301
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Xia Z, White CC, Owen EK, Von Korff A, Clarkson SR, McCabe CA, Cimpean M, Winn PA, Hoesing A, Steele SU, Cortese ICM, Chitnis T, Weiner HL, Reich DS, Chibnik LB, De Jager PL. Genes and Environment in Multiple Sclerosis project: A platform to investigate multiple sclerosis risk. Ann Neurol 2015; 79:178-89. [PMID: 26583565 DOI: 10.1002/ana.24560] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 10/21/2015] [Accepted: 11/14/2015] [Indexed: 11/06/2022]
Abstract
The Genes and Environment in Multiple Sclerosis project establishes a platform to investigate the events leading to multiple sclerosis (MS) in at-risk individuals. It has recruited 2,632 first-degree relatives from across the USA. Using an integrated genetic and environmental risk score, we identified subjects with twice the MS risk when compared to the average family member, and we report an initial incidence rate in these subjects that is 30 times greater than that of sporadic MS. We discuss the feasibility of large-scale studies of asymptomatic at-risk subjects that leverage modern tools of subject recruitment to execute collaborative projects.
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Affiliation(s)
- Zongqi Xia
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Charles C White
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Emily K Owen
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Alina Von Korff
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Sarah R Clarkson
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Cristin A McCabe
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Maria Cimpean
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Phoebe A Winn
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Ashley Hoesing
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Sonya U Steele
- Division of Neuroimmunology and Neurovirology, National Institute for Neurologic Diseases and Stroke, Bethesda, MD
| | - Irene C M Cortese
- Division of Neuroimmunology and Neurovirology, National Institute for Neurologic Diseases and Stroke, Bethesda, MD
| | - Tanuja Chitnis
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA
| | - Howard L Weiner
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA
| | - Daniel S Reich
- Division of Neuroimmunology and Neurovirology, National Institute for Neurologic Diseases and Stroke, Bethesda, MD
| | - Lori B Chibnik
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Philip L De Jager
- Program in Translational Neuropsychiatric Genomics and Partners Multiple Sclerosis Center, Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
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302
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Zhu Z, Liang Z, Liany H, Yang C, Wen L, Lin Z, Sheng Y, Lin Y, Ye L, Cheng Y, Chang Y, Liu L, Yang L, Shi Y, Shen C, Zhou F, Zheng X, Zhu J, Liang B, Ding Y, Zhou Y, Yin X, Tang H, Zuo X, Sun L, Bei JX, Liu J, Yang S, Yang W, Cui Y, Zhang X. Discovery of a novel genetic susceptibility locus on X chromosome for systemic lupus erythematosus. Arthritis Res Ther 2015; 17:349. [PMID: 26635088 PMCID: PMC4669597 DOI: 10.1186/s13075-015-0857-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 11/09/2015] [Indexed: 01/21/2023] Open
Abstract
Introduction Systemic lupus erythematosus (SLE) is an autoimmune connective tissue disease affecting predominantly females. To discover additional genetic risk variants for SLE on the X chromosome, we performed a follow-up study of our previously published genome-wide association study (GWAS) data set in this study. Methods Twelve single nucleotide polymorphisms (SNPs) within novel or unpublished loci with P-value < 1.00 × 10−02 were selected for genotype with a total of 2,442 cases and 2,798 controls(including 1,156 cases and 2,330 controls from central China, 1,012 cases and 335 controls from southern China and 274 cases and 133 controls from northern China) using Sequenom Massarry system. Associaton analyses were performed using logistic regression with sample region as a covariate through PLINK 1.07 software. Results Combined analysis in discovery and central validation dataset discovered a novel locus rs5914778 within LINC01420 associated with SLE at genome-wide significance (P = 1.00 × 10−08; odds ratio (OR) = 1.32). We also confirmed rs5914778 in the southern Chinese sample cohort (P = 5.31 × 10−05; OR = 1.51), and meta-analysis of the samples from the discovery, central and southern validations regions provided robust evidence for the association of rs5914778 (P = 5.26 × 10−12; OR = 1.35). However, this SNP did not show association with SLE in the northern sample (P = 0.33). Further analysis represent the association of northern was significantly heterogeneous compared to central and southern respectively. Conclusions Our study increases the number of established susceptibility loci for SLE in Han Chinese population and has further demonstrated the important role of X-linked genetic risk variants in the pathogenesis of SLE in Chinese Han population. Electronic supplementary material The online version of this article (doi:10.1186/s13075-015-0857-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhengwei Zhu
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China. .,Department of Dermatology, China-Japan Friendship Hospital, East Street Cherry Park, Chaoyang District, Beijing, 100029, China.
| | - Zhuoyuan Liang
- Department of Nephrology, Jiangmen Central Hospital, Jiangmen, Guangdong, 529030, China.
| | - Herty Liany
- Human Genetics, Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore.
| | - Chao Yang
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China. .,Department of Dermatology, China-Japan Friendship Hospital, East Street Cherry Park, Chaoyang District, Beijing, 100029, China.
| | - Leilei Wen
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Zhiming Lin
- Department of Rheumatology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, 510630, China.
| | - Yujun Sheng
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Yan Lin
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Lei Ye
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Yuyan Cheng
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Yan Chang
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Lu Liu
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Lulu Yang
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Yinjuan Shi
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Changbing Shen
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Fusheng Zhou
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Xiaodong Zheng
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Jun Zhu
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Bo Liang
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Yantao Ding
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Yi Zhou
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Xianyong Yin
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Huayang Tang
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Xianbo Zuo
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Liangdan Sun
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Jin-Xin Bei
- Human Genetics, Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore.
| | - Jianjun Liu
- Human Genetics, Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore. .,Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.
| | - Sen Yang
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong, China. .,Centre for Genomic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital, East Street Cherry Park, Chaoyang District, Beijing, 100029, China.
| | - Xuejun Zhang
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China. .,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, 230032, China.
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303
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Atanasovska B, Kumar V, Fu J, Wijmenga C, Hofker MH. GWAS as a Driver of Gene Discovery in Cardiometabolic Diseases. Trends Endocrinol Metab 2015; 26:722-732. [PMID: 26596674 DOI: 10.1016/j.tem.2015.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/20/2015] [Accepted: 10/25/2015] [Indexed: 01/23/2023]
Abstract
Cardiometabolic diseases represent a common complex disorder with a strong genetic component. Currently, genome-wide association studies (GWAS) have yielded some 755 single-nucleotide polymorphisms (SNPs) encompassing 366 independent loci that may help to decipher the molecular basis of cardiometabolic diseases. Going from a disease SNP to the underlying disease mechanisms is a huge challenge because the associated SNPs rarely disrupt protein function. Many disease SNPs are located in noncoding regions, and therefore attention is now focused on linking genetic SNP variation to effects on gene expression levels. By integrating genetic information with large-scale gene expression data, and with data from epigenetic roadmaps revealing gene regulatory regions, we expect to be able to identify candidate disease genes and the regulatory potential of disease SNPs.
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Affiliation(s)
- Biljana Atanasovska
- Molecular Genetics Section, Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Molecular Genetics Section, Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | - Marten H Hofker
- Molecular Genetics Section, Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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304
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Bentham J, Morris DL, Graham DSC, Pinder CL, Tombleson P, Behrens TW, Martín J, Fairfax BP, Knight JC, Chen L, Replogle J, Syvänen AC, Rönnblom L, Graham RR, Wither JE, Rioux JD, Alarcón-Riquelme ME, Vyse TJ. Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus. Nat Genet 2015; 47:1457-1464. [PMID: 26502338 PMCID: PMC4668589 DOI: 10.1038/ng.3434] [Citation(s) in RCA: 575] [Impact Index Per Article: 63.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 10/02/2015] [Indexed: 12/12/2022]
Abstract
Systemic lupus erythematosus (SLE) is a genetically complex autoimmune disease characterized by loss of immune tolerance to nuclear and cell surface antigens. Previous genome-wide association studies (GWAS) had modest sample sizes, reducing their scope and reliability. Our study comprised 7,219 cases and 15,991 controls of European ancestry, constituting a new GWAS, a meta-analysis with a published GWAS and a replication study. We have mapped 43 susceptibility loci, including ten new associations. Assisted by dense genome coverage, imputation provided evidence for missense variants underpinning associations in eight genes. Other likely causal genes were established by examining associated alleles for cis-acting eQTL effects in a range of ex vivo immune cells. We found an over-representation (n = 16) of transcription factors among SLE susceptibility genes. This finding supports the view that aberrantly regulated gene expression networks in multiple cell types in both the innate and adaptive immune response contribute to the risk of developing SLE.
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Affiliation(s)
- James Bentham
- Division of Genetics and Molecular Medicine, King's College London, UK
| | - David L Morris
- Division of Genetics and Molecular Medicine, King's College London, UK
| | | | | | - Philip Tombleson
- Division of Genetics and Molecular Medicine, King's College London, UK
| | | | - Javier Martín
- Instituto de Parasitología y Biomedicina López Neyra, CSIC, Granada, Spain
| | - Benjamin P Fairfax
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lingyan Chen
- Division of Genetics and Molecular Medicine, King's College London, UK
| | | | - Ann-Christine Syvänen
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars Rönnblom
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Joan E Wither
- Toronto Western Research Institute (TWRI), University Health Network, Toronto, Ontario, Canada
| | - John D Rioux
- Université de Montréal, Montreal, Quebec, Canada
- Montreal Heart Institute, Montreal, Quebec, Canada
| | - Marta E Alarcón-Riquelme
- Centro de Genómica e Investigación Oncológica (GENYO), Pfizer-Universidad de Granada-Junta de Andalucía, Granada, Spain
| | - Timothy J Vyse
- Division of Genetics and Molecular Medicine, King's College London, UK
- Division of Immunology, Infection and Inflammatory Disease, King's College London, UK
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305
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Simchovitz A, Soreq L, Soreq H. Transcriptome profiling in Parkinson's leukocytes: from early diagnostics to neuroimmune therapeutic prospects. Curr Opin Pharmacol 2015; 26:102-9. [PMID: 26609801 DOI: 10.1016/j.coph.2015.10.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 10/19/2015] [Accepted: 10/24/2015] [Indexed: 02/07/2023]
Abstract
Parkinson's disease (PD) involves motor symptoms reflecting the progressive degeneration of dopaminergic neurons in the substantia nigra. However, diagnosis is only enabled late in the disease, limiting treatment to palliative assistance. Here, we review recently generated transcriptional profiling datasets from blood and brain RNA of human PD cohorts and animal models that may offer unprecedented progress in PD research. Specifically, advanced analysis techniques demonstrated functionally inter-related underlying impairments of RNA metabolism and neuroimmune signalling processes. Identifying novel biomarkers in serum and nucleated blood cells, including protein networks and non-coding RNAs can drive discovery of the molecular mechanisms involved and reveal new targets for therapeutic intervention, posing a dual diagnosis/treatment opportunity for limiting the exacerbation of neuroinflammatory events in PD.
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Affiliation(s)
- Alon Simchovitz
- Department of Biological Chemistry and The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Lilach Soreq
- Department of Molecular Neuroscience, UCL Institute of Neurology (ION), Queen Square, London WC1N 3BG, UK
| | - Hermona Soreq
- Department of Biological Chemistry and The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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306
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Link VM, Gosselin D, Glass CK. Mechanisms Underlying the Selection and Function of Macrophage-Specific Enhancers. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2015; 80:213-21. [PMID: 26582787 DOI: 10.1101/sqb.2015.80.027367] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Macrophages populate every tissue of the body and play vital roles in homeostasis, pathogen elimination, and tissue healing. These cells possess the ability to adapt to a multitude of abruptly changing and complex environments. Furthermore, different populations of resident tissue macrophages each show their own defining gene signatures. The enhancer repertoire of these cells underlies both the cellular identity of a given subset of resident macrophage population and their ability to dynamically alter, in an efficient manner, their gene expression programs in response to internal and external signals. Notably, transcription is pervasive at active enhancers and enhancer RNAs, or eRNAs, are tightly correlated to regulated transcription of protein-coding genes. Furthermore, selection and establishment of enhancers is a dynamic and plastic process in which activation of intracellular signaling pathways by factors present in a macrophage's environment play a determining role. Here, we review recent studies providing insights into the distinct mechanisms that contribute to the selection and function of enhancers in macrophages and the relevance of studying these mechanisms to gain a better understanding of complex human diseases.
