CD33: increased inclusion of exon 2 implicates the Ig V-set domain in Alzheimer's disease susceptibility

Abstract

We previously demonstrated that the Alzheimer's disease (AD) associated risk allele, rs3865444(C), results in a higher surface density of CD33 on monocytes. Here, we find alternative splicing of exon 2 to be the primary mechanism of the genetically driven differential expression of CD33 protein. We report that the risk allele, rs3865444(C), is associated with greater cell surface expression of CD33 in both subjects of European and African-American ancestry and that there is a single haplotype influencing CD33 surface expression. A meta-analysis of the two populations narrowed the number of significant SNPs in high linkage disequilibrium (LD) (r(2) > 0.8) with rs3865444 to just five putative causal variants associated with increased protein expression. Using gene expression data from flow-sorted CD14(+)CD16(-) monocytes from 398 healthy subjects of three populations, we show that the rs3865444(C) risk allele is strongly associated with greater expression of CD33 exon 2 (pMETA = 2.36 × 10(-60)). Western blotting confirms increased protein expression of the full-length CD33 isoform containing exon 2 relative to the rs3865444(C) allele (P < 0.0001). Of the variants in strong LD with rs3865444, rs12459419, which is located in a putative SRSF2 splice site of exon 2, is the most likely candidate to mediate the altered alternative splicing of CD33's Immunoglobulin V-set domain 2 and ultimately influence AD susceptibility.

Figure 1.

A single haplotype in the CD33 locus is associated with greater CD33 expression on the cell surface of monocytes. (A) rs3865444^C is significantly associated with greater CD33 surface expression in a meta-analysis of monocyte-derived data from ROSMAP/CHAP EA and AA subjects (n = 390, P = 2.1 × 10⁻²¹). (B) Upper panel: Within the CD33 locus, meta-analysis of the ROSMAP/CHAP EA and AA CD33 monocyte surface expression data distills the significant SNPs to a group of five variants in high LD, one of which is likely to be the causal variant. rs3865444 is one of those five variants. Lower panel: Using conditional analysis to adjust for the effect of rs3865444, we find no significant residual associations with CD33 surface expression in the CD33 locus. The y-axis scale is inverted relative to the upper panel. This image was produced using LocusZoom (27).

Figure 2.

The CD33 locus is associated with greater mRNA expression of CD33 exon 2, which encodes an Ig V-set domain. (A) Using a SI to deconvolve gene-level and exon-specific expression, rs3865444^C is significantly associated with a greater mRNA expression of CD33 exon 2 (n = 398, P = 2.36 × 10⁻⁶⁰) quantified using a microarray platform and RNA from ex vivo, cytometrically sorted monocytes from ImmVar EA, AA and EAA subjects. The CD33 locus is not significantly associated with expression of other CD33 exons in monocytes. (B) CD33 is a type 1 transmembrane glycoprotein expressed on the surface of myeloid cells. Full-length CD33^M consists of a signal peptide, an extracellular Ig V-set sialic-acid binding domain, an extracellular Ig C2-set domain, a transmembrane region, and a cytosolic domain containing immunoreceptor tyrosine-based inhibitory motifs. The alternatively spliced CD33^m isoform lacks the Ig V-set domain encoded by exon 2 (13). The figure is not drawn to scale.

Figure 3.

rs3865444^C is the best candidate causal variant for association with the mRNA SI of CD33 exon 2 in monocytes. (A) In the ImmVar EA and AA populations, rs3865444 is the most significant SNP for association with the mRNA SI of CD33 exon 2 (p_EA = 1.6 × 10⁻²³; p_AA = 2.9 × 10⁻⁶). In the ImmVar EAA population, multiple SNPs in high LD with rs3865444 are associated with the SI of exon 2. (B) In a meta-analysis (upper panel) of the EA, AA and EAA populations, rs3865444 is the most significant SNP for association with the SI of CD33 exon 2 (P = 2.36 × 10⁻⁶⁰) (top panel), and, after conditioning on rs3865444 and rs12459419, there are no significant genetic associations with the SI of exon 2 (lower panel). These images were produced using LocusZoom (27).

Figure 4.

Western blot analysis confirms the association between rs3865444^C and increased abundance of the full-length CD33^M isoform in monocytes. (A) In purified, ex vivo monocytes isolated from healthy subjects in the PhenoGenetic cohort, western blot analysis indicates that full-length CD33^M isoform is expressed at low levels in individuals with the protective rs3865444^AA genotype compared with individuals with the risk rs3865444^CC genotype. (B) As quantified by densitometric analysis, this association is statistically significant (P < 0.0001). (C) The truncated CD33^m isoform has no significant association with rs3865444 genotype (P = 0.75).