Cell-type-resolved mRNA 3'-end remodeling in Alzheimer's disease

Alternative polyadenylation diversifies messenger RNAs by altering coding sequences and 3' untranslated regions, but its organization across human brain cell types and disruption in neurodegeneration remain poorly understood. By analyzing 3'-capture single-nucleus RNA sequencing data of 6.3 million nuclei from the prefrontal cortex of 1,494 human donors, we defined 108,768 polyadenylation sites across 25,274 genes, most of which were absent from the GENCODE polyadenylation-site annotation. Polyadenylation-site usage was strongly cell-type-specific and revealed regulatory differences not captured by gene expression. With increasing Alzheimer's disease clinicopathological severity, excitatory neurons, oligodendrocytes and immune cells showed increased distal-site preference, including reduced relative usage of intronic sites and increased distal 3' untranslated region usage in synaptic and RNA-processing genes. External single-nucleus data supported neuronal and oligodendrocyte patterns, while complementary analyses of purified microglia supported selected immune-cell findings. Integrative analyses of cleavage and polyadenylation factor expression, co-regulated usage networks, sequence motifs and published perturbations prioritized the cleavage factor Im complex as a candidate regulator. These findings identify cell-type-specific messenger RNA 3'-end remodeling as a reproducible dimension of Alzheimer's disease molecular pathology that is only partly captured by gene-level analyses.