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Affiliation(s)
- Verena M Link
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0651 Faculty of Biology, Department II, Ludwig-Maximilians Universität München, Planegg-Martinsried 82152, Germany
| | - David Gosselin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0651
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093-0651 Department of Medicine, University of California, San Diego, La Jolla, California 92093-0651
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307
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Messemaker TC, Huizinga TW, Kurreeman F. Immunogenetics of rheumatoid arthritis: Understanding functional implications. J Autoimmun 2015. [DOI: 10.1016/j.jaut.2015.07.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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308
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Lewin A, Saadi H, Peters JE, Moreno-Moral A, Lee JC, Smith KGC, Petretto E, Bottolo L, Richardson S. MT-HESS: an efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues. Bioinformatics 2015; 32:523-32. [PMID: 26504141 PMCID: PMC4743623 DOI: 10.1093/bioinformatics/btv568] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 09/03/2015] [Indexed: 01/22/2023] Open
Abstract
MOTIVATION Analysing the joint association between a large set of responses and predictors is a fundamental statistical task in integrative genomics, exemplified by numerous expression Quantitative Trait Loci (eQTL) studies. Of particular interest are the so-called ': hotspots ': , important genetic variants that regulate the expression of many genes. Recently, attention has focussed on whether eQTLs are common to several tissues, cell-types or, more generally, conditions or whether they are specific to a particular condition. RESULTS We have implemented MT-HESS, a Bayesian hierarchical model that analyses the association between a large set of predictors, e.g. SNPs, and many responses, e.g. gene expression, in multiple tissues, cells or conditions. Our Bayesian sparse regression algorithm goes beyond ': one-at-a-time ': association tests between SNPs and responses and uses a fully multivariate model search across all linear combinations of SNPs, coupled with a model of the correlation between condition/tissue-specific responses. In addition, we use a hierarchical structure to leverage shared information across different genes, thus improving the detection of hotspots. We show the increase of power resulting from our new approach in an extensive simulation study. Our analysis of two case studies highlights new hotspots that would remain undetected by standard approaches and shows how greater prediction power can be achieved when several tissues are jointly considered. AVAILABILITY AND IMPLEMENTATION C[Formula: see text] source code and documentation including compilation instructions are available under GNU licence at http://www.mrc-bsu.cam.ac.uk/software/.
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Affiliation(s)
- Alex Lewin
- Department of Mathematics, Brunel University London
| | - Habib Saadi
- Department of Epidemiology and Biostatistics, Imperial College London, London
| | - James E Peters
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, MRC Biostatistics Unit, Cambridge Institute of Public Health, Cambridge
| | | | - James C Lee
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge
| | - Kenneth G C Smith
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge
| | - Enrico Petretto
- MRC Clinical Sciences Centre, Imperial College London, London, UK, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Leonardo Bottolo
- Department of Mathematics, Imperial College London, London, UK and Department of Medical Genetics, University of Cambridge
| | - Sylvia Richardson
- MRC Biostatistics Unit, Cambridge Institute of Public Health, Cambridge
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309
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Song F, Qian Y, Peng X, Han G, Wang J, Bai Z, Crack PJ, Lei H. Perturbation of the transcriptome: implications of the innate immune system in Alzheimer's disease. Curr Opin Pharmacol 2015; 26:47-53. [PMID: 26480202 DOI: 10.1016/j.coph.2015.09.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 09/29/2015] [Accepted: 09/30/2015] [Indexed: 12/01/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease with broad impact. Although Aβ and tau have been proposed as the key molecules in the disease mechanism, comprehensive understanding of AD pathogenesis requires a systemic view at the genomic level. From studies on the brain transcriptome of AD, we have gradually realized the contribution of the immune system to AD development. Recent explorations on the blood transcriptome of AD patients have revealed robust immune activation in the peripheral blood. The combination of transcriptome studies and other types of studies has further elucidated the roles of specific immune pathways in distinct cell types during AD development and highlighted the critical contributions from immune genes such as TREM2.
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Affiliation(s)
- Fuhai Song
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ying Qian
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xing Peng
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Guangchun Han
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Jiajia Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zhouxian Bai
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Peter J Crack
- Department of Pharmacology and Therapeutics, University of Melbourne, Parkville, Australia
| | - Hongxing Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, China.
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310
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Croteau-Chonka DC, Rogers AJ, Raj T, McGeachie MJ, Qiu W, Ziniti JP, Stubbs BJ, Liang L, Martinez FD, Strunk RC, Lemanske RF, Liu AH, Stranger BE, Carey VJ, Raby BA. Expression Quantitative Trait Loci Information Improves Predictive Modeling of Disease Relevance of Non-Coding Genetic Variation. PLoS One 2015; 10:e0140758. [PMID: 26474488 PMCID: PMC4608673 DOI: 10.1371/journal.pone.0140758] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 09/30/2015] [Indexed: 11/24/2022] Open
Abstract
Disease-associated loci identified through genome-wide association studies (GWAS) frequently localize to non-coding sequence. We and others have demonstrated strong enrichment of such single nucleotide polymorphisms (SNPs) for expression quantitative trait loci (eQTLs), supporting an important role for regulatory genetic variation in complex disease pathogenesis. Herein we describe our initial efforts to develop a predictive model of disease-associated variants leveraging eQTL information. We first catalogued cis-acting eQTLs (SNPs within 100kb of target gene transcripts) by meta-analyzing four studies of three blood-derived tissues (n = 586). At a false discovery rate < 5%, we mapped eQTLs for 6,535 genes; these were enriched for disease-associated genes (P < 10−04), particularly those related to immune diseases and metabolic traits. Based on eQTL information and other variant annotations (distance from target gene transcript, minor allele frequency, and chromatin state), we created multivariate logistic regression models to predict SNP membership in reported GWAS. The complete model revealed independent contributions of specific annotations as strong predictors, including evidence for an eQTL (odds ratio (OR) = 1.2–2.0, P < 10−11) and the chromatin states of active promoters, different classes of strong or weak enhancers, or transcriptionally active regions (OR = 1.5–2.3, P < 10−11). This complete prediction model including eQTL association information ultimately allowed for better discrimination of SNPs with higher probabilities of GWAS membership (6.3–10.0%, compared to 3.5% for a random SNP) than the other two models excluding eQTL information. This eQTL-based prediction model of disease relevance can help systematically prioritize non-coding GWAS SNPs for further functional characterization.
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Affiliation(s)
- Damien C. Croteau-Chonka
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Angela J. Rogers
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, School of Medicine, Stanford University, Stanford, California, United States of America
| | - Towfique Raj
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Michael J. McGeachie
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Weiliang Qiu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - John P. Ziniti
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Benjamin J. Stubbs
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Liming Liang
- Departments of Biostatistics and Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Fernando D. Martinez
- Arizona Respiratory Center and BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Robert C. Strunk
- Division of Allergy, Immunology and Pulmonary Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Robert F. Lemanske
- University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
| | - Andrew H. Liu
- Division of Allergy and Clinical Immunology, Department of Pediatrics, National Jewish Health and University of Colorado School of Medicine, Denver, Colorado, United States of America
| | - Barbara E. Stranger
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Vincent J. Carey
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Benjamin A. Raby
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- BWH Pulmonary Genetics Center, Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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311
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Larochelle A, Bellavance MA, Michaud JP, Rivest S. Bone marrow-derived macrophages and the CNS: An update on the use of experimental chimeric mouse models and bone marrow transplantation in neurological disorders. Biochim Biophys Acta Mol Basis Dis 2015; 1862:310-22. [PMID: 26432480 DOI: 10.1016/j.bbadis.2015.09.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 09/17/2015] [Accepted: 09/25/2015] [Indexed: 12/12/2022]
Abstract
The central nervous system (CNS) is a very unique system with multiple features that differentiate it from systemic tissues. One of the most captivating aspects of its distinctive nature is the presence of the blood brain barrier (BBB), which seals it from the periphery. Therefore, to preserve tissue homeostasis, the CNS has to rely heavily on resident cells such as microglia. These pivotal cells of the mononuclear lineage have important and dichotomous roles according to various neurological disorders. However, certain insults can overwhelm microglia as well as compromising the integrity of the BBB, thus allowing the infiltration of bone marrow-derived macrophages (BMDMs). The use of myeloablation and bone marrow transplantation allowed the generation of chimeric mice to study resident microglia and infiltrated BMDM separately. This breakthrough completely revolutionized the way we captured these 2 types of mononuclear phagocytic cells. We now realize that microglia and BMDM exhibit distinct features and appear to perform different tasks. Since these cells are central in several pathologies, it is crucial to use chimeric mice to analyze their functions and mechanisms to possibly harness them for therapeutic purpose. This review will shed light on the advent of this methodology and how it allowed deciphering the ontology of microglia and its maintenance during adulthood. We will also compare the different strategies used to perform myeloablation. Finally, we will discuss the landmark studies that used chimeric mice to characterize the roles of microglia and BMDM in several neurological disorders. This article is part of a Special Issue entitled: Neuro Inflammation edited by Helga E. de Vries and Markus Schwaninger.
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Affiliation(s)
- Antoine Larochelle
- Neuroscience Laboratory, CHU de Québec Research Center, Department of Molecular Medicine, Faculty of Medicine, Laval University, 2705 Laurier Blvd., Québec G1V 4G2, Canada
| | - Marc-André Bellavance
- Neuroscience Laboratory, CHU de Québec Research Center, Department of Molecular Medicine, Faculty of Medicine, Laval University, 2705 Laurier Blvd., Québec G1V 4G2, Canada
| | - Jean-Philippe Michaud
- Neuroscience Laboratory, CHU de Québec Research Center, Department of Molecular Medicine, Faculty of Medicine, Laval University, 2705 Laurier Blvd., Québec G1V 4G2, Canada
| | - Serge Rivest
- Neuroscience Laboratory, CHU de Québec Research Center, Department of Molecular Medicine, Faculty of Medicine, Laval University, 2705 Laurier Blvd., Québec G1V 4G2, Canada.
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312
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Quinn EM, Coleman C, Molloy B, Dominguez Castro P, Cormican P, Trimble V, Mahmud N, McManus R. Transcriptome Analysis of CD4+ T Cells in Coeliac Disease Reveals Imprint of BACH2 and IFNγ Regulation. PLoS One 2015; 10:e0140049. [PMID: 26444573 PMCID: PMC4596691 DOI: 10.1371/journal.pone.0140049] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/21/2015] [Indexed: 12/16/2022] Open
Abstract
Genetic studies have to date identified 43 genome wide significant coeliac disease susceptibility (CD) loci comprising over 70 candidate genes. However, how altered regulation of such disease associated genes contributes to CD pathogenesis remains to be elucidated. Recently there has been considerable emphasis on characterising cell type specific and stimulus dependent genetic variants. Therefore in this study we used RNA sequencing to profile over 70 transcriptomes of CD4+ T cells, a cell type crucial for CD pathogenesis, in both stimulated and resting samples from individuals with CD and unaffected controls. We identified extensive transcriptional changes across all conditions, with the previously established CD gene IFNy the most strongly up-regulated gene (log2 fold change 4.6; Padjusted = 2.40x10-11) in CD4+ T cells from CD patients compared to controls. We show a significant correlation of differentially expressed genes with genetic studies of the disease to date (Padjusted = 0.002), and 21 CD candidate susceptibility genes are differentially expressed under one or more of the conditions used in this study. Pathway analysis revealed significant enrichment of immune related processes. Co-expression network analysis identified several modules of coordinately expressed CD genes. Two modules were particularly highly enriched for differentially expressed genes (P<2.2x10-16) and highlighted IFNy and the genetically associated transcription factor BACH2 which showed significantly reduced expression in coeliac samples (log2FC -1.75; Padjusted = 3.6x10-3) as key regulatory genes in CD. Genes regulated by BACH2 were very significantly over-represented among our differentially expressed genes (P<2.2x10-16) indicating that reduced expression of this master regulator of T cell differentiation promotes a pro-inflammatory response and strongly corroborates genetic evidence that BACH2 plays an important role in CD pathogenesis.
