Leveraging Context-Specific eQTL to Inform BMD GWAS

PROJECT SUMMARY: Osteoporosis, characterized by decreased bone mineral density (BMD) and increased fracture risk, is a serious public health issue. Genome-wide association studies (GWASs) have identified hundreds of associations for BMD; however, most of the specific genes driving these associations remain unknown. This project aims to bridge this gap by leveraging context-specific expression quantitative trait loci (eQTLs) to identify the potential causal genes underlying BMD-associated loci. The goal of this project is to use context-specific eQTL discovery in mesenchymal lineage (CD45-) cells to identify potential causal genes and then use cutting-edge CRISPR-based approaches to begin to understand how they impact cells of the mesenchymal lineage. In Aim 1, we will use single-cell and bulk RNA-sequencing of bone marrow-derived mesenchymal stem cells (MSCs) cultured under osteogenic conditions, to map eQTLs that are active during osteogenic differentiation and in response to osteogenic stimuli. We will then integrate context-specific eQTLs with BMD GWAS data through colocalization and Mendelian Randomization analyses, pinpointing candidate genes likely responsible for BMD associations. In Aim 2, we will functionally validate genes using targeted Perturb-seq and in vitro and in vivo CRISPR-based inactivation/activation (CRISPRi/a) approaches. We will assess the role of these genes in osteoblast function and bone formation. This work has the potential to uncover novel regulatory mechanisms in bone biology and identify therapeutic targets to treat and prevent osteoporosis. Ultimately, this project will provide important insights into how genetic variation influences context-specific gene expression and how this impacts mesenchymal cell differentiation, BMD, and osteoporosis.