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SNP located in an AluJb repeat downstream of TMCO1, rs4657473, is protective for POAG in African Americans.
- Source :
-
The British journal of ophthalmology [Br J Ophthalmol] 2019 Oct; Vol. 103 (10), pp. 1530-1536. Date of Electronic Publication: 2019 Mar 12. - Publication Year :
- 2019
-
Abstract
- Aims: To determine the association of single nucleotide polymorphisms (SNPs) downstream from the TMCO1 gene with primary open-angle glaucoma (POAG) in African Americans (AA).<br />Methods: AA subjects were recruited for the Primary Open-Angle African American Glaucoma Genetics (POAAGG) study from the Scheie Eye Institute and its satellite sites in Philadelphia. A region containing an AluJb repeat and seven SNPs, including rs4656461 near the TMCO1 gene, were PCR-Sanger sequenced from POAAGG cases (n=1537) and controls (n=1570). Association between POAG and SNPs near TMCO1 was investigated by logistic regression analysis. Phenotypic trait associations with these SNPs were assessed by analysis of variance. Electrophoretic mobility shift assay (EMSA) was performed to assess the affinity of human T-box 5 (TBX5) protein for a predicted binding motif in the TMCO1 region. Dual Luciferase assays were performed by transfecting recombinant plasmids containing the region surrounding the above SNPs in HEK293T and trabecular meshwork cells.<br />Results: The SNP rs4657473 (C>T) was associated with POAG; the TT genotype was protective (OR 0.20, 95% CI 0.09 to 0.42; p<0.001). No significant associations were found between the TMCO1 variants and phenotypic traits. EMSA confirmed the affinity of TBX5 for a predicted binding motif containing TMCO1 SNP rs4657475. Luciferase assays demonstrated a regulatory function for the genomic region around SNP rs4656561, located within AluJb repeat.<br />Conclusion: Our results demonstrate that a SNP downstream of TMCO1, rs4657473, is associated with POAG in an AA population. Our studies suggest a regulatory role for the previously POAG-associated locus near the TMCO1 gene that may affect gene expression.<br />Competing Interests: Competing interests: None declared.<br /> (© Author(s) (or their employer(s)) 2019. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)
- Subjects :
- Aged
Aged, 80 and over
Case-Control Studies
Electrophoretic Mobility Shift Assay
Female
Genotyping Techniques
HEK293 Cells
Humans
Intraocular Pressure
Male
Middle Aged
Plasmids genetics
Polymerase Chain Reaction
Trabecular Meshwork
Transfection
Black or African American genetics
Alu Elements genetics
Calcium Channels genetics
Glaucoma, Open-Angle genetics
Polymorphism, Single Nucleotide
Subjects
Details
- Language :
- English
- ISSN :
- 1468-2079
- Volume :
- 103
- Issue :
- 10
- Database :
- MEDLINE
- Journal :
- The British journal of ophthalmology
- Publication Type :
- Academic Journal
- Accession number :
- 30862618
- Full Text :
- https://doi.org/10.1136/bjophthalmol-2018-313086