Integrative genomics and single-cell CRISPRi screening dissect Alzheimer GWAS non-coding variants regulating TSPAN14

Area of Science:

• Genomics
• Neuroscience
• Molecular Biology

Background:

• Genome-wide association studies (GWASs) identify numerous genetic loci associated with complex diseases like Alzheimer disease (AD).
• Functional characterization of these identified loci to pinpoint causal variants and genes remains a significant challenge in AD research.

Purpose of the Study:

• To develop and apply a systematic variant-to-gene (V2G) mapping framework for Alzheimer disease (AD).
• To identify cell-type-specific regulatory elements and effector genes underlying AD genetic risk.

Main Methods:

• Integration of ten brain-relevant genomics datasets (e.g., Capture C, ATAC-seq, RNA-seq) to fine-map AD GWAS variants.
• Single-cell CRISPR interference (CRISPRi) Perturb-seq screen in human microglial cells (HMC3) to functionally validate candidate regulatory regions.
• Analysis of variant-gene associations and downstream effects on gene expression and cellular pathways.

Main Results:

• Identified 93 candidate causal variants and 94 effector genes for 35 AD loci.
• Validated 21 variant-gene pairs using CRISPRi screening.
• Discovered a microglial-specific enhancer at the TSPAN14 locus, where the AD-risk haplotype alters TSPAN14 expression, disrupts cell-adhesion pathways, and reduces IL-6 and IL-8 secretion.

Conclusions:

• The study establishes a robust V2G mapping framework for cell-type-specific functional genomics in AD.
• Identified TSPAN14 as a key gene regulated by microglial enhancers, implicating its role in AD pathogenesis.
• Provides critical insights into the functional consequences of AD-associated genetic variants for future therapeutic strategies.