Funded Awards

Updated: December 5, 2017

The CBC seeks to stimulate collaboration among scientists at Northwestern University, the University of Chicago, and the University of Illinois at Chicago that will transform research at the frontiers of biomedicine. CBC funding opportunities have enabled our three member institutions to create a novel and innovative collaborative effort, linking researchers, resources, and facilities to enable fundamental breakthroughs in scientific understanding. To learn more about the CBC funded awards, scroll down and click on the individual award titles or choose from the following award categories:

Current Award Programs:  Catalyst Awards
Past Award Programs:  Lever Awards  I  Spark Awards  I  HTS Awards  I  Postdoctoral Research Awards  I  Scholars Program  I  Exploratory Workshops


 

Funded Catalyst Awards

2017 Spring Round

PIs: Narayanan Kasthuri (UChicago) and Irina Balyasnikova (NU) for the project:
The Connectome of Newly Born Neurons
Type of Award: Catalyst
Date Awarded: September 2017
Amount Awarded: $ 235,371.00

Abstract: Brain diseases are an enormous economic burden worldwide. Stem cell therapy promises to help by rewiring malfunctioning brains: replacing damaged neurons and their connections with new neurons derived from stem cells (SCNs). This promise remains unfulfilled. The sheer complexity of brains (e.g. ~ 100 billion neuronal connections made by ~ 100 million neurons in the mouse) has stymied understanding of fundamental questions about stem cells and brains: how do stem cells navigate this vast ‘jungle’ of nerve cells to arrive at specific sites? How do they connect with neurons already connected to other neurons by thousands of pre-existing connections? We have developed a multi-scale brain mapping imaging platform that reconstructs stem cell derived neurons specifically over entire brains and, with nanometer precision, identifies their neuronal connections. By providing definitive answers about how stem cells integrate into brains, we will identify future targets for improving stem cell therapy for brain diseases.

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PIs: Jaehyuk Choi (NU) and Jun Huang (UChicago) for project:
Novel Single-Cell Analyses of Tumor-Specific T-cells in Merkel Cell Carcinoma
Type of Award: Catalyst
Date Awarded: September 2017
Amount Awarded: $ 250,000.00

Abstract: Despite significant advances in cancer immunotherapy, it is still unclear why the responses to these potentially curative treatments are heterogeneous. This is partally because of our inability, until recently, to identify and characterize, a patient’s entire repertoire of anti-tumor T cells. Current approaches can only detect functionally competent tumor antigen-specific T cells. To overcome this obstacle, we have developed novel single-cell technologies that allow for efficient isolation and comprehensive functional interrogation of tumor-specific T cells. These methods have better sensitivity and defined specificity than current approaches. We propose to validate our approach on Merkel cell carcinoma (MCC), a uniquely immunogenic cancer ideally suited for this study. We will utilize orthogonal single-cell and population based assays to comprehensively elucidate the number and the functional readiness of MCC-specific T cells. These experiments promise to improve our understanding of the immunological heterogeneity present among MCC patients and will validate a novel analytical pipeline that has potentially broad applicability.

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PIs: Ernesto Bongarzone and Steven Roth (UIC), and Joshua Leonard (NU) for project:
Targeted Delivery of Biomolecules to the CNS via Extracellular Vesicles
Type of Award: Catalyst
Date Awarded: September 2017
Amount Awarded: $ 250,000.00

Abstract: The complex structure of the central nervous system (CNS) and its privileged circulatory isolation by the blood-brain barrier pose challenges for delivering therapeutic molecules. A novel means to overcome these challenges is to leverage the advantageous properties of extracellular vesicles (EVs). EVs are cellularly-secreted nanoparticles that transfer RNA, lipids, and proteins to recipient cells via endocytosis and membrane fusion. EVs are highly attractive as therapeutic delivery vehicles, since they exhibit favorable stability, non-toxicity, are non-immunogenic, and may cross the blood-brain barrier (BBB). However, efficiently directing EVs to specific cells remains a limitation. In this proposal, we will use our distinct and complementary expertise to develop novel vehicles for delivering therapeutics to the CNS, by engineering EVs to express surface recognition proteins that direct their uptake by key cells involved in most disease processes in the brain – neurons and oligodendrocytes (OLs). The PIs will leverage their years of experience with the retina and optic nerve, and the spinal cord, as target regions for testing this central hypothesis.

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2016 Fall Round

PIs: Jingyi Fei (UChicago) and Alfonso Mondragon (NU) for project:
Probing the Kinetics of tRNA Recognition by T-box Riboswitch at the Single-molecule Level
Type of Award: Catalyst
Date Awarded: March 2017
Amount Awarded: $ 250,000.00

Abstract: RNA molecules play many roles in the cell, including as regulatory elements to control gene expression at both transcriptional and translational levels. In bacteria, some RNA elements, termed T-box riboswitches, directly affect protein production by responding to the level and aminoacylation state of tRNA molecules. The regulation involves recognition and binding of one RNA molecule by another RNA molecule concomitant with conformational changes in the RNA molecules. We propose to study the kinetic mechanism of this regulation using single-molecule fluorescence techniques. By monitoring individual riboswitch molecules as they interact with tRNAs, we aim to discern the series of functional steps that lead to regulation. The approach we propose is novel and challenging and promises to provide information that cannot be obtain in other manner and help obtain a more complete vista on the way these important molecules work.

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PIs: Laura Sanchez (UIC) and Mark Mandel (NU) for project:
Capturing Host-Microbiome Chemical Communication
Type of Award: Catalyst
Date Awarded: March 2017
Amount Awarded: $ 249,652.00

Abstract: A major area of research is now dedicated to how beneficial bacteria–our “microbiome”–are required for nutrient acquisition, immune and tissue development, and to preferentially occupy niches that otherwise can be overtaken by pathogens. Bacteria dedicate up to 25 % of their genetic material to chemistry, but little is known about how bacteria use chemistry in a host. Therefore a major question now is to understand how chemical communication between the host and colonizing microbe mediate specific interactions. This proposal uses a model system and cutting-edge chemical methods to ask specifically (1) How does the chemical signature of a specific bacterium impact its ability to colonize the host, and (2) What are the key chemical signatures at the host interface during the dynamic process of bacterial colonization? This proposal integrates the technological expertise of the Sanchez Laboratory and the animal and genetic expertise of the Mandel Laboratory.

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PIs: Keith Tyo (NU) and Scott Franzblau (UIC) for project:
A Novel Antibiotic Strategy Exploiting Metabolite Self-Toxicity
Type of Award: Catalyst
Date Awarded: March 2017
Amount Awarded: $ 250,000.00

Abstract: Strains of multidrug resistant Mycobacterium tuberculosis (M. tb) are appearing faster than new antibiotics, threatening a wide-spread re-emergence. This trend is true for many infectious bacteria, and the NIH has made combating antibiotic resistance a key priority. The standard drugging approach of directly inhibiting essential pathways may be exhausted. We propose a fundamentally different approach that could target a new set of non-essential M. tb proteins. Native metabolites that act as competitive inhibitors (CIs) at high levels, can be artificially raised by drug combinations. This proposal seeks to identify potentially toxic native CIs and devise strategies to increase their concentration by modulating enzymatic producers/consumers of the CI (PCI/CCI). If successful, a whole range of compounds that target non-essential enzymes (PCI/CCI) could be made antimicrobial by potentiating this self-toxicity.

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PIs: Jae-Won Shin (UIC) and William Miller (NU) for project:
Single-cell Level Biophysical Control of Platelet Production from Megakaryocytes
Type of Award: Catalyst
Date Awarded: March 2017
Amount Awarded: $ 250,000.00

Abstract: More than 2 million units of platelets are transfused every year in the U.S. Disruption of the supply and a 5-day shelf life can result in critical shortages. Also, platelets are stored at 22°C, so there is risk of bacterial contamination. Thus, it would be very useful to generate platelets on demand. Platelets are made from megakaryocytes (MKs) in marrow, but it remains challenging to efficiently produce platelets outside the body. Platelet biogenesis is highly biophysical: mature MKs in marrow extend tendrils called proplatelets into a neighboring blood vessel, and are fragmented by blood shear to form platelets. However, it remains unknown how this process can be recapitulated to achieve efficient platelet generation. By combining the expertise of Dr. Shin at the University of Illinois at Chicago and Dr. Miller at Northwestern University, we hope to develop novel engineering strategies to maximize the biophysical control of platelet production from MKs.

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PIs: Gregory Schwartz (NU) and Jeremy Segal (UChicago) for project:
Establishing a Comprehensive Typology of Retinal Ganglion Cells
Type of Award: Catalyst
Date Awarded: March 2017
Amount Awarded: $ 250,000.00

Abstract: This project brings together state-of-the-art techniques from genomics and electrophysiology to create a comprehensive parts list of retinal ganglion cells (RGCs), the output neurons of the retina that carry visual information to the brain. The combination of detailed functional and transcriptomic information from individual cells will, for the first time, link specific genetic markers to each RGC type. The information in this parts list will usher in a revolution in our understanding of the vertebrate visual system. Researchers will be able to label particular RGC types throughout development, trace their specific connectivity in the brain, and pinpoint their behavioral implications using cell type-specific ablations. Classifying the diversity of neurons in the brain has been recognized as a vital missing piece in the quest to understand the circuit basis of neurological disease. Our work will serve as a template for classification efforts elsewhere in the brain.

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PIs: Jason Wertheim (NU) and Jeffrey Hubbell (UChicago) for project:
Restoring the Renal Extracellular Matrix Using Engineered Growth Factors
Type of Award: Catalyst
Date Awarded: March 2017
Amount Awarded: $ 248,299.00

Abstract: Far more patients with end-stage kidney disease are waiting for a kidney transplant (>100,000) than the available supply of donor kidneys (<18,000 in 2015), and this shortfall continues to worsen. One novel approach to develop replacement tissues involves removing endogenous cells from an incompatible kidney to produce a three-dimensional (3D) extracellular matrix (ECM) scaffold that can support stem cell differentiation and regeneration of renal tissue. Growth factors signal cells to migrate, proliferate, and differentiate, essential tasks for kidney regeneration, but have not been harnessed for medical applications due to systemic side effects related to escape into the bloodstream. To overcome this limitation, we have engineered growth factors (eGFs) that bind to ECM proteins at the site of administration. We propose to discover new binding sites for eGFs that target specific proteins retained in kidney-derived ECM scaffolds to augment pluripotent stem cell-mediated development of renal tissue.  PERMALINK



2016 Spring Round

PIs: Ankur Saxena (UIC) and Victoria E. Prince (UChicago) for project:
In Vivo Multicellular Dynamics of Neural Crest Stem Cell Migration
Type of Award: Catalyst
Date Awarded: June 2016
Amount Awarded: $ 250,000.00

Abstract: To find solutions for human birth defects, we must understand how vertebrate embryonic development goes awry, but first we must understand how it occurs correctly. The complexity of vertebrate embryogenesis has led to a pressing need for context-dependent, quantitative information regarding how progenitor cells interact system-wide and cooperatively give rise to a variety of cell types and structures. Therefore, we investigate outstanding questions in developmental neurobiology in their natural context, i.e. in vivo, and are particularly intrigued by how the migration of neural crest stem cells produces a variety of neuronal and non-neuronal derivatives. This proposal embraces advances in imaging technologies to observe, manipulate, and quantitate cell-cell interactions and migration at unprecedented spatiotemporal resolution in live zebrafish embryos. The resulting sharper view of systems-level cell biology can shed new light on vertebrate stem cell behavior, the formation of complex body plans, cancer metastasis, and a host of other processes.

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PIs: Chuan He (UChicago) and Yongchao Ma (NU) for project:
Deciphering RNA Methylation in Regulating Neuronal Functions in Health and Disease
Type of Award: Catalyst
Date Awarded: June 2016
Amount Awarded: $ 250,000.00

Abstract: RNA methylation on N6-adenosine is emerging as a critical regulator of RNA function and metabolism. Neurological diseases, including spinal muscular atrophy (SMA), fragile X syndrome, and ALS, share pathogenic mechanisms involving defective RNA metabolism. However, the role of RNA methylation in mammalian neurons and neurological disorders has not been explored. We recently found that fragile X mental retardation protein (FMRP) binds specifically to consensus RNA methylation motifs. In addition, SMN (survival motor neuron) protein, whose expression is disrupted in SMA, interacts with FMRP; while SMA disease-associated SMN mutants can’t interact. We hypothesize that FMRP and SMN read/interpret RNA methylation to regulate RNA localization, degradation and translation. Defects in these mechanisms are particularly exacerbated in polarized neurons with long neurites. Successful completion of the proposed studies will identify FMRP and SMN as new methylated RNA readers, and set the stage for functional investigation of RNA methylation in neurons and neurological diseases.

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PIs: Sadie Wignall (NU) and Michael Glotzer (UChicago) for project:
Spatial and Temporal Dissection of Mouse Meiotic Chromosome Segregation
Type of Award: Catalyst
Date Awarded: June 2016
Amount Awarded: $ 250,000.00

Abstract: Sexually reproducing organisms utilize a specialized cell division program called meiosis to reduce their chromosome number by half to generate haploid gametes. Meiosis in females is especially error-prone and this vulnerability has a profound impact on human health: ~10-25% of human embryos have chromosomal abnormalities, largely as a result of problems during oocyte meiosis. However, despite the importance of oocyte meiosis for successful reproduction, much remains to be learned about how these cells segregate chromosomes. The Wignall lab has discovered a surprising new way that chromosomes segregate in oocytes of the nematode C. elegans, but it is unknown whether this mechanism also operates in humans or other mammals. Here, we will leverage technology developed by the Glotzer lab to answer this question, potentially yielding insight into why so many errors occur during this important and specialized cell division.

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PIs: D. Allan Drummond (UChicago) and Laura Lackner (NU) for project:
Asymmetric Inheritance of a Regulatory Memory by Organelle Tethering
Type of Award: Catalyst
Date Awarded: June 2016
Amount Awarded: $ 250,000.00

Abstract: Stresses such as heat and oxidation cause protein aggregates to form in cells. In assymetrically dividing cells, aggregates containing misfiled proteins are preferentially retained in older cells by becoming tethered to organelles: mitochondria and the endoplasmic reticulum (ER). This has been interpreted as reducing transmission of irreversibly damaged proteins to young cells, which would rejuvenate the cell lineage each generation. Yet, this interpretation is based on studies of foreign proteins, and is challenged by the recent systems-level work in the Drummond lab demonstrating the reversibility of most endogenous stress-induced aggregates, suggesting an alternative regulatory interpretation. By joining forces with the Lackner lab, which has deep expertise in mitochondrial and ER tethering, we propose as integrated biochemical and imaging study of tether-mediated asymmetric aggregate retention. This new collaboration will bring powerful new methods to bear on the fundamental question of how cells selectively transmit information about past events to offspring.

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PIs: Michael Rust (UChicago) and Ravi Allada (NU) for project:
Transplanting a Prokaryotic Oscillator to Animals to Restore Circadian Clock Function
Type of Award: Catalyst
Date Awarded: August 2016
Amount Awarded: $ 250,000.00

Abstract: Life on Earth evolved circadian clocks to optimally align behavior and physiology to the 24-hour environment. Molecular circadian oscillators are found in virtually all organs and tissues and disrupted circadian timing is a hallmark of cardiometabolic, oncological, and neuropsychiatric diseases. Major advances in understanding the fundamental biochemical basis of these circadian timers have been made, culminating in the ability to reconstitute a free running circadian oscillator in a test tube using only three cyanobacterial proteins. These discoveries in prokaryotes open up the possibility of applying synthetic biology approaches to recover and optimize circadian timing in animals using a transgenic oscillator network. Yet the transplantation of complex dynamic systems from prokaryotes to eukaryotes remains a major barrier. Building on our respective expertise in bacterial and animal clocks, we will engineer clock circuits based on bacterial oscillators, which we term “Kai-meras” to generate, restore and tune circadian rhythms in animals.

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2015 Fall Round

PIs: Yuan He (NU), Joseph Piccirilli and Jonathan Staley (UChicago) for project:
Towards the Visualization of Spliceosomal Intermediates
Type of Award: Catalyst
Date Awarded: February 2016
Amount Awarded: $ 200,000.00

Abstract: Our genes are interrupted by nonsense that must be removed during the expression of our genes into proteins, the workhorses of the cell. In gene expression, a gene is first transcribed into a messenger made of RNA, which is similar to DNA. Then, the nonsense is excised and the instructions are spliced together. Lastly, the message is translated to protein. Each step is catalyzed by a macromolecular machine. An understanding of how these machines work requires their visualization at each stage of operation. For over a decade, the transcriptional and translational machinery have been visualized at numerous stages, whereas the first visualization of the splicing machinery has only just been reported. This advance has been enabled by exciting technical breakthroughs in electron microscopy. With our complementary expertise in electron microscopy and splicing machinery, we are uniquely positioned to exploit these breakthroughs to visualize the operation of the splicing machine.

