Identifying Genes Associated with Alzheimer’s Disease Using Gene-Based Polygenic Risk Score

Article type: Research Article

Authors: Lai, Dongbing^{a; *} | Zhang, Michael^a | Li, Rudong^a | Zhang, Chi^a | Zhang, Pengyue^b | Liu, Yunlong^a | Gao, Sujuan^b | Foroud, Tatiana^a

Affiliations: [a] Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA | [b] Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA

Correspondence: [*] Correspondence to: Dongbing Lai, PhD, 410 W. 10^th Street, HS 4000, HITS, Indianapolis, IN 46202-3002, USA. Tel.: +1 317 278 9544; Fax: +1 317 278 1100; E-mail: dlai@iu.edu.

Abstract: Background: Except APOE, Alzheimer’s disease (AD) associated genes identified in recent large-scale genome-wide association studies (GWAS) had small effects and explained a small portion of heritability. Many AD-associated genes have even smaller effects thereby sub-threshold p-values in large-scale GWAS and remain to be identified. For some AD-associated genes, drug targeting them may have limited efficacies due to their small effect sizes. Objective: The purpose of this study is to identify AD-associated genes with sub-threshold p-values and prioritize drugs targeting AD-associated genes that have large efficacies. Methods: We developed a gene-based polygenic risk score (PRS) to identify AD genes. It was calculated using SNPs located within genes and having the same directions of effects in different study cohorts to exclude cohort-specific findings and false positives. Gene co-expression modules and protein-protein interaction networks were used to identify AD-associated genes that interact with multiple other genes, as drugs targeting them have large efficacies via co-regulation or interactions. Results: Gene-based PRS identified 389 genes with 164 of them not previously reported as AD-associated. These 389 genes explained 56.12% –97.46% SNP heritability; and they were enriched in brain tissues and 164 biological processes, most of which are related to AD and other neurodegenerative diseases. We prioritized 688 drugs targeting 64 genes that were in the same co-expression modules and/or PPI networks. Conclusions: Gene-based PRS is a cost-effective way to identify AD-associated genes without substantially increasing the sample size. Co-expression modules and PPI networks can be used to identify drugs having large efficacies.

Keywords: Alzheimer’s disease, gene-based polygenic risk score, gene-targeting drugs, gene co-expression module, protein-protein interaction network, SNP heritability

DOI: 10.3233/JAD-230510

Journal: Journal of Alzheimer's Disease, vol. 96, no. 4, pp. 1639-1649, 2023