Meta-analysis of gene–environment-wide association scans accounting for education level identifies additional loci for refractive error

This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/Myopia is the most common human eye disorder and it results from complex genetic and environmental causes. The rapidly increasing prevalence of myopia poses a major public health challenge. Here, the CREAM consortium performs a joint meta-analysis to test single-nucleotide polymorphism (SNP) main effects and SNP × education interaction effects on refractive error in 40,036 adults from 25 studies of European ancestry and 10,315 adults from 9 studies of Asian ancestry. In European ancestry individuals, we identify six novel loci (FAM150B-ACP1, LINC00340, FBN1, DIS3L-MAP2K1, ARID2-SNAT1 and SLC14A2) associated with refractive error. In Asian populations, three genome-wide significant loci AREG, GABRR1 and PDE10A also exhibit strong interactions with education (P<8.5 × 10(-5)), whereas the interactions are less evident in Europeans. The discovery of these loci represents an important advance in understanding how gene and environment interactions contribute to the heterogeneity of myopia

Genetic Variants on Chromosome 1q41 Influence Ocular Axial Length and High Myopia

As one of the leading causes of visual impairment and blindness, myopia poses a significant public health burden in Asia. The primary determinant of myopia is an elongated ocular axial length (AL). Here we report a meta-analysis of three genome-wide association studies on AL conducted in 1,860 Chinese adults, 929 Chinese children, and 2,155 Malay adults. We identified a genetic locus on chromosome 1q41 harboring the zinc-finger 11B pseudogene ZC3H11B showing genome-wide significant association with AL variation (rs4373767, β = −0.16 mm per minor allele, Pmeta = 2.69×10−10). The minor C allele of rs4373767 was also observed to significantly associate with decreased susceptibility to high myopia (per-allele odds ratio (OR) = 0.75, 95% CI: 0.68–0.84, Pmeta = 4.38×10−7) in 1,118 highly myopic cases and 5,433 controls. ZC3H11B and two neighboring genes SLC30A10 and LYPLAL1 were expressed in the human neural retina, retinal pigment epithelium, and sclera. In an experimental myopia mouse model, we observed significant alterations to gene and protein expression in the retina and sclera of the unilateral induced myopic eyes for the murine genes ZC3H11A, SLC30A10, and LYPLAL1. This supports the likely role of genetic variants at chromosome 1q41 in influencing AL variation and high myopia

GENES AND SIGNALING PATHWAYS UNDERLYING POSTNATAL AND MYOPIA DEVELOPMENT IN MOUSE SCLERA

Ph.DDOCTOR OF PHILOSOPH

Effects of wild type Serum Amyloid A1.1 and its derivative proteins on the cholesterol efflux activity

Serum Amyloid A (SAA) is known to be important in atherogenesis although the mechanisms are unclear. It is shown to promote cholesterol efflux activity of cells in several studies and may prevent atherosclerosis by promoting cholesterol efflux in foam cells of the atherosclerotic lesions. Therefore, it is important to elucidate the mechanism of SAA-mediated cholesterol efflux. Human Embryonic Kidney (HEK) 293 cells were first transfected to produce endogenous wild type SAA1.1, mutated SAA1.1 without the N-terminal lipid binding domain and mutated SAA1.1 with an amino acid substitution of Glycine to Aspartic acid at the 8th amino acid. The SAA1.1 concentration in cells and culture medium were measured with Enzyme-linked immunosorbent assay (ELISA) to determine SAA1.1 expression. After transfected cells were labeled with 3H cholesterol, their cholesterol effluxes were determined by measuring the radioactivity of cell lysate and culture medium. The results showed that secreted SAA1.1 promoted a significant increase in cholesterol efflux activity of HEK293 cells. The signal peptide of SAA1.1 was also demonstrated to be important for protein secretion. Hence, secreted SAA1.1 is shown to promote cholesterol efflux through its interaction at cell membrane in this study.Bachelor of Science in Biological Science

The chromosome 1q41 region and its association with axial length in the Asian cohorts.

