Research into the structural bases of biological function.
Labs In This Area
Structural and biochemical basis of chromatin folding and chromosome condensation
The folding of DNA within nuclei and chromosomes is one of the great mysteries of biology, impacts gene regulation and influences heredity. At the most basic level, DNA is wrapped around histones in the nucleosome to form an extended “beads-on-a-string” chromatin fiber. Chromosome conformation capture, involving chemical cross-linking of chromatin followed by restriction digestion, ligation and high-throughput DNA sequencing (Hi-C), detects further folding of the chromatin fiber. Hi-C has revealed “topologically associating domains” (TADs), regions of intra-chromosomal self-association that are interspersed with regions of little or no such self interaction, which are prevalent throughout metazoans. By applying Hi-C to the polytene chromosomes of Drosophila, I established that polytene bands are equivalent to TADs, connecting chromatin folding inferred from Hi-C with direct, physical observations from light microscopy. Furthermore, TADs are conserved between polytene and diploid cells identifying the polytene band-interband pattern as a general principle of interphase chromosome architecture. Chromatin between TADs exists in a fully extended state, whereas TADs, which are up to 30-foldmore condensed, reflect the next higher level of stable chromosome folding.
Through experimental and computational improvements to the Hi-C method, I mapped chromatin interactions at sub-kilobase resolution, the highest resolution for a metazoan genome to-date. This allowed me to determine the locations of chromatin loops across the Drosophila genome. Loops were frequently located within domains of polycomb-repressed chromatin. Loop boundaries or “anchors” were frequently associated with the protein Polycomb, a subunit of Polycomb Repressive Complex 1 (PRC1). Promoters located at PRC1 loop anchors regulate some of the most important developmental genes and are less likely to be expressed than those not at PRC1 loop anchors. Although DNA looping has most commonly been associated with enhancer–promoter communication, these results indicate that loops are also associated with gene repression.
These advances have significantly furthered our understanding of nuclear organization, but DNA folding at the scale of tens-of-nanometers and beyond is still largely undetermined. Enhancers, cis-regulatory regions often located a distance from gene promoters, are important for tissue specific gene expression and malfunction in cancer. Enhancers are often found within TADs and intra-TAD chromatin folding influences proper gene regulation by modulating enhancer-promoter interactions. Disrupting TAD structure pathogenically rewires these interactions in human disease, so determining how TADs fold is of great interest. At the highest level of DNA folding, mitotic chromosomes are one of the most recognizable structures in cell biology, yet a detailed understanding of their internal structure has remained elusive. Faithful propagation of mitotic chromosomes underlies cellular heredity, so it is important to relate chromatin folding within interphase TADs to chromosome condensation during metaphase. My lab combines concepts and approaches from structural biology with methods and analytical tools from molecular biology and genomics to determine the structural basis of chromatin condensation within TADs and mitotic chromosomes. A combination of molecular biology, biochemistry, genomics and imaging will pave the way for a deeper understanding of chromatin structure as well as unravel principles.
Visit the Eagen Lab Website.
For more information, visit the faculty profile page of Kyle Eagen
View lab publications via PubMed.
Structural Biology, X-ray Crystallography, Macromolecular Structure/Function-GTPase mechanism, Signal Recognition Particle (SRP) targeting complex and Mitochondrial protein Miro, among others
a. Tetrameric galectin from cynachyrella sp.
b. Hydrogen bonding structure at the N/G domain interface of Ffh.
c. The Ffh/FtsY GTPase heterodimer highlighting its buried nucleotide pair.
We determine the three-dimensional structures of proteins in order to understand the structural basis for and functional mechanisms of interactions between proteins and between proteins and small molecules that play important roles cell biology.
