Functional analysis of PDZ domain - PDZ ligand interactions

Scaffold proteins with PDZ domains are known to coordinate multiple signaling molecules and to couple membrane events to the underlying cytoskeleton. Using genetic and molecular approaches we are investigating the role of PDZ domain containing scaffold proteins in T cell receptor signaling and intestinal epithelial biology. We are particularly interested in understanding how scaffold proteins modulate positive and negative signaling outputs following T cell receptor activation.

Given the central importance of PDZ complexes in establishing and maintaining polarity and their link to epithelial cancers of the gastrointestinal tract, we are interested in identifying PDZ domain proteins and PDZ ligands that function as oncogenes and tumor suppressors. We have generated knockout ES cells and mice of a number of novel PDZ domain proteins:

1. To define the biochemical functions of these proteins
2. To track signaling in vivo using GFP/RFP tagged proteins
3. To elucidate the roles of these proteins in immunity and cancer
4. To use integrative genomics approaches to gain insights into the role of PDZ ligands in immunity and epithelial cancers

The genetic analysis of signal transduction pathways that determine host cell responses to microbes

Several known serum response element (SRE) activators are critical regulators of actin cytoskeletal functions. It is also known that activators of the SRE are co-opted or mimicked by pathogenic bacteria to facilitate actin-mediated invasion or attachment. We propose using the SRE as a marker for actin reorganization and believe that novel SRE activators may play previously unknown roles in host-pathogen interactions. Utilizing a robotized luciferase based assay system, we have identified many novel activators of the serum response element. Our primary goal is to delineate molecular pathways that mediate host cell actin cytoskeletal changes in response to bacteria. We will also use computational approaches to prioritize activators and shRNA based experiments to validate predictions. We believe that functional pathway analysis of novel activators will provide important insight into the pathogenesis of human infections and IBD.

Functional analysis of novel IBD loci/genes

Crohn's disease (CD) and ulcerative colitis (UC) are idiopathic inflammatory disorders of the gastrointestinal tract known as the inflammatory bowel diseases (IBD). There is growing evidence that genetic variation plays an important role in the determination of individual susceptibility to disease. Ongoing collaborative studies with Mark Daly of the Broad Institute and John Rioux of the Montreal Heart Institute have resulted in the discovery of novel IBD loci in Crohn's disease.

We are currently developing molecular approaches (knockout/knockin mice, biochemistry, proteomics and computational approaches) to identify the functional implications of the novel regulatory polymorphisms discovered in IBD.

Systems biology approaches to understand human disease signaling networks

The discovery of important mediators and effectors involved in immunity requires a deeper exploration of how these function as integrated systems. Especially of interest are the cellular components and regulatory networks which interact dynamically within temporal, spatial and pathophysiological contexts. We are pursuing integrative systems approaches that closely couple genome-wide experimentation with bioinformatics and computational methods.

We hope to gain additional insights about the immune system in terms of the underlying interaction and regulatory networks that define functional modules at the host-pathogen interface. In addition the team of computational biologists and mathematicians in the group are developing testable models using information from genome-wide studies and high-throughput screens to gain insight into molecular mechanisms of autoimmune disorders.