Basic Science and Pathogenesis

Despite evidence that Alzheimer's Disease (AD) is a highly heritable disease, there remains substantial "missing" heritability, likely due to the clinical and neuropathologic heterogeneity inherent in the disease. Here, we leverage sensitive longitudinal cognitive measures as endophenotypes in a rare variant analysis to identify novel genetic drivers of cognitive decline in aging and disease.

We leveraged 8 cohorts of cognitive aging with whole genome sequencing data from the AD Sequencing Project to conduct rare variant analyses of multiple domains of cognition (N = 8,481; mean age=73; 56% female; 52% cognitively unimpaired). Harmonized scores for memory, executive function, and language were derived using confirmatory factor analysis models. Longitudinal scores were generated for each domain using linear mixed model regressions. Participants of European ancestry inferred using SNPweights and 1000G reference panel were included. Variants included had a minor allele frequency < 0.01 and were annotated as a high or moderate impact SNP using VEP. We performed SKAT-O testing for genes with at least two variants contributing and with a minimum aggregate minor allele count >10. All tests were adjusted for sex, baseline age at cognitive assessment, sequencing center and platform, and the first 5 principal components of genetic ancestry. Correction for multiple comparisons was completed using the false discovery rate (FDR) procedure.

We identified 9 genes associated with our cognitive domains. Two genes (APOE, PSEN1) were associated with baseline memory (both p_FDR=0.07), one (PEDS1-UBE2V1) with baseline language (p_FDR=0.01), and six (HPN, HPN-AS1, GAB1, CXCL3, SIGIRR, PLA2G4A) with executive function decline (p_FDR range=0.01-0.08). SIGIRR, PLA2G4A, and HPN all had high impact variants contributing to the gene score that were significantly associated with executive function decline.

These results highlight novel rare variants associated with cognition. GAB1 is an AGORA nominated gene target for potential AD treatment. Decreased expression was found in cholinergic neurons in AD patients and decreased learning and memory in a mouse model of AD. PLA2G4A has increased expression in AD patients that is evident in early stages but is decreased in healthy aging brains. Future work will incorporate other ancestries.