Integrating human brain proteomes with genome-wide association data implicates new proteins in Alzheimer's disease pathogenesis

Abstract

Genome-wide association studies (GWAS) have identified many risk loci for Alzheimer's disease (AD)^1,2, but how these loci confer AD risk is unclear. Here, we aimed to identify loci that confer AD risk through their effects on brain protein abundance to provide new insights into AD pathogenesis. To that end, we integrated AD GWAS results with human brain proteomes to perform a proteome-wide association study (PWAS) of AD, followed by Mendelian randomization and colocalization analysis. We identified 11 genes that are consistent with being causal in AD, acting via their cis-regulated brain protein abundance. Nine replicated in a confirmation PWAS and eight represent new AD risk genes not identified before by AD GWAS. Furthermore, we demonstrated that our results were independent of APOE e4. Together, our findings provide new insights into AD pathogenesis and promising targets for further mechanistic and therapeutic studies.

Extended Data Fig. 1. Quantile-quantile plots for the discovery and replication PWAS of AD

Quantile-quantile plot for A) the discovery PWAS of AD (λ = 1.36; λ₁₀₀₀ = 1.003) and B) confirmatory PWAS of AD (λ = 1.39; λ₁₀₀₀ = 1.003).

Extended Data Fig. 2. Overlap of significant genes between AD and other traits

Overlap between results of the AD PWAS and PWAS for other traits. All the PWAS used the discovery ROS/MAP proteomic dataset (n=376) and GWAS summary results from Caucasian individuals. The following outcomes were tested: clinical AD GWAS (N=63,926), amyotrophic lateral sclerosis (ALS; N=80,610), body mass index (BMI; N=681,275), height (N=693,529), neuroticism (N=390,278), Parkinson’s disease (PD; N=1,474,097), and waist-to-hip ratio adjusting for BMI (WHRadjBMI; N=694,649). Significant genes considered for overlap are those with FDR p<0.05.

Extended Data Fig. 3. Quantile-quantile plot for the TWAS of AD

Quantile-quantile plot for the TWAS of AD (λ = 1.22; λ₁₀₀₀ = 1.002).

Extended Data Fig. 4. Single cell-type expression

Single-cell type expression for AD PWAS-significant genes with evidence of causality in AD. Using human brain single-cell RNA-sequencing data profiled from the dPFC, we found that 6 genes (of the 11 genes) had evidence of enrichment in a cell type at FDR p < 0.05. Enrichment testing was performed using Wilcoxon rank sum test, as implemented by the Seurat package, and multiple testing was accounted for by FDR adjusted for 17,775 tested genes. CARHSP1 showed enrichment in oligodendrocytes. CTSH showed enrichment in astrocytes and microglia. DOC2A, ICA1L, PLEKHA1, and SNX32 were enriched in excitatory neurons.

Extended Data Fig. 5. Genetic principal components of genetic ancestry for each dataset

Genetic principal components of genetic ancestry for each dataset. The first two genetic principal components for individuals in each dataset are plotted (grey boxes) with individuals from the 1000G CEU dataset (purple triangles) for A) the discovery proteomic dataset, B) the replication proteomic dataset, and C) the transcriptomic dataset.

Figure 1:

Manhattan plot for the discovery AD PWAS integrating the AD GWAS (N=455,258) with the discovery ROS/MAP proteomes (N=376). Each point represents a single test of association between a gene and AD ordered by genomic position on the x axis and the association strength on the y axis as the -log₁₀ p value of a z-score test. The discovery PWAS identified 13 genes whose cis-regulated brain protein abundances were associated with AD at FDR p< 0.05. The red horizontal line reflects the significant threshold of FDR p <0.05 and is set at the highest unadjusted p value that is below that threshold (p = 2.6×10⁻⁴).