepted: 05/06/2015] [Indexed: 02/06/2023]
Abstract
The Stanley Neuropathology Consortium Integrative Database (SNCID, http://sncid.stanleyresearch.org) is a data-mining tool that includes 379 neuropathology data sets from hippocampus, as well as RNA-Seq data measured in 15 well-matched cases in each of four groups: schizophrenia, bipolar disorder (BPD), major depression (MD) and unaffected controls. We analyzed the neuropathology data from the hippocampus to identify those abnormalities that are shared between psychiatric disorders and those that are specific to each disorder. Of the 379 data sets, 20 of them showed a significant abnormality in at least one disorder as compared with unaffected controls. GABAergic markers and synaptic proteins were mainly abnormal in schizophrenia and the two mood disorders, respectively. Two immune/inflammation-related co-expression modules built from RNA-seq data from both schizophrenia and controls combined were associated with disease status, as well as negatively correlated with the GABAergic markers. The correlation between immune-related modules and schizophrenia was replicated using microarray data from an independent tissue collection. Immune/inflammation-related co-expression modules were also built from RNA-seq data from BPD cases or from MD cases but were not preserved when using data from control cases. Moreover, there was no overlap in the genes that comprise the immune/inflammation response-related modules across the different disorders. Thus, there appears to be differential activation of the immune/inflammatory response, as determined by co-expression of genes, which is associated with the major psychiatric disorders and which is also associated with the abnormal neuropathology in the disorders.
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Affiliation(s)
- S Kim
- Stanley Brain Research Laboratory, Stanley Medical Research Institute, Rockville, MD, USA
| | - Y Hwang
- Department of Bio and Brain Engineering, KAIST, Yuseong-gu, Daejeon, Korea
| | - M J Webster
- Stanley Brain Research Laboratory, Stanley Medical Research Institute, Rockville, MD, USA
| | - D Lee
- Department of Bio and Brain Engineering, KAIST, Yuseong-gu, Daejeon, Korea
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24
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Wang C, Aleksic B, Ozaki N. Glia-related genes and their contribution to schizophrenia. Psychiatry Clin Neurosci 2015; 69:448-61. [PMID: 25759284 DOI: 10.1111/pcn.12290] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/08/2015] [Indexed: 12/24/2022]
Abstract
Schizophrenia, a debilitating disease with 1% prevalence in the general population, is characterized by major neuropsychiatric symptoms, including delusions, hallucinations, and deficits in emotional and social behavior. Previous studies have directed their investigations on the mechanism of schizophrenia towards neuronal dysfunction and have defined schizophrenia as a 'neuron-centric' disorder. However, along with the development of genetics and systematic biology approaches in recent years, the crucial role of glial cells in the brain has also been shown to contribute to the etiopathology of schizophrenia. Here, we summarize comprehensive data that support the involvement of glial cells (including oligodendrocytes, astrocytes, and microglial cells) in schizophrenia and list several acknowledged glia-related genes or molecules associated with schizophrenia. Instead of purely an abnormality of neurons in schizophrenia, an additional 'glial perspective' provides us a novel and promising insight into the causal mechanisms and treatment for this disease.
