Deciphering the Regulation and Expression of APOE in Alzheimer's Disease

This goal of this project is to unravel the complete landscape of APOE transcripts to better understand the regulation APOE function and its involvement in Alzheimer’s disease. In aim 1 I will use targeted long-read RNA sequencing to identify APOE transcripts in brain regions analysed in Braak and Braak staging and Aß progression from patients with Alzheimer’s disease and controls. In aim 2 I will quantify the transcript expression and perform spatial transcriptomic analyses to map where transcripts of interest are expressed. In aim 3 I will leverage publicly available and previously generated datasets to assess clinical correlations with specific APOE transcript usage and whether genetic variability regulates the inclusion of certain transcripts.

The APOE gene confers the most significant genetic risk for Alzheimer’s disease (AD) and other forms of dementia. Most of the risk associated with APOE is due to a variant known as e4. However, the e4 variant does not tell the full story as additional important risk factors within or near APOE are yet to be unravelled. We hypothesize that changes to the APOE RNA molecule – the template produced by DNA that also translates into proteins, the building blocks in the body – may contribute to the risk of AD. Thus, the primary aim of this study is to understand how APOE RNA is regulated and how this contributes to AD.
One particular gene may produce a number of different versions of the same RNA template, known as transcripts. We have previously shown that one such APOE RNA transcript induces risk of AD and is more prevalent in severe cases of the disease. The proposed project will use a new technology called long-read RNA-sequencing to explore the full landscape of APOE RNA transcripts in AD. We will also explore whether the usage of specific APOE RNA transcripts exist mainly within neuronal cells or microglia, the immune cells of the brain. Lastly, we will explore how such transcript usage may correlate with disease in large publicly available datasets.
This proposal will reveal how APOE transcripts are regulated and may therefore be suitable therapeutic targets to ameliorate the effect of APOE and the e4 variant.

This project involves a recently developed, yet to be published, long-read RNA sequencing approach which can target any candidate gene and simultaneously multiplex samples. The result is full-length transcript sequences from which a complete understanding of splicing and APOE gene structure can be achieved. Additionally, paired with spatial transcriptomics, in brain samples from patients with Alzheimer’s disease, this will give us an understanding of APOE in the Alzheimer’s brain previously not achieved.

A complete annotation of APOE gene structure and transcript diversity will let us better understand the mechanism of pathogenesis and to more comprehensively ascertain the Alzheimer’s disease risk associated with the APOE locus. This will also offer the potential to target specific disease relevant transcripts by means of antisense oligonucleotide technologies. Additionally, understanding how the quantitative regulation of certain APOE transcript occurs and where they are expressed will undoubtedly lead to the development of novel models to study the disease.