Cerebrospinal fluid APOE levels: an endophenotype for genetic studies for Alzheimer's disease

Abstract

The apolipoprotein E (APOE) genotype is the major genetic risk factor for Alzheimer's disease (AD). We have access to cerebrospinal fluid (CSF) and plasma APOE protein levels from 641 individuals and genome-wide genotyped data from 570 of these samples. The aim of this study was to test whether CSF or plasma APOE levels could be a useful endophenotype for AD and to identify genetic variants associated with APOE levels. We found that CSF (P = 8.15 × 10(-4)) but not plasma (P = 0.071) APOE protein levels are significantly associated with CSF Aβ(42) levels. We used Mendelian randomization and genetic variants as instrumental variables to confirm that the association of CSF APOE with CSF Aβ(42) levels and clinical dementia rating (CDR) is not because of a reverse causation or confounding effect. In addition the association of CSF APOE with Aβ(42) levels was independent of the APOE ε4 genotype, suggesting that APOE levels in CSF may be a useful endophenotype for AD. We performed a genome-wide association study to identify genetic variants associated with CSF APOE levels: the APOE ε4 genotype was the strongest single-genetic factor associated with CSF APOE protein levels (P = 6.9 × 10(-13)). In aggregate, the Illumina chip single nucleotide polymorphisms explain 72% of the variability in CSF APOE protein levels, whereas the APOE ε4 genotype alone explains 8% of the variability. No other genetic variant reached the genome-wide significance threshold, but nine additional variants exhibited a P-value <10(-6). Pathway mining analysis indicated that these nine additional loci are involved in lipid metabolism (P = 4.49 × 10(-9)).

Figure 1.

Correlation of CSF and plasma levels. CSF APOE levels are significantly lower in individuals with low CSF Aβ₄₂ levels. CSF and plasma levels of APOE were measured on 641 samples from the Knight-ADRC and ADNI using the rules based medicine human discovery MAP panel version 1. (A) CSF and plasma APOE levels show very low correlation (R²= 0.01). Plasma (B) and CSF (D) APOE levels in clinically defined cases and controls. CSF Aβ₄₂ was used to define individuals with likely Aβ brain deposition (cases or presymptomatic cases) and individuals without Aβ brain deposition (controls). Plasma (C) and CSF (E) APOE levels in individuals with low or high CSF Aβ₄₂ levels. The P-value is for the association of plasma/CSF APOE levels without including APOE genotype as a covariate. The P-value in parenthesis was calculated including the APOE genotype as a covariate. (F) CSF APOE levels in cases and controls stratified by the APOE genotype. No significant differences were found between cases and controls in any strata. (G) CSF APOE levels in individuals with high and low CSF Aβ₄₂ levels stratified by the APOE genotype.

Figure 2.

The APOE genotype influences plasma and CSF APOE levels. (A) The APOE genotype shows a strong association with plasma APOE levels and explains 24% of the variability in plasma APOE levels. Gender was included as a covariate in the analysis. (B) The APOE genotype shows a strong association with CSF APOE levels and explains 12% of the variability in CSF APOE levels. Age and gender were included in the analysis as covariates. (C) The APOE genotype is strongly associated with CSF APOE levels in clinically defined cases. (D) The APOE genotype is strongly associated with CSF APOE levels in clinically defined controls. (E) The APOE genotype is strongly associated with CSF APOE levels in individuals with low CSF Aβ₄₂ levels. (F) The APOE genotype is strongly associated with CSF APOE levels in individuals with high CSF Aβ₄₂ levels.

Figure 3.

Mendelian randomization: graphical illustration of the structural model.

Figure 4.

The Manhattan plot and the Q–Q plot for the GWAS for CSF APOE levels. (A) Within each chromosome, shown on the x-axis, the results are plotted left to right from the p-terminal end. Horizontal dashed lines indicate P-value thresholds of 1 × 10^–5 and 5 × 10^–8 (genome-wide significance). (B) Quantile–quantile (Q–Q) plot. No evidence of systematic inflation of P-values was found (λ = 1.007). The plots compare additive model statistics to those expected under the null distribution using fixed-effects for all analyzed imputed SNPs passing quality control criteria in the studies.