Transcriptomic_analysis_of_iPS_derived_neurons_and_macrophages_containing_Alzheimer_s_and_Parkinson_s_disease_mutations
Alzheimer's disease (AD) and Parkinson's disease (PD) are severe neurodegenerative conditions that are common in the elderly (AD >10%, PD 1-2%), and for which there are currently no effective therapies. Although both diseases have distinct neuropathological features, the causal chain of mechanisms responsible for onset or progression of either disease remains largely unknown. Hence, there has been substantial interest in genome wide approaches to discover novel potential drug targets for AD and PD{Lambert 2013, Nalls 2014, Zhang 2013}. Although recent studies have not been without success, there remain three major limitations that this proposal seeks to address:  1. Genome wide association studies (GWAS) have identified multiple loci that contain causal genetic variants (along with variants associated due to linkage disequilibrium). Despite large sample sizes, currently only a small proportion of the total genetic variance in disease risk can be explained, implying that many true associations remain undetected (at least at genome wide significance levels). The majority of associated variants are non-coding and are presumed to have gene regulatory effects. However, most have not been well annotated, gene regulatory effects are known to extend up to hundreds of kb, and the causal genes (and hence potential drug targets) remain unidentified.  2. Genome wide expression analyses (GWEA) identify differences in gene expression correlated with disease state. Typically hundreds or thousands of differentially expressed genes are identified. Despite advances in modelling approaches such as causal network analysis, separating correlation from causation remains challenging, especially given that some relevant tissues (brain) can only be studied post mortem.  3. Bioinformatic and statistical analyses rely on limited datasets with partial information, and make assumptions that are difficult to test. Experimental validation in disease relevant human cells, by experimental manipulation of the putatively causal variants or genes, is key evidence needed before resources would be committed to develop potentially therapeutic molecules (e.g. small molecule high throughput screen, or monoclonal antibody development). In a nutshell, GWAS have provided too few high confidence disease genes, GWEA have provided too many genes, and experimental validation is generally lacking.   We will address limitations 1 and 2 by integrating results from GWAS, GWEA, along with genetic-transcriptomic correlations (“eQTL” datasets) and other functional annotation that are becoming available, using recently developed bioinformatic and statistical methods. We will address limitation 3 by functional genetic and genomic experiments in an IPS derived system. Specifically this will involve genome editing using CRISPR in two cell lineages, IPS derived neurons and macrophages, which are two cell types of relevance for neurodegeneration (primarily via cortical neurons and microglia, the resident phagocytic cells of the central nervous system).