Elsevier

The Lancet Neurology

Volume 19, Issue 10, October 2020, Pages 840-848
The Lancet Neurology

Articles
Identification of novel risk loci and causal insights for sporadic Creutzfeldt-Jakob disease: a genome-wide association study

https://doi.org/10.1016/S1474-4422(20)30273-8Get rights and content

Summary

Background

Human prion diseases are rare and usually rapidly fatal neurodegenerative disorders, the most common being sporadic Creutzfeldt-Jakob disease (sCJD). Variants in the PRNP gene that encodes prion protein are strong risk factors for sCJD but, although the condition has similar heritability to other neurodegenerative disorders, no other genetic risk loci have been confirmed. We aimed to discover new genetic risk factors for sCJD, and their causal mechanisms.

Methods

We did a genome-wide association study of sCJD in European ancestry populations (patients diagnosed with probable or definite sCJD identified at national CJD referral centres) with a two-stage study design using genotyping arrays and exome sequencing. Conditional, transcriptional, and histological analyses of implicated genes and proteins in brain tissues, and tests of the effects of risk variants on clinical phenotypes, were done using deep longitudinal clinical cohort data. Control data from healthy individuals were obtained from publicly available datasets matched for country.

Findings

Samples from 5208 cases were obtained between 1990 and 2014. We found 41 genome-wide significant single nucleotide polymorphisms (SNPs) and independently replicated findings at three loci associated with sCJD risk; within PRNP (rs1799990; additive model odds ratio [OR] 1·23 [95% CI 1·17–1·30], p=2·68 × 10−15; heterozygous model p=1·01 × 10−135), STX6 (rs3747957; OR 1·16 [1·10–1·22], p=9·74 × 10−9), and GAL3ST1 (rs2267161; OR 1·18 [1·12–1·25], p=8·60 × 10−10). Follow-up analyses showed that associations at PRNP and GAL3ST1 are likely to be caused by common variants that alter the protein sequence, whereas risk variants in STX6 are associated with increased expression of the major transcripts in disease-relevant brain regions.

Interpretation

We present, to our knowledge, the first evidence of statistically robust genetic associations in sporadic human prion disease that implicate intracellular trafficking and sphingolipid metabolism as molecular causal mechanisms. Risk SNPs in STX6 are shared with progressive supranuclear palsy, a neurodegenerative disease associated with misfolding of protein tau, indicating that sCJD might share the same causal mechanisms as prion-like disorders.

Funding

Medical Research Council and the UK National Institute of Health Research in part through the Biomedical Research Centre at University College London Hospitals National Health Service Foundation Trust.

Introduction

Prion diseases are fatal neurodegenerative conditions in humans and animals caused by the propagation of prions: atypical infectious agents comprised solely or predominantly of host prion protein.1 Prions are thought to propagate through a process of binding to normal prion protein, induction of conformational change by templating, and fission of the polymeric assembly. Prion diseases can be acquired from exposure to prions in the diet, or through medical or surgical procedures, which can result in public health crises. The cattle prion disease, bovine spongiform encephalopathy (BSE), which transmitted to mostly young British and other European adults as variant Creutzfeldt-Jakob disease (vCJD),2 led to enhanced clinical surveillance for all prion diseases worldwide. Inherited prion disease, caused only by mutations of the prion protein gene (PRNP), causes approximately 10–15% of the annual incidence of all prion diseases in most countries.3 The most common type of human prion disease is sporadic CJD (sCJD), a rapidly progressive dementia with a lifetime risk of approximately one in 5000, which occurs predominantly in older adults.4, 5 Other than age and polymorphisms at PRNP, no risk factors for sCJD are known, leaving only speculative explanations for sporadic prion formation.

