The cysteine proteinase inhibitor cystatin C harbors a haplotype associated with increased risk of AMD and Alzheimer’s disease and decreased plasma levels of its mature form

Abstract

Purpose : A missense SNP (rs1064039) in the cystatin C gene (CST3) is known to be associated with both AMD and Alzheimer’s disease (AD). A previously published GWAS (n= 9,978) identified that a SNP (rs6048952) adjacent to CST3 (11.2kb downstream of the aforementioned missense SNP) is associated with cystatin C plasma level. We undertook a linkage disequilibrium (LD) analysis around the CST3 locus to determine if LD exists between the two SNPs. Subsequent deduction of haplotypes will shed light on the directionality of the relationship between the two phenotypes: AMD/AD risk and cystatin C plasma levels.

Methods : Linkage disequilibrium (LD) was calculated from the phased genotype data of a Caucasian sample (n = 503) taken from Phase 3 of the 1000 Genomes Project. Calculation of LD was performed using the coefficient of determination (R²). Visualization of LD and haplotype analysis was performed using Haploview (Broad Institute).

Results : We find that high LD exists between the two SNPs (R² = 0.91), essentially forming two major haplotypes. We represent these two haplotypes as T-G and A-A, corresponding to the nucleotides at rs6048952-rs1064039 SNPs respectively. Haplotype frequencies are estimated to be 72% and 28% respectively. We deduce that it is the A-A haplotype (also known as variant B cystatin C) that is associated with decreased cystatin C plasma levels and increased risk of both AMD and Alzheimer’s disease.

Conclusions : To our knowledge this is the first time that these two phenotype-genotype associations have been brought together through knowledge of a shared haplotype. This suggests that the mechanistic link between the missense genetic polymorphism in CST3 and its associated risk of AD and AMD is, at least in part, through plasma levels of cystatin C likely consequential to decreased secretion. This mechanism is supported by previous in-vitro studies showing that RPE cells and fibroblasts expressing variant B CST3 exhibit reduced secretion of cystatin C compared with wildtype cells. This finding invites further investigation into the link between decreased plasma cystatin C levels and the increased risk of both AMD and AD risk, with the potential to explore cystatin C replacement therapy for patients homozygous for variant B CST3.

This is an abstract that was submitted for the 2016 ARVO Annual Meeting, held in Seattle, Wash., May 1-5, 2016.