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      Systems genetics identifies a role for Cacna2d1 regulation in elevated intraocular pressure and glaucoma susceptibility

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          Abstract

          Glaucoma is a multi-factorial blinding disease in which genetic factors play an important role. Elevated intraocular pressure is a highly heritable risk factor for primary open angle glaucoma and currently the only target for glaucoma therapy. Our study helps to better understand underlying genetic and molecular mechanisms that regulate intraocular pressure, and identifies a new candidate gene, Cacna2d1, that modulates intraocular pressure and a promising therapeutic, pregabalin, which binds to CACNA2D1 protein and lowers intraocular pressure significantly. Because our study utilizes a genetically diverse population of mice with known sequence variants, we are able to determine that the intraocular pressure-lowering effect of pregabalin is dependent on the Cacna2d1 haplotype. Using human genome-wide association study (GWAS) data, evidence for association of a CACNA2D1 single-nucleotide polymorphism and primary open angle glaucoma is found. Importantly, these results demonstrate that our systems genetics approach represents an efficient method to identify genetic variation that can guide the selection of therapeutic targets.

          Abstract

          Elevated intraocular pressure (IOP) is a heritable risk factor for primary open angle glaucoma. Using forward mouse genetics, cell biology, pharmacology and human genetic data, the authors identify CACNA2D1 as an IOP risk gene that can be therapeutically targeted by the drug pregabalin in animal models.

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          Most cited references56

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          Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function.

          Patterns of gene expression in the central nervous system are highly variable and heritable. This genetic variation among normal individuals leads to considerable structural, functional and behavioral differences. We devised a general approach to dissect genetic networks systematically across biological scale, from base pairs to behavior, using a reference population of recombinant inbred strains. We profiled gene expression using Affymetrix oligonucleotide arrays in the BXD recombinant inbred strains, for which we have extensive SNP and haplotype data. We integrated a complementary database comprising 25 years of legacy phenotypic data on these strains. Covariance among gene expression and pharmacological and behavioral traits is often highly significant, corroborates known functional relations and is often generated by common quantitative trait loci. We found that a small number of major-effect quantitative trait loci jointly modulated large sets of transcripts and classical neural phenotypes in patterns specific to each tissue. We developed new analytic and graph theoretical approaches to study shared genetic modulation of networks of traits using gene sets involved in neural synapse function as an example. We built these tools into an open web resource called WebQTL that can be used to test a broad array of hypotheses.
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            A new set of BXD recombinant inbred lines from advanced intercross populations in mice

            Background Recombinant inbred (RI) strains are an important resource for mapping complex traits in many species. While large RI panels are available for Arabidopsis, maize, C. elegans, and Drosophila, mouse RI panels typically consist of fewer than 30 lines. This is a severe constraint on the power and precision of mapping efforts and greatly hampers analysis of epistatic interactions. Results In order to address these limitations and to provide the community with a more effective collaborative RI mapping panel we generated new BXD RI strains from two independent advanced intercrosses (AI) between C57BL/6J (B6) and DBA/2J (D2) progenitor strains. Progeny were intercrossed for 9 to 14 generations before initiating inbreeding, which is still ongoing for some strains. Since this AI base population is highly recombinant, the 46 advanced recombinant inbred (ARI) strains incorporate approximately twice as many recombinations as standard RI strains, a fraction of which are inevitably shared by descent. When combined with the existing BXD RI strains, the merged BXD strain set triples the number of previously available unique recombinations and quadruples the total number of recombinations in the BXD background. Conclusion The combined BXD strain set is the largest mouse RI mapping panel. It is a powerful tool for collaborative analysis of quantitative traits and gene function that will be especially useful to study variation in transcriptome and proteome data sets under multiple environments. Additional strains also extend the value of the extensive phenotypic characterization of the previously available strains. A final advantage of expanding the BXD strain set is that both progenitors have been sequenced, and approximately 1.8 million SNPs have been characterized. This provides unprecedented power in screening candidate genes and can reduce the effective length of QTL intervals. It also makes it possible to reverse standard mapping strategies and to explore downstream effects of known sequence variants.
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              Genome-wide association study identifies susceptibility loci for open angle glaucoma at TMCO1 and CDKN2B-AS1.

              We report a genome-wide association study for open-angle glaucoma (OAG) blindness using a discovery cohort of 590 individuals with severe visual field loss (cases) and 3,956 controls. We identified associated loci at TMCO1 (rs4656461[G] odds ratio (OR) = 1.68, P = 6.1 × 10(-10)) and CDKN2B-AS1 (rs4977756[A] OR = 1.50, P = 4.7 × 10(-9)). We replicated these associations in an independent cohort of cases with advanced OAG (rs4656461 P = 0.010; rs4977756 P = 0.042) and two additional cohorts of less severe OAG (rs4656461 combined discovery and replication P = 6.00 × 10(-14), OR = 1.51, 95% CI 1.35-1.68; rs4977756 combined P = 1.35 × 10(-14), OR = 1.39, 95% CI 1.28-1.51). We show retinal expression of genes at both loci in human ocular tissues. We also show that CDKN2A and CDKN2B are upregulated in the retina of a rat model of glaucoma.
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                Author and article information

