Research Project
10490490
Abstract Osteoporosis is a devastating disease of bone that impacts over 10 million Americans. While the cellular basis for osteoporosis includes an imbalance in bone formation by osteoblasts and bone resorption by osteoclasts, there are relatively few validated, clinically relevant genes in osteoporosis. There is a significant need to discover new genes that influence osteoporosis pathogenesis. These discoveries will then permit us to achieve the long-term goal of developing new therapies to both prevent and treat this debilitating disease. The existing collaboration between the Hankenson and Grant laboratories has been focused on understanding the functional significance of genome wide association study (GWAS) signals associated with bone mass, osteoporosis, and fracture risk. We have developed methods to use those signals to identify novel genes putatively involved in disease pathogenesis. While GWAS efforts by numerous research groups have been successful in discovering genomic variants robustly associated with bone mineral density (BMD) and fracture, GWAS only reports signals associated with a given trait and not necessarily culprit genes. Our approach for this proposal is to utilize a computationally advanced, multi-step process that integrates genome level data to identify novel osteoblast and osteoclast genes. This ?genome-wide variant to gene mapping? effort combines RNA-seq, ATAC-seq and high-resolution chromatin conformation capture methods to implicate culprit effector genes. We have already used this approach in osteoblast lineage cells and 30% of osteoporosis-associated GWAS signals were shown to have direct physical contact with genes in these cells, totaling 86 putative target genes. Several of these targets (ex. EPDR1, ING3) have already had functional follow-up. However, many more need functional follow-up and there are still 70% of osteoporosis associated GWAS loci that remain unresolved. Importantly, our initial work was focused only on discovering osteoblast- associated genes, and thus genes that play a role in osteoclasts were not revealed. Furthermore, our published work to date has only focused on one time-point during the osteoblast differentiation process, thus genes that play roles at later points in cell differentiation have not been discovered. This comprehensive application will functionalize GWAS findings, and in doing so, reveal novel genes that are involved in regulating bone formation and resorption. Our pipeline from gene discovery to gene validation has been robustly tested and thus far, although our sampling has been small, we have had a 100% hit rate for validating putative effector genes. Thus, it is our hypothesis that we can uncover many more BMD effector genes by conducting high resolution ?genome-wide variant to gene mapping? in osteoclasts and osteoblasts. The relevance of genes will be validated using both in vitro and in vivo approaches in mouse models. Upon completion, we will provide the bone community with new targets to pursue for understanding mechanism.
