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Gaofeng Wang, William K. Scott, William Cade, Brenda Court, Kylee L. Spencer, Stephen G. Schwartz, Jaclyn L. Kovach, Anita Agarwal, Jonathan L. Haines, Margaret A. Pericak-Vance; Functional Analysis Of The Chromosome 10q26 Locus In Age-related Macular Degeneration. Invest. Ophthalmol. Vis. Sci. 2011;52(14):5244.
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© ARVO (1962-2015); The Authors (2016-present)
A locus at chromosome 10q26 has been repeatedly and consistently genetically linked and associated to the disease and represents one of the strongest genetic effects in AMD. Uncertainty remains, however, about which gene(s) in the chromosome 10q26 locus confers risk for AMD. This study is to functionally analyze the role of the genes ARMS2 and HTRA1 in age-related macular degeneration.
Quantitative PCR was conducted to measure gene expression level of HTRA1 and ARMS2. Rapid amplification of cDNA ends (RACE) assay was performed to characterize the ARMS2 transcripts in human retina. Mass spectrometry was applied to determine ARMS2 protein sequence. In situ hybridization and immunohistochemistry was used to localize ARMS2 in human retina.
We confirmed that there are no statistically significant effects of genotypes at the AMD-associated promoter variant rs11200638 on HTRA1 expression. We then focused on the ARMS2 gene, in which the strongly associated variants such as rs10490924 (A69S change) are potentially functional. We first verified the transcription stop site and found that the transcription start site (TSS) of ARMS2 in human retina is 220 bp upstream of the annotated start site in the genome database (NCBI GRCh37). More importantly, we identified a novel splice variant which uses TG at the genomic DNA position (chr10:124,216,608-124,216,609) as an alternative splice acceptor. The novel splice variant (designated as isoform-B) is expressed at a much higher level in whole eye tissues than is the annotated transcript (designated as isoform A). Furthermore, isoform-B, not isoform-A, is preferentially and significantly more highly expressed in the choroid/RPE than the retina (P<0.05). We are now determining protein sequence of ARMS2 and morphological ARMS2 expression in human retina.
The function of SNP rs11200638 on HTRA1 expression remains inconsistent.. ARMS2 is a potential functional gene in human retina, with multiple splice variants and proteins isoforms. The exact functions of ARMS2 in human retina need further studies.
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