The Conklin Lab studies the mechanisms by which hormone receptors direct the development and function of complex tissues, including those found in the cardiovascular system. The focus of our research is on the largest known family of receptors for hormones and drugs, the G protein–coupled receptors (GPCRs), which include over 700 human genes. We combine genetic knockouts, designer GPCRs and bioinformatics techniques in order to gain a basic understanding of hormone signaling in mice and pluripotent embryonic stem (ES) cells. More recently we have derived induced pluripotent stem (iPS) cells from patients with human genetic heart rhythm disorders such as Long QT syndrome. These studies should allow us to directly study to role of GPCR signaling in human myocytes with specific human genetic diseases.

Significance:
GPCRs are the target for some of the most widely used pharmaceuticals to treat diseases that involve virtually all tissues in the body. Although our primary focus is on the process of ES cell differentiation into cardiovascular tissues, our work also encompasses the effects of pharmaceutical intervention on bone development, neurobiology and cell migration.

Approaches and Contributions: The late Richard Feynman once said, “What I cannot create, I do not understand.” Although this principle is well known in the field of engineering, we are just beginning to understand its application in biology. Our research utilizes bioinformatics programs, along with receptor engineering and advanced methods for measuring pharmacological responses. Since all GPCRs share a common design, they are ideal for testing synthetic signaling systems and mapping common signaling pathways.

New Receptors to Rewire Signaling Pathways: We have engineered GPCRs called RASSLs (receptors activated by small synthetic ligands, see Coward et al 1998), that are unresponsive to endogenous natural hormones, but can still be activated via synthetic small-molecule drugs. We have successfully expressed RASSLs in a wide variety of tissues, and have experienced success in controlling responses such as heart rate. These first RASSLs have proven to be catalysts in the examination of GPCR signaling in complex systems, including bone development, taste, and olfactory development. In recent years, we have been able to develop RASSLs that can activate all the major GPCR pathways (see Conklin, Nature Methods, 2008). Internationally, RASSLs are currently used in several laboratories in order to answer basic questions in neurobiological, endocrine and cardiovascular studies.

Stem Cells as a Model System: Our functional genomic experiments focus on GPCR signaling pathways in pluripotent ES cell-derived cardiac myocytes. We use high-throughput gene inactivation methods, including siRNA and gene trapping in ES cells, and then analyze ES cell-derived cardiomyocytes. We are also studying ES cell differentiation at the level of gene transcription and alternative splicing that guide cell transition from ESCs into cardiomyocytes. We are actively involved with BayGenomics, a large-scale, academic collaboration whose goal is the inactivation of all genes in murine ESCs (www.genetrap.org). The effects of this approach have been demonstrated in a recent study that showed that genetic alterations (AKAP-10 trap) in ESC -derived cardiac myocytes alter the electrical responses to hormones, such as acetylcholine, in a phenotype that was reproduced in mice derived from these ES cells. More recently we have are using human iPS cells for similar signaling studies. As we move forward with our research, we will continue to focus on studies that have synergy between stem cell biology, mouse genetics and human genetics.

Bioinformatics, GenMAPP and WikiPathways: The efforts of our pathway-oriented bioinformatics team have produced a free, publicly distributed software package, GenMAPP (Gene Map Annotator and Pathway Profiler). GenMAPP is now used by researchers world-wide, with over 17,000 unique registrations in 40 countries, and more than 400 publications citing the program. More recently we have developed first public pathway wiki (www.WikiPathways.org) to empower any researcher to contribute to our public pathway knowledge. We are in the process of expanding these open source programs in order to provide comprehensive genome-wide, pathway-oriented analysis for twenty species and all types of functional genomic data, including genetic variation and disease association studies, in an effort to provide more complete analysis of the data collected in functional genomic experiments.

Some questions addressed in ongoing studies:

* What are the GPCR signals that drive growth and differentiation of pluripotent stem cells into cardiac myocytes, bone, endocrine and other cell types?

* What are the drugs that can be used to control adult cardiac function via GPCRs?

* How can whole-genome SNP and expression data be best visualized in the context of biological pathways in order to provide insights into human disease?