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PIs: Howard Shuman (UChicago) and Heather Pinkett (NU) for project:
Spatiotemporal Control of Protein Function: Ligand Activation of TEV Protease
Type of Award: Catalyst
Date Awarded: February 2016
Amount Awarded: $ 200,000.00

Abstract: Protein complexes carry out essentially all activities of living cells. Although remarkable progress has been made in determining the three dimensional structures of individual proteins, the detailed structures of multi-protein complexes are much more difficult to unravel. Even more challenging is to find out which parts of complexes interact with one another while carrying out their function. The proposed work will develop a simple method to precisely cleave protein complexes with a “protease” that can be targeted to specific sites in protein complexes. The main goal of the proposed work is to develop new forms of the protease that can be turned on by the presence of a small molecule that stabilizes special mutant forms of the protease. This will provide a new method to study protein structure and function.

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PIs: Hyunyoung Jeong (UIC) and Eugene Chang (UChicago) for project:
Role of Gut Microbiota in Determining Drug Efficacy and Toxicity
Type of Award: Catalyst
Date Awarded: February 2016
Amount Awarded: $ 199,998.00

Abstract: Unintentional drug over- or under-dosing is an enormous clinical problem. For example, In 2007, approximately 27,000 unintentional drug overdose deaths occurred in the United States (one death every 19 minutes). Inter-individual variability in the rate of drug elimination is a key contributor to this. Yet, what causes the variability remains uncertain. Potential roles of human genetic differences (among individuals) in the inter-individual variability have been extensively studied over the last 30 years, but we are still unable to predict the rate of drug elimination based on the genetic information alone. Identification of novel factors that cause the variability in drug elimination will lay a foundation for the design of optimal drug therapy and thus enable us to accomplish precision medicine. We propose herein to explore gut microbiota (the aggregate of microorganisms residing in the gut) as a potential contributor to inter- individual variability in drug elimination.

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PIs: Jason MacLean and Stephanie Palmer (UChicago) and David Schwab (NU) for project:
Reading the cortical code for natural motion
Type of Award: Catalyst
Date Awarded: February 2016
Amount Awarded: $ 199,555.00

Abstract: Discovering the language the brain uses to represent the world is a difficult challenge. Currently, our best models are unable to explain 90% of the activity of the visual area of the brain when viewing natural scenes. The current theoretical framework for visual processing in the brain is based on static models that neglect neuron-neuron interactions. Our work takes into account the connected and dynamic nature of real neural activity and makes use of new experimental and computational techniques to improve our model of the brain’s code for motion. In this proposal, we aim to uncover the set of neural activity patterns that are preferentially driven by salient visual input, such as the trajectory of a threatening predator, as opposed to background motion, like the fluttering of leaves in the wind, to optimally predict the future trajectory of moving objects in the world – a key computation performed in neocortex.

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PIs: Christopher Gomez (UChicago) and Jeffrey Savas (NU) for project:
Overlapping cistrons within mammalian mRNAs
Type of Award: Catalyst
Date Awarded: February 2016
Amount Awarded: $ 200,000.00

Abstract: We discovered that the CACNA1A calcium channel gene is actually bi-cistronic, meaning that it can generate two distinct proteins, the calcium channel protein plus a separate transcription factor protein we named 1ACT. This contradicts the “One gene-one polypeptide hypothesis” of Beadle and Tatum (Nobel Prize, 1958). Although exceptions had previously been found, this is the most complete evidence to date for bi-cistronic, protein-encoding vertebrate genes. We have found additional evidence that other ion channel genes contain a second cistron that also encode transcription factors, suggesting a novel gene expression strategy. Curiously mutations of several of these genes leads to complex disease relevant phenotypes, possibly owing to the effect of the mutation on both proteins. We aim to identify the set of bi-cistronic genes that express structural proteins in tandem with transcription factors which inform disease mechanisms.

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PIs: Raymond Roos (UChicago) and Brian Kay (UIC) for project:
Darpins: A New Generation of Protein Therapeutics in Neurodegenerative Diseases
Type of Award: Catalyst
Date Awarded: February 2016
Amount Awarded: $ 200,000.00

Abstract: For many neurodegenerative diseases, antibodies have been used to knockdown cognate proteins that are thought to be pathogenic because they misfold and aggregate; however, antibodies have several shortcomings that limit their effectiveness. This proposal focuses on designed ankyrin repeat proteins (DARPins), which lack many of the shortcomings of antibodies. We recently generated DARPins against mutant (mt) SOD1, which is believed to misfold and cause 20% of cases of familial amyotrophic lateral sclerosis (FALS). We aim to characterize the DARPins and determine whether they prolong survival of ALS in mtSOD1 transgenic mice. We will also test whether mtSOD1 DARPins can react with the normal SOD1 in sporadic ALS, since recent data suggest that sporadic ALS involves abnormalities in the SOD1 protein similar to that seen with mtSOD1. Our studies may lead to new therapeutic directions in ALS and provide a proof of principle concerning the use of DARPins in neurodegenerative diseases.

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2015 Spring Round

PIs: Jason Brickner (NU) and Alexander Ruthenburg (UChicago) for project:
Biochemical Reconstruction of Epigenetic Transcriptional Memory
Type of Award: Catalyst
Date Awarded: September 2015
Amount Awarded: $ 200,000.00

Abstract: Cells respond to environmental signals through changes in gene expression. Previous experience can profoundly alter a cell’s response to environmental signals for multiple generations. Understanding the molecular basis of such adaptive mechanisms may reveal how the environment, aging and lifestyle can have a long-term impact on physiology. The Brickner laboratory has discovered a highly conserved, broadly utilized mechanism called epigenetic transcriptional memory that persists for generations, poising genes for more rapid expression. Using cell biological, genetic and molecular approaches, the Brickner lab has defined important aspects of this phenomenon. However, to fully understand transcriptional memory will require a new approach. Drawing on tools and expertise from the Ruthenburg laboratory, we propose to biochemically reconstitute transcriptional memory in a test tube. This new collaboration will serve as a powerful platform to identify new players in this process and to test mechanistic hypotheses about epigenetic inheritance.

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PIs: Hao F. Zhang and Yevgenia Kozorovitskiy (NU), and Patrick La Riviere (UChicago) for project:
Deep Brain Super-Resolution Imaging of Neuronal Architechture
Type of Award: Catalyst
Date Awarded: September 2015
Amount Awarded: $ 200,000.00

Abstract: The goal of this project is to demonstrate the feasibility of a first-of-its-kind super-resolution optical technology for in vivo deep-brain imaging of neuronal architecture. Our long-term goal is to understand and sculpt neural circuit plasticity through in vivo imaging and neuromodulation, which may transform how we understand and treat neurological diseases, such as Alzheimer’s and Parkinson’s diseases. The 2014 Nobel Prize in Chemistry for achieving nanoscale spatial resolution in optical imaging underscores the significance of optical nanoscopic imaging. However, none of the existing optical nanoscopic imaging technologies can be applied to tissue imaging beyond 100-μm depth. We fill this gap by developing a deep-penetrating (greater than 500 μm) optical technology that can achieve a spatial resolution of at least 100 nm , referred to as two- photon scanning patterned illumination microscopy. During the technology development process, we will image nanosphere phantoms, brain slices, and fluorescently-labeled mouse brain in vivo.

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PIs: Bryan Dickinson (UChicago) and David Gius (NU) for project:
Fluorescent Probes for Live-Cell Imaging of Sirtuin Activity: Applications to Breast Cancer
Type of Award: Catalyst
Date Awarded: September 2015
Amount Awarded: $ 200,000.00

Abstract: Personalized cancer therapy identifies subgroups of patients who will benefit from specific therapies strategies. The Gius lab has identified a subgroup of estrogen positive (ER+) luminal B human breast cancer that exhibits decreased SIRT3 expression or monoallelic deletion using murine models and human breast cancer samples, suggesting SIRT3 is a new target for therapeutic strategies. However, the role of SIRT3 activity in disease progression is unknown, in large part to due a dearth of tools for measuring endogenous activity. The Dickinson lab will design and synthesize a new class of chemical fluorescent probes to measure SIRT3 lysine deacetylation in living systems. Both labs will work together to validate each new tool using in vitro analyses, cell culture, and in vivo murine models. Together, both labs will apply the probes to uncover the mechanistic roles of SIRT3 in breast carcinogenesis, aiming to eventually use these new tools and models to investigate novel therapeutic predictors.

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2014 Fall Round

PIs: Fotini Gounari (UChicago) and Brad Merrill (UIC) for project:
Mapping the Regulation of Wnt Signaling with β-Cat-eleon: A Fluorescent β-catenin “timer”
Type of Award: Catalyst
Date Awarded: February 2015
Amount Awarded: $ 200,000.00

Abstract: All animals possess a version of the Wnt signaling pathway, which transmits signals from outside of cells to DNA in the nucleus. These signals specify cell identities in embryos, and control stem cells in adults. In humans, deregulated Wnt signaling causes cancer in several organs, including the colon, blood, mammary gland and liver. Despite the importance of Wnt signaling, it is not clear how the pathway stimulates its many of its physiological effects. We will develop a novel method of detecting Wnt signaling, named “β-cat-eleon”, which will identify new ways in which Wnt controls cell identities and identify new genetic regulators of Wnt signaling. This research is needed to map how Wnt signaling informs the cell about its environment and the genes needed for this process. Such discoveries are paramount for understanding what goes wrong in diseases such as cancer.

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PIs: Michael Caffrey and Arnon Lavie (UIC), and Balaji Manicassamy (UChicago) for project:
Role of Dynamics in the Structure and Function of Intrinsically Metastable Proteins
Type of Award: Catalyst
Date Awarded: February 2015
Amount Awarded: $ 200,000.00

Abstract: Many proteins function as nanomachines in which conformational changes are prerequisite for their function. Classic examples include myosin-actin in muscle contraction, ATP synthase for ATP generation and active transport, G-Protein Coupled Receptors that relay extracellular signals (GPCR, and the family of proteins that mediate fusion of biological membranes, which are the focus of this proposal. In each of the above cases, an external trigger leads to an alternative conformation relative to the intrinsically metastable (IM) pre-trigger state. Not surprisingly, maintenance of this IM conformation is highly regulated and its destabilization or stabilization may disrupt fundamental biological pathways. Whereas disruption of the IM state often leads to disease, we propose that this vulnerability can be exploited for therapeutic purposes. In this work we have chosen as model system the well-characterized examples of IM proteins that mediate virus fusion with the host cell, a key step in virus infectivity. We hypothesize that local dynamic motions determine the propensity of the IM state transitioning to the alternative stable conformation. Additionally, we suggest that stabilizing or destabilizing mutations, or small molecule agonists or antagonists, can disrupt conformational changes, and function, by altering local dynamics.

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PIs: Jonna Frasor and Terry Moore (UIC), and Geoffrey Greene (UChicago) for project:
Photoaffinity-based Protein Profiling Approach to Discover Estrogen Receptor/ Coactivator Inhibitors
Type of Award: Catalyst
Date Awarded: March 2015
Amount Awarded: $ 199,330.00

Abstract: The estrogen receptor (ER) is expressed in ~75% of breast cancers. Patients who have estrogen receptor-positive (ER+) breast cancer are typically prescribed endocrine therapy, but 1/3 of these cases will fail, for various reasons. It is important to note that ER is still expressed and active in 80- 85% of these therapy-resistant cancers; thus, new ways of targeting ER in breast cancer are needed. Association of ER with coactivators is an important step in ER+ breast cancer, and we will target this interaction as a new potential therapy. Because this interaction is still involved in the majority of endocrine resistant breast cancers, this approach should work in most of these cases and could revolutionize breast cancer therapy.

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PIs: Michael Walsh (UIC) and Aliya Husain (UChicago) for project:
Label-free Chemical Imaging: Early Detection of Heart Transplant Rejection
Type of Award: Catalyst
Date Awarded: April 2015
Amount Awarded: $ 199,745.00

Abstract: Heart transplant remains the most effective long-term treatment of end-stage heart failure. However, despite great surgical success with heart transplants, cardiac allograft rejection, remains a major cause of transplant failure. There are three main types of rejection, acute cellular rejection (ACR), chronic allograft vasculopathy (CAV) and antibody-mediated rejection (AMR). ACR is relatively well understood and treatable while AMR is less well understood and has been associated with worse outcomes including a greatly increased risk for developing CAV. The current gold standard for AMR diagnosis is staining for the protein C4d, however this is a fairly late stage marker of AMR at which point damage has already been done. We propose to develop chemical imaging, which allows for the label-free acquisition of rich-biochemical images that can be used for disease diagnosis. The goals of this proposal are to; 1) Identify a ‘biochemical signature’ of AMR and 2) Identify patients undergoing AMR earlier than is possible using current approaches.

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PIs: Peng Ji (NU) and Amittha Wickrema (UChicago) for project:
Nuclear Opening and Histone Release in Mammalian Terminal Erythropoiesis
Type of Award: Catalyst
Date Awarded: March 2015
Amount Awarded: $ 200,000.00

Abstract: Mammalian red blood cell development involves a dramatic nuclear condensation that is essential for differentiation. However, the mechanism of nuclear condensation is poorly understood. In an effort to fully understand the mechanism of nuclear condensation, we studied nuclear condensation in a temporal fashion using a mouse erythropoiesis model and discovered the presence of a unique nuclear opening from which major histones, except one type of histones, H2AZ, are released out of the nucleus. Based on these novel observations we hypothesize that caspase-3-mediated regulation, and direct involvement of H2AZ in histone replacement and nuclear release are responsible for chromatin condensation during mouse and human red blood cell development. Successful accomplishment of the proposed research will reveal a novel facet of red blood cell development, which could provide critical insights in the pathogenesis of certain red cell diseases with defective nuclear condensation and/or terminal differentiation.

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PIs: Brian Murphy and Rachel Poretsky (UIC), and George Wells (NU) for project:
Co-occurance and Implications of Antibiotic Production and Resistance Genes in the Environment
Type of Award: Catalyst
Date Awarded: March 2015
Amount Awarded: $ 199,982.00

Abstract: Microorganisms have been the primary source of clinically used antibiotics for nearly a century, though the constant rediscovery of known compounds using traditional drug discovery approaches has not kept pace with evolving resistance to existing antibiotic treatments. Since nature is a reservoir for antibiotics and antibiotic resistance genes, it is critical that we understand how these genes are distributed in the environment in order to reveal patterns of co- occurrence, and develop a targeted approach to antibiotic-lead discovery from environmental microorganisms. In this study, we will use advanced sequencing techniques and data analysis to map the occurrence of antibiotic production and resistance genes emanating from wastewater treatment plants that discharge into Lake Michigan and Lake Erie. This information will be used to predict how antibiotic production and resistance genes are transmitted in nature and will facilitate the development of a more targeted approach toward the discovery of antimicrobials.

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2014 Spring Round

PIs: Erik Andersen (NU) and Ilya Ruvinsky (UChicago) for project:
Uncovering ‘Missing Heritability’ in Any Experimentally Tractable Model Organism
Type of Award: Catalyst
Date Awarded: August 2014
Amount Awarded: $ 200,000.00

Abstract: Completion of the human genome project provided a first glimpse at our genetic blueprint. However, the DNA sequence is only part of the story – we must be able to interpret that genetic information. Previous studies showed that many traits, including disease susceptibility, are inherited in families, suggesting that identifying causal genes could be invaluable to diagnosis and treatment of these conditions. Over the past ten years, hundreds of genes that contribute to common disease have been identified. However, to our great surprise, they only predict a small fraction of the differences in disease susceptibility. How is it that these diseases have a strong genetic component yet we fail to identify most of the important genes? Plausible explanations range from genetic to statistical mechanisms. Importantly, none of these explanations can be feasibly tested in humans. Because these experiments are cost-prohibitive or impossible to do in humans, we propose to leverage the power of a model organism routinely used in biomedical research to rapidly test each of these hypotheses. Specifically, using Caenorhabditis elegans, we will: first create a large panel of reagents paired with high-throughput assays to achieve statistical power beyond what is possible in humans; this effort will define the bounds for genetic correlation studies in multicellular animals and second develop additional experimental measurement paradigms to determine how genetic contributions are altered by variable environments. Our project will empirically explore a vexing question, namely why genes identified so far explain little of the differences we see among individuals. It will thus contribute both to basic understanding of genetics and to the practical problem of identifying hereditary bases of susceptibility to common diseases in humans. This research effort will help to establish a long-term collaboration between two research groups that share common interests and possess complementary expertise.

