Research
Broadly, the work in our lab addresses a deficiency in our field relating to the lack of a functional understanding of genetic associations. The lab is concentrating on projects to characterize the functional consequences of common and rare variants in genes associated with bleeding or thrombosis risk. These experiments attempt to address the clinical problem where patients who receive genetic testing have “variants of unknown significance” identified in their genomes. The goal is to create useful clinical information about the functional consequences of variants discovered in GWAS, linkage and next generation sequencing experiments. Our lab employs a variety of genetic, molecular and cellular experimentation leading to a better mechanistic understanding of human genetic variation and the determinants of thrombosis and bleeding risk.
Genome Sequencing in Venous Thromboembolic Disease
Through national and international collaborations, we directed the examination of the coding DNA sequence from ~400 individuals with VTE. We compared this sequence to ~6000 individuals without VTE. We utilized an emerging framework of rare variant association testing, a gene collapsing method, in order to identify genes that harbor more “damaging” variants in cases compared to controls. In doing so, we confirmed the contribution of loss of function of three known natural anticoagulant genes to VTE as well as discovering a new gene for thrombophilia, STAB2. In our preliminary study, about 8% of individuals with VTE had at least one copy of STAB2 bearing a loss of function or damaging mutation compared to 2% of the controls. Our laboratory group is now focusing on the functional characterization of STAB2 which encodes stabilin-2, a scavenger receptor expressed on the venous epithelium in the spleen and liver sinusoids. We are performing experiments to determine how loss of function mutations in this receptor lead to increased risk for VTE. For example, we are studying the variants of STAB2 identified in the VTE study and looking in vitro to understand how the variant protein is expressed and delivered to the cell surface compared to wild-type. We are also searching for procoagulant plasma ligands that stabilin-2 normally clears from the circulation through a proximity labeling system. The goal is to expand our knowledge of stabilin-2 function in thrombosis risk, further understand the role of rare genetic variants in VTE and to provide better risk predictions for families with a history of VTE.
Desch lab also performs genetic screens to increase our understanding of human genetic variation's impact on hemostatic function. For example, we are focused on the deep mutational scan of anti-coagulant genes such as SERPINC1, PROC and PROS1. Cloning and functional characterization of every possible single amino acid substitution in these genes will allow for an improved understanding of the critical amino acid residues in these anticoagulant proteins and aid in the interpretation of human genetic sequencing results.
An additional area of interest in Desch Lab relates to bleeding disorders and von Willebrand factor biology. We are using whole genome and focused CRISPR "knock out" screens in endothelial cells to determine which proteins are required for the packaging and controlled secretion of von Willebrand factor. This data may help inform the reasons why ~30% of individuals with low plasma VWF levels do not have a known damaging mutation in VWF.
A library of cells expressing eGFP tagged antithrombin can be screened with flow cytometry. Cells expressing mutant AT that causes defects in secretion will have higher intracellular fluorescence compared to cells bearing AT mutants with normal secretion. To screen for mutations that alter the anticoagulant function of antithrombin, we will perform flow cytometry on a library of cells expressing AT mutants on the surface of the cell. Cells will be incubated with antithrombin ligands and labelled with antibodies for flow cytometry.