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Affiliation(s)
- Chenyao Wang
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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25
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Erburu M, Cajaleon L, Guruceaga E, Venzala E, Muñoz-Cobo I, Beltrán E, Puerta E, Tordera R. Chronic mild stress and imipramine treatment elicit opposite changes in behavior and in gene expression in the mouse prefrontal cortex. Pharmacol Biochem Behav 2015; 135:227-36. [DOI: 10.1016/j.pbb.2015.06.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/28/2015] [Accepted: 06/01/2015] [Indexed: 01/22/2023]
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Wang X, Cairns MJ. Understanding complex transcriptome dynamics in schizophrenia and other neurological diseases using RNA sequencing. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2015; 116:127-52. [PMID: 25172474 DOI: 10.1016/b978-0-12-801105-8.00006-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
How the human brain develops and adapts with its trillions of functionally integrated synapses remains one of the greatest mysteries of life. With tremendous advances in neuroscience, genetics, and molecular biology, we are beginning to appreciate the scope of this complexity and define some of the parameters of the systems that make it possible. These same tools are also leading to advances in our understanding of the pathophysiology of neurocognitive and neuropsychiatric disorders. Like the substrate for these problems, the etiology is usually complex-involving an array of genetic and environmental influences. To resolve these influences and derive better interventions, we need to reveal every aspect of this complexity and model their interactions and define the systems and their regulatory structure. This is particularly important at the tissue-specific molecular interface between the underlying genetic and environmental influence defined by the transcriptome. Recent advances in transcriptome analysis facilitated by RNA sequencing (RNA-Seq) can provide unprecedented insight into the functional genomics of neurological disorders. In this review, we outline the advantages of this approach and highlight some early application of this technology in the investigation of the neuropathology of schizophrenia. Recent progress of RNA-Seq studies in schizophrenia has shown that there is extraordinary transcriptome dynamics with significant levels of alternative splicing. These studies only scratch the surface of this complexity and therefore future studies with greater depth and samples size will be vital to fully explore transcriptional diversity and its underlying influences in schizophrenia and provide the basis for new biomarkers and improved treatments.
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Affiliation(s)
- Xi Wang
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, Callaghan, New South Wales, Australia
| | - Murray J Cairns
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, The University of Newcastle, Callaghan, New South Wales, Australia; The Schizophrenia Research Institute, Sydney, Australia.
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Horváth S, Mirnics K. Schizophrenia as a disorder of molecular pathways. Biol Psychiatry 2015; 77:22-8. [PMID: 24507510 PMCID: PMC4092052 DOI: 10.1016/j.biopsych.2014.01.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 01/02/2014] [Accepted: 01/05/2014] [Indexed: 12/21/2022]
Abstract
Over the last decade, transcriptome studies of postmortem tissue from subjects with schizophrenia revealed that synaptic, mitochondrial, immune system, gamma-aminobutyric acidergic, and oligodendrocytic changes are all integral parts of the disease process. The combined genetic and transcriptomic studies argue that the molecular underpinnings of the disease are even more varied than the symptomatic diversity of schizophrenia. Ultimately, to decipher the pathophysiology of human disorders in general, we will need to understand the function of hundreds of genes and regulatory elements in our genome and the consequences of their overexpression and reduced expression in a developmental context. Furthermore, integration of knowledge from various data sources remains a monumental challenge that has to be systematically addressed in the upcoming decades. In the end, our success in interpreting the molecular changes in schizophrenia will depend on our ability to understand the biology using innovative ideas and cannot depend on the hope of developing novel, more powerful technologies.
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Affiliation(s)
- Szatmár Horváth
- Department of Psychiatry; Department of Psychiatry, University of Szeged, Szeged, Hungary
| | - Károly Mirnics
- Department of Psychiatry; Vanderbilt Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, Tennessee; Department of Psychiatry, University of Szeged, Szeged, Hungary.
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Ramasamy A, Trabzuni D, Guelfi S, Varghese V, Smith C, Walker R, De T, Coin L, de Silva R, Cookson MR, Singleton AB, Hardy J, Ryten M, Weale ME. Genetic variability in the regulation of gene expression in ten regions of the human brain. Nat Neurosci 2014; 17:1418-1428. [PMID: 25174004 PMCID: PMC4208299 DOI: 10.1038/nn.3801] [Citation(s) in RCA: 485] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 07/30/2014] [Indexed: 12/12/2022]
Abstract
Germ-line genetic control of gene expression occurs via expression quantitative trait loci (eQTLs). We present a large, exon-specific eQTL data set covering ten human brain regions. We found that cis-eQTL signals (within 1 Mb of their target gene) were numerous, and many acted heterogeneously among regions and exons. Co-regulation analysis of shared eQTL signals produced well-defined modules of region-specific co-regulated genes, in contrast to standard coexpression analysis of the same samples. We report cis-eQTL signals for 23.1% of catalogued genome-wide association study hits for adult-onset neurological disorders. The data set is publicly available via public data repositories and via http://www.braineac.org/. Our study increases our understanding of the regulation of gene expression in the human brain and will be of value to others pursuing functional follow-up of disease-associated variants.
