RNA isoform diversity, splicing variants and switching in single cells of the Alzheimer’s disease brain

Alzheimer's disease (AD) is the most common cause of dementia, yet its molecular causes remain incompletely understood. RNA diversity in part arising from dysregulated splicing may contribute to AD pathogenesis, however the ability to interrogate the resulting full-length isoforms in single brain cells has been technologically limited. Here we report the use of PacBio Kinnex long-read sequencing combined with 10X Genomics single-cell preparations to identify both annotated and unannotated RNA isoforms. Eight AD and seven non-diseased post-mortem human brains yield ~70,000 single nuclei showing diverse, differentially expressed and switched transcripts in multiple genes. Cell-type-specific isoform expression and variants with intra-exonic junctions associated with reverse transcriptase-mediated somatic gene recombination are also detected. Novel isoforms are altered in AD, with examples of CHI3L1 and SEPTIN4. Kinnex detection of RNA isoforms from single nuclei highlights vast isoform diversity amongst brain cell types, representing an under-explored element in AD and other brain disorders.