                Contributors
                mjablonski@uthsc.edu
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                24 November 2017
                24 November 2017
                2017
                : 8
                : 1755
                Affiliations
                [4 ]ISNI 0000 0001 2164 3847, GRID grid.67105.35, Department of Epidemiology and Biostatistics, Institute of Computational Biology, , Case Western Reserve University School of Medicine, ; Cleveland, OH 44106 USA
                [6 ]ISNI 000000041936754X, GRID grid.38142.3c, Department of Ophthalmology, , Harvard Medical School, Massachusetts Eye and Ear Infirmary, ; Boston, MA 02298 USA
                [9 ]ISNI 0000 0004 1936 7961, GRID grid.26009.3d, Department of Ophthalmology, , Duke University Eye Center, ; Durham, NC 27705 USA
                [10 ]ISNI 0000 0001 2167 3675, GRID grid.14003.36, University of Wisconsin Institute for Clinical and Translational Research, ; Madison, WI 53705 USA
                [11 ]ISNI 0000000122483208, GRID grid.10698.36, Department of Ophthalmology, , UNC School of Medicine, ; Chapel Hill, NC 27517 USA
                [12 ]ISNI 0000 0004 1936 8294, GRID grid.214572.7, Department of Ophthalmology and Visual Sciences, , University of Iowa, ; Iowa City, IA 52242 USA
                [13 ]Eye Doctors of Washington DC, Washington, DC 20036 USA
                [14 ]ISNI 0000 0004 0383 8052, GRID grid.417124.5, Glaucoma Research Center, , Wills Eye Hospital, ; Philadelphia, PA 19107 USA
                [15 ]ISNI 0000 0004 0378 8294, GRID grid.62560.37, Channing Division of Network Medicine, , Brigham and Women’s Hospital, ; Boston, MA 02115 USA
                [16 ]ISNI 000000041936754X, GRID grid.38142.3c, Harvard T.H. Chan School of Public Health, ; Boston, MA 02115 USA
                [17 ]ISNI 0000 0004 1936 8606, GRID grid.26790.3a, Department of Ophthalmology, Bascom Palmer Eye Institute, , University of Miami, ; Miami, FL 33136 USA
                [18 ]ISNI 0000000086837370, GRID grid.214458.e, Department of Ophthalmology, Kellogg Eye Center, , University of Michigan, ; Ann Arbor, MI 48105 USA
                [19 ]ISNI 0000 0001 2284 9329, GRID grid.410427.4, Department of Cellular Biology and Anatomy, , Augusta University, ; Augusta, GA 30901 USA
                [20 ]ISNI 0000 0004 1936 8606, GRID grid.26790.3a, John P. Hussman Institute for Human Genomics, , University of Miami, ; Miami, FL 33136 USA
                [21 ]ISNI 0000 0001 2156 6140, GRID grid.268154.c, Department of Ophthalmology, , West Virginia University, ; Morgantown, WV 26506 USA
                [22 ]ISNI 0000 0001 2164 3847, GRID grid.67105.35, Department of Ophthalmology and Visual Sciences, , Case Western Reserve University, ; Cleveland, OH 44106 USA
                [23 ]ISNI 0000 0001 0002 2427, GRID grid.420243.3, Department of Ophthalmology, Einhorn Clinical Research Center, , New York Eye and Ear Infirmary, ; New York, NY 10003 USA
                [24 ]ISNI 0000 0001 2109 4251, GRID grid.240324.3, Department of Ophthalmology, , NYU Langone Medical Center, ; New York, NY 10016 USA
                [25 ]ISNI 0000 0004 0414 313X, GRID grid.418456.a, Dr. John T. Macdonald Foundation Department of Human Genetics, John P. Hussman Institute for Human Genomics, , University of Miami Health System, ; Miami, FL 33136 USA
                [26 ]ISNI 0000000087342732, GRID grid.240952.8, Department of Ophthalmology, , Stanford University Medical Center, ; Stanford, CA 94303 USA
                [27 ]ISNI 0000 0004 0459 167X, GRID grid.66875.3a, Department of Ophthalmology, , Mayo Clinic, ; Rochester, MN 85259 USA
                [28 ]ISNI 0000000087342732, GRID grid.240952.8, Department of Genetics, , Stanford University Medical Center, ; Stanford, CA 94305 USA
                [29 ]ISNI 0000 0001 2171 9311, GRID grid.21107.35, Department of Ophthalmology, Wilmer Eye Institute, , The Johns Hopkins University School of Medicine, ; Baltimore, MD 21287 USA
                [30 ]ISNI 0000 0001 2180 6431, GRID grid.4280.e, Singapore Eye Research Institute, , National University of Singapore, ; Singapore, 168751 Singapore
                [31 ]ISNI 000000040459992X, GRID grid.5645.2, Department of Epidemiology, , Erasmus Medical Center, ; Rotterdam, GE 3015 The Netherlands
                [32 ]ISNI 0000 0004 0367 2697, GRID grid.1014.4, Department of Ophthalmology, , Flinders University, ; Adelaide, SA 5042 Australia
                [33 ]ISNI 000000040459992X, GRID grid.5645.2, Department of Epidemiology, , Erasmus Medical Center, ; Rotterdam, GE 3015 The Netherlands
