Altered gene expression in excitatory neurons is associated with Alzheimer's disease and its higher incidence in women

INTRODUCTION: Alzheimer's disease (AD) is a neurodegenerative disorder involving interactions between different cell types in the brain. Previous single‐cell and bulk expression Alzheimer's studies have reported conflicting findings about the key cell types and cellular pathways whose expression is primarily altered in this disease. We re‐analyzed these data in a uniform, coherent manner aiming to resolve and extend past findings. Our analysis sheds light on the observation that females have higher AD incidence than males. METHODS: We re‐analyzed three single‐cell transcriptomics datasets. We used the software Model‐based Analysis of Single‐cell Transcriptomics (MAST) to seek differentially expressed genes comparing AD cases to matched controls for both sexes together and each sex separately. We used the GOrilla software to search for enriched pathways among the differentially expressed genes. Motivated by the male/female difference in incidence, we studied genes on the X‐chromosome, focusing on genes in the pseudoautosomal region (PAR) and on genes that are heterogeneous across individuals or tissues for X‐inactivation. We validated findings by analyzing bulk AD datasets from the cortex in the Gene Expression Omnibus. RESULTS: Our results resolve a contradiction in the literature, showing that by comparing AD patients to unaffected controls, excitatory neurons have more differentially expressed genes than do other cell types. Synaptic transmission and related pathways are altered in a sex‐specific analysis of excitatory neurons. PAR genes and X‐chromosome heterogeneous genes, including, for example, BEX1 and ELK1, may contribute to the difference in sex incidence of Alzheimer's disease. GRIN1, stood out as an overexpressed autosomal gene in cases versus controls in all three single‐cell datasets and as a functional candidate gene contributing to pathways upregulated in cases. DISCUSSION: Taken together, these results point to a potential linkage between two longstanding questions concerning AD pathogenesis, involving which cell type is the most important and why females have a higher incidence than males. HIGHLIGHTS: By reanalyzing three, published, single‐cell RNAseq datasets, we resolved a contradiction in the literature and showed that when comparing AD patients to unaffected controls, excitatory neurons have more differentially expressed genes than do other cell types. Further analysis of the published single‐cell datasets showed that synaptic transmission and related pathways are altered in a sex‐specific analysis of excitatory neurons. Combining analysis of single‐cell datasets and publicly available bulk transcriptomics datasets revealed that X‐chromosome genes, such as BEX1, ELK1, and USP11, whose X‐inactivation status is heterogeneous may contribute to the higher incidence in females of Alzheimer's disease.