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PIs: Zhijian Qian (UIC) and Wei Du (UChicago) for project:
Control of Hematopoietic Stem Cell Expansion by Inhibition of Axin Polymerization
Type of Award: Catalyst
Date Awarded: August 2014
Amount Awarded: $ 200,000.00

Abstract: Cell based therapies represent promising treatment strategies for many diseases at the frontier of medicine and are often limited by the ability to generate sufficient amount of stem/progenitor cells. The beta-catenin signaling pathway is highly conserved between flies and mammalian systems and plays critical roles in controlling the self-renewal, proliferation, and differentiation of many types of stem/progenitor cells. However little is known of how the beta-catenin signaling can be controlled to specifically modulate stem/progenitor cell self-renewal and proliferation without affecting their differentiation. While null mutants of Drosophila Axin, a key negative regulator of beta-catenin pathway, affects both stem/progenitor cell self-renewal, proliferation, and differentiation, recent studies from the Du lab revealed that disrupting the DIX domain of Axin, which blocks Axin polymerization, only promoted stem/progenitor cell self-renewal, proliferation, but did not affect their differentiation. These observations suggest that inhibition of Axin polymerization can potentially be used to specifically control stem/progenitor cell self-renewal and proliferation without affecting their differentiation. This discovery sparked a new collaboration with the Qian lab at UIC, who has significant expertise studying the roles of the Wnt signaling in hematopoietic stem cells (HSCs). The new collaboration is aimed at developing a novel approach to modulate HSCs self-renewal and proliferation without affecting their differentiation. For this proposal, the Qian lab will generate a mouse model with Axin polymerization mutation in HSCs and will test the effects of disrupting Axin polymerization on HSC self-renewal, proliferation, and differentiation. The Du lab will develop high-throughput cell imaging based assays for Axin polymerization and will screen for compounds that can inhibit Axin polymerization. These studies will potentially lead to the identification of compounds that can promote the expansion of HSCs in vitro and improve clinical outcomes for HSC transplantation.

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PIs: Norbert Scherer (UChicago) and Oliver Cossairt (NU) for project:
Development of a 3D Snapshot Holographic Microscope for Volumetric Live Cell Imaging
Type of Award: Catalyst
Date Awarded: August 2014
Amount Awarded: $ 199,633.00

Abstract: We propose to develop a 3D Snapshot Holographic Microscope (3D-SHM) capable of imaging whole live cells in all 3 dimensions in a single “snapshot.” The instrument combines independent developments in the Cossairt and Scherer/Jureller labs. This will enable imaging motion (dynamics) of cellular processes by brightfield, darkfield, and fluorescence microscopy modalities. A specific goal is developing greater understanding of intracellular transport and secretion of insulin granules in living cells. However, other biological and non-biological processes and systems can be studied with the 3D-SHM.

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PIs: Mark Mandel (NU) and Nancy Freitag (UIC) for project:
Klebsiella Pneumoniae Pathogenesis in Immunocompetent and Immunosuppressed Hosts
Type of Award: Catalyst
Date Awarded: August 2014
Amount Awarded: $ 200,000.00

Abstract: Hospital-acquired bacterial infections are an insidious public health threat. In recent years patient deaths have been linked to a new class of superbugs, Carbapenem-resistant Enterobacteriaceae (CRE), which are primarily Klebsiella pneumoniae (Kpn) and Escherichia coli bacteria (1). There has been a pronounced alarm about the rising threats posed by these bacteria; PBS Frontline has called them “Nightmare Bacteria” and the NY Times announced “Deadly Bacteria That Resist Strongest Drugs Are Spreading”. The Centers for Disease Control and Prevention (CDC) has labeled CRE bacteria as one of the top threats to public health (1). Unfortunately, they are resistant to modern antibiotics. This proposal applies proven modern genetic approaches to discover which bacterial genes and proteins are required to cause these lethal infections. It further explores whether propofol, the most commonly-used anesthetic drug for surgeries and intubation, increases patient susceptibility to CRE infection. Together, these studies will lead to a greater understanding of hospital-acquired CRE infections as well as the identification of Kpn proteins that can be targeted for novel therapies to eliminate hospital-based transmission of this deadly pathogen. This proposal addresses new complementary avenues of investigation for both the Mandel and Freitag Laboratories.

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2013 Fall Round

PIs: Russell R. Reid and Tong-Chuan He (UChicago), and Guillermo Ameer (NU) for project:
Craniofacial Tissue Engineering with Citric-Acid Based Nanocomposite Scaffolds
Type of Award: Catalyst
Date Awarded: April 2014
Amount Awarded: $ 166,008.00

Abstract: Craniofacial skeletal defects secondary to trauma (e.g., war or other ballistic injury), tumor, or congenital disease present challenging problems for reconstructive surgeons. One limitation in the repair of these defects lies in the finite supply of autologous tissue (i.e., bone) available. Engineering bone using osteoinductive scaffolds and cells capable of expansion and differentiation is a promising strategy. Two significant challenges exist: 1) in vivo induction of readily available stem cells that are effective towards craniofacial defect healing and 2) designing novel biomaterials that are amenable to such defects and provides a three-dimensional architecture for appropriate defect healing. Multidisciplinary strategies are required that combine materials science, cell biology, and clinical sciences effectively and seamlessly. Our project therefore mandates a multi-institutional approach that involves disciplines from two independent academic institutions, whose strengths are: 1. Molecular biology/animal model studies that have established the potency of BMP-9 in inducing stem cell osteogenesis both in vitro and in vivo (University of Chicago); 2. Biomaterials for tissue engineering applications, specifically novel, citric-acid based nanocomposite scaffolds (Northwestern University).

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PIs: Tao Pan and Marsha Rosner (UChicago), and Hidayatullah G. Munshi (NU) for project:
Extra-translational Function of Transfer RNA as Regulators of Cellular Processes
Type of Award: Catalyst
Date Awarded: January 2014
Amount Awarded: $ 199,998.00

Abstract: Communications between cellular processes are essential in homeostasis and in cellular response to environmental change. Protein synthesis is a major process that consumes a vast amount of materials and energy in the cell. Hence, coordination of protein synthesis activity with other cellular processes such as cell cycle control, histone modification, membrane trafficking and so on should be crucial for cell physiology. We have discovered recently that tRNAs may serve as a major class of communicators in the cell. We found that tRNAs bind to a wide array of cellular proteins such as the mitogen-activated protein kinase kinase (MEK), histone methyltransferase 1, GTP-binding protein SAR1a, farnesyl-transferase, glutathione synthetase, and phosphoenolpyruvate carboxykinase; none was known previously to interact with any nucleic acids. We hypothesize that tRNA binding regulates the activity of these proteins in response to the translation activity in the cell. When translation activity is high, only a small amount of tRNA is available, and these tRNA-protein interactions are present only at low levels. When translation activity decreases, more tRNA becomes available to increase the level of these tRNA- protein interactions in order to up- or down-regulate the cellular processes these proteins participate in. Here, we propose to test this hypothesis for the MEK-tRNA interaction in vitro and in non-tumorigenic and pancreatic cancer cells. Aim 1 will validate MEK-tRNA interaction in non- tumorigenic and pancreatic cancer cells. Aim 2 will test MEK binding to tRNA in vitro, and generate MEK mutants that disrupt binding. Aim 3 will test the physiological effect of such MEK mutants in 3D cell cultures. Our results should reveal a potential new paradigm for cellular communications involving RNA-protein interactions.

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PIs: Phoebe A. Rice (UChicago) and H. Steven Seifert (NU) for project:
Structural Basis for RecA Filament Nucleation by the Neisseria PilE G Quadruplex Motif
Type of Award: Catalyst
Date Awarded: March 2014
Amount Awarded: $ 200,000.00

Abstract: All organisms, from viruses to bacteria to humans need to be able to mix DNA sequences. This ability to recombine DNA corrects mistakes in DNA, allows for evolution to work, and provides genetic diversity. The RecA protein is the central enzyme that allows cells to mix DNA sequences and is therefore one of the most well-studied enzymes known. The human pathogens Neisseria gonorrhoeae and Neisseria meningitidis use RecA to initiate a specialized form of recombination that helps evade the immune system called antigenic variation. Antigenic variation requires an alternative form of DNA called a guanine quartet or G4 structure, and we have recently shown that the RecA protein binds the G4 structure required for antigenic variation. This work will use structural assays to define how RecA binds the G4 structure.

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PIs: Lee Miller (NU) and Sliman Bensmaia (UChicago) for project:
Probing Somatosensory Representations in the Brainstem of Awake Monkeys
Type of Award: Catalyst
Date Awarded: April 2014
Amount Awarded: $ 200,000.00

Abstract: We seek CBC Catalyst funding toward a collaborative effort among senior and junior faculty at Northwestern University and the University of Chicago, including neuroscientists, a biomedical engineer and a neurosurgeon, to achieve the first recordings of signals from the cuneate nucleus (CN) in awake animals. CN is a tiny, previously inaccessible, structure at the base of the brainstem that is the gateway for sensory signals from our arms to our brain. A Catalyst award will allow us to generate foundational scientific data that will illuminate the poorly understood role of CN in processing information about somatosensation–our sense of touch and limb position. Furthermore, these experiments will allow us to establish the scientific foundation for a groundbreaking longer-term effort: to use CN as a neural interface to restore touch and proprioception for amputees and patients with spinal cord injury.

The neural basis of many aspects of somatosensation are well known: The properties of afferents innervating the skin, joints, and muscles have been studied and modeled extensively, as have those of neurons in somatosensory cortex. However, the role of CN in somatosensory processing is largely unknown. Anatomical studies have revealed the location of different types of ascending inputs within CN and the presence of descending, cortical inputs, but the functional properties of CN neurons have never been probed in awake animals because of the technical difficulty of accessing this structure. To fill this gap, we will implant an electrode array in the CN of Rhesus macaques using a unique, bioinspired adhesive. We will record the activity of CN neurons while the monkeys perform a variety of sensory and motor tasks. Preliminary results enabled by the Catalyst award will fill a significant gap in knowledge about somatosensory processing, while opening an exciting new avenue for the development of sensory neuroprostheses.

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PIs: Michael J. Federle (UIC) and Matthew Tirrell (UChicago) for project:
Immunotherapy-Mediated Interference of Bacterial Quorum Sensing
Type of Award: Catalyst
Date Awarded: February 2014
Amount Awarded: $ 200,000.00

Abstract: Our society faces a significant moment in modern health care where many antibiotics have lost their effectiveness in treating life-threatening and debilitating diseases due to the emergence of multi-drug resistant bacteria. New antibiotics are desperately needed; yet because antibiotics inhibit growth or kill bacteria, they drive the evolution of bacteria to become drug-resistant and make antimicrobial drugs a non-ideal long-term strategy to treat infectious diseases. An alternative approach is to use anti-virulence strategies that target the underlying causes of disease without inhibiting bacterial growth, limiting the capacity for bacteria to develop treatment resistance. The Federle lab has discovered several new signaling pathways that are responsible for microbial cell-to-cell communication and play a prominent role in their ability to cause disease. Our approach utilizes the Tirrell Lab’s ability to synthesize immunostimulatory biomaterials in order to generate antibodies specifically aimed at bacterial communication pathways. The Federle lab will utilize methodologies developed in the group to assess activity and function of the antibodies. Together, we will test the hypothesis that antibodies generated to disrupt bacterial communication hold the potential to inhibit pathogenesis.

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PIs: Godfrey S. Getz (UChicago) and Edward Thorp (NU) for project:
ApoA-I Mediated Regulation of Inflammation and Heart Repair after Heart Attack
Type of Award: Catalyst
Date Awarded: March 2014
Amount Awarded: $ 199,954.00

Abstract: Increased lipids/lipoproteins are a significant risk factor in the progression of heart failure after heart attack/myocardial infarction (MI). Impaired wound healing in the heart is associated with heightened inflammation and reduced ratios of high density lipoprotein (HDL) in the blood. Besides its role during the transport of cholesterol in the circulation, HDL has also been implicated as a regulator of key cellular events during cardiovascular disease. For example, HDL has anti-apoptotic activity, especially in endothelial cells, which is critical during angiogenesis after ischemia. Importantly, HDL levels predict morbidity and mortality after MI in humans. Recent evidence interestingly highlights HDL as a suppressor of immune cell proliferation. This is a revealing insight as mobilization of the immune response directly impacts heart repair. Herein we hypothesize that inflammation resolution and heart repair after heart attack is enhanced by ApoA-I, a significant component of HDL. This will be examined for the first time in an ApoA- I deficient mouse model by measuring cardiac function and immune cell trafficking to the heart after experimental MI. Because of the high clinical occurrence of secondary MIs, we will also examine the influence of ApoA-I on MI-induced enhancement of atherosclerosis, as well as the complementary effect of MI on HDL function. Finally, the therapeutic potential of this pathway will be tested with APOA-I peptide mimetics. Taken together, these studies will lay the ground work to determine for the first time the significance of ApoA-I after heart attack at a physiological level and its therapeutic potential.

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2013 Spring Round

PIs: Stephen J. Kron (UChicago) and Preston T. Snee (UIC) for project:
Radiation-guided delivery of quantum dot theranostic nanoparticles
Type of Award: Catalyst
Date Awarded: September 2013
Amount Awarded: $ 200,000.00

Abstract: The emerging field of “theranostics” (therapeutic diagnostics) has found powerful applications in cancer. Here, a single agent might serve both as a chemotherapy and as a contrast agent to image the tumor and gauge the effects of therapy. Recent advances have been in engineering nanomaterials to combine an imaging probe with the capacity to deliver a molecular payload. The Kron lab at UC hopes to apply theranostics to radiotherapy (RT), using imaging to improve treatment planning and to improve outcomes by the delivery of radiosensitizers. They hope to exploit the newly described radiation-enhanced permeability and retention (R-EPR) effect. Here, radiation disrupts the endothelial barrier between the bloodstream and tumor, permitting macromolecules and nanoparticles to flow in. This discovery has sparked a new collaboration with the Snee group at UIC, pioneers in fluorescent quantum dot (QD) chemistry, aimed at developing novel imaging and drug delivery agents. While QDs are bright and stable nanoparticle fluorophores, the complexity of synthesis and functionalization has prevented their broad applications in biology. Snee has developed novel chemistry to achieve high solubility and stability as well as to coat QDs with drugs and DNA. For this project, Snee will develop synthetic methods to produce near-infrared (NIR) fluorescent QDs, allowing their detection within living mice, and to coat the QDs so they circulate freely in the blood while carrying payloads such as chemotherapy drugs or gene therapies. Kron will then optimize R-EPR delivery of these QD theranostic agents, using imaging to follow the accumulation of QDs in the tumor and to monitor the effects on tumor responses to radiation. Demonstrating the ability to target and eliminate tumors with radiation- guided nanoparticle theranostics can be rapidly translated to significantly improve the value of radiosurgery for cancer.

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PIs: Andrei Karginov (UIC) and Michael Glotzer (UChicago) for project:
An “And-Gate” for Optogenetic Control Of Protein Kinases
Type of Award: Catalyst
Date Awarded: September 2013
Amount Awarded: $ 200,000.00

Abstract: A vast array of cellular behaviors are regulated by a class of enzymes called kinases that catalyze the covalent addition of negatively charged phosphate groups to specific sites on other proteins. This simple, reversible modification controls diverse processes including, but not limited to, cellular organization, intercellular communication, as well as cell growth, division, migration, and death. An individual kinase can regulate distinct processes by acting on different substrates at different subcellular sites. In order to decipher the complex functions of different kinases, it would be extremely beneficial to be able to control the time, place, and duration in which a particular kinase is active. However, we currently lack the tools to control kinases with this precision. In independent work, Drs. Karginov and Glotzer had developed tools that address portions of this goal. Dr. Karginov developed a method to control kinases by the use of a small molecule activator; this provides a degree of temporal control. Dr. Glotzer’s lab has developed a method to control protein- protein interactions with light; this provides general spatial and temporal control, but not control of kinase activity. By combining our technologies and refining the hybrid technology, we seek to generate active forms of specific kinases at any desired subcellular site. If successful, these tools will further our understanding of the functions of this critically important class of enzymes.

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PIs: Michael Jewett (NU) and Jared Lewis (UChicago) for project:
Engineering Prokaryotic Translation for Artificial Metalloenzyme Production
Type of Award: Catalyst
Date Awarded: September 2013
Amount Awarded: $ 200,000.00

Abstract: The extraordinary synthetic capability of protein biosynthesis has driven extensive efforts to engineer translation systems to create proteins containing unnatural amino acids (UAAs). However, UAA incorporation efficiency is ca. 1000x lower than that of natural AAs due to the challenge of re-engineering a system of nearly 80 separate macromolecules. We will identify and eliminate bottlenecks in this system to enable incorporation of organometallic (M)UAAs into proteins. Specifically, we will study MUAA bioavailability, explore interactions between EF-Tu and MUAA-tRNAs, and evolve the entire translation system for maximal MUAA incorporation efficiency. Our work will expand understanding of the translation apparatus, provide a general platform to incorporate any UAA of interest, and facilitate direct expression of a new class of artificial metalloenzymes (ArMs). ArMs combine the selectivity and evolvability of enzymes with the bond forming capabilities of organometallic catalysts. We are particularly interested in non-biogenic metal complexes (e.g., Pd, Ir, and Rh) to promote site-specific C-H functionalization reactions. Such reactions are not currently possible using small molecule catalysts, and they could greatly expand the scope of metabolic engineering for chemical synthesis and enable new methods for direct interrogation of biomolecules in vivo.

