Using genetic variability in whole transcriptome expression in cells and tissues to understand the pathogenesis of Parkinson's and Alzheimer's disease

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Parkinson's and Alzheimer's disease (PD & AD) are common diseases that affect the brain, causing certain cells to die. When these cells are lost people experience, amongst other problems, difficulty remembering recent events in the case of AD and difficulties moving in the case of PD. At the moment these diseases affect over 1 million people in the United Kingdom with a devastating impact on patients and their families. Since both these diseases become more common with age, the number of sufferers is likely to increase as the number of elderly people rises in the UK. Unfortunately, at the moment we know relatively little about why certain people suffer from these diseases and until we do it is hard for researchers and doctors to develop effective treatments. In the past 3 years scientists have been able to show that some individuals have common changes in their DNA (the instruction manual for all the building blocks needed to make the human body) that put them at higher risk of developing these conditions. Although this has been an amazing step forward, it has not been easy for scientists to understand how these changes in the DNA, termed genetic risk factors, act to help cause disease. Many people believe that one way in which these genetic risk factors might cause disease is by changing how much or the way in which particular genes (the basic building blocks) are expressed in brain cells. In order to check this, researchers need to make measurements about the genetic variation an individual carries and link this information to the genes they express in their cells.Although this type of investigation is particularly challenging for diseases that affect the brain, it is possible and meeting those challenges is the aim of this project. One of the difficulties is accurately measuring the amount of the gene expressed in the right cells in the brain. The brain is extremely complex and even within a single region there are many different types of cells. We will address this problem by making use of a technique called laser capture microdissection to obtain pure collections of cells from brain regions relevant to PD and AD. In this technique, using very thin slices of the human brain tissue, we shoot out just the cells we are interested in collecting with a high power laser and then extract the RNA (the gene copies) from the pellets we shoot out. Another advance is the advent of new technology for measuring all the genes expressed in a single cell type or tissue sample. This technology is called "RNA-seq" or "whole transcriptome sequencing" and it allows us to measure all kinds of gene product from any gene. It also allows us to measure the relative quantities of alternative versions of the same gene, and to measure these quantities in such a way that the influence of genetic risk factors can be more sensitively detected by directly comparing the relative product quantities in individuals who happen to have both a "good" and a "bad" copy of a given genetic variant. We believe that we are in an ideal position to complete this project and so add important insights to the understanding of PD and AD. We already have many of the RNA samples needed to perform this study and while some new RNA samples will be created during the project, through our close collaboration with the MRC Sudden Death Brain and Tissue Bank in Edinburgh we have the brain samples needed to do this (all of which have been donated for research). We have also already carried out extensive analysis of DNA from these samples, which means that the new information we generate during this grant can be quickly and cost-effectively added to existing sources of data in order to progress this research. As a final benefit, all the data we will generate on the human brain will be made publically available so that other scientists interested in understanding how the human brain works in health and disease can use this information.