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

## TL;DR

This study explores RNA diversity in single brain cells from Alzheimer’s disease patients, revealing new isoforms and splicing patterns that may contribute to the disease.

## Contribution

The novel use of PacBio Kinnex long-read sequencing with single-cell RNA analysis uncovers previously undetected isoforms and splicing variants in Alzheimer’s disease.

## Key findings

- Thousands of single nuclei from AD and non-diseased brains showed diverse and differentially expressed RNA isoforms.
- Cell-type-specific isoform expression and novel isoforms like CHI3L1 and SEPTIN4 were altered in AD.
- Reverse transcriptase-mediated somatic gene recombination was associated with intra-exonic junctions in AD brains.

## Abstract

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 yielded ~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 were also detected. Novel isoforms, including CHI3L1 and SEPTIN4, were altered in AD. Kinnex sequencing of RNA isoforms from single nuclei detected vast isoform diversity amongst brain cell types, representing an under-explored element in AD and other brain disorders.