Isoform Remodeling and Promoter Switching Identify Altered Transcriptional Regulation in Alzheimer's Disease Frontal...

Alzheimer's disease (AD) is associated with transcriptional dysregulation, but gene-level analyses may overlook isoform changes. We investigated how differential isoform usage, promoter selection, and splicing contribute to transcriptome remodeling in the AD frontal cortex.

We analyzed Oxford Nanopore long-read RNA sequencing data from frontal cortex of six individuals with AD and six controls. Transcripts were quantified using Bambu, and differential isoform usage was assessed using IsoformSwitchAnalyzeR. Promoter usage and SUPPA2-derived percent-spliced-in values were tested using beta regression. Transcription factor motif enrichment was evaluated at differentially used promoters. Transcript-level effects were compared with an independent short-read cohort.

We identified 109 isoform-switching events involving 96 isoforms across 86 genes, including CLSTN3, SNCA, BECN1, USP10, and EGFR. Several switches altered predicted nonsense-mediated decay sensitivity. Eleven genes exhibited promoter switching, comprising 46 differentially used promoters: 31 with increased and 15 with decreased usage in AD. These promoters were enriched for 179 TF motifs. IRF7, IRF8, IRF9, and STAT1::STAT2 motifs were top-ranked among promoters with increased usage, whereas NFKB1 and NFKB2 motifs were top-ranked among those with decreased usage. Targeted analysis identified 14 significant differential splicing events with sex-associated effects, including BECN1. Although cross-platform concordance was weak, 16 of 26 transcripts with large effects in both datasets changed concordantly, and 13 showed large, concordant effects of similar magnitude.

AD-associated transcriptome remodeling extends beyond gene-level abundance to include changes in isoform proportions, promoter selection, and transcript structure. These findings implicate transcription initiation and RNA processing as complementary layers of dysregulation in AD.