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Affiliation(s)
- Adaikalavan Ramasamy
- Department of Medical & Molecular Genetics, King’s College London, Guy’s Hospital, London, UK
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK
| | - Daniah Trabzuni
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sebastian Guelfi
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK
| | - Vibin Varghese
- Department of Medical & Molecular Genetics, King’s College London, Guy’s Hospital, London, UK
| | - Colin Smith
- Department of Neuropathology, MRC Sudden Death Brain Bank Project, University of Edinburgh, Edinburgh, UK
| | - Robert Walker
- Department of Neuropathology, MRC Sudden Death Brain Bank Project, University of Edinburgh, Edinburgh, UK
| | - Tisham De
- School of Public Health, Faculty of Medicine, Imperial College London, London, UK
| | | | | | - Lachlan Coin
- Institute of Molecular Bioscience, The University of Queensland, Brisbane St Lucia, Queensland, Australia
| | - Rohan de Silva
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK
| | - Mark R Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - John Hardy
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK
| | - Mina Ryten
- Department of Medical & Molecular Genetics, King’s College London, Guy’s Hospital, London, UK
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London (UCL) Institute of Neurology, London, UK
| | - Michael E Weale
- Department of Medical & Molecular Genetics, King’s College London, Guy’s Hospital, London, UK
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Quednow BB, Brzózka MM, Rossner MJ. Transcription factor 4 (TCF4) and schizophrenia: integrating the animal and the human perspective. Cell Mol Life Sci 2014; 71:2815-35. [PMID: 24413739 PMCID: PMC11113759 DOI: 10.1007/s00018-013-1553-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 12/04/2013] [Accepted: 12/30/2013] [Indexed: 02/06/2023]
Abstract
Schizophrenia is a genetically complex disease considered to have a neurodevelopmental pathogenesis and defined by a broad spectrum of positive and negative symptoms as well as cognitive deficits. Recently, large genome-wide association studies have identified common alleles slightly increasing the risk for schizophrenia. Among the few schizophrenia-risk genes that have been consistently replicated is the basic Helix-Loop-Helix (bHLH) transcription factor 4 (TCF4). Haploinsufficiency of the TCF4 (formatting follows IUPAC nomenclature: TCF4 protein/protein function, Tcf4 rodent gene cDNA mRNA, TCF4 human gene cDNA mRNA) gene causes the Pitt-Hopkins syndrome-a neurodevelopmental disease characterized by severe mental retardation. Accordingly, Tcf4 null-mutant mice display developmental brain defects. TCF4-associated risk alleles are located in putative coding and non-coding regions of the gene. Hence, subtle changes at the level of gene expression might be relevant for the etiopathology of schizophrenia. Behavioural phenotypes obtained with a mouse model of slightly increased gene dosage and electrophysiological investigations with human risk-allele carriers revealed an overlapping spectrum of schizophrenia-relevant endophenotypes. Most prominently, early information processing and higher cognitive functions appear to be associated with TCF4 risk genotypes. Moreover, a recent human study unravelled gene × environment interactions between TCF4 risk alleles and smoking behaviour that were specifically associated with disrupted early information processing. Taken together, TCF4 is considered as an integrator ('hub') of several bHLH networks controlling critical steps of various developmental, and, possibly, plasticity-related transcriptional programs in the CNS and changes of TCF4 expression also appear to affect brain networks important for information processing. Consequently, these findings support the neurodevelopmental hypothesis of schizophrenia and provide a basis for identifying the underlying molecular mechanisms.