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PIs: Robert Daum (UChicago) and Michael E. Johnson (UIC) for project:
A Novel Antimicrobial Strategy Against Methicillin-Resistant S Aureus (MRSA)
Type of Award: Catalyst
Date Awarded: September 2013
Amount Awarded: $ 200,000.00

Abstract: Staphylococcus aureus (Staph) is the most common cause of bacterial skin infections and an important cause of invasive disease and life threatening illness. Methicillin (Mc) is a penicillin antibiotic that was once the mainstay for treatment of Staph infections. However, strains that are Mc-resistant (known by the acronym, MRSA) have been increasing in prevalence and virulence in recent years. Since MRSA strains are resistant to nearly all penicillin antibiotics and are often resistant to other antibiotic classes as well, new antibiotics are desperately needed to treat MRSA infections. We propose to identify chemical inhibitors of an important Staph antibiotic sensing system called vraTSR that can be used in combination with Mc or its modern day chemical relative, oxacillin (Ox), to treat MRSA infections. We reason that combining such an inhibitor with Ox will effectively treat patients that are infected with MRSA strains. Our idea is to find inhibitors of VraTSR, a system that is required by MRSA strains to stay resistant to Ox. Therefore, this proposal specifically seeks to identify chemical inhibitors of VraTSR that can block resistance and move these inhibitors closer to the clinical marketplace.

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PIs: Jie Liang and Amy Kenter (UIC), and John Marko (NU) for project:
Characterizing in Vivo Chromatin Folding Landscape of IgH locus on Chromosome 12
Type of Award: Catalyst
Date Awarded: September 2013
Amount Awarded: $ 199,998.00

Abstract: Gene expression is controlled by combinations of regulatory elements that interact over long distances. Chromosome conformation capture (3C) and related techniques have led to the discovery of looping interactions among distant chromosomal elements, thereby providing a mechanism for long range enhancer function. However, the looping events responsible for immunoglobulin (Ig) gene rearrangements, which are key events in the assembly of functional Ig genes required for mature humoral immune responses, are currently unknown. Aberrant V(D)J joining occurs at surprisingly high frequency and often leads to recurrent chromosomal translocations with specific oncogenes. The chromosomal translocations originating from aberrant V(D)J joining are precipitating factors in leukemiagenesis. Recurrent nonrandom chromosomal translocations may be due to spatial proximity of broken chromosomal ends at the time of V(D)J joining. We present here two highly inter-related projects that requires the expertise of each investigator to create exciting new synergies with the potential for cutting edge new technologies and experimental insights. Using new methodology under development by Dr. Kenter, a defined segment of chromatin will be isolated in vivo and its biophysical properties will be measured by Dr. Marko using his single-chromatin fiber nano-tweezers technology. Dr. Kenter has generated massively parallel large scale measurements of long range chromosomal interactions spanning the Igh locus and the surrounding areas. Using this information, Dr. Liang will apply his novel sequential Monte Carlo algorithms, built upon a polymer chromosome model of explicitly constructed chromatin chains , to assemble ensemble 3D chromatin structures of the Igh locus. This information will be leveraged to better understand sites within the Igh locus that are at high risk for chromosomal translocations and the propensity toward leukemia and lymphoma, and will lay the groundwork for efficient large scale modeling of full chromosomes.

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PIs: Thomas Gajewski and Haochu Huang (UChicago), and Xiaozhong Wang (NU) for project:
Identifying Immune Evasion Mechanisms in Tumors Via a Genome-Wide shRNA Screen
Type of Award: Catalyst
Date Awarded: September 2013
Amount Awarded: $ 199,998.00

Abstract: Tumors and the host immune system interact in an intricate and dynamic manner. Many pieces of evidence suggest that the immune system can prevent tumor formation, yet tumors do occur in individuals with a competent immune system. It has long been thought that the tumor- suppressing actions of the immune system result in the selection of tumor variants that are invisible to the immune system or have acquired other mechanisms to evade or suppress immune attack. Indeed, some tumors that recur after successful immunotherapy often possess immunoresistant phenotypes. Thus it is critical to understand the mechanisms by which tumors become refractory to immune attack. We propose to study these mechanisms in a well-controlled tumor model where tumors are killed by tumor specific CD8+ T cells. We will use a genome-wide shRNA library to knock-down genes in tumor cells to screen for tumor variants that escape the immune attack. Understanding these mechanisms will help us to develop better immunotherapy for cancer.

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2012 Fall Round

PIs: Tian Wang (UIC) and Hans-Georg Simon (NU) for project:
Proteomic Characterization of Epicardial-Myocardial Signaling and Regenerative Activity
Type of Award: Catalyst
Date Awarded: February 2013
Amount Awarded: $ 200,000.00

Abstract: Each year, about 650,000 people in the United States survive a heart attack only to have a scar replace the damaged muscle tissue. The loss of muscle can have severe consequences over time, often leading to congestive heart failure and death. As the infarcted heart does not heal by itself, one of the goals of regenerative medicine is to replace the damaged tissue with viable muscle that is physiologically normal in its contractile and conductive properties. Current research in cardiac repair is focused on the use of stem cells, an approach that has several inherent disadvantages. Recent studies suggest that the epicardium – the outer layer of cells that cover the heart muscle – harbors dormant progenitor cells that can be activated and serve as a source for new cardiomyocytes. Here we seek to capitalize on the expertise in place in two major Chicago research institutions and combine efforts and unique resources in a synergistic manner to identify novel protein targets for the stimulation of epicardial cells for resident-cell-based cardiac repair. The successful outcome of the planned studies will be a significant step forward to enhance cardiac repair in humans.

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PIs: Bruce Lahn (UChicago) and John Crispino (NU) for project:
Dissecting cis versus trans regulation of gene expression using in vitro transcription
Type of Award: Catalyst
Date Awarded: February 2013
Amount Awarded: $ 200,000.00

Abstract: A central focus of biology is how different cell types within a multicellular organism acquire their distinct gene expression patterns. Despite intense research, this important question remains poorly understood, owing chiefly to the complexity of regulatory mechanisms controlling transcription. The current proposal is aimed at bringing one important level of clarity to that complexity, namely, to develop an experimental system capable of dissecting cis versus trans regulation of gene expression. Specifically, we propose to develop a method capable of distinguishing whether the silent state of a gene is caused by diffusible factors acting in trans of the gene or chromatin modifications acting in cis of the gene. As a proof of concept, we will apply this method to the study of gene regulation in blood development. By bringing greater insight into the understanding of cell-type-specific gene regulation, this proposal has the potential to make a significant impact on many areas of biomedicine.

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PIs: Primal de Lanerolle (UIC) and Steven T. Kosak (NU) for project:
Nuclear Actin and Genome Organization
Type of Award: Catalyst
Date Awarded: February 2013
Amount Awarded: $ 200,000.00

Abstract: Why are there no actin filaments in the nucleus? Actin filaments are rampant in the cyto- plasm and the concentration of actin in the nucleus is well-above the concentration needed for the spontaneous polymerization of actin. Still, nuclear actin does not normally polymerize into fila- ments. The presence of actin in the nucleus was first described in 1967 and the absence of nucle- ar actin filaments (NAFs) has bedeviled cell biologists since then. We may have the answer to this paradox. We have found that actin filaments, which form in the nucleus in certain pathological conditions, change the structure of DNA. Therefore, the objective of this proposal is to lay the foundation for understanding how NAFs alter genome organization and what this means in terms of the health and survival of cells. Results from these experiments may yield critical insights into the physiological role of nuclear actin in defining genome form and function and how this role is abrogated in diseases, especially neurodegenerative disorders that are associated with NAFs.

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2012 Spring Round

PIs: John P. O’Bryan (UIC) and Shohei Koide (UChicago) for project:
Development of novel affinity reagents to monitor different activation states of Ras GTPases in cells
Type of Award: Catalyst
Date Awarded: June 2012
Amount Awarded: $ 200,000.00

Abstract: Ras proteins are highly conserved signaling molecules that play critical roles in normal cell growth, and Ras mutations contribute to many forms of human cancer. Thus, molecular mechanisms underlying Ras function has been intensely studied. Ras functions as a molecular switch, cycling between two different states: an active and inactive form. However, we have discovered a third form of Ras that plays an important role in regulating cell signaling. It is generally considered that the third form of Ras exists too transiently in the cell to be functionally important. However, our new discovery suggests that this form is stabilized by interaction with specific proteins also important in cell signaling, thus increasing the lifetime of this form of Ras to a biochemically relevant level that may impact signaling. Our finding is potentially paradigm-shifting in this intensely studied field, and warrants further investigation. A major bottleneck, however, is a lack of suitable research tools. The goal of this proposal is to apply sophisticated protein- engineering technologies to develop biochemical tools that will allow for measurement of the levels of all three forms of Ras. Furthermore, we will use these tools to selectively interfere with the functioning of specific forms of Ras so that we can gain a more complete understanding of their roles in regulating cancer cells.

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PIs: Geoffrey Kansas (NU) and Ravi Salgia (UChicago) for project:
Common bone marrow homing pathways for HSC and SCLC stem cells
Type of Award: Catalyst
Date Awarded: July 2012
Amount Awarded: $ 200,000.00

Abstract: Small cell lung cancer (SCLC) is a nearly invariably fatal disease, with a 5 year survival rate of <10%. This extremely poor prognosis is due almost completely to the strong tendency of malignant cells to metastasize to distant organs, of which the bone marrow (BM) is a major site. However, molecular mechanisms which underlie metastasis of SCLC to BM remain largely unknown. Hematopoietic stem cells (HSC) home to BM via a multistep process entirely analogous to mature leukocyte recruitment to sites of inflammation or infection: selectins initiate recognition of the blood vessel wall by mediating tethering and rolling of leukocytes along the endothelium; chemokines on the lumenal surface activate integrins on the rolling cells; and these activated integrins mediate firm arrest and subsequent transmigration into the tissue. In the case of HSC, it is known that the endothelial selectins (E- and P-selectin) are constitutively expressed on BM sinusoidal endothelium and mediate the initial rolling step, that the chemokine CXCL12/SDF-1 binding to its monogamous receptor CXCR4 on HSC mediates the second step, and that the broadly expressed integrin VLA-4 on HSC mediates the third step via binding to its cellular ligand on BM endothelium VCAM-1. Each of these molecules may also comprise part of the HSC “niche”, the specialized microenvironment in the BM responsible for HSC maintenance, regulation and survival. We have shown that 100% of SCLC cells also express CXCR4, and scattered reports suggest that at least some SCLC can express glycan ligands for the endothelial selectins. These findings suggest that SCLC, and by implication other BM-tropic metastatic cancers, “hijack” the normal homing pathway used by HSC. If true, this would represent a major advance in understanding the molecular basis of metastasis, and should provide an array of targets for preclinical and translational studies.

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PIs: Richard Longnecker (NU), Lijun Rong (UIC) and Bernard Roizman, ScD (UChicago) for project:
Genome Wide siRNA Screen for Host Factors Required for Human Herpesvirus (HHV) Latency
Type of Award: Catalyst
Date Awarded: September 2012
Amount Awarded: $ 200,000.00

Abstract: The proposed research focuses on two human herpes viruses (HHVs), herpes simplex 1 (HSV-1) and Epstein-Barr virus (EBV). These viruses represent divergent members of the HHV family that infect humans and cause a range of diseases that can be life threatening. The divergence in their gene content is reflected in their life-styles. Whereas HSV-1 establishes latency in neurons, causes encephalitis and is a major cause of blindness in USA, EBV establishes latency in white blood cells and is associated with a wide range of human cancers. In principle viruses depend and subvert cellular gene products to do the work for them. The focus of this proposal takes into account this fundamental finding and centers on two key questions: The first is what genes enable the two human herpes viruses to actively replicate at the site of initial infection yet remain silent (latency) for years at a time in neurons (HSV-1) or B cells (EBV). The second key question is what cellular genes are responsible for either establishment or termination of latent state. Because EBV and HSV-1 establish latency in very different cells, we hypothesize that these viruses will have commonalities and differences with the cellular genes that enable them to replicate in some cells and establish latent, silent infections in others. We propose to use highly efficient state of the art screening methods to identify the cellular genes that are required for regulating the latent phase of these two viruses. We predict that HSV-1 and EBV require both common and different cell factors for the latent life cycle phase. The identification of cellular genes required for establishment and maintenance will allow development of novel therapeutics effective against a broad range of human herpes viruses.

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PIs: Brian Kay (UIC), Eric Weiss and Milan Mrksich (NU) for project:
Genome-scale identification of protein docking interactions
Type of Award: Catalyst
Date Awarded: August 2012
Amount Awarded: $ 197,394.00

Abstract: Networks of interacting proteins inside cells direct their behavior. When functioning properly, these systems ensure correct organization and function of cells in normal tissues. In contrast, their derangement can lead to deadly and debilitating illnesses, notably cancer and age-related disorders. It is therefore critical to understand the rules that govern protein interactions in both healthy and diseased cells. A specific class of interactions has proven both centrally important and incredibly difficult to identify and study: brief, dynamic associations through short “docking motifs”. In essence, these motifs are like “words” through which proteins recognize each other. Such interactions are critical for proper function, as they localize proteins such as kinases to different parts of the cell and contribute to substrate specificity. Using a new computational method, we found that there are probably hundreds more of these words than previously understood. For the vast majority of them no function is known. This project will develop and combine two new approaches to study thousands of these potential docking motif interactions in a single experiment. The groups of Milan Mrksich at NWU and Brian Kay at UIC will pursue these novel screening approaches, and the group of Eric Weiss at NWU will develop ways to parallelize production of proteins for analysis. Overall, this promises to provide unique insight into a crucial part of cellular “wiring diagrams” that is currently missing from contemporary molecular biology.

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2011 Fall Round

PIs: Alan Leff (UChicago) and Terry Vanden Hoek (UIC) for project:
Design and Delivery of TAT Fusion Proteins for CPR
Type of Award: Catalyst
Date Awarded: January 2012
Amount Awarded: $ 200,000.00

Abstract: Cardiac arrest is a leading cause of death among women and men in the United States, with a greater public health impact than cancer, HIV, stroke or infectious diseases. Despite this public health challenge, no drugs have been developed for cardiopulmonary resuscitation (CPR) that improve long-term survival after cardiac arrest. Only a few therapies—use of a defibrillator, CPR with high quality chest compressions, and mild cooling—appear to improve long-term survival after cardiac arrest. These interventions affect most the heart and brain, but how these interventions such as cooling “work” in the heart and brain is not known. Recent clinical experience suggests that patients can survive remarkably long periods of cardiac arrest that exceed 30 minutes. These patients return back to work and home neurologically intact if CPR and cooling are optimized. This experience suggests that new approaches that further optimize CPR and cooling treatments could significantly improve public health. This work builds a new collaboration between CPR researchers at the University of Illinois who are studying mechanisms of CPR and cooling protection, and investigators at the University of Chicago who specialize in the development of therapeutic fusion proteins. These proteins are designed to gain rapid access to critical organs rapidly and specifically block endogenous proteins causing disease. We propose to design new proteins that will mimic the effects of cooling in the heart and brain by inhibiting phosphatase enzymes that block tissue survival responses during CPR.

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PIs: Chuan He (UChicago) and Jung-Hyun Min (UIC) for project:
Capturing Kinetically Labile Protein Assemblies on DNA
Type of Award: Catalyst
Date Awarded: January 2012
Amount Awarded: $ 200,000.00

Abstract: Control and maintenance of the human genome is carried out by proteins that assemble at specific DNA sites, driven by highly specific and often labile interactions. These biologically critical interactions are difficult to study because of challenges in preparing large and complex protein machines and in assembling them on DNA in a stable manner for detailed characterization. We propose a strategy against these challenges by combining the unique strengths of two groups: The Min group (UIC) can produce complex proteins for biochemical and structural analysis using a new “MultiBac” system; and the He group (U of Chicago) uses chemical crosslinking technologies to stabilize protein-DNA and protein-protein interactions. We will apply our joined forces to determine the structures of previously intractable protein-DNA complexes, focusing on detailed biochemical characterization of binding events, to answer questions such as: how do proteins assemble in the right place on the DNA out of myriad possible locations? What are the architectures of the assembly that control the biological process? We select two areas of the highest scientific interest to showcase our approach:(1) All cells rely on efficient DNA damage repair complexes such as XPC, yet it is unknown how this recognizes DNA lesions within a vast genome. We will capture XPC on DNA and analyze the assembly events during the damage repair process.