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Affiliation(s)
- Emma M. Quinn
- Department of Clinical Medicine, Trinity College Dublin, Trinity Centre, St James’s Hospital, Dublin, 8, Ireland
| | - Ciara Coleman
- Department of Clinical Medicine, Trinity College Dublin, Trinity Centre, St James’s Hospital, Dublin, 8, Ireland
| | - Ben Molloy
- Department of Clinical Medicine, Trinity College Dublin, Trinity Centre, St James’s Hospital, Dublin, 8, Ireland
| | - Patricia Dominguez Castro
- Department of Clinical Medicine, Trinity College Dublin, Trinity Centre, St James’s Hospital, Dublin, 8, Ireland
| | - Paul Cormican
- Animal and Bioscience Research Department, Grange Research Centre, Teagasc, Dunsany, Ireland
| | - Valerie Trimble
- Department of Clinical Medicine, Trinity College Dublin, Trinity Centre, St James’s Hospital, Dublin, 8, Ireland
| | - Nasir Mahmud
- Department of Clinical Medicine, Trinity College Dublin, Trinity Centre, St James’s Hospital, Dublin, 8, Ireland
| | - Ross McManus
- Department of Clinical Medicine, Trinity College Dublin, Trinity Centre, St James’s Hospital, Dublin, 8, Ireland
- * E-mail:
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313
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Chan G, White CC, Winn PA, Cimpean M, Replogle JM, Glick LR, Cuerdon NE, Ryan KJ, Johnson KA, Schneider JA, Bennett DA, Chibnik LB, Sperling RA, Bradshaw EM, De Jager PL. CD33 modulates TREM2: convergence of Alzheimer loci. Nat Neurosci 2015; 18:1556-8. [PMID: 26414614 PMCID: PMC4682915 DOI: 10.1038/nn.4126] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 09/02/2015] [Indexed: 12/26/2022]
Abstract
Here, we report results from a protein quantitative trait analysis in monocytes from 226 individuals to evaluate cross-talk between Alzheimer loci. We find that the NME8 locus influences PTK2B and that the CD33 risk allele leads to greater TREM2 expression. Further, we observe (1) a decreased TREM1/TREM2 ratio with a TREM1 risk allele, (2) decreased TREM2 expression with CD33 suppression, and (3) elevated cortical TREM2 mRNA expression with amyloid pathology.
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Affiliation(s)
- Gail Chan
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Charles C White
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Phoebe A Winn
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Maria Cimpean
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Joseph M Replogle
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Laura R Glick
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Nicole E Cuerdon
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Katie J Ryan
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Keith A Johnson
- Harvard Medical School, Boston, Massachusetts, USA.,Center for Alzheimer's Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Lori B Chibnik
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Reisa A Sperling
- Harvard Medical School, Boston, Massachusetts, USA.,Center for Alzheimer's Research and Treatment, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Elizabeth M Bradshaw
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Philip L De Jager
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Department of Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
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314
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Flores Saiffe Farías A, Jaime Herrera López E, Moreno Vázquez CJ, Li W, Prado Montes de Oca E. Predicting functional regulatory SNPs in the human antimicrobial peptide genes DEFB1 and CAMP in tuberculosis and HIV/AIDS. Comput Biol Chem 2015; 59 Pt A:117-25. [PMID: 26447748 DOI: 10.1016/j.compbiolchem.2015.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 01/04/2023]
Abstract
Single nucleotide polymorphisms (SNPs) in transcription factor binding sites (TFBSs) within gene promoter region or enhancers can modify the transcription rate of genes related to complex diseases. These SNPs can be called regulatory SNPs (rSNPs). Data compiled from recent projects, such as the 1000 Genomes Project and ENCODE, has revealed essential information used to perform in silico prediction of the molecular and biological repercussions of SNPs within TFBS. However, most of these studies are very limited, as they only analyze SNPs in coding regions or when applied to promoters, and do not integrate essential biological data like TFBSs, expression profiles, pathway analysis, homotypic redundancy (number of TFBSs for the same TF in a region), chromatin accessibility and others, which could lead to a more accurate prediction. Our aim was to integrate different data in a biologically coherent method to analyze the proximal promoter regions of two antimicrobial peptide genes, DEFB1 and CAMP, that are associated with tuberculosis (TB) and HIV/AIDS. We predicted SNPs within the promoter regions that are more likely to interact with transcription factors (TFs). We also assessed the impact of homotypic redundancy using a novel approach called the homotypic redundancy weight factor (HWF). Our results identified 10 SNPs, which putatively modify the binding affinity of 24 TFs previously identified as related to TB and HIV/AIDS expression profiles (e.g. KLF5, CEBPA and NFKB1 for TB; FOXP2, BRCA1, CEBPB, CREB1, EBF1 and ZNF354C for HIV/AIDS; and RUNX2, HIF1A, JUN/AP-1, NR4A2, EGR1 for both diseases). Validating with the OregAnno database and cell-specific functional/non functional SNPs from additional 13 genes, our algorithm performed 53% sensitivity and 84.6% specificity to detect functional rSNPs using the DNAseI-HUP database. We are proposing our algorithm as a novel in silico method to detect true functional rSNPs in antimicrobial peptide genes. With further improvement, this novel method could be applied to other promoters in order to design probes and to discover new drug targets for complex diseases.
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Affiliation(s)
- Adolfo Flores Saiffe Farías
- Personalized Medicine Laboratory (LAMPER), Medical and Pharmaceutical Biotechnology, Guadalajara Unit, Research Center of Technology and Design Assistance of Jalisco State, National Council of Science and Technology (CIATEJ AC, CONACYT), Av. Normalistas 800, Col. Colinas de la Normal, CP 44270 Guadalajara, Jalisco, Mexico.
| | - Enrique Jaime Herrera López
- Industrial Biotechnology, CIATEJ AC, Zapopan Unit, CONACYT, Camino Arenero 1227, Col. El Bajío del Arenal, CP 45019 Zapopan, Jalisco, Mexico.
| | - Cristopher Jorge Moreno Vázquez
- Personalized Medicine Laboratory (LAMPER), Medical and Pharmaceutical Biotechnology, Guadalajara Unit, Research Center of Technology and Design Assistance of Jalisco State, National Council of Science and Technology (CIATEJ AC, CONACYT), Av. Normalistas 800, Col. Colinas de la Normal, CP 44270 Guadalajara, Jalisco, Mexico.
| | - Wentian Li
- The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, 350 Community Dr. Manhasset, NY 11030, USA.
| | - Ernesto Prado Montes de Oca
- Personalized Medicine Laboratory (LAMPER), Medical and Pharmaceutical Biotechnology, Guadalajara Unit, Research Center of Technology and Design Assistance of Jalisco State, National Council of Science and Technology (CIATEJ AC, CONACYT), Av. Normalistas 800, Col. Colinas de la Normal, CP 44270 Guadalajara, Jalisco, Mexico; Molecular Biology Laboratory, Biosafety Area, Medical and Pharmaceutical Biotechnology, Guadalajara Unit, CIATEJ AC, CONACYT, Av. Normalistas 800, Col. Colinas de la Normal, CP 44270 Guadalajara, Jalisco, Mexico.
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315
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Richard AC, Ferdinand JR, Meylan F, Hayes ET, Gabay O, Siegel RM. The TNF-family cytokine TL1A: from lymphocyte costimulator to disease co-conspirator. J Leukoc Biol 2015; 98:333-45. [PMID: 26188076 PMCID: PMC4763597 DOI: 10.1189/jlb.3ri0315-095r] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 06/10/2015] [Accepted: 06/19/2015] [Indexed: 12/12/2022] Open
Abstract
Originally described in 2002 as a T cell-costimulatory cytokine, the tumor necrosis factor family member TNF-like factor 1A (TL1A), encoded by the TNFSF15 gene, has since been found to affect multiple cell lineages through its receptor, death receptor 3 (DR3, encoded by TNFRSF25) with distinct cell-type effects. Genetic deficiency or blockade of TL1A-DR3 has defined a number of disease states that depend on this cytokine-receptor pair, whereas excess TL1A leads to allergic gastrointestinal inflammation through stimulation of group 2 innate lymphoid cells. Noncoding variants in the TL1A locus are associated with susceptibility to inflammatory bowel disease and leprosy, predicting that the level of TL1A expression may influence host defense and the development of autoimmune and inflammatory diseases.
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Affiliation(s)
- Arianne C Richard
- *Immunoregulation Section, Autoimmunity Branch, NIAMS, National Institutes of Health, Bethesda, Maryland, USA; Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - John R Ferdinand
- *Immunoregulation Section, Autoimmunity Branch, NIAMS, National Institutes of Health, Bethesda, Maryland, USA; Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Françoise Meylan
- *Immunoregulation Section, Autoimmunity Branch, NIAMS, National Institutes of Health, Bethesda, Maryland, USA; Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Erika T Hayes
- *Immunoregulation Section, Autoimmunity Branch, NIAMS, National Institutes of Health, Bethesda, Maryland, USA; Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Odile Gabay
- *Immunoregulation Section, Autoimmunity Branch, NIAMS, National Institutes of Health, Bethesda, Maryland, USA; Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Richard M Siegel
- *Immunoregulation Section, Autoimmunity Branch, NIAMS, National Institutes of Health, Bethesda, Maryland, USA; Cambridge Institute for Medical Research and Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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316
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Romanoski CE, Link VM, Heinz S, Glass CK. Exploiting genomics and natural genetic variation to decode macrophage enhancers. Trends Immunol 2015; 36:507-18. [PMID: 26298065 PMCID: PMC4548828 DOI: 10.1016/j.it.2015.07.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/15/2015] [Accepted: 07/17/2015] [Indexed: 12/18/2022]
Abstract
The mammalian genome contains on the order of a million enhancer-like regions that are required to establish the identities and functions of specific cell types. Here, we review recent studies in immune cells that have provided insight into the mechanisms that selectively activate certain enhancers in response to cell lineage and environmental signals. We describe a working model wherein distinct classes of transcription factors define the repertoire of active enhancers in macrophages through collaborative and hierarchical interactions, and discuss important challenges to this model, specifically providing examples from T cells. We conclude by discussing the use of natural genetic variation as a powerful approach for decoding transcription factor combinations that play dominant roles in establishing the enhancer landscapes, and the potential that these insights have for advancing our understanding of the molecular causes of human disease.
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Affiliation(s)
- Casey E Romanoski
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA
| | - Verena M Link
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA; Faculty of Biology, Department II, Ludwig-Maximilians Universität München, Planegg-Martinsried 85152, Germany
| | - Sven Heinz
- Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, USA.
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317
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C5orf30 is a negative regulator of tissue damage in rheumatoid arthritis. Proc Natl Acad Sci U S A 2015; 112:11618-23. [PMID: 26316022 DOI: 10.1073/pnas.1501947112] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The variant rs26232, in the first intron of the chromosome 5 open reading frame 30 (C5orf30) locus, has recently been associated with both risk of developing rheumatoid arthritis (RA) and severity of tissue damage. The biological activities of human C5orf30 are unknown, and neither the gene nor protein show significant homology to any other characterized human sequences. The C5orf30 gene is present only in vertebrate genomes with a high degree of conservation, implying a central function in these organisms. Here, we report that C5orf30 is highly expressed in the synovium of RA patients compared with control synovial tissue, and that it is predominately expressed by synovial fibroblast (RASF) and macrophages in the lining and sublining layer of the tissue. These cells play a central role in the initiation and perpetuation of RA and are implicated in cartilage destruction. RASFs lacking C5orf30 exhibit increased cell migration and invasion in vitro, and gene profiling following C5orf30 inhibition confirmed up-regulation of genes involved in cell migration, adhesion, angiogenesis, and immune and inflammatory pathways. Importantly, loss of C5orf30 contributes to the pathology of inflammatory arthritis in vivo, because inhibition of C5orf30 in the collagen-induced arthritis model markedly accentuated joint inflammation and tissue damage. Our study reveal C5orf30 to be a previously unidentified negative regulator of tissue damage in RA, and this protein may act by modulating the autoaggressive phenotype that is characteristic of RASFs.
