CWOW

Research Projects

Project 1

PI: Allison Goate, Daniel Geschwind, Martin Kampmann

Legend: Overview of Project 1. We will test the hypothesis that H1 and H2 haplotypes have a significant effect on gene expression in multiple cell types by integrating RNA-sequencing (gene expression), ATAC-seq, Hi-C (epigenetics and chromatin structure), ISO-seq (splicing) and proteomics data, along with multi-OMIC single cell sequencing approaches (Figure 1). Combining these different levels of OMICs data and annotations will enable prediction of the most likely functional variants associated with haplotypic differences in gene regulation. We will validate these putative functional variants using high-throughput CRISPRa/i-based functional genomic screens to directly test the impact of H1- and H2-specific variants on gene expression.

The goal of Project 1 is to understand the changes in gene expression, regulation and splicing conferred by the H2 inversion in i) human brain tissue, in individuals of European and African ancestries, ii) individual cell types by assessing cell-autonomous effects in iPSC-derived neurons, astrocytes and microglia, and iii) iPSC-derived assembloids to investigate the interaction between haplotype and cell-cell interactions.

Project 2

PI: Allison Goate, Daniel Geschwind, Martin Kampmann

Legend: Overview of Project 2. We hypothesize that the H1/H2 haplotypes modulates expression of the pathogenic phenotypes associated with specific MAPT variants. We will assess the effect of H2 haplotype on gene expression, chromatin structure and splicing in a cell type-specific manner in i) human brain tissue from carriers with pathogenic P301L and V337M MAPT mutations and ii) iPSC-derived assembloids carrying the same mutations on either an H1/H1 or H2/H2 background. We will test our hypothesis that H2-specific pathways and regulatory mechanisms may modify or confer protection against the pathogenic impact of these mutations by integrating single-nuclear in both brain tissue and (assembloids) via multi-omics sequencing approaches to pair the gene expression and chromatin profiles in the same individual cells, with bulk ISO-seq (splicing) and proteomics data, as well as functional validation of disease-related Tau phenotypes. We will then validate the functional consequences of key haplotype-associated regulatory regions containing candidate common causal variants on disease-related Tau phenotypes and gene expression in both H1 and H2 haplotypes.

The goal of Project 2 is to determine the mechanisms by which the MAPT inversion region haplotypes modify the impact of both common and rare MAPT FTD-associated variants on gene expression and Tau-related phenotypes. We will assess the effect of H2 haplotype on gene expression, chromatin structure and splicing in a cell type-specific manner in i) human brain tissue from carriers of pathogenic P301L and V337M MAPT mutations and ii) iPSC-derived assembloids carrying the same mutations on either an H1/H1 or H2/H2 background.