(2) DNA hydroxymethylation by TET-family enzymes has recently been shown as critical epigenetic marking that controls gene regulation. Yet how TET locates and processes target DNA sites is unknown. We will trap and characterize TET and its cofactor proteins during this vital epigenetic operation. Our success will represent major discoveries in genetic mechanisms, create a long-term collaboration between a junior (Min) and senior faculty (He) in CBC and lead to joint federal grants for applying the approach to diverse biological systems.

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PIs: David Eddington and Jalees Rehman (UIC), and Navdeep Chandel (NU) for project:
Oxygen Sensing in Endothelial Progenitor Cells
Type of Award: Catalyst
Date Awarded: January 2012
Amount Awarded: $ 200,000.00

Abstract: The majority of cardiovascular deaths are due to narrowing of blood vessels (e.g., atherosclerosis) which leads to reduced oxygen supply in vital organs. The discovery of intrinsic “vessel wall repair system” consisting of endothelial progenitor cells (EPCs) raises the possibility of developing novel approaches to treat cardiovascular disease. It is postulated that EPCs activated by tissue hypoxia proliferate and thus repair damaged blood vessels or help build new vessels to restore oxygen supply. A reduction in tissue oxygen content (hypoxia) may be sensed by EPCs, and if true, it constitutes a potent signal to activate EPCs and promote repair of new blood vessels, but it is not known whether and how EPCs sense hypoxia. EPC numbers and activity are often reduced in patients with vascular diseases such as high blood pressure or diabetes, which may explain in part why their EPCs are unable to repair blood vessels or build new blood vessels. Thus, understanding how hypoxia regulates the regenerative potential of EPCs becomes imperative to understand EPC-based treatment in patients with suppressed EPC function. Since little is known about mechanisms underlying oxygen sensing EPCs, by combining the expertise of Drs. Eddington and Rehman at UIC and Dr. Chandel at Northwestern University, we hope to identify novel key regulators of EPC hypoxia activation. Ultimately, we envision this research will lead to therapies that improve EPC function and promote repair of blood vessels.

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PIs: Lucia Rothman-Denes and Douglas Bishop (UChicago), Konrad Kording and Keith Tyo (NU) for project:
A Molecular Chart Recorder
Type of Award: Catalyst
Date Awarded: January 2012
Amount Awarded: $ 200,000.00

Abstract: The interplay between millions of neurons allows us to perceive our environment and choose successful actions. Brain scientists, in an attempt to understand this interplay, need to record from progressively more neurons. Neuroscience relies on new developments in recording technology and thus far this progress is largely driven by physics — thin wires and optical sensors are used to read out signals. We propose to shrink the size of a recording setup by orders of magnitude to produce a molecular tape recorder – that writes time-varying neural activities onto individual DNA molecules.We will design a system so that it essentially copies just one long DNA molecule (template) during a neuroscience experiment. Some DNA polymerases (DNAP) are capable of copying roughly 1 base pair every millisecond. The position of a base-pair along this molecule thus corresponds to the time it was copied (our “chart”). We will engineer the DNAP so that it makes copying mistakes whenever Ca2+ is high (our “recorder”). If neurons are active, intracellular calcium concentrations increase. Consequently base pairs copied while Ca2+ concentrations were high will have many copying mistakes. Comparing with the template we can thus read out a chart of intracellular Ca2+ concentration. After the experiment, the animal will be killed, the brain will be cut into small pieces and the DNA in neurons will be sequenced and converted into a Calcium chart (our “read out”). This resulting calcium chart characterizes neural activities as a function of time.

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2011 Spring Round

PIs: Jun Yin (UChicago) and Hiroaki Kiyokawa (NU) for project:
Identify Cell Cycle-Regulatory Substrates Ubiquitinated by the Apoptosis Inhibitor BRUCE
Type of Award: Catalyst
Date Awarded: July 2011
Amount Awarded: $ 200,000.00

Abstract: BRUCE is a member of the IAP (Inhibitors of Apoptosis Proteins) family, which can suppress programmed cell death (apoptosis). Recently BRUCE has also been found to participate in the assembly of a super cellular structure called midbody ring and regulate the proper change of cell shape during cell division. It is still a mystery how BRUCE combines and coordinates these diverse functions in a single protein at different stages of the cell cycle. Much of the interpretation of BRUCE’s function is based on its C-terminal E2 domain that mediates the transfer of ubiquitin (Ub) to other cellular proteins. Ub attachment to proteins triggers their degradation thus BRUCE may be a key regulator of the life span of other proteins in the cell. Our goal in this application is to systematically identify the ubiquitination targets of BRUCE in order to elucidate how BRUCE regulates cell division and cell death.

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PIs: Adilson Motter (NU) and Sean Crosson (UChicago) for project:
An approach to identify drug targets that select against antibiotic resistance
Type of Award: Catalyst
Date Awarded: September 2011
Amount Awarded: $ 199,972.00

Abstract: Diseases caused by microbial infection are the second leading cause of death worldwide (WHO World Health Report, 2004). Perhaps the greatest current challenge in the treatment of such infections is the development of new classes of antibiotics. Between 1935 and 1968, 14 classes of antibiotics were developed — representing novel mechanisms of action. Since 1970 only 5 new classes have been introduced into the clinic, two of which are limited to topical use (Alanis 2005). In all cases, bacterial resistance to these drugs arose a few years after their introduction (Walsh 2003). There are, therefore, two major problems to consider in the development of new antibiotic drugs:1) the identification of novel targets, and

2) the development of approaches that will limit the evolution of resistance in bacteria.

Using the tools of metabolic network modeling (Motter) and bacterial genetics (Crosson), we will identify new drug targets that are less likely to develop resistance and refine approaches to select against resistance for existing antibiotics.

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2010 Fall Round

PIs: Amittha Wickrema (UChicago) and Hongmei Jiang (NU) for project:
Uncovering Early Genetic Aberrations in Myelodysplastic Syndromes
Type of Award: Catalyst
Date Awarded: March 2011
Amount Awarded: $ 200,000.00

Abstract: Myelodysplastic syndromes (MDS) are a group of diseases in the bone marrow cells that are considered cancerous. Many patients with MDS are initially diagnosed with anemia without an underlying cause but slowly progress to MDS and acute myeloid leukemia (AML). The disease is mostly prevalent in older patients (over 60 years of age) and the disease affects several blood cell types although the disease mostly manifests in red blood cell precursors. Currently there are no tests available to precisely diagnose the disease at very early stage. Chromosomal changes and cytogenetic aberrations are not prominent in the early stages of the disease. Therefore, current diagnostic methods are not sufficient to predict which patients with unexplained anemia will develop MDS and AML. Our grant proposal is aimed at uncovering very early genetic aberrations of MDS using the latest DNA sequencing technology and data analysis methods. Following identification of early defects in DNA we will test the normal function of these genes in a unique cellular model we have developed. Overall these studies will discover new ways to detect and predict the onset of MDS very early providing an opportunity to intervene in the treatment of MDS before the disease becomes aggressive.

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PIs: Steven T. Rosen (NU) and Fotini Gounari (UChicago) for project:
The Molecular Basis of Genomic Instability: A Genome Wide Approach
Type of Award: Catalyst
Date Awarded: January 2011
Amount Awarded: $ 200,000.00

Abstract: Cancer cells have unstable genomes and show significant diversions from normal cells. These include major alterations in the copy number of chromosomes, translocations of parts of a chromosome to another as well as local inversions of chromosomes. Major and smaller scale cryptic changes are present in almost all cancers. Their link to carcinogenesis is best established in leukemia/lymphoma, where specific translocations and the resulting activation of cancer genes have been characterized in detail. Certain translocations occur recurrently indicating that specific chromosomal loci are either selectively targeted or selected during transformation. How are these loci chosen and what molecular mechanisms are involved is unclear. Our hypothesis is that genomically unstable cancers share similar underlying molecular mechanisms, which can be revealed by distinct gene expression properties. The study of these mechanisms requires experimental models that are marked by spontaneous translocations. We have developed an animal model in which genomically unstable T-cell lymphomas show identical translocations to those seen in human leukemia/lymphoma. This model allows us to determine genome wide transcription and chromatin changes that are associated with the state of genomic instability. The findings will be related to human cancer through a collaboration between our two laboratories at the University of Chicago and Northwestern University. These studies will help us understand the mechanisms responsible for genomic instability in cancer and in particular in hematologic malignancies, providing new opportunities for therapeutic intervention.Dr. Rosen is the director of the Northwestern Comprehensive Cancer Center and an international authority in T-cell lymphomas. Dr. Gounari, an immunologist at the University of Chicago, has developed and characterized the animal model and the preliminary work on translocations in leukemia/lymphoma.

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2010 Spring Round

PIs: Aaron Turkewitz (UChicago) and Scott Brady (UIC) for project:
Critical Components in Regulated Secretion
Type of Award: Catalyst
Date Awarded: July 2010
Amount Awarded: $ 200,000.00

Abstract: Neurons require release of critical signaling molecules known as neurotrophins from their target neurons for survival and normal function. Disruptions in this pathway are thought to be a risk factor in diseases like Alzheimer’s, depression, and bipolar disease. Although the regulated secretion of neurotrophins is critical to the development and maintenance of neurons, we do not fully understand how the secretory granules needed to deliver neurotrophins are generated or delivered to where they are needed. A better understanding of this process will illuminate the normal functioning of the neuron and may reveal important insights in how these pathways contribute to Alzheimer’s and affective disorders. We know that critical steps involved in the generation secretory granules like those needed for neurotrophin storage are of ancient evolutionary origin, so we can use the power genetic tools and methods of analysis to identify and analyze these steps in a single-celled organism, Tetrahymena and using this information to define essential homologues involved in neurotrophin storage. By exploiting specific features of Tetrahymena, we have identified a set of genes that conserved in mammalian neurons and may illuminate the mechanisms of neurotrophin storage in human nerve cells, and we therefore propose to undertake a parallel study of these genes in Tetrahymena and in mammalian cells.

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PIs: Richard Ye (UIC) and Neil Kelleher (NU) for project:
Phosphoproteomic analysis of NADPH oxidase activation
Type of Award: Catalyst
Date Awarded: July 2010
Amount Awarded: $ 200,000.00

Abstract: Protein phosphorylation is a major form of post-translational modification known to be important for numerous physiological functions in eukaryotic cells. Top-down mass spectrometry (MS), which analyzes intact proteins, offers several advantages over the traditional bottom-up MS in the characterization of protein phosphorylation. In this application, we propose to extend the top-down MS-based approach from analyzing individual proteins to characterizing multiple proteins for their phosphorylation states within a defined biological system (a “microproteome”). The phagocyte NADPH oxidase is ideally suited for this type of analysis and model development because (1) the essential components of the oxidase complex and their functions have been defined, and (2) the signaling molecules involved in the oxidase assembly and activation have been identified, but their temporal and spatial regulation remains largely uncharacterized. Combining the respective expertise of the two principal investigators in phagocyte biology and MS-based proteomics research, this applications aims to establish novel methodologies for precise analysis of complex biological systems such as those present in phagocytes, cancer cells and stem cells. In Aim 1, we will characterize agonist-dependent phosphorylation of p47phox at multiple sites and develop a model for MS-based analysis of proteins that are extensively and differentially phosphorylated. In Aim 2, we will extend the top-down MS approach from examining individual signaling molecules to simultaneous analysis of multiple kinases within a defined system such as the phagocyte NADPH oxidase. This part of the study takes advantage of autophosphorylation of protein kinases upon activation. Since these phosphorylation events occur at defined sites within the kinase proteins, changes in molecular weight resulting from autophosphorylation at single or multiple sites may be determined rapidly and precisely using top-down MS. A successful completion of the proposed study will not only improve our understanding of the regulatory mechanisms for NADPH oxidase activation, but also obtain much needed information for broad applications of top-down MS-based “precision proteomics” in future studies of complex biological systems.

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PIs: Wonhwa Cho and Daesung Lee (UIC), and Seth Corey (NU) for project:
In situ Imaging of Lipid Signaling Networks
Type of Award: Catalyst
Date Awarded: August 2010
Amount Awarded: $ 200,000.00

Abstract: Membrane lipids play important roles as cellular signaling and regulatory molecules and they control diverse cellular processes, including cell proliferation, apoptosis, metabolism and migration. Perturbations in the lipid- mediated cell regulation contribute to the pathogenesis of human diseases such as inflammation, cancer, diabetes and metabolic diseases. Since lipids are dynamic molecules that are produced, degraded, and transported in a tightly controlled manner, determination of their concentration and movement in a temporally and spatially resolved manner is a key step toward the understanding of a growing myriad of membrane- mediated biological processes and the development of new strategies to diagnose, treat, and prevent human diseases caused by dysfunctional membrane-associated processes. Just as quantitative Ca2+ imaging revolutionized the cell biology in 1980s, quantitative imaging of membrane lipids will have major impact on biology and medicine. We propose to build a library of specific and orthogonal molecular sensors for all major membrane lipids and establish in situ quantitative imaging of multiple lipids. These sensors and imaging methodology will eventually be applied to the systems-level understanding of membrane lipid-mediated cell signaling and regulation.

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2009 Fall Round

PIs: Serdar Bulun (NU), Jonna Frasor and Yang Dai (UIC) for project:
A Systems Biology Understanding of Estrogen Receptor Action
Type of Award: Catalyst
Date Awarded: January 2010
Amount Awarded: $ 200,000.00

Abstract: Women are administered hormones, including selective estrogen receptor modulators (SERMs), which target the estrogen receptor (ER), for a variety of reasons, including preventing growth of hormone-dependent breast tumors, improving bone mineral density, or reducing menopausal symptoms. However, these agents often cause detrimental side-effects in other tissues. One such SERM is tamoxifen. Millions of women have taken tamoxifen to block growth of their ER positive breast tumors. However, this same agent can increase proliferation in the uterus, and in turn increase the risk of uterine cancer. Our goal is to use a combination of novel and complimentary approaches to understand why these drugs have different effects in different tissues. Specifically, we will look at the proteins that interact with ER and the genes that change in response to hormone treatment using a completely unbiased approach. We will create regulatory networks of information based on genome-wide, large scale biological data sets that are generated by us and that we collect from publicly available sources. This proposal is to seek support for an innovative research strategy that requires collaboration among investigators at UIC and NU with complementary expertise in bioinformatics, reproductive endocrinology, and molecular mechanisms of ER action. Because of the diverse approaches to be used in this project, none of the investigators could accomplish this work on their own. We hypothesize that integration of proteomic and genomic data through novel bioinformatics approaches will allow us to identify key mechanisms controlling ER activity in different tissues responses to different ligands, such as estrogen and tamoxifen. This, in turn, may lead to novel therapeutic approaches to target the ER in the treatment of hormone-dependent diseases.

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PIs: Alexander Minella (NU), Marsha Rosner and Robert Rosner (UChicago) for project:
Cell Cycle Regulatory Networks: An Integrative Approach
Type of Award: Catalyst
Date Awarded: November 2009
Amount Awarded: $ 188,000.00

Abstract: Appropriate regulation of cell division is necessary for the normal growth and differentiation of mammalian cells. Loss of cell division controls causes abnormal proliferation, chromosome damage, and, ultimately, progression to diseases such as cancer. Therefore, it is critical for cells to maintain rigorous control of key transition points in the cell division cycle, such as the initiation of DNA replication. In early phases of the cell cycle leading to DNA replication initiation, this control is accomplished in large part by proteins called cyclins and cyclin-dependent kinases. These proteins are necessary for initiating DNA replication and driving cell cycle progression in all organisms, and importantly, they are normally regulated by complex networks that control their activity. To develop a better understanding how diverse regulatory controls on cyclins function together in different cellular contexts, we propose a novel integrative approach that utilizes a multi-disciplinary team of researchers based at Northwestern University and The University of Chicago. We will first develop computational models focused upon the regulation of cyclin E, a key regulator of early cell cycle progression in early mammalian cells. We hypothesize that we can utilize these models to accurately simulate the complex regulation of cyclin E activity. Next, we will use living cell imaging techniques to obtain key data at the single cell level, following experimental manipulations, in order to test and refine our computational models. With these studies, our group aims to develop a robust system, which can be used for generating testable hypotheses to study complexly-regulated components of not only cell cycle machinery but many other cellular processes. Current experimental approaches used by individual laboratories typically focus on studying how genes and proteins are regulated by a single set of molecular controls. We believe the results of our work will enable more unbiased approaches for identifying critical regulatory components, among many, of a given protein within a specific cellular context, which may ultimately be useful in such applications as drug design and molecular diagnostics.