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318
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Dendrou CA, Fugger L, Friese MA. Immunopathology of multiple sclerosis. Nat Rev Immunol 2015; 15:545-58. [PMID: 26250739 DOI: 10.1038/nri3871] [Citation(s) in RCA: 1414] [Impact Index Per Article: 157.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Two decades of clinical experience with immunomodulatory treatments for multiple sclerosis point to distinct immunological pathways that drive disease relapses and progression. In light of this, we discuss our current understanding of multiple sclerosis immunopathology, evaluate long-standing hypotheses regarding the role of the immune system in the disease and delineate key questions that are still unanswered. Recent and anticipated advances in the field of immunology, and the increasing recognition of inflammation as an important component of neurodegeneration, are shaping our conceptualization of disease pathophysiology, and we explore the potential implications for improved healthcare provision to patients in the future.
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Affiliation(s)
- Calliope A Dendrou
- Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology and MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Lars Fugger
- Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology and MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,Clinical Institute, Aarhus University Hospital, DK-8200 Aarhus, Denmark
| | - Manuel A Friese
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, 20246 Hamburg, Germany
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319
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Tsang JS. Utilizing population variation, vaccination, and systems biology to study human immunology. Trends Immunol 2015; 36:479-93. [PMID: 26187853 PMCID: PMC4979540 DOI: 10.1016/j.it.2015.06.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/19/2015] [Accepted: 06/19/2015] [Indexed: 12/27/2022]
Abstract
The move toward precision medicine has highlighted the importance of understanding biological variability within and across individuals in the human population. In particular, given the prevalent involvement of the immune system in diverse pathologies, an important question is how much and what information about the state of the immune system is required to enable accurate prediction of future health and response to medical interventions. Towards addressing this question, recent studies using vaccination as a model perturbation and systems-biology approaches are beginning to provide a glimpse of how natural population variation together with multiplexed, high-throughput measurement and computational analysis can be used to uncover predictors of immune response quality in humans. Here I discuss recent developments in this emerging field, with emphasis on baseline correlates of vaccination responses, sources of immune-state variability, as well as relevant features of study design, data generation, and computational analysis.
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Affiliation(s)
- John S Tsang
- Systems Genomics and Bioinformatics Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases (NIAID), Bethesda, MD 20892, USA; Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), National Institutes of Health, Bethesda, MD 20892, USA.
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320
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Abstract
The past two decades of research into the pathogenesis of Alzheimer disease (AD) have been driven largely by the amyloid hypothesis; the neuroinflammation that is associated with AD has been assumed to be merely a response to pathophysiological events. However, new data from preclinical and clinical studies have established that immune system-mediated actions in fact contribute to and drive AD pathogenesis. These insights have suggested both novel and well-defined potential therapeutic targets for AD, including microglia and several cytokines. In addition, as inflammation in AD primarily concerns the innate immune system - unlike in 'typical' neuroinflammatory diseases such as multiple sclerosis and encephalitides - the concept of neuroinflammation in AD may need refinement.
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321
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Naranbhai V, Fairfax BP, Makino S, Humburg P, Wong D, Ng E, Hill AVS, Knight JC. Genomic modulators of gene expression in human neutrophils. Nat Commun 2015; 6:7545. [PMID: 26151758 DOI: 10.1038/ncomms8545] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 05/19/2015] [Indexed: 12/12/2022] Open
Abstract
Neutrophils form the most abundant leukocyte subset and are central to many disease processes. Technical challenges in transcriptomic profiling have prohibited genomic approaches to date. Here we map expression quantitative trait loci (eQTL) in peripheral blood CD16+ neutrophils from 101 healthy European adults. We identify cis-eQTL for 3281 neutrophil-expressed genes including many implicated in neutrophil function, with 450 of these not previously observed in myeloid or lymphoid cells. Paired comparison with monocyte eQTL demonstrates nuanced conditioning of genetic regulation of gene expression by cellular context, which relates to cell-type-specific DNA methylation and histone modifications. Neutrophil eQTL are markedly enriched for trait-associated variants particularly autoimmune, allergy and infectious disease. We further demonstrate how eQTL in PADI4 and NOD2 delineate risk variant function in rheumatoid arthritis, leprosy and Crohn's disease. Taken together, these data help advance understanding of the genetics of gene expression, neutrophil biology and immune-related diseases.
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Affiliation(s)
- Vivek Naranbhai
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Benjamin P Fairfax
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Seiko Makino
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Peter Humburg
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Daniel Wong
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Esther Ng
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Adrian V S Hill
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
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322
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Gibson G, Powell JE, Marigorta UM. Expression quantitative trait locus analysis for translational medicine. Genome Med 2015; 7:60. [PMID: 26110023 PMCID: PMC4479075 DOI: 10.1186/s13073-015-0186-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Expression quantitative trait locus analysis has emerged as an important component of efforts to understand how genetic polymorphisms influence disease risk and is poised to make contributions to translational medicine. Here we review how expression quantitative trait locus analysis is aiding the identification of which gene(s) within regions of association are causal for a disease or phenotypic trait; the narrowing down of the cell types or regulators involved in the etiology of disease; the characterization of drivers and modifiers of cancer; and our understanding of how different environments and cellular contexts can modify gene expression. We also introduce the concept of transcriptional risk scores as a means of refining estimates of individual liability to disease based on targeted profiling of the transcripts that are regulated by polymorphisms jointly associated with disease and gene expression.
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Affiliation(s)
- Greg Gibson
- Center for Integrative Genomics, School of Biology, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Joseph E Powell
- Centre for Neurogenetics and Statistical Genomics, Queensland Brain Institute, University of Queensland, St Lucia, Brisbane, QLD 4072 Australia ; The Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072 Australia
| | - Urko M Marigorta
- Center for Integrative Genomics, School of Biology, Georgia Institute of Technology, Atlanta, GA 30332 USA
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323
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Wes PD, Holtman IR, Boddeke EW, Möller T, Eggen BJ. Next generation transcriptomics and genomics elucidate biological complexity of microglia in health and disease. Glia 2015; 64:197-213. [DOI: 10.1002/glia.22866] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 05/11/2015] [Indexed: 12/11/2022]
Affiliation(s)
| | - Inge R. Holtman
- Department of NeuroscienceSection Medical Physiology, University of Groningen, University Medical Center GroningenGroningen The Netherlands
| | - Erik W.G.M. Boddeke
- Department of NeuroscienceSection Medical Physiology, University of Groningen, University Medical Center GroningenGroningen The Netherlands
| | | | - Bart J.L. Eggen
- Department of NeuroscienceSection Medical Physiology, University of Groningen, University Medical Center GroningenGroningen The Netherlands
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324
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Abstract
Autoimmune diseases affect up to approximately 10% of the population. While rare Mendelian autoimmunity syndromes can result from monogenic mutations disrupting essential mechanisms of central and peripheral tolerance, more common human autoimmune diseases are complex disorders that arise from the interaction between polygenic risk factors and environmental factors. Although the risk attributable to most individual nucleotide variants is modest, genome-wide association studies (GWAS) have the potential to provide an unbiased view of biological pathways that drive human autoimmune diseases. Interpretation of GWAS requires integration of multiple genomic datasets including dense genotyping, cis-regulatory maps of primary immune cells, and genotyped studies of gene expression in relevant cell types and cellular conditions. Improved understanding of the genetic basis of autoimmunity may lead to a more sophisticated understanding of underlying cellular phenotypes and, eventually, novel diagnostics and targeted therapies.
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325
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Esposito F, Sorosina M, Ottoboni L, Lim ET, Replogle JM, Raj T, Brambilla P, Liberatore G, Guaschino C, Romeo M, Pertel T, Stankiewicz JM, Martinelli V, Rodegher M, Weiner HL, Brassat D, Benoist C, Patsopoulos NA, Comi G, Elyaman W, Martinelli Boneschi F, De Jager PL. A pharmacogenetic study implicates SLC9a9 in multiple sclerosis disease activity. Ann Neurol 2015; 78:115-27. [PMID: 25914168 DOI: 10.1002/ana.24429] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 04/17/2015] [Accepted: 04/17/2015] [Indexed: 02/06/2023]
Abstract
OBJECTIVE A proportion of multiple sclerosis (MS) patients experience disease activity despite treatment. The early identification of the most effective drug is critical to impact long-term outcome and to move toward a personalized approach. The aim of the present study is to identify biomarkers for further clinical development and to yield insights into the pathophysiology of disease activity. METHODS We performed a genome-wide association study in interferon-β (IFNβ)-treated MS patients followed by validation in 3 independent cohorts. The role of the validated variant was examined in several RNA data sets, and the function of the presumed target gene was explored using an RNA interference approach in primary T cells in vitro. RESULTS We found an association between rs9828519(G) and nonresponse to IFNβ (pdiscovery = 4.43 × 10(-8)) and confirmed it in a meta-analysis across 3 replication data sets (preplication = 7.78 × 10(-4)). Only 1 gene is found in the linkage disequilibrium block containing rs9828519: SLC9A9. Exploring the function of this gene, we see that SLC9A9 mRNA expression is diminished in MS subjects who are more likely to have relapses. Moreover, SLC9A9 knockdown in T cells in vitro leads an increase in expression of IFNγ, which is a proinflammatory molecule. INTERPRETATION This study identifies and validates the role of rs9828519, an intronic variant in SLC9A9, in IFNβ-treated subjects, demonstrating a successful pharmacogenetic screen in MS. Functional characterization suggests that SLC9A9, an Na(+) -H(+) exchanger found in endosomes, appears to influence the differentiation of T cells to a proinflammatory fate and may have a broader role in MS disease activity, outside of IFNβ treatment.