                [34 ]ISNI 0000 0001 2294 1395, GRID grid.1049.c, Statistical Genetics, , QIMR Berghofer Medical Research Institute, ; Brisbane, QLD 4006 Australia
                [35 ]ISNI 000000040459992X, GRID grid.5645.2, Department of Epidemiology, , University Medical Center of Rotterdam, ; Rotterdam, GE 3015 The Netherlands
                [36 ]ISNI 0000 0001 2322 6764, GRID grid.13097.3c, Department of Ophthalmology, , King’s College London, ; London, SE5 9RS UK
                [37 ]ISNI 0000 0004 1936 826X, GRID grid.1009.8, Department of Ophthlmology, Menzies Institute for Medical Research, , University of Tasmania, ; Tasmania, 7000 Australia
                [38 ]ISNI 0000 0001 0726 5157, GRID grid.5734.5, Ophthalmology, Inselspital, University Hospital Bern, , University of Bern, ; Bern, 3010 Switzerland
                [39 ]ISNI 0000 0004 0640 0021, GRID grid.14013.37, Faculty of Medicine, , University of Iceland, ; Reykjavik, 101 Iceland
                [40 ]ISNI 0000000121885934, GRID grid.5335.0, Department of Public Health and Primary Care, , University of Cambridge, ; Cambridge, CB2 1TN England
                [41 ]ISNI 0000 0001 2180 6431, GRID grid.4280.e, Department of Biochemistry, , National University of Singapore, ; Singapore, 117596 Singapore
                [42 ]ISNI 000000040459992X, GRID grid.5645.2, Department of Ophthalmology, , Erasmus Medical Center, ; Rotterdam, GE 3015 The Netherlands
                [43 ]ISNI 0000 0004 1936 9297, GRID grid.5491.9, Clinical and Experimental Sciences, Faculty of Medicine, , University of Southampton, ; Southampton, SO17 1BJ UK
                [44 ]GRID grid.410670.4, Centre for Eye Research Australia, University of Melbourne, , Royal Victorian Eye and Ear Hospital, ; Melbourne, VIC 3002 Australia
                [45 ]ISNI 0000 0001 2294 1395, GRID grid.1049.c, Statistical Genetics, , QIMR Berghofer Medical Research Institute Royal Brisbane Hospital, ; Brisbane, QLD 4006 Australia
                [46 ]ISNI 0000 0004 1937 0482, GRID grid.10784.3a, Department of Ophthalmology and Visual Sciences, , The Chinese University of Hong Kong, ; Hong Kong, Hong Kong
                [47 ]ISNI 0000 0001 2107 3311, GRID grid.5330.5, Institute of Human Genetics, , Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), ; Erlangen, 91054 Germany
                [48 ]deCODE genetics/Amgen, Inc., Reykjavik, IS-101 Iceland
                [49 ]ISNI 0000 0004 1936 7988, GRID grid.4305.2, MRC Human Genetics Unit, , The University of Edinburgh, ; Edinburgh, EH4 2XU Scotland
                [50 ]ISNI 0000 0001 2167 3675, GRID grid.14003.36, McPherson Eye Research Institute, , University of Wisconsin-Madison, ; Madison, WI 53705 USA
                [51 ]ISNI 0000 0001 2180 3484, GRID grid.13648.38, Clinic for General and Interventional Cardiology, , University Heart Center Hamburg, ; Hamburg, 20246 Germany
                [1 ]ISNI 0000 0004 0386 9246, GRID grid.267301.1, Department of Ophthalmology, The Hamilton Eye Institute, , The University of Tennessee Health Science Center, ; Memphis, TN 38163 USA
                [2 ]ISNI 0000 0004 0386 9246, GRID grid.267301.1, Department of Pharmaceutical Sciences, , The University of Tennessee Health Science Center, ; Memphis, TN 38163 USA
                [3 ]ISNI 0000000103426662, GRID grid.10251.37, Department of Pharmaceutics, College of Pharmacy, , Mansoura University, ; Mansoura, 35516 Egypt
                [5 ]ISNI 0000 0001 2322 6764, GRID grid.13097.3c, Department of Twin Research and Genetic Epidemiology, , King’s College London, ; London, WC2R 2LS UK
                [7 ]ISNI 0000 0004 0386 9246, GRID grid.267301.1, Department of Anatomy and Neurobiology, , The University of Tennessee Health Science Center, ; Memphis, TN 38163 USA
                [8 ]ISNI 0000 0004 0386 9246, GRID grid.267301.1, Department of Genetics, Genomics and Informatics, , The University of Tennessee Health Science Center, ; Memphis, TN 38163 USA
                Author information
                http://orcid.org/0000-0002-4001-8702
                http://orcid.org/0000-0002-4021-3559
                Article
                837
                10.1038/s41467-017-00837-5
                5701146
                29176626
                93adba42-715c-44e7-8a87-bf2fc549b414
                © The Author(s) 2017

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 1 December 2016
                : 28 June 2017
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