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PIs: Lonnie Shea (NU) and Deborah Tonetti (UIC) for project:
High throughput signaling pathway analysis during cellular organization into structures
Type of Award: Catalyst
Date Awarded: February 2010
Amount Awarded: $ 200,000.00

Abstract: Cells sense cues from the local environment and respond by initiating signals leading to a variety of cellular decisions such as cell growth, cell death, cell division or maturation. In cancer, an altered microenvironment may induce erroneous cellular responses, or the cell may erroneously respond to a normal environment. Quantifying the activity of the signaling pathways within normal and cancer cells as a function of the environmental cues may identify critical pathways leading to the formation of normal or abnormal tissue structures, which provides fundamental insight into the cell-environment interaction and could ultimately be used as a diagnostic in patient specific therapies. The proposed research to develop and apply a system to measure the signaling activity represents a collaboration between Prof. Shea, a bioengineer at Northwestern University and Prof. Tonetti at UIC, a breast cancer researcher. Prof Shea has developed a screening system that allows the defined modification of the extracellular environment and at the same time can detect and quantify multiple signaling pathways within cells, which will be expanded with the proposed research. Prof Tonetti has an extensive history of research involving signaling pathways in cancer cells, and has begun investigating the dependence upon the environmental context. This collaboration will apply defined microenvironments and the system for signaling pathway quantification to models of breast cancer to identify the pathways responsible for formation of normal and abnormal tissue structures, which have been observed in patients. Successful completion of these studies will lay the foundation to connect the microenvironment, cell signaling, and cellular responses to the organization of cells into functional tissues, which has numerous implications such as regenerative medicine, cancer, and stem cells. Additionally, this system has the potential to identify targets for therapeutic intervention and to understand the mechanistic basis of multiple diseases.

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2009 Spring Round

PIs: Michael Glotzer and Tobin Sosnick (UChicago), and Eric Weiss (NU) for project:
Genetically Encoded Control of Protein Function with Light
Type of Award: Catalyst
Date Awarded: September 2009
Amount Awarded: $ 200,000.00

Abstract: Biologists aim to understand in a detailed way how cells change shape, move, and divide. These behaviors are tightly regulated within the cell, and failures of the control systems lead to disease. Perturbation experiments, in which the experimenter makes controlled changes to a system and observes the results, are an important way of learning how biological systems function. However, no convenient method is available to perturb cellular control systems at specific sub-cellular locations and in real time. Because illumination through the microscope is one of the most precise perturbations one can make to a living cell, we propose to fill this technological gap by creating a convenient tool for activating or deactivating these systems using light.

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PIs: Sergey Kozmin (UChicago) and Paul Schumacker (NU) for project:
New Molecular Tools to Study Cancer Metabolic Reprogramming
Type of Award: Catalyst
Date Awarded: September 2009
Amount Awarded: $ 200,000.00

Abstract: Cell-permeable small organic molecules are useful for dissecting complex metabolic and signaling networks. Such compounds function by modulating the protein activity directly, providing a complementary approach to the widely employed gene replacement and RNA interference strategies. We propose to develop an arsenal of new small-molecule tools to study altered energy metabolism in cancer. Due to the increased dependency of tumor cells on glycolysis, and its likely role in promoting cell proliferation, survival and invasion, understanding of the nature of reprogrammed energy metabolism in cancer cells is of significant current interest. This study will help in identifying the underlying reasons for major alterations in energy producing pathways employed in rapidly proliferating cells and will test the possibility of targeting such cells selectively both in vitro and in vivo.

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PIs: Chuan He (UChicago) and Scott Franzblau (UIC) for project:
Virulence and Latency Regulation in M. tuberculosis
Type of Award: Catalyst
Date Awarded: June 2009
Amount Awarded: $ 200,000.00

Abstract: It is estimated that one third of the world’s population is infected with Mycobacteria tuberculosis (Mtb). In about 90% of infected people, Mtb persists throughout the life of the host in a largely non-replicating (“latent”) state that causes no disease and against which antibiotics are ineffective. However, a change in the environmental conditions surrounding the bacterium (i.e. when the host becomes immune compromised) can make the bacterium exit the latent state and become pathogenic. Unfortunately, very little is known about the underlying molecular mechanisms and regulators that control the virulence and latency of Mtb. This proposal combines expertise from the Franzblau laboratory in the Institute of Tuberculosis Research (ITR) at the University of Illinois at Chicago (UIC) and the He laboratory from the University of Chicago (UofC) to address this fundamental question. We propose that reactive oxygen species (ROS) produced by host immune systems is a key signal that is sensed by Mtb and affects virulent states of the pathogen. Our proposed study will provide systems level and mechanism level understanding of the regulatory pathways involved in virulence and latency regulation in Mtb. This new knowledge will lead to a paradigm shift for how we treat Mtb infections: instead of screening for traditional bactericidal or bacteriostatic antibiotics that are less effective against Mtb in the latent state we may develop compounds that can either shut down the virulence of Mtb or activate exit of Mtb from the latent state and then eliminate the active forms with existing antibiotics that work well against actively replicating bacilli.

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2008 Fall Round

PIs: Sangram Sisodia (UChicago) and Robert Vassar (NU) for project:
Investigating the in vivo Interactomes of BACE1 and APP
Type of Award: Catalyst
Date Awarded: December 2008
Amount Awarded: $ 200,000.00

Abstract: Alzheimer’s disease is an incurable neurodegenerative disease characterized by the accumulation of amyloid plaques – deposits of protein in the brain whose main constituent is the Abeta peptide, which is itself derived from the metabolism of a larger protein called APP. Reducing the Abeta load in the brain is a major goal of Alzheimer’s research, and to accomplish this, many strategies aim to inhibit the metabolism of APP. Cleavage of APP by the enzyme BACE1 is required to generate Abeta. Thus, understanding which proteins APP and BACE1 interact with is important because 1) this aids in the design of small molecule drugs, and 2) if APP metabolism or BACE1 activity are to be inhibited, an understanding of their natural function is critical. Although many studies have investigated the metabolism of APP in cultured cells, confirmation of these results in animal studies has not yet been achieved. Moreover, very little is known about BACE1 interacting proteins, and these proteins likely contribute to delivering BACE1 and APP into the same cellular compartment for cleavage of APP into Abeta. Thus, we aim to generate a transgenic mouse that expresses APP and BACE1 containing a peptide tag. By using these tagged proteins as “bait” in the living animal, we can subsequently purify them and those proteins with which they are bound. Analyzing the purified material and comparing it to a protein database will confirm binding partners identified by cell culture studies and identify new binding partners with new specific therapeutic targets.

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PIs: Stephen Kron and Stephen Kent (UChicago), and Brian Kay (UIC) for project:
Proteolysis-inducing Peptides as Tools for Chemical Genetics
Type of Award: Catalyst
Date Awarded: January 2009
Amount Awarded: $ 199,333.00

Abstract: In this Catalyst proposal, an interdisciplinary team consisting of Stephen Kent and Stephen Kron at The University of Chicago and Brian Kay at the University of Illinois at Chicago will work together to investigate a new approach to testing protein function in cells. They will pursue development of ProTaPs, Proteolysis Targeting Peptides, as a tool for chemical manipulation of cellular proteins. In detail, ProTaPs consist of three functionalities: a targeting peptide that binds to specific protein target, a domain that binds to an E3 ubiquitin ligase to induce polyubiquitination and a cell penetrating peptide to deliver the ProTaP to its site of action. These three functionalities can be synthesized independently as peptide modules and then linked together by native chemical ligation. This modular approach allows great flexibility, so that a large number of ProTaPs can be synthesized and tested in parallel. Treating cells with a ProTaP will rapidly induce ubiquitin-proteasome dependent destruction of the target protein. We hope to validate ProTaPs alongside knockouts and knockdowns as a tool for analysis of gene functions, but also as a novel route to validating proteins as targets for therapeutics. This new tool will be used to analyze chromatin modification and protein assembly at DNA double strand breaks. We will identify a small number of key target proteins and exploit phage display to discover high affinity and high specificity binding peptides that will tether a ProTaPs to each of these proteins. Because ProTaPs can be used much like a drug, they will allow determination of the requirements for normal responses to DNA damage, such as modification of histone proteins, recruitment and assembly of DNA damage signaling and repair proteins, and for assembly of the characteristic protein complex at the double strand break site. They will exploit a GFP fusion to 53BP1, a protein that rapidly localizes to DNA breaks, as a fluorescent reporter for changes in chromatin modification or protein assembly. By examining changes in the characteristic relocalization of GFP-53BP1 from diffuse nuclear distribution to discrete foci at double strand break sites and then tracking whether the persistence of the foci is normal, we will be able to determine whether a ProTaPs has disrupted a key function in the DNA damage response. This work will identify new mechanisms and targets in DNA damage response and provide useful data on the approach of targeting chromatin as a route to radiosensitization. Developing a new tool to help understand protein function in the response to DNA damage may have broad consequences. The new drug-like molecules to be studied here may provide leads for a new class of drugs that will enhance the effects of radiation on tumors, with the potential for major impact on the treatment of metastatic cancer.

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2008 Spring Round

PIs: Bruce T. Lahn (UChicago) and John A. Kessler (NU) for project:
Testing the ‘Occlusis’ Model of Cell Fate Restriction
Type of Award: Catalyst
Date Awarded: August 2008
Amount Awarded: $ 200,000.00

Abstract: A gene’s transcriptional output is the combined product of two inputs: diffusible factors in the cellular milieu acting in trans, and the biochemical state of chromatin acting in cis. Although many studies in the field of epigenetics have pointed to the possibility that genes could be silenced by cis-acting, chromatin-based mechanisms, there is as yet no ready experimental system for ascertaining whether the silent state of a gene is indeed the result of cis rather than trans regulation. To address this problem, we have recently developed a cell fusion strategy with which it is possible to dissect out the relative contribution of cis versus trans mechanisms to gene silencing. The strategy entails fusing two disparate cell types and searching for genes differentially expressed between the two genomes of fused cells. Any differential expression can be causally attributed to cis mechanisms because the two genomes of fused cells share a single homogenized milieu. Using this strategy, we uncovered the presence of many ‘occluded’ genes in the genome – defined as genes existing in a state of transcriptional competency whereby they are silenced by cis-acting mechanisms in a manner that blocks them from responding to the trans-acting milieu of the cell. Here, we propose to further develop the cell-fusion-based approach for identifying and analyzing occluded genes. Specifically, we intend to pursue the following aims: (1) to test whether the occluded state of a gene, once acquired during development, is essentially irreversible; (2) to explore the biochemical mechanisms underlying gene occlusion.The identification and analysis of occluded genes is likely to have important implications for many fields of biology. The following are some examples: (1) knowing the competent/occluded status of genes could be central to studies in systems biology aimed at producing comprehensive circuit diagrams of the regulatory networks within cells; (2) the occlusis model could establish an important theoretical framework for studies of developmental biology and stem cell biology, especially the mechanisms underlying cell fate restriction; (3) genome-wide maps of occluded genes might offer a more fundamental molecular definition of cell type identity; (4) the description of competent/occluded status of genes provides a novel functional readout of the genome with which the biological significance of chromatin signatures such as DNA methylation and histone modifications could be better interpreted; and (5) disruption of the competent/occluded status of genes by environmental, genetic or stochastic factors might contribute to aging and disease processes such as cancer. For these reasons, we believe that the proposed work has the potential to make a significant impact on a broad swath of biomedical research.

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2007 Fall Round

PIs: Wonhwa Cho and Hui Lu (UIC), and Eduardo Perozo (UChicago) for project:
Spatiotemporal Dynamics of Cellular Protein Networks on Membranes
Type of Award: Catalyst
Date Awarded: January 2008
Amount Awarded: $ 200,000.00

Abstract: 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.

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PIs: E. McNally (UChicago), P. Schumacker and H. Ardehali (NU), and R. J. Solaro (UIC) for project:
Proteomic Analysis of Mitochondrial and Sarcomeric Proteins in Cardiomyopathy
Type of Award: Catalyst
Date Awarded: January 2008
Amount Awarded: $ 199,992.00

Abstract: 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 Genomic and 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 perform genetic analysis in patients with CM. These studies would not be possible without close collaboration among the involved groups. We believe CCGPC will build the infrastructure to make Chicago the leading heart failure research center in the world. The CCGPC 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.

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PIs: Lawrence Miller (UIC) and Jerrold Turner (UChicago) for project:
Multiplexed Imaging of Transient Molecular Complex Dynamics in vivo
Type of Award: Catalyst
Date Awarded: January 2008
Amount Awarded: $ 200,000.00

Abstract: 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 needs 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 the 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.

 PERMALINK


PIs: Harinder Singh and Aaron Dinner (UChicago), and John Crispino (NU) for project:
Gene Regulatory Networks Directing Hematopoietic Cellular Fates
Type of Award: Catalyst
Date Awarded: January 2008
Amount Awarded: $ 200,000.00

Abstract: 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.

 PERMALINK



2007 Spring Round

PIs: Erik J. Sontheimer (NU), Jonathan P. Staley and Manyuan Long (UChicago) for project:
Gene Regulation by Natural Antisense RNAs in Yeast
Type of Award: Catalyst
Date Awarded: August 2007
Amount Awarded: $ 236,000.00

Abstract: Cells and organisms depend on the proper functioning of their genes, many of which encode proteins that carry out essential cellular tasks. Most genes must restrict their activities to specific cell types, developmental stages, or environmental circumstances, and inappropriate gene expression causes or contributes to many diseases, including cancer. Therefore, the expression of a gene into protein must be controlled properly to maintain human health. Genes are comprised of DNA, which forms the famous double helical structure discovered by Watson and Crick. Gene expression initially involves the production of RNA, which is a chemical cousin of DNA. RNA, like DNA, has the capacity to form a double helix, and the formation of a double helix can affect RNA function and, as a consequence, gene expression. Despite this potential, the degree to which cells use RNA double helices to control gene expression is poorly understood. This study will begin to uncover the true extent of RNA double helix formation in a single cell type, and will enable researchers to test the roles of RNA double helices in specific cellular processes, including those that affect human health and disease.

 PERMALINK


PIs: Joseph Bass (NU), Graeme I. Bell (UChicago) and Nissim Hay (UIC) for project:
Chicago Consortium in Diabetes and Obesity Genetics
Type of Award: Catalyst
Date Awarded: July 2007
Amount Awarded: $ 249,000.00

Abstract: Over the past decade, an epidemic of obesity and diabetes has swept our nation and present estimates indicate that greater than one in three children born in 2007 will be affected with these disorders. Together, diabetes and obesity result in over 200,000 deaths annually and exert a devastating toll due to blindness, kidney failure, heart disease and stroke. In the Chicago area, research at Northwestern/ENH and the Universities of Chicago and Illinois has transformed our understanding of the underlying cause of disease, however the infrastructure needed to carry these advances to the next stage of development has not been realized. The present proposal, for a “Chicago Consortium in Diabetes and Obesity Genetics”, seeks to capitalize on the expertise already in place in three major Chicago research institutions through the creation of an umbrella program to generate state-of-the-art disease models and application of novel analytic methods (“proteomic” and “array”) that will ultimately translate into new treatments for patients with diabetes and obesity. The Consortium will focus on integration of three of the most conserved and ancient pathways involved in diabetes and obesity and consolidate efforts and resources to identify new targets for intervention that will provide a springboard for subsequent funding applications from the National Institutes of Health. The benefit of a strong preclinical Consortium will also have a cascade of positive effects within each University by opening future opportunities for collaborative studies in genetics and translational research and providing a pool of trainees committed to improving the health of individuals with these prevalent disorders.

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2006 Fall Round

PIs: Philippe Cluzel (UChicago) and John F. Marko (NU) for project:
Systems Analysis of Chromosome Dynamics in Single Bacteria
Type of Award: Catalyst
Date Awarded: January 2007
Amount Awarded: $ 200,000.00

Abstract: The 20th century has seen systematic discovery and characterization of the molecules which are the building blocks of cells: DNA, proteins, and RNA. Thanks to recently completed genomic projects, one now has an extensive molecular-biological “parts list” for cells. The upcoming challenge for biology in the 21st century is to go beyond this exhaustive list and to understand how the parts work together as a whole to bring a cell to life. Our research project seeks to tackle this challenge through experiments on live single cells of the bacterium E. coli. We will study how the physical organization of the E. coli chromosome impacts the expression of the genetic information in a live cell. Our approach will be based on simultaneous measurement of time-space evolution of chromosome shape, and expression of chromosomal genes in single E. coli cells, using a combination of cutting-edge fluorescence visualization techniques. Since the organization of the chromosome is controlled by proteins which are synthesized according to instructions encoded into the DNA sequence on that same chromosome, our project seeks to understand an example of a feedback system common to all living cells: the coupled dynamics of chromosome structure and gene expression. We anticipate that lessons learned from our proposed studies in E. coli will guide future studies of gene expression dynamics in more complex cells.