One focus is the GTPases of the Signal Recognition Particle (SRP), Ffh and FtsY. We currently seek to understand the structural basis for regulation of assembly of their heterodimeric targeting complex. The complex is mediated by a remarkable composite GTPase active site, but how this “GTPase core” regulates (and is regulated by) cotranslational targeting remains an important focus of research. Key publication: Focia (2004) Heterodimeric GTPase Core of the SRP Targeting ComplexScience 303 p373-7
We have collaborated with the laboratory of Geoffrey Swanson (Northwestern University, Pharmacology) and Ryuichi Sakai (Hokkaido University) to determine the structure of a novel tetrameric galectin from a marine sponge. Key publication: Freymann (2012) Structure of a tetrameric galectin from Cinachyrella sp.Acta CrystD68 p1163-74
Currently we are collaborating with Sarah Rice (Northwestern University, Cell & Molecular Biology) to understand the mitochondrial protein Miro, a key regulator of Ca-dependent mitochondrial transport. The protein comprises unusually coupled Ca-binding EF hand / GTPase-fold pairs. We seek to determine the structural role for small molecule ligands (i.e. calcium, GTP) in the regulation of this important protein. Key publication: Klosowiak (2013) Structural coupling of the EF hand and C-terminal GTPase domains in the mitochondrial protein MiroEMBO Rep.14 p968-74
We have also initiated a proposal to determine structures of novel members of the bloodstream trypanosome surface coat proteins (VSGs) in order to understand a previously unrecognized minimal structural motif that is widely conserved among unrelated trypanosomal surface proteins.
For more information, visit the faculty profile of Douglas Freymann, PhD.
See Dr. Freymann's publications in PubMed.
Research Assistant Professor:
Pamela FociaStructural Biology Facility Manager, Robert H. Lurie Comprehensive Cancer Center
Mechanisms of signal transmission across the membrane via the cell-surface receptors
This laboratory is interested in cancer, neural development and reproduction-related structural mechanisms of how extracellular signals (e.g., growth factors, adhesion molecules and morphogens) are translated into intracellular signals by plasma membrane receptors. We use biophysical methods (crystallography, calorimetry, surface plasmon resonance, analytical ultracentrifugation, etc.) in combination with functional studies to define the physiological states and binding processes of these receptors and their complexes with ligands. Our research targets include receptor tyrosine kinases, Semaphorin and its receptors and leucine-rich-repeat-containing G-protein coupled-receptors.
For more information, visit the faculty profile of Xiaolin He, PhD.
See Dr. He's publications in PubMed.
Contact Dr. He at 312-503-8030 or the He Lab at 312-503-8029.
The Kelleher Group has three primary lines of research focused on Top Down Proteomics, Natural Products Discovery and Biosynthesis and Chromatin Oncobiology and DNA-Damage. An underlying focus, driving all lines of research, is our continued push towards optimizing instrumentation and bioinformatic approaches to best suit the unique needs of a Top Down analysis.
The main focus for our Top Down Proteomics subgroup is to push the limits for whole proteome analysis of mammalian cells, striving for a future in which Top Down analysis rivals that of Bottom Up in the number of protein identifications per run. Recently, we have seen progress toward this very goal with the introduction of a separation platform specifically designed to minimize the most common problem in Top Down Proteomics, intact protein separations. This platform effectively reduces sample complexity and separates proteins depending on size, resulting in an opportunity for the scientist to select the optimal analysis method for the sample.
Our Natural Products subgroup is focused on the discovery and biosynthesis of novel natural products. Developments from this subgroup include the introduction of the PrISM platform, geared towards the identification of natural products synthesized by nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) without prior knowledge of a gene sequence. This is made possible by our ability to detect a phosphopantetheinyl (Ppant) ejection marker ion for NRPS/PKS thiolation domains. We also work in collaboration with groups from other universities to provide mass spectrometry analysis of novel biochemical systems.
We also have a long-standing interest in histone analysis. Our Chromatin Oncobiology and DNA-Damage subgroup continues to dig deeper into the "histone code", a complex mixture of post-translational modifications that together determine a host of cellular processes. We are interested in visualizing dynamic histone PTM changes simultaneously on multiple sites. Through application of technology developed in our Top Down Proteomics subgroup, we are able to apply "Precision Proteomics" to histone analysis.
View lab publications via PubMed.