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Affiliation(s)
- Boris B. Quednow
- Department of Psychiatry, Psychotherapy and Psychosomatics, Experimental and Clinical Pharmacopsychology, Psychiatric Hospital, University of Zurich, Lenggstrasse 31, 8032 Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Magdalena M. Brzózka
- Department of Psychiatry, Molecular and Behavioral Neurobiology, Ludwig-Maximillians-University, Nussbaumstr. 7, 80336 Munich, Germany
| | - Moritz J. Rossner
- Department of Psychiatry, Molecular and Behavioral Neurobiology, Ludwig-Maximillians-University, Nussbaumstr. 7, 80336 Munich, Germany
- Research Group Gene Expression, Max-Planck-Institute of Experimental Medicine, Hermann-Rein-Str. 3, Goettingen, 37075 Germany
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Ganesh S, Chasman D, Larson M, Guo X, Verwoert G, Bis J, Gu X, Smith A, Yang ML, Zhang Y, Ehret G, Rose L, Hwang SJ, Papanicolau G, Sijbrands E, Rice K, Eiriksdottir G, Pihur V, Ridker P, Vasan R, Newton-Cheh C, Raffel LJ, Amin N, Rotter JI, Liu K, Launer LJ, Xu M, Caulfield M, Morrison AC, Johnson AD, Vaidya D, Dehghan A, Li G, Bouchard C, Harris TB, Zhang H, Boerwinkle E, Siscovick DS, Gao W, Uitterlinden AG, Rivadeneira F, Hofman A, Willer CJ, Franco OH, Huo Y, Witteman JC, Munroe PB, Gudnason V, Palmas W, van Duijn C, Fornage M, Levy D, Psaty BM, Chakravarti A, Newton-Cheh C, Johnson T, Gateva V, Tobin M, Bochud M, Coin L, Najjar S, Zhao J, Heath S, Eyheramendy S, Papadakis K, Voight B, Scott L, Zhang F, Farrall M, Tanaka T, Wallace C, Chambers J, Khaw KT, Nilsson P, van der Harst P, Polidoro S, Grobbee D, Onland-Moret N, Bots M, Wain L, Elliott K, Teumer A, Luan J, Lucas G, Kuusisto J, Burton P, Hadley D, McArdle W, Brown M, Dominiczak A, Newhouse S, Samani N, Webster J, Zeggini E, Beckmann J, Bergmann S, Lim N, Song K, Vollenweider P, Waeber G, Waterworth D, Yuan X, Groop L, Orho-Melander M, Allione A, Di Gregorio A, Guarrera S, Panico S, Ricceri F, Romanazzi V, Sacerdote C, Vineis P, Barroso I, Sandhu M, Luben R, Crawford G, Jousilahti P, Perola M, Boehnke M, Bonnycastle L, Collins F, Jackson A, Mohlke K, Stringham H, Valle T, Willer C, Bergman R, Morken M, Döring A, Gieger C, Illig T, Meitinger T, Org E, Pfeufer A, Wichmann H, Kathiresan S, Marrugat J, O’Donnell C, Schwartz S, Siscovick D, Subirana I, Freimer N, Hartikainen AL, McCarthy M, O’Reilly P, Peltonen L, Pouta A, de Jong P, Snieder H, van Gilst W, Clarke R, Goel A, Hamsten A, Peden J, Seedorf U, Syvänen AC, Tognoni G, Lakatta E, Sanna S, Scheet P, Schlessinger D, Scuteri A, Dörr M, Ernst F, Felix S, Homuth G, Lorbeer R, Reffelmann T, Rettig R, Völker U, Galan P, Gut I, Hercberg S, Lathrop G, Zeleneka D, Deloukas P, Soranzo N, Williams F, Zhai G, Salomaa V, Laakso M, Elosua R, Forouhi N, Völzke H, Uiterwaal C, van der Schouw Y, Numans M, Matullo G, Navis G, Berglund G, Bingham S, Kooner J, Paterson A, Connell J, Bandinelli S, Ferrucci L, Watkins H, Spector T, Tuomilehto J, Altshuler D, Strachan D, Laan M, Meneton P, Wareham N, Uda M, Jarvelin MR, Mooser V, Melander O, Loos R, Elliott P, Abecasis G, Caulfield M, Munroe P. Effects of long-term averaging of quantitative blood pressure traits on the detection of genetic associations. Am J Hum Genet 2014; 95:49-65. [PMID: 24975945 DOI: 10.1016/j.ajhg.2014.06.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/03/2014] [Indexed: 01/11/2023] Open
Abstract
