Summary: Researchers have identified multiple new genetic risk factors for Alzheimer’s disease and for progressive supranuclear palsy (PSP), using high-throughput functional screening to pinpoint variants that alter gene regulation.
Source: UCLA
A UCLA-led research team has used large-scale functional assays to identify dozens of genetic variants and several new risk genes linked to Alzheimer’s disease (AD) and the rarer tauopathy progressive supranuclear palsy (PSP). Their approach narrows the gap between genome-wide association study (GWAS) signals and the causal regulatory changes that drive neurodegenerative disease risk.
Published in the journal Science, the study applies massively parallel reporter assays (MPRAs) together with CRISPR-based validation to test thousands of candidate noncoding variants at loci previously associated with AD and PSP. The results support a model in which many common variants, each with small individual effects, together disrupt specific transcriptional programs in particular brain cell types and thereby increase disease risk.
GWAS have successfully mapped genomic regions linked to AD and other disorders, but each associated locus typically contains many correlated markers due to linkage disequilibrium, making it difficult to identify the actual functional variants and the genes they influence. This study demonstrates a practical, scalable roadmap for moving from association signals to likely causal regulatory variants and their target genes.
Using MPRAs, the investigators simultaneously tested 5,706 noncoding single-nucleotide variants drawn from 25 AD-associated loci and nine PSP-associated loci. The screen identified 320 functional regulatory variants (frVars) that altered transcriptional activity in their assay. To validate these MPRA findings, the team performed pooled CRISPR screens and targeted CRISPR perturbations in multiple cell types, confirming regulatory effects for a subset of high-confidence variants.
Lead authors combined high-throughput reporter assays with CRISPR droplet sequencing (CROP-seq) and CRISPR excision in induced pluripotent stem cell–derived neurons, microglia, and astrocytes. From 42 prioritized variants, validation experiments confirmed 19 functional variants and implicated 20 candidate risk genes across 11 loci. Among the genes supported by their data are C4A, PVRL2 and APOC1 for Alzheimer’s disease, and PLEKHM1 and KANSL1 for PSP, along with further validation for over a dozen previously suggested genes.
The study also links disease-associated variants to cell type–specific regulatory elements: AD-associated frVars were enriched in microglial enhancers, while PSP frVars were enriched in neuronal and, to a lesser extent, oligodendrocyte enhancers. Many frVars overlap known functional annotations and are predicted to disrupt transcription factor binding sites, indicating pathways by which noncoding variants can alter gene expression in disease-relevant cell types.
The authors highlight an additive mechanism in PSP where multiple loci converge to disrupt a core set of transcription factors that operate together in specific cell types. In PSP, their data point to a neuronal SP1-driven regulatory network, illustrating how distributed regulatory variation can converge on shared molecular pathways. This suggests that therapeutic strategies targeting regulatory networks, rather than single genes, may be promising.
Dr. Dan Geschwind, the study’s corresponding author, emphasized that high-throughput functional testing does not replace detailed mechanistic experiments but provides an efficient intermediate step to prioritize variants and genes for follow-up in cellular and animal models. Yonatan Cooper, the lead author, noted that integrating multiple experimental methods strengthens confidence in variant interpretation and will be essential for future research and clinical annotation of disease-associated variation.
About this genetics research news
Author: Press Office
Source: UCLA
Contact: Press Office – UCLA
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Original Research: Closed access.
“Functional regulatory variants implicate distinct transcriptional networks in dementia” by Yonatan A. Cooper et al. Science
Abstract
Functional regulatory variants implicate distinct transcriptional networks in dementia
INTRODUCTION
Genome-wide association studies have revealed many loci linked to complex traits, including neurodegenerative diseases, but most susceptibility signals lie in noncoding regions and span multiple correlated variants. Massively parallel reporter assays (MPRAs) enable high-throughput functional testing of noncoding variation but have been underused in neurodegeneration research. Here, MPRAs combined with CRISPR validation identify likely causal regulatory variants underlying Alzheimer’s disease and progressive supranuclear palsy, two conditions connected by intracellular tau protein aggregation.
RATIONALE
AD and PSP cause substantial morbidity and lack disease-modifying therapies. Pinpointing causal genetic variants and their downstream target genes is a crucial first step toward mechanistic insight and therapeutic development. High-throughput functional assays offer a route to prioritize variants for detailed mechanistic follow-up.
RESULTS
The authors assayed 5,706 noncoding single-nucleotide variants from 25 AD and nine PSP loci in HEK293T cells by MPRA, identifying 320 functional regulatory variants across 27 loci. AD-associated frVars were enriched in microglial enhancers while PSP frVars were enriched in neuronal and oligodendrocyte enhancers. Most frVars overlapped existing functional annotations and many were predicted to disrupt transcription factor binding. Validation with CRISPR approaches confirmed 19 functional variants and implicated 20 risk genes, including C4A, PVRL2 and APOC1 for AD and PLEKHM1 and KANSL1 for PSP. The data indicate that frVars converge on transcription factor networks with cell type–specific activity, implicating a neuronal SP1-driven network in PSP pathogenesis.
CONCLUSION
This study provides a systematic functional map of common noncoding variants contributing to AD and PSP risk and demonstrates the value of integrating MPRAs with CRISPR validation. The findings support a model in which polygenic, cell type–specific regulatory effects on gene networks underlie disease susceptibility and point to new candidate genes and network-level targets for therapeutic investigation.