Next, to assess the robustness of our results, we performed a replication analysis using RNA-Seq data from the Mount Sinai Brain Bank (MSSB)25 involving 301 samples from Alzheimer’s disease and control brains (Supplementary Note). Of the 84 genes with differentially spliced intron clusters in ROSMAP, 52 (including APP, PFKP, and NDRG2) were significant at a Bonferroni-corrected P < 0.05 thresholds in the MSBB data and the effect sizes are highly correlated between the two datasets (Pearson’s r=0.35; P <6.75× 10−14) (Fig. 2c; Supplementary Fig. 4; Supplementary Table 8). This constitutes an independent replication of specific, aberrant splicing alterations in Alzheimer’s disease brains. Finally, to further validate and explore the mechanism of our observations, we analyzed RNA-Seq data derived from 3 control induced pluripotent stem cells (iPSC)-derived neurons (iN) and the same iN line overexpressing Tau: differential intron excision was noted for 42 genes (FDR < 0.05), of which 11 genes overlap with the Alzheimer’s disease-associated splicing in the cortex including APP, PICALM, and NDRG2 (Fig. 2d; Supplementary Table 9). Despite the small sample size, these in vitro data suggest that