Blood pressure (BP) is a heritable, quantitative trait with intraindividual variability and susceptibility to measurement error. Genetic studies of BP generally use single-visit measurements and thus cannot remove variability occurring over months or years. We leveraged the idea that averaging BP measured across time would improve phenotypic accuracy and thereby increase statistical power to detect genetic associations. We studied systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP), and pulse pressure (PP) averaged over multiple years in 46,629 individuals of European ancestry. We identified 39 trait-variant associations across 19 independent loci (p < 5 × 10(-8)); five associations (in four loci) uniquely identified by our LTA analyses included those of SBP and MAP at 2p23 (rs1275988, near KCNK3), DBP at 2q11.2 (rs7599598, in FER1L5), and PP at 6p21 (rs10948071, near CRIP3) and 7p13 (rs2949837, near IGFBP3). Replication analyses conducted in cohorts with single-visit BP data showed positive replication of associations and a nominal association (p < 0.05). We estimated a 20% gain in statistical power with long-term average (LTA) as compared to single-visit BP association studies. Using LTA analysis, we identified genetic loci influencing BP. LTA might be one way of increasing the power of genetic associations for continuous traits in extant samples for other phenotypes that are measured serially over time.
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McKenzie M, Henders AK, Caracella A, Wray NR, Powell JE. Overlap of expression quantitative trait loci (eQTL) in human brain and blood. BMC Med Genomics 2014; 7:31. [PMID: 24894490 PMCID: PMC4066287 DOI: 10.1186/1755-8794-7-31] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 05/20/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Expression quantitative trait loci (eQTL) are genomic regions regulating RNA transcript expression levels. Genome-wide Association Studies (GWAS) have identified many variants, often in non-coding regions, with unknown functions and eQTL provide a possible mechanism by which these variants may influence observable phenotypes. Limited access and availability of tissues such as brain has led to the use of blood as a substitute for eQTL analyses. METHODS Here, we evaluate the overlap of eQTL reported in published studies conducted in blood and brain tissues to assess the utility of blood as an alternative to brain tissue in the study of neurological and psychiatric conditions. Expression QTL results from eight published brain studies were compared to blood eQTL identified in from a meta-analysis involving 5,311 individuals. We accounted for differences in SNP platforms and study design by using SNP proxies in high linkage disequilibrium with reported eQTL. The degree of overlap between studies was calculated by ascertaining if an eQTL identified in one study was also identified in the other study. RESULTS The percentage of eQTL overlapping for brain and blood expression after adjusting for differences in sample size ranged from 13 - 23% (mean 19.2%). Amongst pairs of brain studies eQTL overlap ranged from 0 - 35%, with higher degrees of overlap found for studies using expression data collected from the same brain region. CONCLUSION Our results suggest that whenever possible tissue specific to the pathophysiology of the disease being studied should be used for transcription analysis.