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Affiliation(s)
- Federica Esposito
- Department of Neurology and Neurorehabilitation, San Raffaele Scientific Institute, Milan, Italy.,Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Melissa Sorosina
- Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Linda Ottoboni
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Elaine T Lim
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA
| | - Joseph M Replogle
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Program for Medical and Population Genetics, Broad Institute, Cambridge, MA.,Program in Translational Neuropsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Towfique Raj
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Program for Medical and Population Genetics, Broad Institute, Cambridge, MA.,Program in Translational Neuropsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Paola Brambilla
- Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Giuseppe Liberatore
- Department of Neurology and Neurorehabilitation, San Raffaele Scientific Institute, Milan, Italy.,Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Clara Guaschino
- Department of Neurology and Neurorehabilitation, San Raffaele Scientific Institute, Milan, Italy.,Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Marzia Romeo
- Department of Neurology and Neurorehabilitation, San Raffaele Scientific Institute, Milan, Italy
| | - Thomas Pertel
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA
| | - James M Stankiewicz
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA
| | - Vittorio Martinelli
- Department of Neurology and Neurorehabilitation, San Raffaele Scientific Institute, Milan, Italy.,Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Mariaemma Rodegher
- Department of Neurology and Neurorehabilitation, San Raffaele Scientific Institute, Milan, Italy.,Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Howard L Weiner
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA
| | - David Brassat
- Department of Neurology, Purpan Hospital and Mixed Unit of Research 1043, University of Toulouse, Toulouse, France
| | - Christophe Benoist
- Harvard Medical School, Boston, MA.,Program for Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Nikolaos A Patsopoulos
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA.,Program for Medical and Population Genetics, Broad Institute, Cambridge, MA.,Program in Translational Neuropsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Giancarlo Comi
- Department of Neurology and Neurorehabilitation, San Raffaele Scientific Institute, Milan, Italy.,Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Wassim Elyaman
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA.,Program in Translational Neuropsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Filippo Martinelli Boneschi
- Department of Neurology and Neurorehabilitation, San Raffaele Scientific Institute, Milan, Italy.,Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Philip L De Jager
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, MA.,Harvard Medical School, Boston, MA.,Program for Medical and Population Genetics, Broad Institute, Cambridge, MA.,Program in Translational Neuropsychiatric Genomics, Institute for the Neurosciences, Department of Neurology, Brigham and Women's Hospital, Boston, MA
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326
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Pierson E, Koller D, Battle A, Mostafavi S. Sharing and Specificity of Co-expression Networks across 35 Human Tissues. PLoS Comput Biol 2015; 11:e1004220. [PMID: 25970446 PMCID: PMC4430528 DOI: 10.1371/journal.pcbi.1004220] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 03/02/2015] [Indexed: 01/21/2023] Open
Abstract
To understand the regulation of tissue-specific gene expression, the GTEx Consortium generated RNA-seq expression data for more than thirty distinct human tissues. This data provides an opportunity for deriving shared and tissue specific gene regulatory networks on the basis of co-expression between genes. However, a small number of samples are available for a majority of the tissues, and therefore statistical inference of networks in this setting is highly underpowered. To address this problem, we infer tissue-specific gene co-expression networks for 35 tissues in the GTEx dataset using a novel algorithm, GNAT, that uses a hierarchy of tissues to share data between related tissues. We show that this transfer learning approach increases the accuracy with which networks are learned. Analysis of these networks reveals that tissue-specific transcription factors are hubs that preferentially connect to genes with tissue specific functions. Additionally, we observe that genes with tissue-specific functions lie at the peripheries of our networks. We identify numerous modules enriched for Gene Ontology functions, and show that modules conserved across tissues are especially likely to have functions common to all tissues, while modules that are upregulated in a particular tissue are often instrumental to tissue-specific function. Finally, we provide a web tool, available at mostafavilab.stat.ubc.ca/GNAT, which allows exploration of gene function and regulation in a tissue-specific manner.
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Affiliation(s)
- Emma Pierson
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | | | - Daphne Koller
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | - Alexis Battle
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | - Sara Mostafavi
- Department of Computer Science, Stanford University, Stanford, California, United States of America
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327
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Replogle JM, Chan G, White CC, Raj T, Winn PA, Evans DA, Sperling RA, Chibnik LB, Bradshaw EM, Schneider JA, Bennett DA, De Jager PL. A TREM1 variant alters the accumulation of Alzheimer-related amyloid pathology. Ann Neurol 2015; 77:469-77. [PMID: 25545807 DOI: 10.1002/ana.24337] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 11/23/2014] [Accepted: 12/21/2014] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Genome-wide association studies have linked variants in TREM2 (triggering receptor expressed on myeloid cells 2) and TREML2 with Alzheimer disease (AD) and AD endophenotypes. Here, we pursue a targeted analysis of the TREM locus in relation to cognitive decline and pathological features of AD. METHODS Clinical, cognitive, and neuropathological phenotypes were collected in 3 prospective cohorts on aging (n = 3,421 subjects). Our primary analysis was an association with neuritic plaque pathology. To functionally characterize the associated variants, we used flow cytometry to measure TREM1 expression on monocytes. RESULTS We provide evidence that an intronic variant, rs6910730(G) , in TREM1, is associated with an increased burden of neuritic plaques (p = 3.7 × 10(-4) ), diffuse plaques (p = 4.1 × 10(-3) ), and Aβ density (p = 2.6 × 10(-3) ) as well as an increased rate of cognitive decline (p = 5.3 × 10(-3) ). A variant upstream of TREM2, rs7759295(C) , is independently associated with an increased tau tangle density (p = 4.9 × 10(-4) ), an increased burden of neurofibrillary tangles (p = 9.1 × 10(-3) ), and an increased rate of cognitive decline (p = 2.3 × 10(-3) ). Finally, a cytometric analysis shows that the TREM1 rs6910730(G) allele is associated with decreased TREM1 expression on the surface of myeloid cells (p = 1.7 × 10(-3) ). INTERPRETATION We provide evidence that 2 common variants within the TREM locus are associated with pathological features of AD and aging-related cognitive decline. Our evidence suggests that these variants are likely to be independent of known AD variants and that they may work through an alteration of myeloid cell function.
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Affiliation(s)
- Joseph M Replogle
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, MA; Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA; Harvard Medical School, Boston, MA
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328
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Wen X, Luca F, Pique-Regi R. Cross-population joint analysis of eQTLs: fine mapping and functional annotation. PLoS Genet 2015; 11:e1005176. [PMID: 25906321 PMCID: PMC4408026 DOI: 10.1371/journal.pgen.1005176] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 03/25/2015] [Indexed: 12/19/2022] Open
Abstract
Mapping expression quantitative trait loci (eQTLs) has been shown as a powerful tool to uncover the genetic underpinnings of many complex traits at molecular level. In this paper, we present an integrative analysis approach that leverages eQTL data collected from multiple population groups. In particular, our approach effectively identifies multiple independent cis-eQTL signals that are consistent across populations, accounting for population heterogeneity in allele frequencies and linkage disequilibrium patterns. Furthermore, by integrating genomic annotations, our analysis framework enables high-resolution functional analysis of eQTLs. We applied our statistical approach to analyze the GEUVADIS data consisting of samples from five population groups. From this analysis, we concluded that i) jointly analysis across population groups greatly improves the power of eQTL discovery and the resolution of fine mapping of causal eQTL ii) many genes harbor multiple independent eQTLs in their cis regions iii) genetic variants that disrupt transcription factor binding are significantly enriched in eQTLs (p-value = 4.93 × 10(-22)).
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Affiliation(s)
- Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
- * E-mail: (XW); (RPR)
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
- Department of Clinical and Translational Sciences, Wayne State University, Detroit, MI, USA
- * E-mail: (XW); (RPR)
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329
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Thériault P, ElAli A, Rivest S. The dynamics of monocytes and microglia in Alzheimer's disease. ALZHEIMERS RESEARCH & THERAPY 2015; 7:41. [PMID: 25878730 PMCID: PMC4397873 DOI: 10.1186/s13195-015-0125-2] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Alzheimer’s disease (AD) is the most common neurodegenerative disorder affecting older people worldwide. It is a progressive disorder mainly characterized by the presence of amyloid-beta (Aβ) plaques and neurofibrillary tangles within the brain parenchyma. It is now well accepted that neuroinflammation constitutes an important feature in AD, wherein the exact role of innate immunity remains unclear. Although innate immune cells are at the forefront to protect the brain in the presence of toxic molecules including Aβ, this natural defense mechanism seems insufficient in AD patients. Monocytes are a key component of the innate immune system and they play multiple roles, such as the removal of debris and dead cells via phagocytosis. These cells respond quickly and mobilize toward the inflamed site, where they proliferate and differentiate into macrophages in response to inflammatory signals. Many studies have underlined the ability of circulating and infiltrating monocytes to clear vascular Aβ microaggregates and parenchymal Aβ deposits respectively, which are very important features of AD. On the other hand, microglia are the resident immune cells of the brain and they play multiple physiological roles, including maintenance of the brain’s microenvironment homeostasis. In the injured brain, activated microglia migrate to the inflamed site, where they remove neurotoxic elements by phagocytosis. However, aged resident microglia are less efficient than their circulating sister immune cells in eliminating Aβ deposits from the brain parenchyma, thus underlining the importance to further investigate the functions of these innate immune cells in AD. The present review summarizes current knowledge on the role of monocytes and microglia in AD and how these cells can be mobilized to prevent and treat the disease.
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Affiliation(s)
- Peter Thériault
- Department of Molecular Medicine, Neuroscience Laboratory, CHU de Québec Research Center (CHUL), Faculty of Medicine, Laval University, 2705 Laurier Boulevard, Quebec City, QC G1V 4G2 Canada
| | - Ayman ElAli
- Department of Molecular Medicine, Neuroscience Laboratory, CHU de Québec Research Center (CHUL), Faculty of Medicine, Laval University, 2705 Laurier Boulevard, Quebec City, QC G1V 4G2 Canada
| | - Serge Rivest
- Department of Molecular Medicine, Neuroscience Laboratory, CHU de Québec Research Center (CHUL), Faculty of Medicine, Laval University, 2705 Laurier Boulevard, Quebec City, QC G1V 4G2 Canada
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330
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Kamimura D, Stofkova A, Nishikawa N, Atsumi T, Arima Y, Murakami M. Immune cell gateways in the central nervous system regulated by regional neural stimulations. ACTA ACUST UNITED AC 2015. [DOI: 10.1111/cen3.12198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Daisuke Kamimura
- Molecular Neuroimmunology; Institute for Genetic Medicine; Graduate School of Medicine; Hokkaido University; Sapporo Hokkaido Japan
| | - Andrea Stofkova
- Molecular Neuroimmunology; Institute for Genetic Medicine; Graduate School of Medicine; Hokkaido University; Sapporo Hokkaido Japan
| | - Naoki Nishikawa
- Molecular Neuroimmunology; Institute for Genetic Medicine; Graduate School of Medicine; Hokkaido University; Sapporo Hokkaido Japan
| | - Toru Atsumi
- Molecular Neuroimmunology; Institute for Genetic Medicine; Graduate School of Medicine; Hokkaido University; Sapporo Hokkaido Japan
| | - Yasunobu Arima
- Molecular Neuroimmunology; Institute for Genetic Medicine; Graduate School of Medicine; Hokkaido University; Sapporo Hokkaido Japan
| | - Masaaki Murakami
- Molecular Neuroimmunology; Institute for Genetic Medicine; Graduate School of Medicine; Hokkaido University; Sapporo Hokkaido Japan
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Zhang Y, Yang J, Zhang J, Sun L, Hirankarn N, Pan HF, Lau CS, Chan TM, Lee TL, Leung AMH, Mok CC, Zhang L, Wang Y, Shen JJ, Wong SN, Lee KW, Ho MHK, Lee PPW, Chung BHY, Chong CY, Wong RWS, Mok MY, Wong WHS, Tong KL, Tse NKC, Li XP, Avihingsanon Y, Rianthavorn P, Deekajorndej T, Suphapeetiporn K, Shotelersuk V, Ying SKY, Fung SKS, Lai WM, Wong CM, Ng IOL, Garcia-Barcelo MM, Cherny SS, Cui Y, Sham PC, Yang S, Ye DQ, Zhang XJ, Lau YL, Yang W. Genome-wide search followed by replication reveals genetic interaction of CD80 and ALOX5AP associated with systemic lupus erythematosus in Asian populations. Ann Rheum Dis 2015; 75:891-8. [PMID: 25862617 DOI: 10.1136/annrheumdis-2014-206367] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 03/22/2015] [Indexed: 12/20/2022]
Abstract
OBJECTIVES Genetic interaction has been considered as a hallmark of the genetic architecture of systemic lupus erythematosus (SLE). Based on two independent genome-wide association studies (GWAS) on Chinese populations, we performed a genome-wide search for genetic interactions contributing to SLE susceptibility. METHODS The study involved a total of 1 659 cases and 3 398 controls in the discovery stage and 2 612 cases and 3 441 controls in three cohorts for replication. Logistic regression and multifactor dimensionality reduction were used to search for genetic interaction. RESULTS Interaction of CD80 (rs2222631) and ALOX5AP (rs12876893) was found to be significantly associated with SLE (OR_int=1.16, P_int_all=7.7E-04 at false discovery rate<0.05). Single nuclear polymorphism rs2222631 was found associated with SLE with genome-wide significance (P_all=4.5E-08, OR=0.86) and is independent of rs6804441 in CD80, whose association was reported previously. Significant correlation was observed between expression of these two genes in healthy controls and SLE cases, together with differential expression of these genes between cases and controls, observed from individuals from the Hong Kong cohort. Genetic interactions between BLK (rs13277113) and DDX6 (rs4639966), and between TNFSF4 (rs844648) and PXK (rs6445975) were also observed in both GWAS data sets. CONCLUSIONS Our study represents the first genome-wide evaluation of epistasis interactions on SLE and the findings suggest interactions and independent variants may help partially explain missing heritability for complex diseases.
