Basic Science and Pathogenesis

Pathogenic variants in presenilin 1 (PSEN1) or presenilin 2 (PSEN2) cause familial Alzheimer's disease (AD). Recent long-read RNA sequencing of PSEN2 revealed cryptic exon inclusion and differential regulation of the 3' untranslated region (3'UTR) in sporadic AD. Notably, two-thirds of PSEN2 reads harbored the canonical short 3'UTR, while the other third contained an extended ∼4kb long 3'UTR. Given that 3'UTRs contain critical regulatory elements, we sought to determine the functional significance of PSEN2 3'UTR isoforms in AD.

To develop in vitro models to assess PSEN2 3'UTR isoforms, we designed constructs containing the PSEN2 3'UTR short and long isoforms to overexpress in either HMC3 human microglial or SH-SY5Y human neuroblastoma cell lines. Since miRNAs are known to target 3'UTRs, we also completed homogenate and synaptosome small RNA sequencing on AD and control samples to profile miRNA expression. Finally, we tested whether PSEN2 3'UTR length or inclusion of cryptic exon 9B altered cellular localization in human frontal cortex samples using BaseScope in-situ hybridization.

We primarily detected short PSEN2 in the cytoplasm with significantly reduced levels in AD versus control frontal cortex. Conversely, long PSEN2 was retained in the nucleus and expressed at similar levels between cases and controls. These findings are relevant for PSEN2 expression studies as in vitro findings indicated increased long PSEN2 3'UTR isoform abundance relative to the short PSEN2 3'UTR. Small RNA sequencing analysis identified 53 homogenate and 76 synaptosome miRNAs with significant differential regulation in AD, including one miRNA, miR-34c, that was significantly downregulated in both fractions. The long PSEN2 3'UTR contains 10 binding sites for 5 miRNAs with significant differential regulation in AD brains relative to controls, including 3 miRNAs with significant synaptosome downregulation (miR-346, miR-326, and miR-548p), and 2 miRNAs with significant homogenate downregulation (miR-217) and upregulation (miR-890).

Collectively, our data establish 1) an in vitro model to test PSEN2 3'UTR isoforms, 2) miRNA expression differences in human AD synaptosome and homogenate fractions, and 3) decreased PSEN2 transcript signal in human AD frontal cortex tissue. Elucidating the functional significance of PSEN2 3'UTR isoform regulation will further our understanding of AD.