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Affiliation(s)
- Marna McKenzie
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Anjali K Henders
- Queensland Institute of Medical Research, Brisbane, Herston, Australia
| | - Anthony Caracella
- Queensland Institute of Medical Research, Brisbane, Herston, Australia
| | - Naomi R Wray
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Joseph E Powell
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
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Ellis SE, Gupta S, Ashar FN, Bader JS, West AB, Arking DE. RNA-Seq optimization with eQTL gold standards. BMC Genomics 2013; 14:892. [PMID: 24341889 PMCID: PMC3890578 DOI: 10.1186/1471-2164-14-892] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 12/10/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RNA-Sequencing (RNA-Seq) experiments have been optimized for library preparation, mapping, and gene expression estimation. These methods, however, have revealed weaknesses in the next stages of analysis of differential expression, with results sensitive to systematic sample stratification or, in more extreme cases, to outliers. Further, a method to assess normalization and adjustment measures imposed on the data is lacking. RESULTS To address these issues, we utilize previously published eQTLs as a novel gold standard at the center of a framework that integrates DNA genotypes and RNA-Seq data to optimize analysis and aid in the understanding of genetic variation and gene expression. After detecting sample contamination and sequencing outliers in RNA-Seq data, a set of previously published brain eQTLs was used to determine if sample outlier removal was appropriate. Improved replication of known eQTLs supported removal of these samples in downstream analyses. eQTL replication was further employed to assess normalization methods, covariate inclusion, and gene annotation. This method was validated in an independent RNA-Seq blood data set from the GTEx project and a tissue-appropriate set of eQTLs. eQTL replication in both data sets highlights the necessity of accounting for unknown covariates in RNA-Seq data analysis. CONCLUSION As each RNA-Seq experiment is unique with its own experiment-specific limitations, we offer an easily-implementable method that uses the replication of known eQTLs to guide each step in one's data analysis pipeline. In the two data sets presented herein, we highlight not only the necessity of careful outlier detection but also the need to account for unknown covariates in RNA-Seq experiments.
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Affiliation(s)
- Shannon E Ellis
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Simone Gupta
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Foram N Ashar
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Joel S Bader
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Andrew B West
- Department of Neurology, University of Alabama School of Medicine, Birmingham, USA
| | - Dan E Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
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Forstner AJ, Degenhardt F, Schratt G, Nöthen MM. MicroRNAs as the cause of schizophrenia in 22q11.2 deletion carriers, and possible implications for idiopathic disease: a mini-review. Front Mol Neurosci 2013; 6:47. [PMID: 24367288 PMCID: PMC3851736 DOI: 10.3389/fnmol.2013.00047] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 11/17/2013] [Indexed: 12/18/2022] Open
Abstract
The 22q11.2 deletion is the strongest known genetic risk factor for schizophrenia. Research has implicated microRNA-mediated dysregulation in 22q11.2 deletion syndrome (22q11.2DS) schizophrenia-risk. Primary candidate genes are DGCR8 (DiGeorge syndrome critical region gene 8), which encodes a component of the microprocessor complex essential for microRNA biogenesis, and MIR185, which encodes microRNA 185. Mouse models of 22q11.2DS have demonstrated alterations in brain microRNA biogenesis, and that DGCR8 haploinsufficiency may contribute to these alterations, e.g., via down-regulation of a specific microRNA subset. miR-185 was the top-scoring down-regulated microRNA in both the prefrontal cortex and the hippocampus, brain areas which are the key foci of schizophrenia research. This reduction in miR-185 expression contributed to dendritic and spine development deficits in hippocampal neurons. In addition, miR-185 has two validated targets (RhoA, Cdc42), both of which have been associated with altered expression levels in schizophrenia. These combined data support the involvement of miR-185 and its down-stream pathways in schizophrenia. This review summarizes evidence implicating microRNA-mediated dysregulation in schizophrenia in both 22q11.2DS-related and idiopathic cases.
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Affiliation(s)
- Andreas J Forstner
- Institute of Human Genetics, University of Bonn Bonn, Germany ; Department of Genomics, Life and Brain Center Bonn, Germany
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn Bonn, Germany ; Department of Genomics, Life and Brain Center Bonn, Germany
| | - Gerhard Schratt
- Institute of Physiological Chemistry, Philipps-University Marburg Marburg, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn Bonn, Germany ; Department of Genomics, Life and Brain Center Bonn, Germany
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34
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Stranger BE, Raj T. Genetics of human gene expression. Curr Opin Genet Dev 2013; 23:627-34. [PMID: 24238872 DOI: 10.1016/j.gde.2013.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/09/2013] [Accepted: 10/14/2013] [Indexed: 12/31/2022]
Abstract
A steadily growing number of studies have identified and characterized expression quantitative trait loci (eQTLs) in human cell-lines, primary cells, and tissues. This class of variation has been shown to play a role in complex traits, including disease. Here, we discuss how eQTLs have the potential to accelerate discovery of disease genes and functional mechanisms underlying complex traits. We discuss how context-specificity of eQTLs is being characterized at an unprecedented scale and breadth, and how this both informs on the intricacy of human genome function, and has important ramifications for elucidating function of genetic variants of interest, particularly for those contributing to disease.
