Programme 1: Targeted genotyping of candidate SNPs identified by exome sequencing as potential risk factors for Creutzfeldt-Jakob disease.

Background Prion disease susceptibility and disease modification is known to be controlled by genetic factors. The main susceptibility factor and modifier of Creutzfeldt-Jakob disease (CJD) is the PRNP codon 129 genotype, but additional, hitherto unidentified genes are also very likely to be involved. We lead the global effort to identify these genes with over 4500 samples from patients with CJD, contributed from Europe and the US. We have taken different approaches to identify common risk factors of perhaps modest effect, using array technologies, and strong rare risk factors using next generation sequencing.

3 month proposal In our laboratory, gene burden testing of exome sequencing data from 347 sporadic and variant CJD cases and 546 controls, followed by Sanger validation of genes most highly associated with disease, has narrowed down five genes of interest (p<0.01).  However, these findings currently fall short of genome-wide statistical significance due to a lack of power to detect association in the exome study.  The objective of the proposed project is therefore to use custom SNP genotyping arrays to genotype all known rare genetic variants for these five genes in a larger sample of sporadic CJD patients to confirm or discard them as candidate risk factors for the development of CJD, or modifiers of disease progression.

PhD proposal It is hoped that, if successful in generating statistically significant associations of one or more candidate gene/s with CJD, this project will pave the way for functional studies, and ultimately yield new insights into the causes and pathogenesis of the disease, with the aim of identifying new therapeutic targets. We would aim to test hypotheses about the mechanism by which a risk SNP is linked to alteration of a gene product, and how this alteration is linked to the mechanisms of prion disease using cell and animal models.

Programme 1: Epigenetics in prion diseases

Background Epigenetics define a variety of mechanisms that allow heritable changes in gene expression in the absence of DNA mutation. Epigenetic regulation of gene expression is a dynamic and reversible process that establishes normal cellular phenotypes, perpetuate heritable traits in dividing cells but also contributes to ageing and diseases. Several lines of evidence point to the importance of epigenetic factors in prion disease, for example, that age is a strong susceptibility factor in acquired and sporadic prion disease, and that cell lines can heritably alter their propensity to propagate prions without genetic changes. Aside from questions about susceptibility and molecular mechanisms, aberrant expression of genes has been reported to provide potential diagnostic or prognostic biomarkers for many human malignancies.

3 month proposal The project will involve profiling gene expression in tissues derived from patients or animals with prion diseases, and in cell lines. These will be determined by next-generation sequencing (NGS) such as RNA sequencing.

PhD proposal The project will aim at identifying epigenetic factors and/or changes in gene expression specific to prion diseases. It will help to understand if, how and when these changes contribute to the diseases. . This project will involve cutting edge technologies and collaborations both within the Unit and with external collaborators.