Deconvolution analysis and differential exon inclusion at the 17q21.31 locus in patients with autopsy-confimed PSP

 Abstract

Progressive supranuclear palsy (PSP) is a neurodegenerative disease characterized by accumulation of hyperphosphorylated microtubule-associated protein tau. While rare kindreds harbor autosomal dominant mutations in the tau gene (MAPT), the majority of cases are sporadic. MAPT mutations that increase splicing of exon 10 cause familial PSP through accumulation of four-repeat (4R) tau. Here we explore if this mechanism plays a role in sporadic PSP.

Methods

Publicly available Next Generation RNA sequencing (RNA-seq) data (n=164, cerebellum and neocortex) were analyzed alongside a novel replication cohort (n=40, neocortex). Data were trimmed, aligned, and assessed using STAR, Trimmomatic, FASTQC, and Picard. Differential gene expression was performed using RSEM, with data visualization performed and splicing analysis was conducted using LeafCutter. Data was visualized with ggplot2

Results

Cell type deconvolution analysis generated using BRETIGEA and ggplot2 shows the relative cell type abundance of neurons, astrocytes, oligodendrocytes, OPC, microglia, and endothelial cells in PSP cases compared to controls. The relative cell type abundance for each sample was used as a covariate in determining differentially expressed genes and isoforms. 

PCA plot and volcano plot showing differential expression in cerebellum and temporal cortex in PSP cases compared to controls. Normalized levels of MAPT mRNA in cerebellum and temporal cortex  Differential expression of additional genes in the 17q21.31 locus

Leafcutter results show differential inclusion of exon 10 in PSP cases compared to controls in the temporal cortex. Box plots show the leafcutter-determined change in percent of exon 10 spliced in between cases and controls. 

Total levels of tau mRNA and tau mRNA containing exon 10 were correlated with genes in the whole transcriptome in both the cerebellum and the temporal cortex of PSP cases and controls. 

Conclusion

- Total tau mRNA levels are increased even when cell type is controlled for

- 4R tau mRNA is elevated in cases compared to controls in both brain regions

- After controlling for cell type, PLEKHM1 is differentially expressed in both regions, KANSL1 and ARGHAP27 are differentially expressed in neocortex, LRRC37A is differentially expressed in cerebellum

- Whole transcriptome-wide regressions reveal a large number of gene candidates that significantly correlate with MAPT and 4R MAPT expression