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Affiliation(s)
- Barbara E Stranger
- Section of Genetic Medicine, Department of Medicine, University of Chicago, IL, USA; Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA.
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35
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Iancu OD, Oberbeck D, Darakjian P, Kawane S, Erk J, McWeeney S, Hitzemann R. Differential network analysis reveals genetic effects on catalepsy modules. PLoS One 2013; 8:e58951. [PMID: 23555609 PMCID: PMC3605410 DOI: 10.1371/journal.pone.0058951] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 02/08/2013] [Indexed: 11/19/2022] Open
Abstract
We performed short-term bi-directional selective breeding for haloperidol-induced catalepsy, starting from three mouse populations of increasingly complex genetic structure: an F2 intercross, a heterogeneous stock (HS) formed by crossing four inbred strains (HS4) and a heterogeneous stock (HS-CC) formed from the inbred strain founders of the Collaborative Cross (CC). All three selections were successful, with large differences in haloperidol response emerging within three generations. Using a custom differential network analysis procedure, we found that gene coexpression patterns changed significantly; importantly, a number of these changes were concordant across genetic backgrounds. In contrast, absolute gene-expression changes were modest and not concordant across genetic backgrounds, in spite of the large and similar phenotypic differences. By inferring strain contributions from the parental lines, we are able to identify significant differences in allelic content between the selected lines concurrent with large changes in transcript connectivity. Importantly, this observation implies that genetic polymorphisms can affect transcript and module connectivity without large changes in absolute expression levels. We conclude that, in this case, selective breeding acts at the subnetwork level, with the same modules but not the same transcripts affected across the three selections.
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Affiliation(s)
- Ovidiu D Iancu
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, Oregon, USA.
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Shulha HP, Crisci JL, Reshetov D, Tushir JS, Cheung I, Bharadwaj R, Chou HJ, Houston IB, Peter CJ, Mitchell AC, Yao WD, Myers RH, Chen JF, Preuss TM, Rogaev EI, Jensen JD, Weng Z, Akbarian S. Human-specific histone methylation signatures at transcription start sites in prefrontal neurons. PLoS Biol 2012; 10:e1001427. [PMID: 23185133 PMCID: PMC3502543 DOI: 10.1371/journal.pbio.1001427] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 10/12/2012] [Indexed: 11/18/2022] Open
Abstract
Cognitive abilities and disorders unique to humans are thought to result from adaptively driven changes in brain transcriptomes, but little is known about the role of cis-regulatory changes affecting transcription start sites (TSS). Here, we mapped in human, chimpanzee, and macaque prefrontal cortex the genome-wide distribution of histone H3 trimethylated at lysine 4 (H3K4me3), an epigenetic mark sharply regulated at TSS, and identified 471 sequences with human-specific enrichment or depletion. Among these were 33 loci selectively methylated in neuronal but not non-neuronal chromatin from children and adults, including TSS at DPP10 (2q14.1), CNTN4 and CHL1 (3p26.3), and other neuropsychiatric susceptibility genes. Regulatory sequences at DPP10 and additional loci carried a strong footprint of hominid adaptation, including elevated nucleotide substitution rates and regulatory motifs absent in other primates (including archaic hominins), with evidence for selective pressures during more recent evolution and adaptive fixations in modern populations. Chromosome conformation capture at two neurodevelopmental disease loci, 2q14.1 and 16p11.2, revealed higher order chromatin structures resulting in physical contact of multiple human-specific H3K4me3 peaks spaced 0.5-1 Mb apart, in conjunction with a novel cis-bound antisense RNA linked to Polycomb repressor proteins and downregulated DPP10 expression. Therefore, coordinated epigenetic regulation via newly derived TSS chromatin could play an important role in the emergence of human-specific gene expression networks in brain that contribute to cognitive functions and neurological disease susceptibility in modern day humans.