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Affiliation(s)
- Yan Zhang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Jing Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Jing Zhang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Liangdan Sun
- State Key Laboratory Incubation Base of Dermatology, Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
| | - Nattiya Hirankarn
- Lupus Research Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Chak Sing Lau
- Department of Medicine, Queen Mary Hospital, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Tak Mao Chan
- Department of Medicine, Queen Mary Hospital, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Tsz Leung Lee
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | | | - Chi Chiu Mok
- Department of Medicine, Tuen Mun Hospital, New Territory, Hong Kong, Hong Kong
| | - Lu Zhang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Yongfei Wang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Jiangshan Jane Shen
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Sik Nin Wong
- Department of Paediatrics and Adolescent Medicine, Tuen Mun Hospital, Hong Kong, Hong Kong
| | - Ka Wing Lee
- Department of Medicine, Pamela Youde Nethersole Eastern Hospital, Hong Kong, Hong Kong
| | - Marco Hok Kung Ho
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Pamela Pui Wah Lee
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Brian Hon-Yin Chung
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Chun Yin Chong
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Raymond Woon Sing Wong
- Department of Medicine, Queen Mary Hospital, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Mo Yin Mok
- Department of Medicine, Queen Mary Hospital, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Wilfred Hing Sang Wong
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Kwok Lung Tong
- Department of Medicine, Princess Margaret Hospital, Hong Kong, Hong Kong
| | - Niko Kei Chiu Tse
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, Hong Kong
| | - Xiang-Pei Li
- Department of Rheumatology, Anhui Provincial Hospital, Hefei, China
| | - Yingyos Avihingsanon
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pornpimol Rianthavorn
- Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Kanya Suphapeetiporn
- Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | | | - Wai Ming Lai
- Department of Paediatrics and Adolescent Medicine, Princess Margaret Hospital, Hong Kong, Hong Kong
| | - Chun-Ming Wong
- Department of Pathology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Irene Oi Lin Ng
- Department of Pathology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | | | - Stacey S Cherny
- Department of Psychiatry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Yong Cui
- State Key Laboratory Incubation Base of Dermatology, Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
| | - Pak Chung Sham
- Department of Psychiatry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong LKS Faculty of Medicine, Centre for Genomic Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Sen Yang
- State Key Laboratory Incubation Base of Dermatology, Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
| | - Dong-Qing Ye
- Lupus Research Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Xue-Jun Zhang
- State Key Laboratory Incubation Base of Dermatology, Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, Anhui, China
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong LKS Faculty of Medicine, Centre for Genomic Sciences, The University of Hong Kong, Hong Kong, Hong Kong
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Pihlstrøm L, Rengmark A, Bjørnarå KA, Dizdar N, Fardell C, Forsgren L, Holmberg B, Larsen JP, Linder J, Nissbrandt H, Tysnes OB, Dietrichs E, Toft M. Fine mapping and resequencing of the PARK16 locus in Parkinson’s disease. J Hum Genet 2015; 60:357-62. [DOI: 10.1038/jhg.2015.34] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 03/01/2015] [Accepted: 03/06/2015] [Indexed: 02/04/2023]
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Roederer M, Quaye L, Mangino M, Beddall MH, Mahnke Y, Chattopadhyay P, Tosi I, Napolitano L, Terranova Barberio M, Menni C, Villanova F, Di Meglio P, Spector TD, Nestle FO. The genetic architecture of the human immune system: a bioresource for autoimmunity and disease pathogenesis. Cell 2015; 161:387-403. [PMID: 25772697 PMCID: PMC4393780 DOI: 10.1016/j.cell.2015.02.046] [Citation(s) in RCA: 217] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/22/2014] [Accepted: 02/04/2015] [Indexed: 01/22/2023]
Abstract
Despite recent discoveries of genetic variants associated with autoimmunity and infection, genetic control of the human immune system during homeostasis is poorly understood. We undertook a comprehensive immunophenotyping approach, analyzing 78,000 immune traits in 669 female twins. From the top 151 heritable traits (up to 96% heritable), we used replicated GWAS to obtain 297 SNP associations at 11 genetic loci, explaining up to 36% of the variation of 19 traits. We found multiple associations with canonical traits of all major immune cell subsets and uncovered insights into genetic control for regulatory T cells. This data set also revealed traits associated with loci known to confer autoimmune susceptibility, providing mechanistic hypotheses linking immune traits with the etiology of disease. Our data establish a bioresource that links genetic control elements associated with normal immune traits to common autoimmune and infectious diseases, providing a shortcut to identifying potential mechanisms of immune-related diseases.
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Affiliation(s)
- Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA.
| | - Lydia Quaye
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK; NIHR Biomedical Research Centre at Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Margaret H Beddall
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Yolanda Mahnke
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Pratip Chattopadhyay
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Isabella Tosi
- Cutaneous Medicine Unit, St. John's Institute of Dermatology, King's College London, London SE1 9RT, UK; NIHR Biomedical Research Centre at Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Luca Napolitano
- Cutaneous Medicine Unit, St. John's Institute of Dermatology, King's College London, London SE1 9RT, UK
| | | | - Cristina Menni
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Federica Villanova
- Cutaneous Medicine Unit, St. John's Institute of Dermatology, King's College London, London SE1 9RT, UK; NIHR Biomedical Research Centre at Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Paola Di Meglio
- Cutaneous Medicine Unit, St. John's Institute of Dermatology, King's College London, London SE1 9RT, UK
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK.
| | - Frank O Nestle
- Cutaneous Medicine Unit, St. John's Institute of Dermatology, King's College London, London SE1 9RT, UK; NIHR Biomedical Research Centre at Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
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334
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Pathophysiology of T follicular helper cells in humans and mice. Nat Immunol 2015; 16:142-52. [PMID: 25594465 DOI: 10.1038/ni.3054] [Citation(s) in RCA: 321] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 11/12/2014] [Indexed: 02/08/2023]
Abstract
Follicular helper T cells (TFH cells) compose a heterogeneous subset of CD4(+) T cells that induce the differentiation of B cells into plasma cells and memory cells. They are found within and in proximity to germinal centers in secondary lymphoid organs, and their memory compartment also circulates in the blood. Our knowledge on the biology of TFH cells has increased significantly during the past decade, largely as a result of mouse studies. However, recent studies on human TFH cells isolated from lymphoid organ and blood samples and recent observations on the developmental mechanism of human TFH cells have revealed both similarities and differences between human and mouse TFH cells. Here we present the similarities and differences between mouse and human lymphoid organ-resident TFH cells and discuss the role of TFH cells in response to vaccines and in disease pathogenesis.
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van Luijn MM, Kreft KL, Jongsma ML, Mes SW, Wierenga-Wolf AF, van Meurs M, Melief MJ, der Kant RV, Janssen L, Janssen H, Tan R, Priatel JJ, Neefjes J, Laman JD, Hintzen RQ. Multiple sclerosis-associated CLEC16A controls HLA class II expression via late endosome biogenesis. Brain 2015; 138:1531-47. [PMID: 25823473 DOI: 10.1093/brain/awv080] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 01/26/2015] [Indexed: 01/20/2023] Open
Abstract
C-type lectins are key players in immune regulation by driving distinct functions of antigen-presenting cells. The C-type lectin CLEC16A gene is located at 16p13, a susceptibility locus for several autoimmune diseases, including multiple sclerosis. However, the function of this gene and its potential contribution to these diseases in humans are poorly understood. In this study, we found a strong upregulation of CLEC16A expression in the white matter of multiple sclerosis patients (n = 14) compared to non-demented controls (n = 11), mainly in perivascular leukocyte infiltrates. Moreover, CLEC16A levels were significantly enhanced in peripheral blood mononuclear cells of multiple sclerosis patients (n = 69) versus healthy controls (n = 46). In peripheral blood mononuclear cells, CLEC16A was most abundant in monocyte-derived dendritic cells, in which it strongly co-localized with human leukocyte antigen class II. Treatment of these professional antigen-presenting cells with vitamin D, a key protective environmental factor in multiple sclerosis, downmodulated CLEC16A in parallel with human leukocyte antigen class II. Knockdown of CLEC16A in distinct types of model and primary antigen-presenting cells resulted in severely impaired cytoplasmic distribution and formation of human leucocyte antigen class II-positive late endosomes, as determined by immunofluorescence and electron microscopy. Mechanistically, CLEC16A participated in the molecular machinery of human leukocyte antigen class II-positive late endosome formation and trafficking to perinuclear regions, involving the dynein motor complex. By performing co-immunoprecipitations, we found that CLEC16A directly binds to two critical members of this complex, RILP and the HOPS complex. CLEC16A silencing in antigen-presenting cells disturbed RILP-mediated recruitment of human leukocyte antigen class II-positive late endosomes to perinuclear regions. Together, we identify CLEC16A as a pivotal gene in multiple sclerosis that serves as a direct regulator of the human leukocyte antigen class II pathway in antigen-presenting cells. These findings are a first step in coupling multiple sclerosis-associated genes to the regulation of the strongest genetic factor in multiple sclerosis, human leukocyte antigen class II.
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Affiliation(s)
- Marvin M van Luijn
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Karim L Kreft
- 2 Department of Neurology and MS Center ErasMS, Erasmus MC, University Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - Marlieke L Jongsma
- 3 Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Steven W Mes
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Annet F Wierenga-Wolf
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Marjan van Meurs
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Marie-José Melief
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Rik van der Kant
- 3 Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Lennert Janssen
- 3 Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Hans Janssen
- 3 Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Rusung Tan
- 4 Department of Pathology, Sidra Medical and Research Center, Doha, Qatar 5 BC Children's Hospital and Department of Pathology and Laboratory Medicine, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - John J Priatel
- 5 BC Children's Hospital and Department of Pathology and Laboratory Medicine, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Jacques Neefjes
- 3 Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Jon D Laman
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Rogier Q Hintzen
- 2 Department of Neurology and MS Center ErasMS, Erasmus MC, University Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
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De Jager PL, Hacohen N, Mathis D, Regev A, Stranger BE, Benoist C. ImmVar project: Insights and design considerations for future studies of "healthy" immune variation. Semin Immunol 2015; 27:51-7. [PMID: 25819567 DOI: 10.1016/j.smim.2015.03.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/02/2015] [Accepted: 03/07/2015] [Indexed: 11/18/2022]
Abstract
The Immune Variation (ImmVar) project is one of a series of recent efforts to map the extent of variation in immune function in healthy human subjects. The focus of our initial studies involved a careful mapping of the genetic architecture of the adaptive and innate immunologic transcriptomes. Our studies highlight the shared nature of this immunogenetic architecture across human populations, the important role of context in uncovering effects of genetic variation, and the fact that, over all tested genes, common genetic variation account for a minority of the variance in the immune transcriptome in healthy subjects. Yet, it is an element of the variance that can be measured very precisely and will play an important role in the design of future studies. We therefore discuss how insights from ImmVar and similar studies inform experimental strategies and frame the design of future studies of immune function in health and disease.
