Discovery and Functional Annotation of SIX6 Variants in Primary Open-Angle Glaucoma

PLoS Genetics, May 2014

Glaucoma is a leading cause of blindness worldwide. Primary open-angle glaucoma (POAG) is the most common subtype and is a complex trait with multigenic inheritance. Genome-wide association studies have previously identified a significant association between POAG and the SIX6 locus (rs10483727, odds ratio (OR) = 1.32, p = 3.87×10−11). SIX6 plays a role in ocular development and has been associated with the morphology of the optic nerve. We sequenced the SIX6 coding and regulatory regions in 262 POAG cases and 256 controls and identified six nonsynonymous coding variants, including five rare and one common variant, Asn141His (rs33912345), which was associated significantly with POAG (OR = 1.27, p = 4.2×10−10) in the NEIGHBOR/GLAUGEN datasets. These variants were tested in an in vivo Danio rerio (zebrafish) complementation assay to evaluate ocular metrics such as eye size and optic nerve structure. Five variants, found primarily in POAG cases, were hypomorphic or null, while the sixth variant, found only in controls, was benign. One variant in the SIX6 enhancer increased expression of SIX6 and disrupted its regulation. Finally, to our knowledge for the first time, we have identified a clinical feature in POAG patients that appears to be dependent upon SIX6 genotype: patients who are homozygous for the SIX6 risk allele (His141) have a statistically thinner retinal nerve fiber layer than patients homozygous for the SIX6 non-risk allele (Asn141). Our results, in combination with previous SIX6 work, lead us to hypothesize that SIX6 risk variants disrupt the development of the neural retina, leading to a reduced number of retinal ganglion cells, thereby increasing the risk of glaucoma-associated vision loss.

A PDF file should load here. If you do not see its contents the file may be temporarily unavailable at the journal website or you do not have a PDF plug-in installed and enabled in your browser.

Alternatively, you can download the file locally and open with any standalone PDF reader:

http://www.plosgenetics.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371/journal.pgen.1004372&representation=PDF

Discovery and Functional Annotation of SIX6 Variants in Primary Open-Angle Glaucoma

et al. (2014) Discovery and Functional Annotation of SIX6 Variants in Primary Open-Angle Glaucoma. PLoS Genet 10(5): e1004372. doi:10.1371/journal.pgen.1004372 Discovery and Functional Annotation of SIX6 Variants in Primary Open-Angle Glaucoma Megan Ulmer Carnes 0 Yangfan P. Liu 0 R. Rand Allingham 0 Benjamin T. Whigham 0 Shane Havens 0 Melanie E. Garrett 0 Chunyan Qiao 0 NEIGHBORHOOD Consortium Investigators` 0 Nicholas Katsanis 0 Janey L. Wiggs 0 Louis R. Pasquale 0 Allison Ashley-Koch 0 Edwin C. Oh 0 Michael A. Hauser 0 Greg Gibson, Georgia Institute of Technology, United States of America 0 1 The Center for Human Genetics, Duke University , Durham , North Carolina, United States of America, 2 The Center for Human Disease Modeling, Duke University Medical Center , Durham , North Carolina, United States of America, 3 Department of Ophthalmology, Duke University Medical Center , Durham , North Carolina, United States of America, 4 Department of Ophthalmology, Harvard Medical School , Boston , Massachusetts, United States of America, 5 Beijing Tongren Hospital, Beijing Tongren Eye Center, Beijing Ophthalmology & Visual Sciences Key Laboratory, Capital Medical University , Beijing , China , 6 Channing Division of Network Medicine, Brigham and Women's Hospital , Boston , Massachusetts, United States of America, 7 Department of Medicine, Duke University Medical Center , Durham , North Carolina, United States of America, 8 Department of Neurology, Duke University Medical Center , Durham, North Carolina , United States of America Glaucoma is a leading cause of blindness worldwide. Primary open-angle glaucoma (POAG) is the most common subtype and is a complex trait with multigenic inheritance. Genome-wide association studies have previously identified a significant association between POAG and the SIX6 locus (rs10483727, odds ratio (OR) = 1.32, p = 3.87610211). SIX6 plays a role in ocular development and has been associated with the morphology of the optic nerve. We sequenced the SIX6 coding and regulatory regions in 262 POAG cases and 256 controls and identified six nonsynonymous coding variants, including five rare and one common variant, Asn141His (rs33912345), which was associated significantly with POAG (OR = 1.27, p = 4.2610210) in the NEIGHBOR/GLAUGEN datasets. These variants were tested in an in vivo Danio rerio (zebrafish) complementation assay to evaluate ocular metrics such as eye size and optic nerve structure. Five variants, found primarily in POAG cases, were hypomorphic or null, while the sixth variant, found only in controls, was benign. One variant in the SIX6 enhancer increased expression of SIX6 and disrupted its regulation. Finally, to our knowledge for the first time, we have identified a clinical feature in POAG patients that appears to be dependent upon SIX6 genotype: patients who are homozygous for the SIX6 risk allele (His141) have a statistically thinner retinal nerve fiber layer than patients homozygous for the SIX6 non-risk allele (Asn141). Our results, in combination with previous SIX6 work, lead us to hypothesize that SIX6 risk variants disrupt the development of the neural retina, leading to a reduced number of retinal ganglion cells, thereby increasing the risk of glaucoma-associated vision loss. - Funding: ECO is a NARSAD young investigator. This work was supported by R01EY013315 (MAH), R01EY019126 (MAH), R01EY015543 (RRA), P30 EY005722 (Duke Eye Center); EY015872, EY022305, (JLW); EY015473 and UO1 HG004728 (LRP) Harvard Glaucoma Center for Excellence, and the Margolis Fund (JLW and LRP); Research to Prevent Blindness (JLW, LRP); EY015473 (LRP). A list of the GLAUGEN collaborators is found at The Primary Open-Angle Glaucoma Genes and Environment (GLAUGEN) Study listing on dbGAP, study Accession: http://www.ncbi.nlm.nih.gov/gap/?term=phs000308.v1.p1. December 21, 2010. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. . These authors contributed equally to this work. " ECO and MAH also contributed equally to this work. ` Membership of NEIGHBORHOOD Consortium Investigators is provided in the Acknowledgments. Primary open-angle glaucoma (POAG) is the most common type of glaucoma, a group of diseases that affect approximately 60 million people worldwide and is a leading cause of blindness [1]. Glaucoma is characterized by the progressive death of retinal ganglion cells, leading to optic nerve atrophy and loss of vision. POAG is a complex inherited disorder for which an increasing number of genetic associations have been described, each contributing modestly to disease burden [2,3]. A recent POAG genome-wide association study found a significant genetic association (rs10483727, odds ratio (OR) = 1.32, p = 3.87610211) at the SIX1/SIX6 locus [4]. Variants in the SIX1/ SIX6 locus were first associated with quantitative opt (...truncated)


This is a preview of a remote PDF: http://www.plosgenetics.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371/journal.pgen.1004372&representation=PDF

Megan Ulmer Carnes, Yangfan P. Liu, R. Rand Allingham, Benjamin T. Whigham, Shane Havens, Melanie E. Garrett, Chunyan Qiao, NEIGHBORHOOD Consortium Investigators, Nicholas Katsanis, Janey L. Wiggs, Louis R. Pasquale, Allison Ashley-Koch, Edwin C. Oh, Michael A. Hauser. Discovery and Functional Annotation of SIX6 Variants in Primary Open-Angle Glaucoma, PLoS Genetics, 2014, 5, DOI: 10.1371/journal.pgen.1004372