Sporadic--but not variant--Creutzfeldt-Jakob disease is associated with polymorphisms upstream of PRNP exon 1

Abstract

Human prion diseases have inherited, sporadic, and acquired etiologies. The appearance of the novel acquired prion disease, variant Creutzfeldt-Jakob disease (vCJD), and the demonstration that it is caused by the same prion strain as that causing bovine spongiform encephalopathy, has led to fears of a major human epidemic. The etiology of classical (sporadic) CJD, which has a worldwide incidence, remains obscure. A common human prion-protein-gene (PRNP) polymorphism (encoding either methionine or valine at codon 129) is a strong susceptibility factor for sporadic and acquired prion disease. However, a quantitative-trait-locus study of prion incubation periods in mice has demonstrated an important factor that is close to Prnp but is independent of its coding sequence or that of the nearby prion-like doppel gene (Prnd). We have analyzed the PRNP locus for such tightly linked susceptibility factors. Fifty-six polymorphic sites have been identified within 25 kb of the PRNP open reading frame, including sites within the PRNP promoter and the PRNP 3' untranslated region. These have been characterized in 61 Centre d'Etude du Polymorphisme Humain (CEPH) families, demonstrating extensive linkage disequilibrium around PRNP and the existence of 11 major European PRNP haplotypes. Haplotype frequencies estimated in healthy U.K. control individuals were very similar to those deduced in the CEPH families. A common haplotype was overrepresented in patients with sporadic CJD (sCJD). Through use of a log-linear modeling approach to simultaneously model Hardy-Weinberg and linkage disequilibria, a significant independent association was found between sCJD and a polymorphism upstream of PRNP exon 1 (P=.005), in addition to the strong susceptibility conferred by codon 129 (P=2x10(-8)). However, although our sample size was necessarily small, no association was found between these polymorphisms and vCJD or iatrogenic CJD, in keeping with their having distinct disease mechanisms. In addition, there was no evidence of a PRNP founder effect in the first reported geographical cluster of vCJD.

Figure 1

Line drawing of the PRNP-PRND locus, including the location of SNPs relative to PRNP exons 1 and 2

Figure 2

Haplotype table of the CEPH parents and CEPH grandparents (nontransmitted haplotypes only). Two bases at a single site separated by a slash (/) indicates that there were rare haplotypes in which the second of the two bases shown was found. An asterisk (*) indicates identity with the chimpanzee base. Suspected substitutions are shown in orange. B = most common haplotype with methionine at codon 129, shown in yellow. D = methionine haplotype with a guanine substitution at np 12533, near the PRNP promoter, and thymine at np 28090, near the PRNP 3′ UTR; this haplotype may have been generated by the substitution of guanine at np 12533 on an F (483c) haplotype. E = methionine haplotype similar to B, without substitutions at np 1368 and np 10870 and without the promoter substitution at np 12533 but including the substitution at np 483 that is not found on valine haplotypes; alternatively, E may be a recombinant between B and A, with a break point between np 10870 and np 13436, but here one must account for the presence of cytosine at np 483, only found on methionine haplotypes. U and F = uncommon methionine haplotypes similar to E but with 5′ substitutions; E and F were not distinguished in CEPH grandparents, and therefore the frequencies are combined. E was found in 15 CEPH parents, and F was found in 5 CEPH parents. K and R = two methionine haplotypes whose origin could be best explained by a single 5′ recombination event between A and B; these haplotypes were probably generated by different but nearby recombination break points. In the case of R, the recombination may have occurred on a D or F haplotype with 28090t, with the breakpoint between np 16987 and np 18284; in the case of K, the 5′ recombinant chromosome was probably a rare subset of A, with a substitution of 6266c and a breakpoint between np 13426 and np 13934. A = most common haplotype with valine at codon 129, shown in green. G = valine haplotype similar to A in the 5′ direction from M129V but similar to B in the 3′ direction from M129V. L = valine haplotype, which, like Q below, has a pattern of SNPs similar to the chimpanzee; also found are substitutions unique to this haplotype, including the A117A PRNP ORF silent polymorphism, a polymorphism 31 bp 5′ to the PRNP translation start site (−31), and a common PRNP 3′ UTR polymorphism 881 bp 3′ to the PRNP translation start site (+881), shown in purple. Q = valine haplotype, similar to L and, again, with a number of substitutions found only on this haplotype, shown in blue (nps 5039, 10434, 16713, 18284, 18365, and 31290). Only 8/244 haplotypes, all on valine chromosomes, each found in one parental chromosome only, could not be placed in one of these eight haplotypes. These are not shown.

Figure 3

Table of pairwise D′ (calculated using DNAsp), showing pairwise LD between SNPs