Both common variations and rare non-synonymous substitutions and small insertion/deletions in CLU are associated with increased Alzheimer risk

Abstract

Background: We have followed-up on the recent genome-wide association (GWA) of the clusterin gene (CLU) with increased risk for Alzheimer disease (AD), by performing an unbiased resequencing of all CLU coding exons and regulatory regions in an extended Flanders-Belgian cohort of Caucasian AD patients and control individuals (n = 1930). Moreover, we have replicated genetic findings by targeted resequencing in independent Caucasian cohorts of French (n = 2182) and Canadian (n = 573) origin and by performing meta-analysis combining our data with previous genetic CLU screenings.

Results: In the Flanders-Belgian cohort, we identified significant clustering in exons 5-8 of rare genetic variations leading to non-synonymous substitutions and a 9-bp insertion/deletion affecting the CLU β-chain (p = 0.02). Replicating this observation by targeted resequencing of CLU exons 5-8 in 2 independent Caucasian cohorts of French and Canadian origin identified identical as well as novel non-synonymous substitutions and small insertion/deletions. A meta-analysis, combining the datasets of the 3 cohorts with published CLU sequencing data, confirmed that rare coding variations in the CLU β-chain were significantly enriched in AD patients (OR(MH) = 1.96 [95% CI = 1.18-3.25]; p = 0.009). Single nucleotide polymorphisms (SNPs) association analysis indicated the common AD risk association (GWA SNP rs11136000, p = 0.013) in the 3 combined datasets could not be explained by the presence of the rare coding variations we identified. Further, high-density SNP mapping in the CLU locus mapped the common association signal to a more 5' CLU region.

Conclusions: We identified a new genetic risk association of AD with rare coding CLU variations that is independent of the 5' common association signal identified in the GWA studies. At this stage the role of these coding variations and their likely effect on the β-chain domain and CLU protein functioning remains unclear and requires further studies.

Figure 1

Schematic location of rare CLU coding variants identified in stage I, II and III resequencing. (A) Schematic presentation of CLU gene structure, CLU transcript 1 [NM_001831.2] and CLU protein [NP_001822.2]. Coding variants observed in AD patients only are indicated in red, variants observed in patients and controls in blue, variants detected in control individuals only in green. All predicted pathogenic variants are indicated in bold. After cleavage of the signal peptide, the secreted CLU form (449 AA) contains two coiled-coiled domains (pink), three amphipathic domains (blue) and a cysteine rich region (yellow) with 5 disulfide bridges (grey). Six N-glycosylation sites are marked in purple. For ease of interpretation, amino acids are given for specific CLU domains and for detected protein variants only. (B) Conservation alignment of amino acids of CLU beta-chain variants is shown in different species; Homo sapiens (ENSP00000315130), Gorilla gorilla (ENSGGOP00000016521), Pan troglodytes (ENSPTRP00000034423), Pongo abelii (ENSPPYP00000020696), Macaca mulata (ENSMMUP0000003216), Nomascus leucogenys (ENSNLEP00000020015), Tarsius syrichta (ENSTSYP00000001230), Mus musculus (ENSMUSP00000022616), Rattus norvegicus (ENSRNOP00000022095), Canis lupus familiaris (ENSCAFP00000012350) and Bos taurus (ENSBTAP00000007324). Similar to panel A, patient specific variants are marked in red, variants observed in patients and controls in blue and variants in control individuals in green. All predicted pathogenic variants are marked in bold.