The search for effective treatments for Alzheimer's disease (AD), the leading cause of late-onset dementia, has proven challenging. While recent successes in identifying more than a dozen new genes contributing to late-onset or sporadic AD (sAD) have generated considerable excitement in AD research, it is clear from large population studies including GWAS and whole-exome sequencing projects that many single nucleotide polymorphisms (SNPs) contributing to elevated sAD risk reside in non-coding intragenic or regulatory regions. The biological significance of these noncoding SNPs with respect to sAD pathogenesis is not clear. In the current application, we propose a scalable discovery platform for discerning which AD risk SNPs are associated with functional enhancers in specific neural cell types derived from human induced stem cells (hIPSCs). These hIPSCs, created from fibroblasts of sAD patients with a wealth of phenotypes that clearly lead to AD heterogeneity, will enable us to obtain a high-resolution map of AD risk SNPs associated with enhancers and their putative target genes in varied cell types. We will utilize CRISPR/Cas9/dCas9 technologies to directly determine the cell biological consequences of these AD risk genomic variants via 2D and 3D cytosystems. Our comprehensive strategy will identify novel genetic elements and unexpected regulatory pathways contributing to AD pathogenesis and progression that will lead to new therapeutic avenues.
The multifactorial nature of Alzheimer's disease (AD) underscores gene-network regulatory feedback among various neural cell types as an important aspect of AD pathophysiology. The findings of numerous AD-risk single nucleotide polymorphisms (SNPs) within noncoding regulatory regions lends credence to this view, at the same time challenging new methodologies to address the cell biological significance of these AD risk variants. In this proposal, we will create a discovery platform to identify and validate AD risk SNPs associated with enhancers, and determine the biological significance of these SNPs/enhancers and their target genes in specific neural cell types, in the context of standard cell co-cultures, and cerebral organoids.