The Chicago Biomedical Consortium is pleased to announce four awards as a result of its Fall 2007 Catalyst RFA process. Below are brief summaries of the funded projects.
Gene Regulatory Networks Directing Hematopoietic Cellular Fates
PIs: Harinder Singh, UChicago; John Crispino, NU; Aaron Dinner, UChicago.
Award Amount: $199,538.
Different mammalian cell types turn on subsets of genes that enable the cells to perform distinct
functions within tissues and organ systems. The genetic circuits and switches that control gene
activity and the generation of different cell types are poorly understood. We propose to discover
and comprehensively analyze these circuits using a variety of experimental and theoretical
approaches within the context of the blood and immune system. Detailed knowledge of these
genetic circuits should enable their manipulation to efficiently generate specific blood and
immune cells starting from stem cells. Such knowledge will also provide a new and very
powerful means of assessing diseased states of the blood system such as leukemias and aid in
their diagnosis and therapy.
Multiplexed Imaging of Transient Molecular Complex Dynamics in vivo
PIs: Lawrence Miller, UIC; Jerrold Turner, UChicago.
Award Amount: $200,000.
Proteins interact transiently within multi-component complexes to control a wide variety of biological processes
such as the cell cycle, motility or immune response. In order to understand and model the molecular
mechanisms that underlie biological function, researchers need experimental tools that allow them to elucidate
how the spatial and temporal regulation of a specific protein complex is coupled to a specific activity and a
particular cellular response. Our research seeks to provide a general method for microscopically visualizing
the location and stoichiometry of multiple protein-protein interactions in living cells in real time. Our approach
is based on technology that allows the selective labeling of genetically encoded fusion proteins in living
mammalian cells with cell-permeable small molecules. We will synthesize organic complexes of lanthanide
ions such as terbium or europium that luminesce brightly with very long lifetimes and multiple emission
maxima. The lanthanide probes will enable a facile form of lifetime imaging microscopy that will allow us to
visualize and quantify resonance energy transfer between lanthanide-labeled targets and one or more
fluorophore-labeled proteins. As an initial proof-of-concept, we will use the proposed lanthanide protein
labeling and microscopy technologies to study the biochemical mechanism of cytoskeletal-mediated
remodeling of the tight junction protein complex and its effect on epithelial permeability, a problem not easily
resolvable with existing experimental techniques. Given its generality, we anticipate that the proposed imaging
technology will be easily adopted by other investigators for studying protein dynamics in a wide variety of cell
types.
Proteomic Analysis of Mitochondrial and Sarcomeric Proteins in Cardiomyopathy
PIs: Elizabeth McNally, UChicago; Paul Schumacker, NU; John Solaro, UIC; Hossein Ardehali, NU.
Award Amount: $199,992.
Heart Failure is a major epidemic in the developed world. More than 5 million Americans are
diagnosed with this disorder and our annual expenses related to heart failure approaches $38 billion.
Cardiomyopathy (CM) is defined as the inability of the heart to deliver adequate blood flow to the body
and generally leads to heart failure. Although we have made significant progress in diagnosing and
treating CM, the molecular pathogenesis of this disorder is not totally understood. This is to a great
extent due to limited collaboration among groups that study CM. In June 2006, several lead
investigators from UIC, University of Chicago and Northwestern University started the Chicago Cardiac
Proteomic Center. The purpose of the group was to bring diverse expertise in CM research from
different institutions together to start a de novo collaboration and identify the molecular defects in CM.
The group has met multiple times since last year and our plans and aims have improved significantly.
We hypothesize that the primary defects and triggers of CM are alterations of mitochondrial and
sarcomeric proteins as a consequence of excessive oxidative stress. Mitochondria (also called
the “powerhouse” of the cell”) are organelles that regulate three important cellular processes: 1)
generation of energy, 2) mediating cell death and survival in response to injurious insults, and 3)
production of molecules that cause oxidative stress on cells. Sarcomeric structures are proteins that
mediate force generation by the heart cells and cause beating of the heart. In this proposal, we will use
novel techniques to study whether modifications occur in mitochondrial and sarcomeric proteins in
animal models of CM. We will then apply the knowledge obtained from these studies to patients with
CM. These studies would not be possible without close collaboration among the involved
groups. We believe CCPC will build the infrastructure to make Chicago the leading heart failure
research center in the world. The CCPC is in the process of applying to Center Grants and invited
grants from the National Institute of Health and would use the CBC award as a catalyst for these larger
Center Awards.
Spatiotemporal Dynamics of Cellular Protein Networks on Membranes
PIs: Wonhwa Cho, UIC; Eduardo Perozo, UChicago; Hui Lu, UIC.
Award Amount: $200,000.
Cellular responses to external stimuli are mediated by diverse signal transduction pathways that involve
multiple transmembrane receptors and a large number of cellular proteins. Because dysfunctional or
unregulated cell signaling pathways are known to cause a wide range of human diseases, including cancer,
diabetes, autoimmune diseases, and inflammatory diseases, cell signaling pathways offer many attractive drug
targets, as witnesses by the remarkable success of a signaling kinase inhibitor, Gleevec, against chronic
myelogenous leukemia. Regulation of cell signaling involves a myriad of molecular interactions, including
protein-protein interactions. Determination of the protein-protein interaction network and understanding of their
regulation during cell signaling are the key elements of functional proteomics and systems biology, and may
lead to development of a new generation of specific inhibitors directed toward various signaling pathways. In
general, cellular protein-protein interactions are tightly regulated both spatially and temporally and,
consequently, the success of proteomics and systems biology studies critically depends on the spatiotemporal
resolution of protein-protein interactions. Recent studies have indicated that the spatial regulation is the key to
the successful orchestration of cellular protein interactions and information flow. Furthermore, cellular
membranes serve as the main sites of protein complexes and networks and direct interaction of proteins with
various membrane lipids is critical for spatial regulation of protein networking. The Cho and Lu laboratories
recently developed and/or optimized a bioinformatics-based algorithm for predicting lipid-binding proteins,
high-throughput in vitro and cellular methods for determining lipid binding and subcellular locations of
proteins, cellular single molecule techniques, and a systems biology analysis protocol. On the basis of these
methods as well as structural, spectroscopic, and computational methodologies developed in the Perozo
laboratory, we propose to study the lipid binding properties of all major modular domains that mediate cellular
protein-protein interactions and networking. In this proposal, we will focus on the PDZ domain that is the most
abundant protein interaction module, plays a key role in the localization of a large number of signaling proteins,
and is an important target for drug development. We will predict the lipid-binding PDZ domains, determine their
lipid specificities and membrane binding mechanisms, and finally elucidate how their lipid binding regulates the
spatiotemporal dynamics of signaling complexes and signaling network. These studies will lead to better
understanding of when and where signaling proteins interact with each other and thereby aid in development of
a new type of specific and potent reagents that interfere with or boost particular protein-protein interactions.