Contact the Kelleher Lab at 847-467-1086 or 847-467-4362
Structural properties of prion proteins using yeast as a model organism
Prion diseases belong to a class of fatal, infectious neurodegenerative diseases known as transmissible spongiform encephalopathies (TSEs), including the bovine spongiform encephalopathies (BSE or mad cow disease) in cattle and Creutzfeldt-Jakob disease (CJD) in human. It is generally accepted that the infectious agent of prion disease is a normal host protein (PrPC) that has adopted a pathogenic conformation that is infectious (PrPSc). Remarkably, there are several atypical yeast proteins capable of existing in multiple stable conformations, each of which is associated with distinct phenotypes. Intriguingly, some of the conformations are able to self-propagate and are “infectious.” They are thus referred to as yeast prions. Our laboratory is interested in study this fascinating prion phenomenon using yeast as a model organism. Yeast offers a powerful system that is amenable to biochemical, cell biological and genetic manipulations. We want to obtain information on the structural properties of yeast prions, their mutual interactions and their interactions with other cellular factors, particularly, with molecular chaperones. We have recently discovered that the yeast heat-shock transcription factor (HSF), a master regulator of molecular chaperones’ production, plays an important role in governing the de novo formation and “strain” determination of yeast prion [PSI+]. We are working toward to identify novel cellular factors that are HSF targets and important for yeast prion formation and inheritance. The function of HSF is evolutionally conserved from yeast to human. We hope that results from our yeast prion studies will provide valuable information on the complex etiology of the devastating prion diseases.
Our laboratory is also interested in investigating how common the prion phenomenon in biology is. We wish to identify potential prion proteins from yeast and other non-yeast model organisms through a combined approach of bioinformatics and genetic screenings. Our ultimate goal is to uncover the mechanisms governing the prion conformational switch and to understand the biological significance of the protein conformation based prion-like inheritance.
For more information, visit the faculty profile of Liming Li, PhD.
See Dr. Li's publications in PubMed.
Epstein-Barr virus (EBV) and herpes simplex virus (HSV) entry, replication and pathogenesis.
Research in the Longnecker laboratory focuses on herpes simplex virus (HSV) and Epstein-Barr virus (EBV). These viruses typically cause self-limiting disease within the human population but both can be associated with serious complications. EBV is associated with variety of hematopoietic cancers such as African Burkitt lymphoma, Hodgkin Lymphoma and adult T-cell leukemia. EBV-associated lymphoproliferative disease occurs in individuals with congenital or acquired cellular immune deficiencies. The two notable epithelial diseases associated with EBV infection are nasopharyngeal cancer and oral hairy leukoplakia. Similar to EBV, HSV latent infections are very common in humans. HSV typically does not cause severe disease but is associated with localized mucocutaneous lesions, but in some cases can cause meningitis and encephalitis. The Longnecker laboratory focuses on several aspects of EBV and HSV replication and pathogenesis. First, the molecular basis EBV transformation and how it relates to cancer is being investigated. The laboratory is currently screening selective inhibitors that may be beneficial in EBV-associated cancers such as Hodgkin lymphoma, Burkitt lymphoma and proliferative disorders that occur in HIV/AIDS and transplant patients. Second, the laboratory is investigating herpesvirus latency in the human host and pathogenesis associated with infections in humans. In this regard, the laboratory is developing animal models for EBV and HSV infections. Finally, the laboratory is investigating the function of herpesvirus encoded proteins and the cellular receptors that are important for infection both using in vivo culture models as well as animal models. Ultimately, studies by the Longnecker laboratory may provide insight for the development of novel therapeutics for the treatment of herpesvirus infections in humans and better understanding of the herpesvirus life cycle in the human host
For lab information and more, see Dr. Longnecker's faculty profile
See Dr. Longnecker's publications on PubMed.
Contact Dr. Longnecker at 312-503-0467 or the lab at 312-503-0468 or 312-503-9783.
