Project 1: Determination of molecular differences caused by tauopathy-associated H1 and H2 haplotypes

PROJECT SUMMARY (PROJECT 1) Genetic association between the MAPT H1 haplotype and increased risk for multiple Tauopathies, including Frontotemporal Dementia (FTD) and Progressive Supranuclear Palsy (PSP), is well-established and replicated. Despite this, very little is known regarding the mechanisms behind the differences in disease risk associated with the H1 and H2 haplotypes. To date, comparison of these haplotypes has been restricted to studies of MAPT splicing, as well as associations with clinical phenotypes. However, there has been no investigation of the downstream functional implications of each MAPT haplotype. Our goal is to comprehensively assess the chromatin structure, gene expression and functional consequences of structural differences between the H1 and H2 haplotypes in cells from individuals of European and African ancestry, in order to better understand the mechanisms underlying risk for Tauopathy. The major MAPT haplotypes encompass a 970Kb inversion within the 17q21.31 locus and include many genes in addition to MAPT, as well as extensive genetic and structural variation. We hypothesize that the gross structural differences between haplotypes confer short- and long-range changes in chromatin structure, leading to altered regulation of gene expression within and outside the inversion, and that these changes in neurons and/or glia contribute to risk/protection for tauopathies. We will use 2D and 3D induced pluripotent stem cell (iPSC) models to examine multi-OMIC differences between H1/H1 and H2/H2 and human brain tissue derived from H1/H1 and H2/H2 carriers to validate these changes, followed by CRISPR-based functional genomic screens to test the impact of candidate causal variants on gene expression and function. We propose four specific aims: 1) Use single nuc sequencing, ISOseq and proteomics to characterize chromatin structure, gene/protein expression and splicing in human brain tissue from H1/H1 and H2/H2 carriers, 2) Use RNAseq, HiC, ATACseq, ISOseq and proteomics to characterize cell-autonomous changes in chromatin structure, gene expression and splicing in 2D neuron, astrocyte and microglial cultures from H1/H1 and H2/H2 individuals; 3) Use single cell ATAC/RNAseq to examine effects on gene expression in 3D assembloids from H1/H1 and H2/H2 individuals; 4) Use CRISPRa/i-based assays to test the functional impact of altering haplotype- and cell-specific gene enhancer regions on global gene expression and Tau- isoform expression and splicing. Understanding the mechanisms underlying the protective effects of the H2 haplotype has the potential to uncover new therapeutic strategies for FTD and other neurodegenerative diseases.