 PERMALINK



2006 Spring Round

PIs: Wen-Hsiung Li (UChicago) and Peter C. Nelson (UIC) for project:
Advanced System for Comparative Analysis of Metabolism
Type of Award: Catalyst
Date Awarded: July 2006
Amount Awarded: $ 135,000.00

Abstract: A metabolic process involves a concerted interaction of many cellular components. Understanding complex processes governing metabolism requires a system biology approach and exploration of biological systems at various levels of organization: genomic, metabolic, enzymatic. Here we propose such an approach to studying metabolism to understand metabolic processes and mechanisms of adaptation to environments. Recent progress in genomics, bioinformatics and physiology allows for a systematic exploration of adaptive mechanisms responsible for diversification of biological systems. During evolution, organisms undergo co-adaptive changes such as the complementary changes of protein sequences to accommodate changes in an enzyme’s active site or co-evolution of different steps in metabolic pathways. Therefore, developing a framework for studying evolution of the functional processes and phenotypic variations is essential for interpreting molecular evolution events and for understanding the diversification of metabolism among organisms.The Goal: To understand metabolism and adaptation of organisms to the environment from a system biology viewpoint and to develop tools for identifying variations in metabolic pathways and enzymes among taxonomic groups of organisms.

 PERMALINK


PIs: Alfonso Mondragon (NU) and Tao Pan (UChicago) for project:
Epigenetics of RNA: a systems approach
Type of Award: Catalyst
Date Awarded: July 2006
Amount Awarded: $ 200,000.00

Abstract: While the genome sequence encodes the master plan of how an organism works, adapts, and evolves, epigenetics deals with how this master plan is put into practice through chemical modifications of DNA, protein, and RNA. The epigenetic modifications of DNA selectively regulate gene expression. Epigenetic modifications of proteins are crucial for signal transduction and protein activity regulation.RNA is also epigenetically modified, although this process is not as well studied or understood. Over 100 types of chemical modifications have been identified in thousands of sites in RNA from bacteria to man. However, only a few RNA modifications are essential for life. Instead, many RNA modifications are involved in stress responses and environmental adaptation. An important aspect of RNA modifications is that they may be functionally analogous to protein modifications since many of these modifications are chemically reversible. Reversible modifications would allow sophisticated regulation of the structure and function of modified RNAs.

Our work is concerned with the development of high-throughput methods to study the molecular and mechanistic details of RNA modification enzymes and to study the function of RNA modifications at the genomic level during cell growth and adaptation. Our combination of structural, biochemical and biological approaches should provide a new and unique view of the systems biology of RNA epigenetics.

 PERMALINK


PIs: Martha C. Bohn (NU), Raymond Roos (UChicago) and Scott Brady (UIC) for project:
Viral Vector Translational Resource Center
Type of Award: Catalyst
Date Awarded: July 2006
Amount Awarded: $ 100,000.00

Abstract: The CBC Viral Vector Translational Resource Center will promote gene therapy studies in Chicago in the field of neuroscience, by constructing the viral vectors that are necessary for introducing new DNA into diseased cells. A viral vector is basically an artificial virus and is made using genetic engineering techniques to replace virus genes with genes of scientific interest. The engineered viral vector can be used to infect the patient and instead of causing disease, the viral vector is designed to deliver new healthy genes to specific cells.Gene therapy for human disease is gaining momentum as a direct result of information coming from the genome project. Gene delivery by viral vectors is also useful for generating novel experimental models of disease in animals and for making genetically modified stem cells. The CBC Viral Vector Resource center will produce high quality research-grade stocks of two types of viruses known to be useful for understanding gene function in the nervous system: adeno-associated virus (AAV) and lentivirus (LV). The viruses are modified so that they are merely tools for delivering experimental or therapeutic genes to cells. New virus or disease does not result from infecting cells with these viruses. The viruses will be made for approved projects on a no-strings-attached basis at a subsidized fee for service. The center will also provide advice on the use of these viruses and gene therapy study design.

A Steering Committee composed of faculty at the three institutions will take an active role in promoting the center and approving projects on a scientific merit basis. It is expected that approved projects will lead to novel gene therapies. The CBC center is an important step toward establishing the first National Viral Vector Translational Resource Center in the country to promote gene therapies for neurological disorders.

 PERMALINK


PIs: Richard I. Carthew and San Ming Wang (NU), and Chung-I Wu (UChicago) for project:
Functions and Evolution of micro-RNAs
Type of Award: Catalyst
Date Awarded: July 2006
Amount Awarded: $ 200,000.00

Abstract: In the last century, geneticists have successfully unraveled the molecular basis of many important traits, including some of the most devastating human diseases. Most of these are simple traits that are associated with severe defects in single genes. However, the majority of important and interesting traits, including most hereditary diseases and normal variations among humans, have very complex genetic bases. Hence, searching for groups of genes that can generate complex traits is a potentially rewarding avenue of research. The existence of microRNAs, one of the most fascinating genetic discoveries of the last decade, is promising in this respect. Each microRNA controls a very large number of target genes but all microRNAs carry out the task in much the same way. It is therefore a mechanism that can generate complexity but may at the same time be fundamentally simple. Our research aims at finding out how microRNAs may vary in their production and function between closely related species, or even among members of the same species. Such variability may potentially account for some of the variation in traits, including disease propensity, among individuals.

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Funded HTS Awards

2016 Spring Round
2015 Fall Round
2015 Spring Round
2014 Fall Round
2014 Spring Round
2013 Fall Round
2013 Spring Round

 


 

Funded Postdoctoral Research Awards

2016 Spring Round
2015 Fall Round
2015 Spring Round
2014 Fall Round
2014 Spring Round

 


 

Funded Exploratory Workshops

February 7, 2016
CBC Exploratory Workshop:
Seeing better together – Strategic Cross-Institutional Microscopy Initiatives

June 10, 2014
The CBC Vascular Biology Exploratory Workshop

May 15, 2013
The CBC Exploratory Workshop on Lipoproteins

January 30, 2013
The CBC Exploratory Workshop on Cellular Heterogeneity

January 12, 2013
The CBC Ovarian Cancer Workshop

September 27, 2012
Control of cellular differentiation and gene expression by 5- hydroxymethlcytosine (5-hmc)

 


 

Funded Lever Awards

Lever Award Program ran from 2006 until July 2014. The Program provided matching funds to collaborative teams requesting federal funding of $10 million or more.

May 2015
PIs: Vadim Backman (NU), Lucy Godley (UChicago) and Jack Kaplan (UIC) for project:
Chicago Center for Physical Science-Oncology Innovation and Translation
Type of Award: Lever
Amount Awarded: $ 1,487,992.00

Award Description: The CBC’s sixth Lever Award provides support for the Chicago Center for Physical Science-Oncology Innovation and Translation. Principal Investigators on the Lever are Vadim Backman (NU), Lucy Godley (UChicago) and Jack Kaplan (UIC).  The $1.5 million CBC Lever was awarded in conjunction with a $10 million U54 grant from the National Cancer Institute to fund the Chicago Region Physical Science-Oncology Center (CR-PSOC). The goal of CR-PSOC is to advance the understanding of carcinogenesis by examining the role of physical and chemical forces involved in the transformation of a normal cell into a cancerous one. Specifically, the studies will focus on interrogating changes in both the epigenome and the metallome (the metal ion content of the cell) that contribute to the development of cancer.The CR-PSOC, led by Thomas V. O’Halloran and Jonathan D. Licht, is composed of a multi-disciplinary team of 12 physical scientists and 8 cancer researchers from fields encompassing physics, chemistry, biomedical engineering, biophysics, biochemistry, pharmacology, and hematology-oncology from the three CBC institutions as well as experts in the physical sciences and chromatin fields from outside Chicago, namely MIT, Memorial-Sloan Kettering Cancer Center, and the University of Massachusetts Medical School.

Designed around the theme of “Spatio-Temporal Organization of Chromatin and Information Transfer in Cancer,” the CR-PSOC consists of three interrelated project areas, each focused on different aspects of chromatin structure and function, plus two core facilities, and pilot project, education and outreach programs.

The CBC Lever funds will support the Center’s new instrumentation and shared resources:

  • Nanocytometry Core (Northwestern)
    Leader: Vadim Backman
    It will include Partial Wave Spectroscopy (PWS) and Stochastic Optical Reconstruction Microscopy (STORM) for high resolution microscopy
  • PDX Core (Northwestern)
    Leader: Andrew Mazar

    • Patient-derived xenografts will provide meaningful models of human cancer and enable translation of PSOC innovations
    • Includes funding for investigator pilot studies using PDX models
  • New high precision methylation analysis capabilities through acquisition of an Illumina NextSeq500, to be used in the University of Chicago’s Genomics Core
    Leader: Lucy Godley
  • New ultra-sensitive IC-ICP-mass spectrometer capability to be used in the Quantitative Bioelement Imaging Center at Northwestern
    Leader: Thomas O’Halloran

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May 2012
PIs: Anthony Kossiakoff and Geoffrey Greene (UChicago), Brian Kay (UIC), and Jason Brickner (NU) for project:
Center for Production of Affinity Reagents for Human Transcription Factors: Chicago Synthetic Antibody Pipeline
Type of Award: Lever
Amount Awarded: $ 2,321,520.00

Award Description: The CBC has awarded the fifth Lever Award to scientists from the three CBC member institutions: Tony Kossiakoff (UChicago), Brian Kay (UIC), Geoffrey Greene (UChicago) and Jason Brickner (NU) for a proposal, Center for Production of Affinity Reagents for Human Transcription Factors: Chicago Synthetic Antibody Pipeline (CSAP). The $2.3M CBC Lever Award was awarded in conjunction with an NIH U54 grant, Recombinant Antibody Network (RAN). The goal of the $12.2M NIH grant is to generate renewable, high quality affinity reagents against all human transcription factors. The Lever Award will use the NIH RAN infrastructure to generate affinity reagents for the CBC community against a variety of targets including membrane and soluble proteins, protein complexes and functional RNA. Synthetic antibodies will be generated by phage display and will be stored as plasmids, allowing for low cost regeneration. The consortium is in its early stages so please check the CBC webpage for updates.See also:

Chicago Synthetic Antibody Pipeline (CSAP)

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May 2012
PIs: Andrey Rzhetsky (UChicago), Edwin Cook (UIC), and Richard Morimoto (NU) for project:
Silvio O. Conte Center on the Computational Systems Genomics of Psychiatric Disorders
Type of Award: Lever
Amount Awarded: $ 1,999,431.00

Award Description: The CBC has awarded the fourth Lever Award to a group of scientists from the three CBC member institutions: Andrey Rzhetsky (UChicago), Edwin Cook (UIC), and Richard Morimoto (NU) to support the Silvio O. Conte Center on the Computational Systems Genomics of Psychiatric Disorders. The CBC Lever of $2 million matches a $11.75 million grant from the National Institute of Mental Health: the Silvio O. Conte Center for Basic and Translational Mental Health Research (P-50) award. The new Conte Center, a multi-institutional effort, will be based at the University of Chicago, and will apply data mining strategies to study mental disorders. Specifically the center aims to design and validate a battery of novel analytical tools for the inference of causal relationships among human genomic variations, environmental factors, and more than one neurodevelopmental phenotype, explicitly exploiting the genetic and environmental non-independence of complex (multigenic) disorders.The P50 has four core projects that will study the genome structure of molecular networks involved in psychiatric disorders as well as the effect of genetic and non-genetic variation on the topology and characteristics of these networks.

  • Core Project 1: Pharmacogenomics and Modeling the Joint Effects of Genes and Environment in Psychiatric Disorders
  • Core Project 2: Modeling the temporal succession of phenotypes and environmental cues in the context of latent genetics
  • Core Project 3: Modeling disease risk in the context of molecular networks and gene association or linkage data
  • Core Project 4: Deciphering brain phenotypes through integrative modeling of multiple data types

The CBC Lever Awards are matching grants made to inter-institutional groups that are submitting large-scale grant proposals. The CBC Lever funds supporting the Conte Center will be specifically used for:

  • Enhancing the computational and experimental resources related to the Silvio O. Conte Center for Basic and Translational Mental Health Research (P-50) award, making them available to Chicago-area researchers, whether they are included as Principal Investigators on the P-50 or not.
  • Purchasing computer infrastructure for text mining of large-scale molecular networks, for large-scale study of variants in human genes associated with clinical phenotypes, for analysis of genetic and pharmagenomic data in the context of molecular networks, and to make these analyses maximally useful to a wide group of researchers.
  • Providing technical support and experimental supplies for P-50 and non-P-50 investigators – using the tri-institutional cloud computing infrastructure – for accesssing deep sequencing and proteomics services, as well as testing theories from computational analysis in model biological systems.
  • Supporting extensive educational and outreach activities involving the Chicago-area research community.

For more information about the center visit the Conte Center website.

 PERMALINK


October 2010
PIs: Chad Mirkin and Milan Mrksich (NU), David Eddington (UIC) and Joel Collier (UChicago) for project:
Nanomaterials for Cancer Diagnostics and Therapeutics
Type of Award: Lever
Amount Awarded: $ 2,117,241.00

Award Description: The CBC has awarded a Lever of $2.1 million over three years to establish two core facilities that will develop, fabricate, and disseminate standardized and well-defined matrices and substrates for culturing cancer cells. The facilities will be housed at the University of Illinois at Chicago and at the University of Chicago and operated by a team of dedicated technicians at both sites. The CBC Lever Award matches a $12 million award over five years from the National Cancer Institute (NCI) to help establish a collaborative network of Centers of Cancer Nanotechnology Excellence (CCNEs).CBC Lever Awards are matching grants made to inter-institutional groups that are submitting large-scale grant proposals. The Principal Investigators on the Nanomaterials for Cancer Diagnostics and Therapeutics CBC Lever Award are Chad Mirkin (NU), David Eddington (UIC), Milan Mrksich, (NU) and Joel Collier (UChicago).

The core facilities will have a two-part objective:
(1) Fabricate and Disseminate Tools – the two cores primary effort will be directed towards the preparation of the patterned substrates, peptide amphiphiles and culture devices.
(2) Technical Instruction – the two cores will provide applications specialists who will travel to local laboratories and instruct laboratory members in the use of the tools.

Both the culture tools and technical support will be provided to interested laboratories at no cost. Thus the CBC will provide a mechanism and funding for the translation of NCI-funded research into broad use.

The following foundries are offered to the CBC community through the Nanomaterials for Cancer Diagnostics and Therapeutics Lever Award:

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January 2009
PIs: Sergey Kozmin (UChicago), Karl Scheidt (NU) and Jie Liang (UIC) for project:
Chicago Tri-Institutional Center of Excellence in Chemical Methodologies & Library Development
Type of Award: Lever
Amount Awarded: $ 2,000,000.00

Award Description: The CBC has awarded the second Lever Award to a group of scientists from the three CBC member institutions; Sergey Kozmin (UChicago), Karl Scheidt (Northwestern), Hisashi Yamamoto (UChicago), Vladimir Gevorgyan (UIC), Viresh Rawal (UChicago), Milan Mrksich (NU; at UChicago at the time of the award), and Jie Liang (UIC). The $2 million Lever award matches a $9.2 million award from the National Institutes of Health (NIH) to support the establishment and operation of the Chicago Tri-Institutional Center for Chemical Methods and Library Development (CTCMLD). The CTCMLD will provide significant new resources for biomedical research in the Chicago community and boost drug discovery efforts in the area by advancing high-throughput organic synthesis and integrating the production of new small-molecule libraries with broad biological screening.In order to achieve the maximum impact, the CTCMLD will feature a high degree of collaboration and synergy with several research programs at the University of Chicago, Northwestern University, and University of Illinois at Chicago. Sergey Kozmin (UChicago) will serve as the director of the Center during the initial five year period. The CTCMLD collaborative group will also include exceptional strength in organic synthesis, represented by Karl Scheidt (Northwestern), Hisashi Yamamoto (UChicago), Vladimir Gevorgyan (UIC) and Viresh Rawal (UChicago), as well as the leading expertise in surface engineering of Milan Mrksich (NU; at UChicago at the time of the award) and cheminformatics of Jie Liang (UIC).

CBC Lever Awards are matching grants made to inter-institutional groups that are submitting large-scale grant proposals. Lever Awards are primarily used to establish transformative infrastructure that can be made broadly available to the Chicago scientific community. The CTCMLD represents a high-impact tri-institutional collaboration with projects to be headed by PIs from all three CBC member institutions. The CTCMLD Lever Award will support the following three key initiatives:

1. Enhancing the capabilities of the High-Throughput Synthesis component of the Core Facility of CTCMLD at University of Chicago, by establishing a professionally staffed facility with the state-of-the-art equipment for high-throughput synthesis, purification and analytical characterization of newly generated chemical libraries.