Tolerance mechanisms in autoimmune diabetes and transplantation
1. Tolerance mechanisms for transplantation. We use rodent as well as non-human primate models. These models include allogeneic islet, heart and kidney and xenogeneic islet transplantation. Transplant tolerance is induced by infusion of donor cells treated with the chemical cross-linker ethylcarbodiimide (ECDI). Using a stringent full MHC-mismatched strain combination, we have shown in an allogeneic islet cell transplant model that two infusions of ECDI-treated donor cells prior to and after transplantation led to indefinite graft survival in over 90% of the transplant recipients in the absence of any immunosuppression. This tolerance strategy takes advantage of the tolerogenic recognition of apoptotic donor cells by recipient CD11c dendritic cells and is associated with up-regulation of Tregs and down-regulation of anti-donor T and B cell responses. The same strategy has been applied to allogeneic heart and kidney transplant, as well as xenogeneic islet transplant (rat-to-mouse, pig-to-mouse) with robust tolerance efficacy. We are currently applying the same strategy to monkey-to-monkey (allogeneic) and pig-to-monkey (xenogeneic) islet transplantation. Our ultimate goal is to test this tolerance strategy in human-to-human (allogeneic) and pig-to-human (xenogeneic) solid organ and/or tissue transplantation. Additional ongoing efforts in the lab also focus on: (1) understanding how viral infections at various stages (acute, chronic, latent) can influence tolerance efficacy and stability; (2) collaborating with Shea lab in designing nanoparticle-based cell-free tolerance strategies for allogeneic and xenogeneic transplantation.
2. Proteins with post-translational modifications (PTMs) as neoantigens for autoimmune diabetes. We use the non-obese diabetic (NOD) mouse model to study the role of proteins with PTMs in the pathogenesis of type 1 diabetes. Beta cell secretory proteins are subjected to post-translational modifications such as deamidation and di-sulfide bond formation among others. Such modified proteins/peptides may become neoantigens that can activate endogenous T cells and lead to beta-cell directed autoimmunity. Ongoing efforts in the lab focus on: (1) temporal correlation between the appearance of humoral immunity to proteins/peptides with PTMs and diabetes development; (2) the role of cellular immunity to proteins/peptides with PTMs in the development of diabetes; (3) the role of endogenous enzymatic pathways for the formation of such neoantigens; (4) the role of neoantigens as a diagnostic tool for autoimmune diabetes; (5) the role of neoantigens for more effective tolerance induction strategies for autoimmune diabetes.
3. Circadian Clock regulation in immune cell function and autoimmune diabetes. Disruption of circadian rhythms has been linked to inflammatory diseases, however the precise roles of core clock proteins in the function of immune cells have not been elucidated. Collaborating with the Bass lab, we are investigating the role of BMAL1, one of the core clock proteins, in controlling several fundamental aspects of the immune system. Ongoing efforts in the lab focus on: (1) defining the phenotypic and functional alterations in immune cells caused by disruption of circadian gene regulation; (2) defining the role of circadian gene regulation at the immune cell/beta cell interface and its contribution to the development of autoimmune diabetes; (3) defining the role of circadian gene regulation at the immune cell/transplanted graft interface and its contribution to the development transplant graft rejection.
For more information visit Dr. Luo's faculty profile page
View Dr. Luo's publications at PubMed
Seeking to understand the cellular basis of neurodegeneration.
The long-term goal of my laboratory is to understand the cellular basis of neurodegeneration. We are testing the idea that neurodegeneration results from derangements in relatively few but strategic sub-cellular pathways. By identifying critical components of these pathways one could begin to not only understand the biology of neurodegeneration, but also embark on the design of novel therapeutic agents.
We are currently studying the autosomal dominant disorder Spinocerebellar Ataxia Type 1 (SCA1), a relentless disease that affects cerebellar Purkinje cells and brainstem neurons. This disorder is caused by a polyglutamine expansion in the involved disease protein and is thus similar to a growing number of disorders, including Huntington disease, that share this mutational mechanism. Patients with SCA1 begin to display cerebellar signs characterized by motor incoordination or ataxia in early to mid adulthood. Unfortunately there is no treatment for this disease and patients eventually succumb from the complications of brainstem dysfunction.