Research in context

Evidence before this study

The rarity of sporadic Creutzfeldt-Jakob disease (sCJD) has been limiting in previous genome-wide association studies (GWAS) for disease risk. We searched PubMed on April 9, 2020, with the terms (“prion” OR “creutzfeldt*”) AND (“genome wide association” OR “GWAS”), without language or date restrictions, and identified four relevant publications, including two directly investigating sCJD risk through genome-wide analyses. However, the sample sizes in these studies were not sufficient to identify statistically significant associations outside of the known risk at the prion protein gene (PRNP). Further studies into genetic risk factors for sCJD have primarily utilised targeted replication of putative risk variants or candidate gene studies to propose association.

Added value of this study

Through international collaboration of sample resources, this study is, to our knowledge, the first GWAS to identify genetic variants associated with sCJD risk outside of PRNP, at genome-wide significance. Two of these variants (within STX6 and GAL3ST1) were statistically robust to replication in an independent cohort, with 5208 patients with sCJD in total included in the two-stage study design. Through statistical fine-mapping and analysis of exome sequencing and gene expression data, we propose genes that are likely to be causal, and mechanisms for both novel associations. We used patient brain samples and cell-based assays to further investigate the biological implications of these associations in relevant systems. Two further loci at PDIA4 and BMERB1 were also associated with sCJD risk in gene-based tests.

Implications of all the available evidence

Identification of two novel non-PRNP loci conferring sCJD risk will provide further avenues for research, with increased evidence to support a role of modified intracellular trafficking and sphingolipid metabolism within sCJD biology, providing the potential to inform new therapeutic approaches. With the shared genetic risk of variants within STX6 and those previously identified for the tauopathy progressive supranuclear palsy, this study also supports the notion of a common so-called prion-like causal mechanism for related neurodegenerative disorders and thus potential for shared treatments.

Polymorphisms of PRNP at codons 127, 129, and 219 alter amino acids and are strong genetic risk factors or modifiers of the disease phenotypes.3 Sibling or familial concurrence of sCJD has been reported, but not to the extent that chance concurrence can be eliminated as an explanation. There are no estimates of the heritability of sCJD based on family studies.6 Animal studies have identified acquired prion disease risk factors in Prnp and close by, and provided evidence for susceptible loci on other chromosomes, yet elucidating the causal genes has proven to be challenging.3 Many other neurodegenerative diseases are thought to share fundamental mechanisms with prion diseases, including template-based protein misfolding and spreading of pathology associated with abnormally aggregated proteins in diseased brain tissue. If shared mechanisms exist, this might implicate shared genetic risk factors for these diseases.

This study follows on from previous genome-wide association studies (GWAS) in human prion diseases, which have not been powerful enough to discover non-PRNP risk factors.7, 8, 9, 10 We aimed to identify specific causal genes at risk loci, to allow molecular causal mechanisms for sCJD to be proposed.

Section snippets

Study design and participants

We did a GWAS using samples from patients diagnosed with probable or definite sCJD according to widely accepted criteria, which were provided by specialist or national surveillance centres in countries with populations of predominantly European ancestries (appendix pp 2, 28–32). Diagnostic criteria for probable sCJD varied over the course of sample collection for the study. Using modern diagnostic methods, including real-time quaking-induced conversion assay with CSF, a probable diagnosis

Results

Between 1990 and 2014, we obtained 5208 sCJD samples, of which 4110 were used in the discovery stage and 1098 were used in the replication stage.

In the discovery stage we compared genome-wide genotype data from 4110 patients with probable or definite sCJD from countries of predominantly European ancestries with 13 569 control samples from a similar range of countries (appendix pp 2–3). Imputation using the Michigan server resulted in 6 314 492 high-quality autosomal SNPs after quality control,

Discussion

We report, to our knowledge, the first GWAS in a human prion disease powered to detect alleles with the modest effect sizes typical of complex diseases. We identified new risk factors for sCJD, including variants which appear to have pleiotropic effects in neurodegenerative diseases. Further to the known effects at PRNP codon 129, we report two independently replicated loci and evidence to support the conclusion that risk variants modify the primary sequence of the encoded protein (GAL3ST1) or

Data sharing

Summary statistics are available through the GWAS catalog at National Human Genome Research Institute-European Bioinformatics Institute via study accession number GCST90001389. Further data are available upon request to the corresponding author.

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