Genetic risk factors for variant Creutzfeldt-Jakob disease: a genome-wide association study

Abstract

Background: Human and animal prion diseases are under genetic control, but apart from PRNP (the gene that encodes the prion protein), we understand little about human susceptibility to bovine spongiform encephalopathy (BSE) prions, the causal agent of variant Creutzfeldt-Jakob disease (vCJD).

Methods: We did a genome-wide association study of the risk of vCJD and tested for replication of our findings in samples from many categories of human prion disease (929 samples) and control samples from the UK and Papua New Guinea (4254 samples), including controls in the UK who were genotyped by the Wellcome Trust Case Control Consortium. We also did follow-up analyses of the genetic control of the clinical phenotype of prion disease and analysed candidate gene expression in a mouse cellular model of prion infection.

Findings: The PRNP locus was strongly associated with risk across several markers and all categories of prion disease (best single SNP [single nucleotide polymorphism] association in vCJD p=2.5 x 10(-17); best haplotypic association in vCJD p=1 x 10(-24)). Although the main contribution to disease risk was conferred by PRNP polymorphic codon 129, another nearby SNP conferred increased risk of vCJD. In addition to PRNP, one technically validated SNP association upstream of RARB (the gene that encodes retinoic acid receptor beta) had nominal genome-wide significance (p=1.9 x 10(-7)). A similar association was found in a small sample of patients with iatrogenic CJD (p=0.030) but not in patients with sporadic CJD (sCJD) or kuru. In cultured cells, retinoic acid regulates the expression of the prion protein. We found an association with acquired prion disease, including vCJD (p=5.6 x 10(-5)), kuru incubation time (p=0.017), and resistance to kuru (p=2.5 x 10(-4)), in a region upstream of STMN2 (the gene that encodes SCG10). The risk genotype was not associated with sCJD but conferred an earlier age of onset. Furthermore, expression of Stmn2 was reduced 30-fold post-infection in a mouse cellular model of prion disease.

Interpretation: The polymorphic codon 129 of PRNP was the main genetic risk factor for vCJD; however, additional candidate loci have been identified, which justifies functional analyses of these biological pathways in prion disease.

Figure 1

Flowchart of the genotyping in the tiered study For each tier, the patient and control sample collections used are subsets of those genotypes in the minor groove-binding (MGB) probe study. In the first two tiers, the 117 samples from patients with vCJD are a subset of the 119 used in tiers three and four. In the second tier, the 84 samples from the UK National Blood Service are a subset of the 730 used in the third tier. In the final tier, the 485 samples from patients with sCJD, the 143 samples from patients with kuru, the 122 samples from elderly women, and the 282 samples from healthy young Fore are all subsets of the samples used in the third tier.

Figure 2

QQ (quartile–quartile) plots of different stages of quality control (A) Unfiltered allelic χ² test of vCJD samples versus all UK samples (internal and Welcome Trust Case Control Consortium [WTCCC]) data. (B) Standard filtering allelic χ² test of vCJD versus all UK samples (internal and WTCCC data). (C) Standard filtering with allelic χ² test of vCJD versus only internal UK samples. (D) High-stringency filtering. With standard filtering, the inflation factor used for genomic control of confounding factors was estimated as 1·06 (1·01–1·09). Red dots=observed data. Blue lines=expected data. Broken blue lines=95% CI for expected data.

Figure 3

Physical location and p of allelic test and best of four genetic models (A) SNPs between THRB and RARB, including rs6794719. (B) SNPs upstream of STMN2 including rs1460163. (C) SNPs at the PRNP locus, including rs1799990, rs6107516, and rs6116492, showing trend test (filled circles) and a test comparing vCJD with UK controls with codon 129 methionine homozygous genotypes (empty circles [imputed for WTCCC controls]).

Figure 4

Age of clinical onset of vCJD (red) and sCJD (blue) patients against rs1460163 genotype Clinical onset was defined as the age of the first symptom that progressed into a neurological or neuropsychiatric condition due to prion disease. The central bars indicate mean age of onset; boxes indicate 95% CI of the mean.

Figure 5

Boxplot of Stmn2 and Rarb expression Expression of Stmn2 and Rarb in mouse neuronal cells (GT-1) treated with homogenate of healthy brain (NBHMG) or Rocky Mountain Laboratory scrapie brain homogenate (RML). Median is shown as a thick red horizontal line, IQR by boxes, and largest and smallest observations by whiskers.