Our lab is using live animal (Drosophila and zebrafish), genome-scale approaches to understand biological processes. The lab has two main areas of focus. The first involves the nuclear hormone receptor family of ligand activated transcription factors, which control metabolism, growth, behavior, sexual dimorphism, immunity and aging. The second focuses on the process of RNA transport within cells and how this affects cellular architecture and function.

Hormones are chemicals that circulate within the body and trigger specific responses in target tissues. Steroids, such as the estrogens used to treat or postpone menopause and the muscle building steroids taken by some athletes, are a well known example of these. These particular hormones penetrate cells and elicit responses by binding to a family of proteins called nuclear hormone receptors (NHRs). NHRs control many of the metabolic pathways in our body as well as related processes such as memory, behaviour and aging. Consequently, a large number of human diseases - for example diabetes, obesity and Alzheimers - are caused, or enhanced, by NHR malfunctions. Fortunately, the ability of these proteins to respond to small molecules that move efficiently within the body makes them ideal drug targets. In fact, a disproportionate percentage of the most successful and important pharmaceuticals target specific NHRs. This is despite the fact that hormone partners have yet to be identified for more than half of NHRs.

We have devised new methods to identify the unknown hormone partners in live animals. These methods allow us to screen for compounds that may only work in specific cells or tissues. We can also screen for compounds that do not cross-react with other NHRs, act in the wrong tissues or cause detrimental side effects. These are common problems in drug discovery that usually only come to light during subsequent clinical trials. These studies began with initial studies on the orphan nuclear receptor FTZ-F1 (Guichet et al, 1997;Schwartz et al, 2001). We have since published results ( Reinking et al, 2005) showing that the Drosophila receptor E75 uses heme as a constitutive ligand, which in turn allows it to respond to the signaling gas Nitric oxide. In the animal, this allows it to coordinate metabolism with timed processes such as circadian rhythm and metamorphosis (Caceres et al, 2011). Not surprisingly, we have found that the human orthologues of E75, called Rev-erb alpha and beta, also bind heme and respond to Nitric oxide ( Pardee et al, 2009). Current efforts are focused on the PPAR family of receptors, which are targets of powerful, albeit sometimes dangerous, drugs used to treat metabolic disorders such as type II diabetes.

Until recently, it was thought that the shape and polarity of a cell is controlled by the directed movements of proteins to the sites where they are needed. However, we have shown recently that much of subcellular protein distribution and subsequent activity is controlled by the trafficking of messenger RNAs prior to their conversion into protein. This was first shown with mRNA that encodes a secreted signaling molecule - Drosophila Wg/Wnt ( Simmonds et al, 2001). We showed that localization of wg mRNA is required for the proper localization, processing, secretion and function of the highly conserved and important protein.

Then, to see how prevalent and important the process of mRNA localization is overall, we embarked on a genome scale project to determine the localization of all mRNAs encoded in the Drosophila genome. First, we developed a highly sensitive, spatially accurate and high-throughput method for localizing mRNAs in whole embryos in high throughput. Thus far, we have completed analysis of approximately 1/3 of the fly genome. The results are surprising, with over 70% of mRNAs exhibiting subcellular localization, and with a large assortment of never seen before patterns. These initial results are described in Lecuyer et al, 2007 (editor's pick top paper of the year, Nature). A searchable database with images and descriptions of each mRNA pattern is provided at Fly-fish. We have also initiated analyses of localization in later stage embryos and 3rd instar larvae.

Over the past two decades, tremendous efforts have been made to develop drugs capable of modulating today's most debilitating and costly diseases. However, despite the recent advances offered by genome sequences, the rate of new drug discovery has decreased and costs have gone up. Much of this can be attributed to the simplicity of drug discovery assays, and subsequent attrition due to unforeseen defects and side- effects. An obvious, although difficult solution, would be to develop high throughput drug screens that could be conducted using live animals.

To this end, we have developed a high throughput zebrafish system that allows the visualization and isolation of active drug candidates in live fish (Tiefenbach et al, 2010). We have generated 48 transgenic zebrafish lines, one representing each of the 48 human nuclear receptors, which are one of the most important and successful families of drug target proteins. A couple of screens have already been conducted with tremendous success. One of our discoveries, a drug that is already FDA approved for other indications, looks to have excellent potential for metabolic syndrome diseases such as diabetes.