Testing the transcriptional hypothesis in SCA1 pathogenesis:
One of the earliest features of this disease is change in the gene expression signature within neurons affected in this disease. We are elucidating the pattern of gene expression changes in the vulnerable Purkinje cell population and identifying the contribution of these alterations to pathology.
Testing the role of the vascular and angiogenic factor VEGF in SCA1 pathogenesis.
One of the genes that we have already found to be down-regulated is the neurotrophic and angiogenic factor VEGF. Importantly, we have discovered that genetic or pharmacologic replenishment of VEGF mitigates SCA1 pathogenesis. These results suggest a novel therapeutic strategy for this incurable disease and a possible cross-talk between the degenerating cerebellum and its microvasculature. We are pursuing mechanistic experiments to learn how low VEGF mediates SCA1 pathology. In addition, we are working actively towards testing the potential for VEGF as a therapy in human ataxic disorders.
Testing the role of ataxin-1 misfolding and clearance in disease pathogenesis.
Several studies suggest that ataxin-1 accumulates in neurons because of its inability to be cleared by the protein-misfolding chaperone pathway. We are testing different strategies to promote ataxin-1 clearance.
In addition to spinocerebellar ataxia, we are also studying genetic parkinsonian and dystonic syndromes.
View Dr. Opal's full list of publications at PubMed
Puneet Opal, MD, PhD, at 312-503-4699
Investigating intracellular calcium signaling
Research in the laboratory of Murali Prakriya, PhD, is focused on the molecular and cellular mechanisms of intracellular calcium (Ca2+) signaling. Ca2+ is one of the most ubiquitous intracellular signaling messengers, mediating many essential functions including gene expression, chemotaxis and neurotransmitter release. Cellular Ca2+ signals generally arise from the opening of Ca2+ permeable ion channels, a diverse family of membrane proteins. We are studying Ca2+ signals arising from the opening of a Ca2+ channel sub-type known as the store-operated Ca2+ channel (SOC). SOCs are found in the plasma membranes of virtually all mammalian cells and are activated through a decrease in the calcium concentration ([Ca2+]) in the endoplasmic reticulum (ER), a vast membranous network within the cell that serves as a reservoir for stored calcium. SOC activity is stimulated by a variety of signals such as hormones, neurotransmitters and growth factors whose binding to receptors generates IP3 to cause ER Ca2+ store depletion.
The best-studied SOC is a sub-type known as the Ca2+ release activated Ca2+ (CRAC) channel. CRAC channels are widely expressed in immune cells and generate Ca2+ signals important for gene expression, proliferation and the secretion of inflammatory mediators. Loss of CRAC channel function due to mutations in CRAC channel genes leads to a devastating immunodeficiency syndrome in humans. A major effort in our lab is to understand the molecular mechanisms of CRAC channel function.
Despite the fact that SOCs are found in practically all cells, their properties and functions outside the immune system remain largely unexplored. In order to fill this gap, we have begun investigation of SOC properties and their functions in two major organ systems: in the brain and the lung.
- Neural stem cells (NSCs) express SOCs; robust Ca2+ signals arise from their activation, indicating that SOCs are a major route of Ca2+ entry in NSCs
- CRAC channels serve as a major route of Ca2+ entry in lung epithelial cells; CRAC channel activation leads to robust activation of NFAT and the production of proinflammatory cytokines
See Dr. Prakriya's publications on PubMed.
Contact Dr. Prakriya at 312-503-7030.
Role of bacterial protein toxins in the pathogenesis of Vibrio vulnificus and Vibrio cholerae
My research focuses on the role of secreted protein toxins on bacterial pathogenesis. The toxins we study are members of the MARTX family and are produced by Vibrio cholerae, a pathogen important for the diarrheal disease cholera, and Vibrio vulnificus, a pathogen that causes septicemia and necrotizing fasciitis from seafood consumption as well as wound infections. Our group studies the mechanism of action of these toxins using a combination of cell biology, biochemistry, and structural biology. In addition, we investigate the role of these toxins in pathogenesis using animal and tissue culture models with focus on mechanisms of tissue damage and evasion of innate immune clearance.