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Affiliation(s)
- Hennady P. Shulha
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jessica L. Crisci
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Denis Reshetov
- Department of Human Genetics and Genomics, Vavilov Institute of General Genetics, Moscow, Russian Federation
| | - Jogender S. Tushir
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Iris Cheung
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Rahul Bharadwaj
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Hsin-Jung Chou
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Isaac B. Houston
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Cyril J. Peter
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Amanda C. Mitchell
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Wei-Dong Yao
- New England Primate Center, Southboro, Massachusetts, United States of America
| | - Richard H. Myers
- Department of Neurology, Boston University, Boston, Massachusetts, United States of America
| | - Jiang-fan Chen
- Department of Neurology, Boston University, Boston, Massachusetts, United States of America
| | - Todd M. Preuss
- Yerkes National Primate Research Center/Emory University, Atlanta, Georgia, United States of America
| | - Evgeny I. Rogaev
- Department of Human Genetics and Genomics, Vavilov Institute of General Genetics, Moscow, Russian Federation
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Research Center of Mental Health, Russian Academy of Medical Sciences, Moscow, Russian Federation
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russian Federation
| | - Jeffrey D. Jensen
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Schahram Akbarian
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Departments of Psychiatry and Neuroscience, Friedman Brain Institute, Mount Sinai School of Medicine, New York, New York, United States of America
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Yang X, Murani E, Ponsuksili S, Wimmers K. Association of TLR5 sequence variants and mRNA level with cytokine transcription in pigs. Immunogenetics 2012; 65:125-32. [PMID: 23132291 DOI: 10.1007/s00251-012-0662-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 10/22/2012] [Indexed: 10/27/2022]
Abstract
The Toll-like receptor 5 (TLR5) plays a crucial role in host defense against flagellated bacteria by recognizing flagellin. Accumulating evidence suggests that single nucleotide polymorphisms (SNPs) in TLR5 have an effect on flagellin recognition and are associated with susceptibility/resistance to disease. In this study, we analyzed association of SNPs, including c.834T>G, c.1065T>C, c.1205C>T, c.1246A>T, c.1269G>A, and c.1398C>T, as well as mRNA level of TLR5 with the abundance of transcripts of cytokines in pigs. SNPs c.1246A>T and c.1269G>A were significantly associated with the transcript abundance of interleukin (IL)-2, and SNPs c.834T>G and c.1398C>T with IL-10 (P < 0.05); the haplotypes showed a tendency to affect the transcript abundance of IL-10 (P = 0.0660) and significantly associated with the transcription of TLR5 (P < 0.01); the abundance of transcripts of TLR5 and IL-10 were strongly correlated (P < 0.01). The results indicated that the SNPs, associated with the transcript abundance of cytokines, were related to immune responsiveness mediated by cytokine, which, in turn, would have a role in pig breeding for disease resistance. Furthermore, the positive correlation between the abundance of TLR5 and IL10 suggest a link between TLR5 activation and IL-10 expression in porcine.
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Affiliation(s)
- X Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China
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Shapshak P. Molecule of the month, PDE4DIP. Bioinformation 2012; 8:740-1. [PMID: 23055623 PMCID: PMC3449385 DOI: 10.6026/97320630008740] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 08/04/2012] [Indexed: 11/23/2022] Open
Affiliation(s)
- Paul Shapshak
- Divsion of Infectious Disease and International Health, Department of Medicine and Department of Psychiatry and Behavioral Medicine, USF Morsani School of Medicine, Tampa General Hospital, 1 Tampa Gen Circle, Room G318, Tampa FL 33606 ; Deputy Chief Editor, Bioinformation, India
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