Programme 1

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. We lead the global effort to identify these genes with over 5500 samples from patients with CJD, contributed from Europe and the US. Recently we identified STX6 and GAL3ST1 as risk factors for CJD. Our main aim now is to understand how these risk factors work.

In this proposal we seek to investigate the importance of a new mechanism in prion diseases, underpinned by genetic evidence discovered at UCL: sulfatide metabolism. Sphingolipids are a major class of membrane lipids. Sulfatide, a dominant component of the myelin sheath in the nervous system is synthesised by the cerebroside sulfotransferase (CST) enzyme. At the UCL Institute of Prion Diseases (IoPD) we discovered that a common amino acid variant (V29M) of the sole enzyme involved in the synthesis of sulfatide (GAL3ST1 gene) confers a strongly increased risk of the most common prion disease sporadic Creutzfeldt-Jakob disease (sCJD). Genetic association implies a causal association between sulfatide metabolism and neurodegeneration.

In this PhD proposal we will establish an assay for sulfatides, to measure sulfatide and other sphingolipid metabolite concentrations in biofluids and tissues of patients with prion and other neurodegenerative disorders, determine a direction of effect of the V29M polymorphism of CST on enzyme activity in model systems, and to test hypotheses about the effects of modification of this pathway on propagation of prions and other proteopathic seeds in cellular and animal models (knockout of CST already exists). We have evidence that the protective polymorphism at this enzyme acts to reduce expression, making CST a potentially tractable therapeutic target. In a 3 month rotation project we might pilot assays to test the effects of sulfatide on prion replication in cellular or cell free amplification assays, or a biophysical interaction between sulfatides (or premetabolites) and prion protein. This should be discussed with Prof Simon Mead to get an up to date status of the project.

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 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. Using next generation sequencing, we have identified changes in DNA methylation profiles and in microRNAs expression in prion diseases. Our aim is to decipher if these signatures can provide new biomarkers for the diseases. We also aim to understand how these epigenetic changes contribute to prion disease pathophysiology.

3 month proposal The project will involve profiling DNA methylation and/or gene expression in tissues derived from patients or animals with prion diseases, and in cell lines. Understanding how epigenetics mechanisms play a role in prion diseases will be key to refine diagnosis (biomarkers) and provide avenue for therapeutic interventions. This should be discussed with Dr Emmanuelle Vire to get an up to date status of the project.

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.