See Dr. Satchell's publications on PubMed.
Contact Dr. Satchell at 312-503-2162 or the lab at 312-503-1503.
Research in the Savas lab is aimed at accelerating our understanding of the proteins and proteomes responsible for neurodevelopmental and neurodegenerative diseases.
We use biochemistry with discovery-based mass spectrometry to identify the protein perturbations which drive synaptopathies and proteinopathies. Groups of perturbed proteins serve as pathway beacons which we subsequently characterizes in hopes of finding new pathogenic mechanisms and potential future therapeutic targets.
Please see Dr. Savas' publications on PubMed.
Jeffrey N Savas, PhD
Assistant Professor in Neurology
Bacterial pathogenesis, DNA recombination mechanisms, epithelial cell adherence
Our laboratory studies the pathogenesis of Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhea. This gram-negative bacterium is an obligate human pathogen that has existed within human populations throughout recorded history. We are using a variety of molecular biological, genetic, cell biological and biochemical techniques to investigate the molecular mechanisms controlling gonococcal infection, define mechanisms and pathways of DNA recombination, replication and repair in this human specific pathogen, study the interactions between gonococci and human cells, tissues and the innate immune system and determine how the pilus functions to help mediate genetic transfer and pathogenesis. Our goal is to discover new mechanisms important for the continued existence of this microbe in the human population to further our understanding of how infectious agents have evolved to specifically infect humans.
For lab information and more, see Dr. Seifert's faculty profile.
See Dr. Seifert's publications on PubMed.
Contact Dr. Seifert at 312-503-9788 or the lab at 312-503-9786.
Cell and molecular biology of herpesvirus invasion of the nervous system
We investigate the relationship between infection of the nervous system by herpesviruses and disease outcome. Some of the most traumatic diseases – including polio, rabies and encephalitis – result from infections of the nervous system. In contrast, herpesviruses are highly proficient at infecting the nervous system, yet normally do not cause neurological disease. This is achieved in part by self-imposed restrictions encoded within the viruses that limit viral reproduction and prevent dissemination into the brain. For the individual, this results in a relatively benign infection, yet the virus becomes a life-long occupant of the nervous system that will periodically reemerge at body surfaces to infect others. Unfortunately, this infectious cycle can go awry resulting in several forms of severe disease (i.e. keratitis and encephalitis).
We have pioneered methods to genetically manipulate herpesviruses and visualize individual viruses in living neurons. Using these methods, we are studying the mechanisms by which the virus achieves its stringently controlled infectious cycle. Current genetic manipulations are based on a full-length infectious clone of the herpesvirus genome. The clone was made as a bacterial artificial chromosome (BAC) in E. coli. Transfection of purified E. coli BAC plasmid into permissive eukaryotic cells is sufficient to initiate viral infection, allowing for immediate examination of viral mutant phenotypes in a variety of biological assays. For example, by fusing the green fluorescent protein (GFP) to a structural component of the viral capsid, individual viral particles can be tracked within the axons of living neurons during both entry and egress phases of the infectious cycle. Studies in culture can be complemented by examining the pathogenesis of mutant viruses in rodent models of infection.
Using these methods, we have discovered key aspects of cellular infection, viral assembly and intracellular transport. Looking forward, we are continuing to pursue our multidisciplinary approach of combining neuroscience, cell biology, bacterial genetics and virology to better understand these important pathogens.
For lab information and more, see Dr. Smith's faculty profile.
See Dr. Smith's publications on PubMed.
Contact Dr. Smith at 312-503-3745 or the lab at 312-503-3744.
Research in the Stehlik laboratory focuses on the inflammatory host response during infectious and inflammatory disease with a particular focus on regulation of inflammasomes in phagocytic cells.