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Affiliation(s)
- Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; The Broad Institute, Cambridge, MA 02142, USA.
| | - Nir Hacohen
- The Broad Institute, Cambridge, MA 02142, USA; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Diane Mathis
- Department of Microbiology and Immunobiology, Division of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Aviv Regev
- The Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Barbara E Stranger
- Section of Genetic Medicine, Department of Medicine, University of Chicago, IL 60637, USA; Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Christophe Benoist
- Department of Microbiology and Immunobiology, Division of Immunology, Harvard Medical School, Boston, MA 02115, USA
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del Rosario RCH, Poschmann J, Rouam SL, Png E, Khor CC, Hibberd ML, Prabhakar S. Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms. Nat Methods 2015; 12:458-64. [PMID: 25799442 DOI: 10.1038/nmeth.3326] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 02/06/2015] [Indexed: 12/30/2022]
Abstract
Most disease associations detected by genome-wide association studies (GWAS) lie outside coding genes, but very few have been mapped to causal regulatory variants. Here, we present a method for detecting regulatory quantitative trait loci (QTLs) that does not require genotyping or whole-genome sequencing. The method combines deep, long-read chromatin immunoprecipitation-sequencing (ChIP-seq) with a statistical test that simultaneously scores peak height correlation and allelic imbalance: the genotype-independent signal correlation and imbalance (G-SCI) test. We performed histone acetylation ChIP-seq on 57 human lymphoblastoid cell lines and used the resulting reads to call 500,066 single-nucleotide polymorphisms de novo within regulatory elements. The G-SCI test annotated 8,764 of these as histone acetylation QTLs (haQTLs)—an order of magnitude larger than the set of candidates detected by expression QTL analysis. Lymphoblastoid haQTLs were highly predictive of autoimmune disease mechanisms. Thus, our method facilitates large-scale regulatory variant detection in any moderately sized cohort for which functional profiling data can be generated, thereby simplifying identification of causal variants within GWAS loci.
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Affiliation(s)
| | - Jeremie Poschmann
- Computational and Systems Biology Group, Genome Institute of Singapore, Singapore
| | - Sigrid Laure Rouam
- Computational and Systems Biology Group, Genome Institute of Singapore, Singapore
| | - Eileen Png
- Infectious Diseases Group, Genome Institute of Singapore, Singapore
| | - Chiea Chuen Khor
- 1] Human Genetics Group, Genome Institute of Singapore, Singapore. [2] Singapore Eye Research Institute, Singapore. [3] Department of Opthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Martin Lloyd Hibberd
- 1] Infectious Diseases Group, Genome Institute of Singapore, Singapore. [2] Department of Pathogen Molecular Biology, London School of Hygiene &Tropical Medicine, London, UK
| | - Shyam Prabhakar
- Computational and Systems Biology Group, Genome Institute of Singapore, Singapore
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Hayes CE, Hubler SL, Moore JR, Barta LE, Praska CE, Nashold FE. Vitamin D Actions on CD4(+) T Cells in Autoimmune Disease. Front Immunol 2015; 6:100. [PMID: 25852682 PMCID: PMC4364365 DOI: 10.3389/fimmu.2015.00100] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/23/2015] [Indexed: 12/11/2022] Open
Abstract
This review summarizes and integrates research on vitamin D and CD4+ T-lymphocyte biology to develop new mechanistic insights into the molecular etiology of autoimmune disease. A deep understanding of molecular mechanisms relevant to gene–environment interactions is needed to deliver etiology-based autoimmune disease prevention and treatment strategies. Evidence linking sunlight, vitamin D, and the risk of multiple sclerosis and type 1 diabetes is summarized to develop the thesis that vitamin D is the environmental factor that most strongly influences autoimmune disease development. Evidence for CD4+ T-cell involvement in autoimmune disease pathogenesis and for paracrine calcitriol signaling to CD4+ T lymphocytes is summarized to support the thesis that calcitriol is sunlight’s main protective signal transducer in autoimmune disease risk. Animal modeling and human mechanistic data are summarized to support the view that vitamin D probably influences thymic negative selection, effector Th1 and Th17 pathogenesis and responsiveness to extrinsic cell death signals, FoxP3+CD4+ T-regulatory cell and CD4+ T-regulatory cell type 1 (Tr1) cell functions, and a Th1–Tr1 switch. The proposed Th1–Tr1 switch appears to bridge two stable, self-reinforcing immune states, pro- and anti-inflammatory, each with a characteristic gene regulatory network. The bi-stable switch would enable T cells to integrate signals from pathogens, hormones, cell–cell interactions, and soluble mediators and respond in a biologically appropriate manner. Finally, unanswered questions and potentially informative future research directions are highlighted to speed delivery of etiology-based strategies to reduce autoimmune disease.
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Affiliation(s)
- Colleen Elizabeth Hayes
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison , Madison, WI , USA
| | - Shane L Hubler
- Department of Statistics, College of Letters and Sciences, University of Wisconsin-Madison , Madison, WI , USA
| | - Jerott R Moore
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison , Madison, WI , USA
| | - Lauren E Barta
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison , Madison, WI , USA
| | - Corinne E Praska
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison , Madison, WI , USA
| | - Faye E Nashold
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison , Madison, WI , USA
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Drouin-Ouellet J, St-Amour I, Saint-Pierre M, Lamontagne-Proulx J, Kriz J, Barker RA, Cicchetti F. Toll-like receptor expression in the blood and brain of patients and a mouse model of Parkinson's disease. Int J Neuropsychopharmacol 2015; 18:pyu103. [PMID: 25522431 PMCID: PMC4438545 DOI: 10.1093/ijnp/pyu103] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Accumulating evidence supports a role for the immune system in the pathogenesis of Parkinson's disease. Importantly, recent preclinical studies are now suggesting a specific contribution of inflammation to the α-synuclein-induced pathology seen in this condition. METHODS We used flow cytometry and western blots to detect toll-like receptor 2 and 4 expression in blood and brain samples of Parkinson's disease patients and mice overexpressing human α-synuclein. To further assess the effects of α-synuclein overexpression on the innate immune system, we performed a longitudinal study using Thy1.2-α-synuclein mice that expressed a bicistronic DNA construct (reporter genes luciferase and green fluorescent protein) under the transcriptional control of the murine toll-like receptor 2 promoter. RESULTS Here, we report increases in toll-like receptors 2 and 4 expression in circulating monocytes and of toll-like receptor 4 in B cells and in the caudate/putamen of Parkinson's disease patients. Monthly bioluminescence imaging of Thy1.2-α-synuclein mice showed increasing toll-like receptor 2 expression from 10 months of age, although no change in toll-like receptor 2 and 4 expression was observed in the blood and brain of these mice at 12 months of age. Dexamethasone treatment starting at 5 months of age for 1 month significantly decreased the microglial response in the brain of these mice and promoted functional recovery as observed using a wheel-running activity test. CONCLUSION Our results show that toll-like receptors 2 and 4 are modulated in the blood and brain of Parkinson's disease patients and that overexpression of α-synuclein leads to a progressive microglial response, the inhibition of which has a beneficial impact on some motor phenotypes of an animal model of α-synucleinopathy.
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Affiliation(s)
- Janelle Drouin-Ouellet
- Department of Clinical Neurosciences, John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, United Kingdom (Drs Drouin-Ouellet and Barker); Centre de recherche du CHU de Québec, Québec, QC, Canada (Dr St-Amour, Ms Saint-Pierre, Mr Lamontagne-Proulx, and Dr Cicchetti); Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, Québec, QC, Canada (Dr Kriz); and Département de psychiatrie et neurosciences, Université Laval, Québec, QC, Canada (Drs Kriz and Cicchetti).
| | | | | | | | | | | | - Francesca Cicchetti
- Department of Clinical Neurosciences, John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, United Kingdom (Drs Drouin-Ouellet and Barker); Centre de recherche du CHU de Québec, Québec, QC, Canada (Dr St-Amour, Ms Saint-Pierre, Mr Lamontagne-Proulx, and Dr Cicchetti); Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec, Québec, QC, Canada (Dr Kriz); and Département de psychiatrie et neurosciences, Université Laval, Québec, QC, Canada (Drs Kriz and Cicchetti).
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341
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Gjoneska E, Pfenning AR, Mathys H, Quon G, Kundaje A, Tsai LH, Kellis M. Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease. Nature 2015; 518:365-9. [PMID: 25693568 PMCID: PMC4530583 DOI: 10.1038/nature14252] [Citation(s) in RCA: 380] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 01/22/2015] [Indexed: 12/12/2022]
Abstract
Alzheimer’s disease (AD) is a severe1 age-related neurodegenerative disorder characterized by accumulation of amyloid-β (Aβ) plaques and neurofibrillary tangles, synaptic and neuronal loss, and cognitive decline. Several genes have been implicated in AD, but chromatin state alterations during neurodegeneration remain uncharacterized. Here, we profile transcriptional and chromatin state dynamics across early and late pathology in the hippocampus of an inducible mouse model of AD-like neurodegeneration. We find a coordinated downregulation of synaptic plasticity genes and regulatory regions, and upregulation of immune response genes and regulatory regions, which are targeted by factors that belong to the ETS family of transcriptional regulators, including PU.1. Human regions orthologous to increasing-level enhancers show immune cell-specific enhancer signatures as well as immune cell expression quantitative trait loci (eQTL), while decreasing-level enhancer orthologs show fetal-brain-specific enhancer activity. Notably, AD-associated genetic variants are specifically enriched in increasing-level enhancer orthologs implicating immune processes in AD predisposition. Indeed, increasing enhancers overlap known AD loci lacking protein-altering variants and implicate additional loci that do not reach genome-wide significance. Our results reveal new insights into the mechanisms of neurodegeneration and establish the mouse as a useful model for functional studies of AD regulatory regions.
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Affiliation(s)
- Elizabeta Gjoneska
- 1] The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Andreas R Pfenning
- 1] Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA [2] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Hansruedi Mathys
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Gerald Quon
- 1] Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA [2] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Anshul Kundaje
- 1] Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA [2] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [3] Department of Genetics, Department of Computer Science, Stanford University, Stanford, California 94305, USA
| | - Li-Huei Tsai
- 1] The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Manolis Kellis
- 1] Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA [2] Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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342
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Heinz S, Romanoski CE, Benner C, Glass CK. The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol 2015; 16:144-54. [PMID: 25650801 PMCID: PMC4517609 DOI: 10.1038/nrm3949] [Citation(s) in RCA: 653] [Impact Index Per Article: 72.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The human body contains several hundred cell types, all of which share the same genome. In metazoans, much of the regulatory code that drives cell type-specific gene expression is located in distal elements called enhancers. Although mammalian genomes contain millions of potential enhancers, only a small subset of them is active in a given cell type. Cell type-specific enhancer selection involves the binding of lineage-determining transcription factors that prime enhancers. Signal-dependent transcription factors bind to primed enhancers, which enables these broadly expressed factors to regulate gene expression in a cell type-specific manner. The expression of genes that specify cell type identity and function is associated with densely spaced clusters of active enhancers known as super-enhancers. The functions of enhancers and super-enhancers are influenced by, and affect, higher-order genomic organization.
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Affiliation(s)
| | | | | | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, UC San Diego
- Department of Medicine, UC San Diego
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343
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Albert FW, Kruglyak L. The role of regulatory variation in complex traits and disease. Nat Rev Genet 2015; 16:197-212. [DOI: 10.1038/nrg3891] [Citation(s) in RCA: 684] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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344
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Targeted GAS6 delivery to the CNS protects axons from damage during experimental autoimmune encephalomyelitis. J Neurosci 2015; 34:16320-35. [PMID: 25471571 DOI: 10.1523/jneurosci.2449-14.2014] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Growth arrest-specific protein 6 (GAS6) is a soluble agonist of the TYRO3, AXL, MERTK (TAM) family of receptor tyrosine kinases identified to have anti-inflammatory, neuroprotective, and promyelinating properties. During experimental autoimmune encephalomyelitis (EAE), wild-type (WT) mice demonstrate a significant induction of Gas6, Axl, and Mertk but not Pros1 or Tyro3 mRNA. We tested the hypothesis that intracerebroventricular delivery of GAS6 directly into the CNS of WT mice during myelin oligodendrocyte glycoprotein (MOG)-induced EAE would improve the clinical course of disease relative to artificial CSF (ACSF)-treated mice. GAS6 did not delay disease onset, but significantly reduced the clinical scores during peak and chronic EAE. Mice receiving GAS6 for 28 d had preserved SMI31(+) neurofilament immunoreactivity, significantly fewer SMI32(+) axonal swellings and spheroids and less demyelination relative to ACSF-treated mice. Alternate-day subcutaneous IFNβ injection did not enhance GAS6 treatment effectiveness. Gas6(-/-) mice sensitized with MOG35-55 peptide exhibit higher clinical scores during late peak to early chronic disease, with significantly increased SMI32(+) axonal swellings and Iba1(+) microglia/macrophages, enhanced expression of several proinflammatory mRNA molecules, and decreased expression of early oligodendrocyte maturation markers relative to WT mouse spinal cords with scores for 8 consecutive days. During acute EAE, flow cytometry showed significantly more macrophages but not T-cell infiltrates in Gas6(-/-) spinal cords than WT spinal cords. Our data are consistent with GAS6 being protective during EAE by dampening the inflammatory response, thereby preserving axonal integrity and myelination.
