Investigating MAPT p.R406W Impact on Lysosomal Genes

To evaluate the impact of MAPT p.R406W on lysosomal genes, we queried summary statistics from our previously generated bulk RNAseq data of the insular cortex of MAPT p.R406W (n = 2) and neuropathology-free controls (n = 2) [19 (link)]. Briefly, DNA libraries of individual samples were constructed using the TruSeq Stranded Total RNA Sample Prep with Ribo-Zero Gold kit (Illumina) and then sequenced by the HiSeq 4000 (Illumina). FASTQ files were aligned to human GRCh37 primary assembly. After alignment, Salmon (v. 0.7.2) was used to quantify expression levels of individual genes included in the GENCODE reference genome (GRCh37.75). Differential gene expression was performed using the R (v.3.4.2) package DESeq2 (v.1.18.1) as previously described [19 (link)]. From the summary statistics, we extracted genes that are regulated by Transcription Factor EB (TFEB), defined as: [1 (link)] containing a Coordinated Lysosomal Expression and Regulation (CLEAR) sequence or [2 (link)] being altered by overexpression of TFEB in vitro [37 (link)]. To determine whether genes that are regulated by TFEB and altered in MAPT p.R406W brains were enriched in specific functional pathways, gene enrichment analysis was performed using ToppGene [38 (link)].