Inflammation is a non-specific immune response that occurs in reaction to any type of tissue injury to support tissue repair. Accordingly, acute inflammatory reactions are beneficial; however, chronic and inappropriate inflammation is linked to tissue destruction and disease. Therefore, an important goal is to define strategies to limit these excessive and uncontrolled inflammatory reactions. Inflammasomes are protein platforms that are assembled upon activation of cytosolic pattern recognition receptors to promote activation of the inflammatory caspase-1 and subsequent secretion of its pro-inflammatory cytokine substrates IL-1beta and IL-18 and induction of pyroptotic cell death in monocytes and macrophages. We are investigating the molecular mechanisms that control activation of inflammasomes, which might provide potential targets for developing novel therapies to treat chronic inflammatory diseases. Studies focus to dissect the function of several of these inflammasome activating cytosolic sensors of the Nod-like receptors (NLRs) and AIM2-like receptors (ALRs), and the inflammasome regulatory proteins of the PYD-only protein (POP) and CARD-only protein (COP) families. We primarily focus on macrophages and generated several novel conditional transgenic and knock-out mice to study inflammasomes in response to bacterial and viral infection and sterile tissue damage during autoinflammatory and autoimmune disease, including models for rheumatic disease, Cryopyrinopathies, colitis, sepsis and various bacterial and viral infection models. In addition to mice, we also study this pathway in primary human macrophages from healthy donors and patients. The Stehlik laboratory routinely employs molecular, cellular, biochemical and imaging approaches to dissect these fundamental mechanisms and employ strategies to design novel compounds to interfere with excessive inflammasome responses. If you would like to learn more about our research or join our research group, you are welcome to visit or contact us
View publication from the Stehlik Lab on PubMed
Contact Dr. Stehlik at 312-503-3141 or the Stehlik Lab at 312-503-2191, 312-503-2193 or 312-503-0487
Focusing on the role of protein phosphorylation pathways in disease onset and progression and their potential as drug discovery targets
The role of calmodulin (CaM) mediated signal transduction pathways in physiology and pathophysiology
- Using of emerging technologies to understand how CaM and a CaM-regulated enzyme could be encoded, expressed, regulated and assembled into a calcium signal transduction complex
- Using of integrative (in vivo) chemical biology and molecular genetics to gain insight into how landmark CaM-regulated protein kinases are involved in physiology and pathophysiology
Integrative chemical biology and development of novel therapeutics for attenuation of disease progression
- Using the “smart chemistry” approach integrated with “smart biology” screens for rapid discovery of novel small molecules with potential use in targeting pathophysiology progression related to diseases ranging from neurological disorders, cancer, inflammatory conditions, cardiovascular and pulmonary disease
- Discovering and developing novel small molecule compounds that selectively attenuate the increased production of proteins called proinflammatory cytokines, which can cause tissue injury and disease when produced in excess
We ultimately hope to find, by targeting pathophysiology mechanisms which contribute to disease progression, a series of novel small molecules with potential to be effective against a variety of disorders.
For lab information and more, see Dr. Watterson’s faculty profile
Contact Dr. Watterson at 312-503-0657.
Senior Research Associate
Research Lab Manager
The Wu Laboratory seeks to understand molecular mechanisms regulating gene expression and their involvement in the pathogenesis of age-related diseases, including neurodegeneration and tumor metastasis.
RNA Processing and Neurodegeneration
Accumulating evidence supports that aberrant RNA processing represents a general pathogenic mechanism for neurodegeneration, including dementia and amyotrophic lateral sclerosis (ALS). A number of RNA binding proteins (RBPs) have been associated with neurodegenerative diseases, especially various proteinopathies. Recent studies have defined TDP-43 and FUS proteinopathies, a group of heterogeneous neurodegenerative disorders overlapping with dementia, including frontotemporal lobar degeneration (FTLD) and ALS. Several important questions drive our research: what is physiological function of these RBPs? What are the fundamental mechanisms by which genetic mutations in or aberrant regulation of these RBPs cause neural damage? What are the earliest detectable molecular and cellular events that reflect the neural damage in these devastating neurological diseases? How to reverse/repair the neural damage and slow down the progression of these devastating diseases.
