Rare variants in the endocytic pathway are associated with Alzheimer’s disease, its related phenotypes, and functional consequences

Late-onset Alzheimer’s disease (LOAD) is the most common type of dementia causing irreversible brain damage to the elderly and presents a major public health challenge. Clinical research and genome-wide association studies have suggested a potential contribution of the endocytic pathway to AD, with an emphasis on common loci. However, the contribution of rare variants in this pathway to AD has not been thoroughly investigated. In this study, we focused on the effect of rare variants on AD by first applying a rare-variant gene-set burden analysis using genes in the endocytic pathway on over 3,000 individuals with European ancestry from three large whole-genome sequencing (WGS) studies. We identified significant associations of rare-variant burden within the endocytic pathway with AD, which were successfully replicated in independent datasets. We further demonstrated that this endocytic rare-variant enrichment is associated with neurofibrillary tangles (NFTs) and age-related phenotypes, increasing the risk of obtaining severer brain damage, earlier age-at-onset, and earlier age-of-death. Next, by aggregating rare variants within each gene, we sought to identify single endocytic genes associated with AD and NFTs. Careful examination using NFTs revealed one significantly associated gene, ANKRD13D. To identify functional associations, we integrated bulk RNA-Seq data from over 600 brain tissues and found two endocytic expression genes (eGenes), HLA-A and SLC26A7, that displayed significant influences on their gene expressions. Differential expressions between AD patients and controls of these three identified genes were further examined by incorporating scRNA-Seq data from 48 post-mortem brain samples and demonstrated distinct expression patterns across cell types. Taken together, our results demonstrated strong rare-variant effect in the endocytic pathway on AD risk and progression and functional effect of gene expression alteration in both bulk and single-cell resolution, which may bring more insight and serve as valuable resources for future AD genetic studies, clinical research, and therapeutic targeting.Author summary: Late-onset Alzheimer’s disease (LOAD) is the most common type of dementia and a leading cause of death in the world. Clinical and genetic studies have suggested the potential contribution of the cellular transportation pathway to AD with an emphasis on common variants. In this study, we investigated the effect of rare variants within the cellular transportation pathway and examined three large datasets with over 3,000 individuals with European ancestry. We reported enrichment of rare deleterious variants in the cellular transportation pathway in AD patients from all three datasets. We also observed an elevation of rare deleterious variants in this pathway was associated with individuals with severer brain damages (AD progression), earlier age-at-onset, and earlier age-of-death. By aggregating rare variants in each gene from the cellular transportation pathway, we revealed one gene in which rare variants were significantly associated with the progression of AD. By integrating gene expression data from brain tissues, we identified two additional genes whose rare-variant effect displayed significant influences on gene expression. Taken together, our results demonstrated that rare-variant effect in the cellular transportation pathway is strongly associated with the risk and the progression of AD, which may serve as future clinical and therapeutic targets.