<p>A) Regional plots for AL from the meta-analysis of three Asian GWAS cohorts: SCES, SCORM and SiMES. The association signals in a 1 megabase (Mb) region at chromosome 1q41 from 217,400 kb to 218,400 kb around the top SNP rs4373767 (red diamond) are plotted. The degree of pair-wise LD between the rs4373767 and any genotyped SNPs in this region is indicated by red shading, measured by r². Superimposed on the plots are gene locations and recombination rates in HapMap Chinese and Japanese populations (blue lines). B) LD plot showing pair-wise r² for all the SNPs genotyped in HapMap database residing between rs4428898 and rs7544369, inclusively, at chromosome 1q41. The four identified top SNPs are in red rectangles. The LD plot is generated by Haploview using SNPs (MAF>1%) genotyped on Han Chinese and Japanese samples in the HapMap database. All coordinates are in Build hg18.</p

mRNA expression of <i>ZC3H11B, SLC30A10</i>, and <i>LYPLAL1</i> in human tissues.

<p>Expression of mRNA for the three genes was examined in human brain, placenta, neural retina (retina), retinal pigment epithelium (RPE) and sclera from adult tissues, and retina/RPE and sclera from 24-week gestation fetal tissues using reverse transcription polymerase chain reaction (RT-PCR). Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is a housekeeping gene and was used as an internal control for the quantification of mRNA expression. NTC (No template control) served as a negative control with the use of water rather than cDNA during PCR.</p

Transcription quantification of <i>ZC3H11A</i>, <i>SLC30A10</i>, and <i>LYPLAL1</i> in mouse retina, retinal pigment epithelium, and sclera in induced myopic eyes, fellow eyes, and independent control eyes.

<p>Myopia was induced using −15 diopter negative lenses in the right eye of mice for 6 weeks. Uncovered left eyes were served as fellow eyes and age-matched naive mice eyes were controls. Quantification of mRNA expression in mice neural retina (retina), retinal pigment epithelium (RPE) and sclera using quantitative real-time PCR. The bar represents the fold changes of mRNA for each gene after normalization using <i>GAPDH</i> as reference. The mRNA levels of murine <i>ZC3H11A</i>, a gene that is conserved with respect to <i>ZC3H11B</i> in human, <i>SLC30A10</i> and <i>LYPLAL1</i> in myopic and fellow retina, RPE and sclera are compared with independent controls with <i>P</i>-values as follows: <i>ZC3H11A</i> (retina/RPE/sclera, <i>P</i> = 2.60×10⁻⁵, 2.62×10⁻⁶ and 1.08×10⁻⁴ respectively), <i>SLC30A10</i> (<i>P</i> = 2.00×10⁻⁴, 2.00×10⁻⁴ and 4.02×10⁻⁴ respectively) and <i>LYPLAL1</i> (<i>P</i> = 1.50×10⁻⁴, 1.50×10⁻⁴, 1.54×10⁻⁴ respectively). *P<0.0001.</p

Top SNPs (<i>P_meta</i>-value≤1×10⁻⁵) associated with AL from the meta-analysis in the three Asian cohorts.

a<p>MA, minor allele.</p>b<p>MAF, minor allele frequency in each cohort.</p>c<p>GWAS cohorts. SCES - Singapore Chinese Eye Study; SCORM - Singapore Cohort study of the Risk factors for Myopia; SiMES - Singapore Malay Eye Study.</p>d<p>β, coefficient of linear regression; s.e., standard error for coefficient β. Association between each genetic marker and AL was examined using linear regression, adjusted for age, gender, height and level of education. The effect sizes denote changes in millimeter of AL per each additional copy of the minor allele.</p>e<p><i>P_het</i>, <i>P</i>-value for heterogeneity by Cochran's Q test across three study cohorts.</p