2. Establishing the Hit-to-Lead Development Resource of the CTCMLD at Northwestern University, which will provide unique support for innovative research at the interface of chemistry and biology in Chicago area.

3. Developing a Computational Cheminformatics Core at UIC, which will be used to guide production of small-molecule libraries with favorable physicochemical properties and will facilitate analysis of the compound screening data.

 

Three cores are available to the CBC research community through the Chicago Tri-Institutional Center for Chemical Methods and Library Development (CTCMLD):

  • Library Production Core (located on the University of Chicago campus)
  • Hit-to-Lead Development Resource (HLR) (located at Northwestern University)
  • Computational Cheminformatics Core (located at the University of Illinois at Chicago)

For more information on the cores click here or go directly to the CTCMLD website.

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January 2009
PIs: Kevin White, PhD (UChicago); Robert Grossman, PhD (UChicago; at UIC at the time of the award); Richard Morimoto, PhD (NU); Luis Amaral, PhD (NU) for project:
Chicago Center for Systems Biology
Type of Award: Lever
Amount Awarded: $ 3,000,000.00

Award Description: The CBC has awarded $3 million over three years to help establish the Chicago Center for Systems Biology (CCSB). The CBC Lever Award matches a $15 million award from The National Institute of General Medical Sciences. The CCSB will be one of 10 National Centers for Systems Biology — the first of its kind in Illinois and an outstanding new research resource for the Chicago region. Systems Biology is an emerging field, focusing on the study of complex interactions in biological systems, including everything from the smallest molecules to complete organisms.Kevin White at the University of Chicago will direct the Chicago Center for Systems Biology, which revolves around collaborations among Chicago-area experts in genomics, developmental biology, evolutionary biology, stress and physiology, chemistry and physics and computational professionals who specialize in network modeling and high-performance computing. Combining experimental and computational tools, the CCSB will study the dynamic behavior of gene networks in cells, tissues, and organisms, paying specific attention to transcriptional networks, clusters of master genes that regulate the activity of other genes by directly turning them on or off.

CBC Lever Awards are matching grants made to inter-institutional groups that are submitting large-scale grant proposals. The Principal Investigators on the Lever Award to the CCSB are Luis Amaral (Northwestern), Robert Grossman (University of Chicago; at UIC at the time of the award), Richard Morimoto (Northwestern), and Kevin White (University of Chicago). Lever Awards are primarily used to establish transformative infrastructure that can be made broadly available to the Chicago scientific community. The CCSB Lever Award will support the following four key initiatives:

1. Developing an enhanced imaging core, that uniquely combines microfluidics and confocal microscopy for live imaging of model organisms, tissues, and cells.

2. Cultivating a recombineering and high-throughput cloning core to support genetic modifications to chromosomal sections for human, mouse, Drosophila, and C. elegans genomes.

3. Advancing a computational core that will integrate intimately with the biological driver projects and which will produce software modules that will be useful to a much broader community.

4. Establishing a “CBC Research Fellows Program in Systems Biology” to train the next generation of young scientists in the art of interdisciplinary research in Systems Biology.

The following cores are available to the CBC research community at the Chicago Center for Systems Biology (CCSB):

1. Advanced Imaging Core (AIC)

2. BAC-Recombineering Core

3. Computational Core

For more information about the Chicago Center for Systems Biology (CCSB) click here.

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Funded Spark Awards

Spark Award Program ran from 2008 until August 2011. The Program focused on mid-sized collaborative projects of exceptional creativity. Past CBC Spark Awards are listed below:

August 2011
PIs: Nissim Hay (UIC), Joseph Bass (NU), Graeme Bell and Louis Philipson (UChicago) for project:
Leptin peptide in diabetes: from mechanism to therapeutics
Type of Award: Spark
Amount Awarded: $ 399,597.00

Abstract: Leptin receptor levels are highest in the brain, which is consistent with the primary action of leptin to decrease food intake. However, we hypothesize that, under normal physiological conditions, leptin also plays a key role in the regulation of blood glucose levels through direct effects on the liver and regulation of hepatic glucose production. This effect is more readily evident in insulin-deficient states, common in both type 1 and late type 2 diabetes. We further propose that insulin modulates leptin signaling as abrogation of insulin signaling increases leptin levels in blood and leptin receptor expression in liver. Although this hypothesis challenges the commonly accepted view that leptin exerts its effects through it action in various regions of the brain, there are other observations that provide support for our hypothesis: 1. Liver-specific insulin receptor knockout mice display a 10-fold increase in serum leptin levels as well as a 35- fold increase in leptin receptor levels mRNA in the liver; 2. The level of hepatic leptin receptor is dramatically increased in mice with liver-specific knockout of the downstream insulin receptor signaling molecules IRS1 and PI3 kinase; 3. The expression of hepatic leptin receptor in Akt-deficient mice is markedly increased (data not shown); and 4. Leptin treatment in human patients with lipodystrophy and in multi-tissue Akt-mutant mice (both of which have low leptin levels) normalizes blood glucose levels. Thus, impaired hepatic insulin/PI3K/Akt signaling in the liver is coupled to a marked elevation of leptin receptor levels concomitant with an increase in the levels of circulating leptin. Moreover, deficiency of leptin due to impaired development and/or function of adipose tissue is linked to hepatic overproduction of glucose, increasing insulin resistance and thereby exacerbating diabetes, and fasting hyperglycemia in particular. Surprisingly, the significance of these observations implicating leptin signaling in the regulation of hepatic function are not fully appreciated and need to be further explored to impact clinical practice. Thus, a major goal of this proposal is to challenge the current dogma that leptin exerts its effect on glucose homeostasis exclusively or largely though its effect on the brain. Specifically we will generate hepatic leptin receptor KO mice. These mice will be treated to induce type 1 diabetes and will be subjected to leptin therapy. These mice will also be crossed with Akita mice and the compound mice will be subjected to leptin therapy.

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September 2009
PIs: Anthony Kossiakoff (UChicago), Vladimir Gelfand and Charles Clevenger (NU) for project:
Delivery of synthetic antibodies to probe cell dynamics in live cells
Type of Award: Spark
Amount Awarded: $ 400,000.00

Abstract: Goals: We propose to develop a technology platform for the next generation of affinity reagents and imaging probes that will substantially extend capabilities for observing dynamic events in live cells. Transitions between distinct protein conformations or the formation of multi-protein complexes are fundamental to cellular structures, signaling and regulation. However, current antibody and fluorescent-protein tags are generally insensitive to these subtle, but functionally critical changes in target molecules. To overcome this deficiency we have developed a new technology platform that both generates highly specific affinity-binders that have the capability to identify specific protein complexes and transient conformations and to deliver these probes to living cells with experimental ease and minimal perturbation so they can interrogate cellular dynamics in their native cell environments. As a challenging test-bed to develop and test our new technology, we will generate unique affinity reagents and imaging probes to study core aspects of signaling and motor function essential in cytoskeletal dynamics that cannot be investigated using current methods. This pilot project is only the beginning for what we believe is the full potential for our technology platform. Our long term objective is to assemble a high-throughput pipeline to produce high-affinity synthetic affinity reagents to high-impact protein and RNA targets for use in imaging, localization and inhibition studies in their native cellular environments. We believe it is well within the capability of the technology to automate most of the steps of the pipeline with the aim to create a powerful, compact and affordable core facility-like platform to provide all Chicago area researchers with designer antibodies that can be tailored to particular systems and needs.

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June 2009
PIs: Thomas O’Halloran and Vinayak Dravid (NU) and Jonathan Silverstein (UChicago) for project:
Support for An Innovative CryoSTEM for Element Specific Imaging of Cells and Tissue
Type of Award: Spark
Amount Awarded: $ 379,341.00

Abstract: Support from the two-year Spark Award will be used to fund two scientists who will aid CBC faculty members in using a high-resolution cryo-capable scanning transmission electron microscope (Cryo STEM), soon to be acquired. The microscope is capable of following changes in subcellular distributions of essential or toxic metal ions at the level of a few hundred atoms at a time and offers the unprecedented ability to produce quantitative maps of each relevant element within a biological sample. One CBC-funded scientist will support use of the instrument and train and advise CBC users in sample preparation and data acquisition. A second CBC-funded scientist will make the resulting multidimensional data usable by developing computational methods for 2-D and 3-D volumetric rendering representing the spatial variations in elemental concentrations.This spark award leverages core funding that the team, along with Teresa Woodruff of Northwestern, received from the W. M. Keck Foundation for the purchase and installation of the Cryo STEM. The acquisition of this custom-designed high-resolution electron microscope will bring a novel imaging resource to the Chicago area. While the device will be located on the Northwestern Evanston campus, the full-time staff supported by the CBC will open up use of this unique and exciting technology to researchers from the other CBC member institutions.

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March 2009
PIs: Martin Kreitman and Ilya Ruvinsky (UChicago) and Richard Morimoto (NU) for project:
The Role of Natural Variation and Proteostasis in Complex Disease Traits
Type of Award: Spark
Amount Awarded: $ 400,000.00

Abstract: Our project “The Role of Natural Variation and Proteostasis in Complex Disease Traits”, will attempt to create a new paradigm for studying human diseases with multifactorial genetic and environmental causes. Modern molecular genetics has triumphed over the past decade in the discovery of major mutations causing important human genetic diseases. But many diseases, such as adult-onset diabetes and autism, are not caused by mutations in single genes, but instead are characterized by a complex, and yet unknown, interaction between genetic variations in large number of genes and subtle environmental factors. For these diseases, molecular genetics has been much less successful in deciphering their genetic underpinnings. Our project, a collaboration between two evolutionary geneticists, Dr. Martin Kreitman and Ilya Ruvinsky (Department of Ecology and Evolution, U. Chicago), and a molecular geneticist, Dr. Richard Morimoto (Biochemistry, Molecular and Cell Biology, Northwestern U), proposes a novel way forward by investigating natural variation for susceptibility and severity of complex human disease, recreated in two model organisms, the fruitfly Drosophila melanogaster and the worm Caenorhabditis elegans. The two human diseases we will investigate — neurodegeneration and neonatal diabetes — share a common attribute in that they both result from the inability of targeted cells to respond to physiological stresses imposed by the expression of unstable mutant proteins. The inability of cells to respond to these stresses results in programmed cell death, the direct cause of disease. According to our working hypothesis, a complex diffuse web of interacting naturally occurring polymorphisms in fly, worm and human sets an individual’s ability to respond to genetic or environmental challenges, determining susceptibility to and severity of disease. We will, for the first time, investigate naturally occurring variation affecting disease models in powerful model genetic systems, which we believe has the potential to revolutionize the use of disease these models. The goal of our experiments will be to identify cellular and genetic mechanisms in the worm and fly that influence the severity of these model diseases, taking advantage of the many power genetic and molecular tools available in these model organisms. We believe that commonalities in the worm and fly will also prove to be shared with the human form of the diseases, and that discoveries in these model organisms will therefore be relevant to developing novel therapies to disease. Our findings about effects of genetic variation on the ability of a cell to balance protein synthesis, folding, transport, and degradation (proteostasis), may have broader relevance to other sporadic diseases, in addition to diabetes and neurodegenerative disease. More generally, by integrating the study of natural genetic variation in model organisms with human genetic diseases recreated in these organisms, our research holds the promise of introducing powerful new strategy for deciphering the genetic basis of complex human disease.

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January 2009
PIs: Erik Sontheimer (NU), Alexander Mankin (UIC) and Jonathan Staley (UChicago) for project:
Noncoding RNA Structure, Function, and Evolution
Type of Award: Spark
Amount Awarded: $ 400,000.00

Abstract: Organisms depend on the proper and dynamic functioning of their genes, many of which encode proteins that carry out essential cellular tasks. Additionally, species depend on the evolution of genes to adapt and survive over time. Because inappropriate gene expression causes or contributes to many diseases, including cancer, the expression of genes into proteins must be controlled properly to maintain human health. Genes are comprised of DNA, and the first step of gene expression involves the production of an RNA copy of the gene’s DNA sequence. In many cases the RNA is simply an intermediate that serves as a template for the production of a protein. In other instances, however, the RNA has its own biochemical function beyond the temporary transmission of genetic information, and such RNAs are known as noncoding RNAs (ncRNAs). RNA has increasingly been found to be as important as proteins in executing and regulating gene expression, and the number of known ncRNAs has skyrocketed. However, the boundaries of the ncRNA universe are not yet known, and the functions of most ncRNAs remain mysterious. To meet the challenges and exploit the opportunities of this exciting time in RNA research, we will capitalize on our existing strengths in this area by establishing a Center of Excellence for the investigation of the structure, function and evolution of ncRNAs. Specifically, we aim to discover new modes of ncRNA function, define novel ncRNA populations, explore their structures and interactions with other cellular components, and determine how ncRNA genes evolve. To catalyze these long-term goals, we will expand our capabilities in two areas central to ncRNA research: custom chemical synthesis and bioinformatics. Because ncRNAs are now known to impinge upon nearly all areas of biology, the establishment of an ncRNA research center will benefit the Chicago biomedical community as a whole.

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January 2009
PIs: Keith Thulborn and Y. Jeong (UIC) and Thomas Meade (NU) for project:
Metabolic MR Imaging for Studies of Human Brain Disease
Type of Award: Spark
Amount Awarded: $ 400,000.00

Abstract: The treatment for human disease at the earliest stages requires sensitive, quantitative, and non-destructive diagnostic monitoring methods. Magnetic resonance imaging (MRI) is one of the few technologies capable of localized, nondestructive metabolic characterization without ionizing radiation. The high spatial and temporal resolution of MR imaging provides the means to investigate physiology at the systems level (i.e., whole organisms).This project develops a new dimension of MR imaging to monitor metabolic changes expressed in the earliest stages of disease and during response to treatment. It will focus on obtaining insights into the interrelated problems of developmental and molecular biology and clinical diseases by i. generating MR probes that function as real-time in vivo physiological reporters (exogenous), ii. develop quantitative parameters of metabolic concentrations and rates that reflect tissue health (endogenous) and iii. correlate in vivo image analysis by pharmacokinetic methods. Although applicable to any location in the body, the human brain will be the initial target organ.

Bioscales will be created using MR signals. The signals will be derived from metabolites occurring naturally in the body, or from bioactivated probes that detect specific biochemical processes. New classes of probes will be synthesized and optimized and human and non-human primate MRI studies will be performed at the enhanced sensitivity of 9.4 Tesla to calibrate these bioscales for metabolic modeling of the healthy brain.

These metabolic models will be combined with enhanced MR imaging applicable to clinical field strengths of 3.0 Telsa. This translational approach will result in metabolic imaging for monitoring the earliest stages of diseases, thereby stimulating the development of earlier, and therefore less expensive, interventions. The strategic plan of the NIH emphasizes healthcare cost containment through earlier treatment of disease. Metabolic imaging using both exogenous and endogenous agents is an essential technology for developing such early intervention strategies for humans.

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November 2008
PIs: Robert Goldman and Jonathan Widom (NU), Stephen Kron, Harindar Sighn and Elizabeth McNally (UChicago) for project:
The Chicago Laminome Project
Type of Award: Spark
Amount Awarded: $ 400,000.00

Abstract: The nuclear lamins are members of one of the largest families of proteins. Lamins form mesh-like networks within the nucleus, providing a molecular interface, the lamina, between the membranes surrounding the nucleus and the chromosomes contained inside. In recent years the lamins have been shown to be major components of an extensive regulatory network involved in a wide range of functions, including the control of components of an extensive regulatory network involved in a wide range of functions, including the control of nuclear architecture, the organization, positioning and structure of chromosomes, gene expression, and DNA replication and repair. However, the molecular mechanisms underlying these functions remain largely unknown. There are three lamin genes in humans. Remarkably, over 300 mutations have been identified in one of the human lamin genes, causing nearly 20 different diseases. The lamin A/C gene is one of the most highly mutated genes in humans and is unique for its association with the most diverse disease phenotypes. There is an emerging hypothesis that lamins serve a critical role in the maintenance of cell identity and integrity via regulated protein-protein interactions and associations with specific chromosome structures.The Chicago Laminome Project is a comprehensive approach to understanding lamins in health and disease via tools of systems biology. The City of Chicago had a unique set of internationally recognized leaders who have studied lamins, chromosome structure and function, and proteomics. The Chicago Laminome Project will bring this multi-institutional, multi-disciplinary group together to study the roles of lamins and lamina structure, with the longer term goal of making the Chicago area a widely-recognized center of leadership in this important field of study.

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