Genomic characterisation of Alzheimer's disease risk genes using long-read sequencing

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Alzheimer's disease (AD) is a chronic neurodegenerative disorder that is characterised by progressive neuropathology and cognitive decline. AD starts to appear in the population in people in their 60s, and increases in incidence as people age. Around 500,000 people in the UK have AD, and the condition will make an increasing public health burden as the population ages. There are currently no disease modifying treatments for AD, although some drugs can provide a period of symptomatic relief. Several different therapies may be needed to successfully treat AD, as is the case for diabetes and other common diseases. The classical signatures of AD in the brain are the deposition of amyloid protein into insoluble plaques, and the formation of tau protein tangles in neurons, leading to loss of brain tissue. There is also thought to be extensive inflammation in the brain. Although the pathological changes in the brain associated with AD have been well described, the specific mechanisms involved in the onset and progression of the disease are still unknown. Understanding these processes will be important for the development of novel drugs to treat AD. Therapies for Alzheimer's which try and remove or slow down amyloid protein deposits are currently being evaluated in patients, although it is not yet know if these will work. In order to develop additional therapies, we must focus on the unanswered questions relating to the development and progression of Alzheimer's, such as an understanding of why some people fail to clear amyloid and tau protein from the brain, thus allowing their build-up, how these proteins become toxic to neurons, and the role that inflammation in the brain plays in the disease. In this 4 year PhD studentship these problems will be approached by analysing the expression of specific genes in the brain, already implicated in AD, using a novel genomic sequencing technology that is able to sequence the entire expressed form of the gene, not just small fragments as is currently the case with standard RNA sequencing. This is important as different forms of genes, known as isoforms, with different protein sequence and functions, are known to exist. For example one version of the tau protein is better at stabilising microtubules but also more prone to aggregate in the brain in AD. Alternative splicing and RNA isoforms may dramatically increase the protein-coding potential of the human genome; there is evidence for alternative splicing at >95% of human genes. By using a long-read sequencing method known as small molecule real time sequencing (SMRT), developed by the company Pacific Biosciences (PacBio), the student will examine these long mRNA isoforms in the brains of people who had AD when they died, and better understand their role in disease. Capitalising on our MRC Clinical Research Infrastructure Initiative award, our lab has recently optimised this 'iso-seq' method to enable the generation of full-length cDNA sequences from human brain tissue samples. The student will perform these experiments for genes robustly implicated in AD using 1) a large collection of human post-mortem brain samples donated by volunteers to the MRC London Brainbank for Neurodegenerative Diseases and 2) tissue from well-characterised rodent models of amyloid and tau pathology provided by our industrial partners at Eli Lilly. Iso-seq analysis will be performed on entorhinal cortex tissue (an area of the brain affected early in AD) and cerebellum (which is largely protected from AD pathology) in a large collection of individuals representing the full range of AD pathology. Subsequent changes in transcript isoforms at the same genes will be examined in well-characterised rodent models of amyloid and tau pathology to identify variation associated with the onset and progression of AD neuropathology. This improved understanding of the molecular mechanisms underlying AD may lead to the identification of potential new targets for treatment.