Transcription Factor-Wide Association Studies (TF-WAS) to identify Functional SNPs in Alzheimer's Disease

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder with profound global impact. While Genome-wide Association Studies (GWAS) have revealed genomic variants linked to AD, their translational impact has been limited due to challenges in interpreting the identified genetic associations. To address this challenge, we have devised a novel approach termed Transcription Factor-Wide Association Studies (TF-WAS). By integrating the GWAS, eQTL and transcriptome analyses, we selected 30 AD SNPs in non-coding regions that are likely to be functional. Using human transcription factor (TF) microarrays, we have identified 90 allele-specific TF interactions with 53 unique TFs. We then focused on several interactions involving SMAD4, and further validated them using EMSA, luciferase, and ChIP on engineered genetic backgrounds. This approach holds promise for unraveling the intricacies of not just AD, but any complex disease with available GWAS data, providing insight into underlying molecular mechanisms and clues towards potential therapeutic targets. SNPs are probed to the TF arrays in pairs as a competition assay, with one allele labeled with Cy3 and the other labeled with Cy5. For each pair, the arrays are performed in duplicate, with the allele colors swapped. For example, on one array the Cy3 risk and Cy5 non-risk are probed, while the Cy5 risk and Cy3 non-risk are probed to another array (as indicated in each raw data file name).