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345
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Lewis M, Vyse S, Shields A, Boeltz S, Gordon P, Spector T, Lehner P, Walczak H, Vyse T. UBE2L3 polymorphism amplifies NF-κB activation and promotes plasma cell development, linking linear ubiquitination to multiple autoimmune diseases. Am J Hum Genet 2015; 96:221-34. [PMID: 25640675 PMCID: PMC4320258 DOI: 10.1016/j.ajhg.2014.12.024] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 12/17/2014] [Indexed: 12/13/2022] Open
Abstract
UBE2L3 is associated with increased susceptibility to numerous autoimmune diseases, but the underlying mechanism is unexplained. By using data from a genome-wide association study of systemic lupus erythematosus (SLE), we observed a single risk haplotype spanning UBE2L3, consistently aligned across multiple autoimmune diseases, associated with increased UBE2L3 expression in B cells and monocytes. rs140490 in the UBE2L3 promoter region showed the strongest association. UBE2L3 is an E2 ubiquitin-conjugating enzyme, specially adapted to function with HECT and RING-in-between-RING (RBR) E3 ligases, including HOIL-1 and HOIP, components of the linear ubiquitin chain assembly complex (LUBAC). Our data demonstrate that UBE2L3 is the preferred E2 conjugating enzyme for LUBAC in vivo, and UBE2L3 is essential for LUBAC-mediated activation of NF-κB. By accurately quantifying NF-κB translocation in primary human cells from healthy individuals stratified by rs140490 genotype, we observed that the autoimmune disease risk UBE2L3 genotype was correlated with basal NF-κB activation in unstimulated B cells and monocytes and regulated the sensitivity of NF-κB to CD40 stimulation in B cells and TNF stimulation in monocytes. The UBE2L3 risk allele correlated with increased circulating plasmablast and plasma cell numbers in SLE individuals, consistent with substantially elevated UBE2L3 protein levels in plasmablasts and plasma cells. These results identify key immunological consequences of the UBE2L3 autoimmune risk haplotype and highlight an important role for UBE2L3 in plasmablast and plasma cell development.
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346
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Singh T, Levine AP, Smith PJ, Smith AM, Segal AW, Barrett JC. Characterization of expression quantitative trait loci in the human colon. Inflamm Bowel Dis 2015. [PMID: 25569741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
BACKGROUND Many genetic risk loci have been identified for inflammatory bowel disease and colorectal cancer; however, identifying the causal genes for each association signal remains a challenge. Expression quantitative trait loci (eQTL) studies have identified common variants that induce differential gene expression and eQTLs can be cross-referenced with disease association signals for gene prioritization. However, the genetics of gene expression are highly tissue-specific, and further eQTL datasets from primary tissues are needed. METHODS We have conducted an eQTL discovery study using tissue extracted endoscopically from the terminal ileum and 4 colonic locations of non-inflamed bowel from 65 controls and patients with quiescent inflammatory bowel disease. A genome-wide cis-eQTL analysis was performed on >3,600,000 variants and 13,558 expressed probes. RESULTS We identified 1312 independent eQTLs associated with the differential expression of 1222 genes in rectal mucosa. One hundred seventy-one, 211, 168, and 102 independent eQTLs were identified in the sigmoid, descending colon, ascending colon, and terminal ileum, respectively. Twenty-six percent of genes with rectal eQTLs were novel and unique compared with 7 published eQTL datasets. Rectal eQTLs were significantly enriched for genes expressed in the colon. Examining 163 inflammatory bowel disease risk loci identified 11 tag single-nucleotide polymorphisms that were rectal eQTLs. A colorectal cancer locus at 11q23 contained a rectal eQTL for COLCA2, a protein implicated in colon cancer pathogenesis. CONCLUSIONS This study defines a catalog of ileal and colonic eQTLs. Our data reaffirm the tissue specificity of eQTLs and support the notion that identification of functional variants in relevant tissue can be effective in fine-mapping genetic risk loci.
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Affiliation(s)
- Tarjinder Singh
- *Medical Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; †Division of Medicine, University College London, London, United Kingdom; ‡Department of Gastroenterology, University College London Hospitals NHS Foundation Trust, London, United Kingdom; and §Eastman Dental Institute, University College London, London, United Kingdom
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347
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Abstract
BACKGROUND Many genetic risk loci have been identified for inflammatory bowel disease and colorectal cancer; however, identifying the causal genes for each association signal remains a challenge. Expression quantitative trait loci (eQTL) studies have identified common variants that induce differential gene expression and eQTLs can be cross-referenced with disease association signals for gene prioritization. However, the genetics of gene expression are highly tissue-specific, and further eQTL datasets from primary tissues are needed. METHODS We have conducted an eQTL discovery study using tissue extracted endoscopically from the terminal ileum and 4 colonic locations of non-inflamed bowel from 65 controls and patients with quiescent inflammatory bowel disease. A genome-wide cis-eQTL analysis was performed on >3,600,000 variants and 13,558 expressed probes. RESULTS We identified 1312 independent eQTLs associated with the differential expression of 1222 genes in rectal mucosa. One hundred seventy-one, 211, 168, and 102 independent eQTLs were identified in the sigmoid, descending colon, ascending colon, and terminal ileum, respectively. Twenty-six percent of genes with rectal eQTLs were novel and unique compared with 7 published eQTL datasets. Rectal eQTLs were significantly enriched for genes expressed in the colon. Examining 163 inflammatory bowel disease risk loci identified 11 tag single-nucleotide polymorphisms that were rectal eQTLs. A colorectal cancer locus at 11q23 contained a rectal eQTL for COLCA2, a protein implicated in colon cancer pathogenesis. CONCLUSIONS This study defines a catalog of ileal and colonic eQTLs. Our data reaffirm the tissue specificity of eQTLs and support the notion that identification of functional variants in relevant tissue can be effective in fine-mapping genetic risk loci.
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348
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Abstract
The Estonian Biobank and several other biobanks established over a decade ago are now starting to yield valuable longitudinal follow-up data for large numbers of individuals. These samples have been used in hundreds of different genome-wide association studies, resulting in the identification of reliable disease-associated variants. The focus of genomic research has started to shift from identifying genetic and nongenetic risk factors associated with common complex diseases to understanding the underlying mechanisms of the diseases and suggesting novel targets for therapy. However, translation of findings from genomic research into medical practice is still lagging, mainly due to insufficient evidence of clinical validity and utility. In this review, we examine the different elements required for the implementation of personalized medicine based on genomic information. First, biobanks and genome centres are required and have been established for the high-throughput genomic screening of large numbers of samples. Secondly, the combination of susceptibility alleles into polygenic risk scores has improved risk prediction of cardiovascular disease, breast cancer and several other diseases. Finally, national health information systems are being developed internationally, to combine data from electronic medical records from different sources, and also to gradually incorporate genomic information. We focus on the experience in Estonia, one of several countries with national goals towards more personalized health care based on genomic information, where the unique combination of elements required to accomplish this goal are already in place.
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Affiliation(s)
- L Milani
- Estonian Genome Center, University of TartuTartu, Estonia
| | - L Leitsalu
- Estonian Genome Center, University of TartuTartu, Estonia
- Institute of Molecular and Cell Biology, University of TartuTartu, Estonia
| | - A Metspalu
- Estonian Genome Center, University of TartuTartu, Estonia
- Institute of Molecular and Cell Biology, University of TartuTartu, Estonia
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349
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Lopez de Lapuente A, Pinto-Medel MJ, Astobiza I, Alloza I, Comabella M, Malhotra S, Montalban X, Zettl UK, Rodríguez-Antigüedad A, Fernández O, Vandenbroeck K. Cell-specific effects in different immune subsets associated with SOCS1 genotypes in multiple sclerosis. Mult Scler 2015; 21:1498-512. [PMID: 25623250 DOI: 10.1177/1352458514566418] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/19/2014] [Indexed: 11/15/2022]
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) near SOCS1 are associated with multiple sclerosis (MS), but the most important SNPs in the area and mechanisms by which they influence the disease are unknown. METHODS A haplotype-tagging association study was performed covering 60.5kbp around SOCS1, and the index SNP was validated in a total of 2292 individuals. mRNA expression of SOCS1 and nearby genes was measured in MS patients with different disease courses and healthy controls. SOCS1 protein expression was studied by flow cytometry in a separate cohort of patients and controls. Differentiation and maturation of monocyte-derived dendritic cells (moDCs) were also studied. RESULTS One SNP, rs423674, reached genome-wide significance. No genotype-specific mRNA expression differences were seen, but, by flow cytometry, significant interactions were observed between genotypes for rs423674 and disease activity (relapse or remission) in B cells and regulatory T cells. Furthermore, homozygotes for the risk allele (GG) showed higher levels of CD1a and CD86 than carriers of the protective allele (GT) in immature moDCs and a greater increase of HLA-DR+ cell percentage than GT heterozygotes upon maturation. CONCLUSIONS rs423674, or its genetic proxies, may influence MS risk by modulating SOCS1 expression in a cell-specific manner and by influencing dendritic cell function.
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Affiliation(s)
- Aitzkoa Lopez de Lapuente
- Neurogenomiks Group, Universidad del País Vasco (UPV/EHU), Spain/Achucarro Basque Center for Neuroscience, Spain
| | - María Jesús Pinto-Medel
- Research Laboratory, Clinical Neurosciences Institute, Hospital Regional Universitario Carlos Haya and Fundación IMABIS
| | - Ianire Astobiza
- Neurogenomiks Group, Universidad del País Vasco (UPV/EHU), Spain/Achucarro Basque Center for Neuroscience, Spain
| | - Iraide Alloza
- Neurogenomiks Group, Universidad del País Vasco (UPV/EHU), Spain/ Achucarro Basque Center for Neuroscience, Spain/ IKERBASQUE, Basque Foundation for Science, Spain
| | - Manuel Comabella
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Spain
| | - Sunny Malhotra
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Spain
| | - Xavier Montalban
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Spain
| | - Uwe K Zettl
- University of Rostock, Department of Neurology, Germany
| | | | - Oscar Fernández
- Research Laboratory, Clinical Neurosciences Institute, Hospital Regional Universitario Carlos Haya and Fundación IMABIS
| | - Koen Vandenbroeck
- Neurogenomiks Group, Universidad del País Vasco (UPV/EHU), Spain/ Achucarro Basque Center for Neuroscience, Spain/ IKERBASQUE, Basque Foundation for Science, Spain
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350
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Rothlin CV, Carrera-Silva EA, Bosurgi L, Ghosh S. TAM receptor signaling in immune homeostasis. Annu Rev Immunol 2015; 33:355-91. [PMID: 25594431 DOI: 10.1146/annurev-immunol-032414-112103] [Citation(s) in RCA: 307] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The TAM receptor tyrosine kinases (RTKs)-TYRO3, AXL, and MERTK-together with their cognate agonists GAS6 and PROS1 play an essential role in the resolution of inflammation. Deficiencies in TAM signaling have been associated with chronic inflammatory and autoimmune diseases. Three processes regulated by TAM signaling may contribute, either independently or collectively, to immune homeostasis: the negative regulation of the innate immune response, the phagocytosis of apoptotic cells, and the restoration of vascular integrity. Recent studies have also revealed the function of TAMs in infectious diseases and cancer. Here, we review the important milestones in the discovery of these RTKs and their ligands and the studies that underscore the functional importance of this signaling pathway in physiological immune settings and disease.
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