APOER2 splicing repertoire in Alzheimer's disease: Insights from long-read RNA sequencing.

Disrupted alternative splicing plays a determinative role in neurological diseases, either as a direct cause or as a driver in disease susceptibility. Transcriptomic profiling of aged human postmortem brain samples has uncovered hundreds of aberrant mRNA splicing events in Alzheimer's disease (AD) brains, associating dysregulated RNA splicing with disease. We previously identified a complex array of alternative splicing combinations across apolipoprotein E receptor 2 (APOER2), a transmembrane receptor that interacts with both the neuroprotective ligand Reelin and the AD-associated risk factor, APOE. Many of the human APOER2 isoforms, predominantly featuring cassette splicing events within functionally important domains, are critical for the receptor's function and ligand interaction. However, a comprehensive repertoire and the functional implications of APOER2 isoforms under both physiological and AD conditions are not fully understood. Here, we present an in-depth analysis of the splicing landscape of human APOER2 isoforms in normal and AD states. Using single-molecule, long-read sequencing, we profiled the entire APOER2 transcript from the parietal cortex and hippocampus of Braak stage IV AD brain tissues along with age-matched controls and investigated several functional properties of APOER2 isoforms. Our findings reveal diverse patterns of cassette exon skipping for APOER2 isoforms, with some showing region-specific expression and others unique to AD-affected brains. Notably, exon 15 of APOER2, which encodes the glycosylation domain, showed less inclusion in AD compared to control in the parietal cortex of females with APOE ɛ3/ɛ3 genotype. Also, some of these APOER2 isoforms demonstrated changes in cell surface expression, APOE-mediated receptor processing, and synaptic number. These variations are likely critical in inducing synaptic alterations and may contribute to the neuronal dysfunction underlying AD pathogenesis. Author summary: Alternative splicing enhances genetic diversity by producing various RNA isoforms from a single gene. The gene LRP8, which encodes apolipoprotein E receptor 2 (APOER2), undergoes extensive alternative splicing in the brain. APOER2 is a type I transmembrane receptor that interacts with extracellular ligands, notably the neuroprotective Reelin and APOE, a risk factor associated with Alzheimer's disease (AD). Interestingly, alternative splicing of APOER2 has been shown to be altered in AD; yet the complete repertoire of APOER2 isoforms in both normal and AD-affected brains remained largely unexplored. Our study offers insight into the diverse isoforms of APOER2 in the human brain and their splicing modifications in the context of AD. We discovered a range of combinatorial APOER2 alternative splicing events, leading to a diverse set of isoforms in the human brain. Our analysis revealed both region- and disease-specific APOER2 isoforms, indicating that APOER2 splicing is not only spatially regulated but also undergoes alterations in AD. Moreover, we observed that some of the APOER2 isoforms in AD brains show changes in cell surface expression, receptor processing and synapse numbers. These findings suggest that combinatorial splicing of APOER2 is a critical determinant of its protein function and undergoes significant alterations in AD. [ABSTRACT FROM AUTHOR]