To address these questions, we have established cellular and animal models for both TDP-43 and FUS proteinopathies (Li et al, 2010;Barmada et al, 2010; Chen et al, 2011; Fushimi et al, 2011). Using combined biochemical, biophysical, molecular biology and cell biology approaches, we have begun to examine the molecular pathogenic mechanisms underlying neurotoxicity induced by TDP-43 and FUS. Our recent work using atomic force microscopy (AFM), electron microscopy (EM) and (NMR) approaches has shown the biochemical, biophysical and structural similarities between TDP-43 and classical amyloid proteins (Guo et al, 2011; Xu et al, 2013; Bigio et al, 2013). Our study has defined a minimal amyloidogenic region at the carboxyl terminal domain of TDP-43 that is sufficient for amyloid fibril formation and neurotoxicity (Guo et al, 2011; Zhu et al, unpublished). Using cellular and animal models for FUS proteinopathy, we have begun to identify the earliest detectable cellular damage caused by mutations in and overexpression of the human FUS gene. Our data have provided new insights into pathogenic mechanisms underlying these proteinopathies and suggested candidate targets for developing therapeutic approaches.
A critical step in mammalian gene expression is the removal of introns by the process of pre-mRNA splicing. Alternative pre-mRNA splicing, the process of generating multiple mRNA transcripts from a single genetic locus by alternative selection of distinct splice sites, is one of most powerful mechanisms for genetic diversity and an excellent means for fine-tuning gene activity. Many genes critical for neuronal survival and function undergo extensive alternative splicing. Splicing defects play important roles in neurodegenerative disorders such as dementia and motor neuron diseases. For example, splicing mutations in the human tau gene and imbalance of tau splicing isoforms lead to frontotemporal lobar degeneration with tau-positive pathology (FTLD-tau). To understand mechanisms underlying FTLD-tau, we have set up a model system and developed a number of biochemical, molecular and cell biological assays to study alternative splicing of the human tau gene. Our work has led to the identification of a number of cis-elements and trans-acting RBPs controlling tau alternative splicing (Kar et al, 2006; Wu et al, 2006; Kar et al, 2011; Ray et al, 2011). Our experiments have begun to reveal previously unknown players in FTLD-tau and provided new candidate target genes for developing therapeutic strategy (Donahue et al, 2006; unpublished).
Molecular Mechanisms Regulating Axon Guidance, Cell Migration & Tumor Metastasis
Another line of our research focuses on the cellular and molecular mechanisms regulating cell migration and cancer metastasis. Previous studies from our group and others led to the discovery of Slit as a prototype of neuronal guidance cue. Our studies have shown that Slit interacts with Roundabout (Robo) and acts as a chemorepellent for axons and migrating neurons (Wu et al, 1999; Li et al, 1999;Yuasa-Kawada et al, 2009). Our work has demonstrated that Slit-Robo signaling modulates chemokines and inhibits migration of different types of cells, including cancer cells. The observation that Slit is frequently inactivated in a range of tumors suggests an important role of Slit in tumor suppression. We have established several assays and shown that Slit inhibits invasion and migration of cancer cells, including breast cancer, glioma and prostate cancer. We are using combined molecular and cell biology approaches to dissecting Slit-Robo signaling in neuronal guidance and tumor suppression. Our research has provided new insights into signal transduction pathways mediating Slit function. Enhancing or activating the endogenous mechanisms that restrict or suppress cancer invasion/metastasis will likely provide novel approaches to cancer metastasis.
View a full list of publications by Jane Wu at PubMed
Jane Wu, MD, PhD, at 312-503-0684
Sidan Du, PhD
Research Assistant Professor
Kazuo Fushimi, PhD
Haipeng Cheng, PhD
Yang Li, PhD
Guodong Liu, PhD
Jun Shi, PhD
Warren McGee (MSTP)
Hearing and cochlear amplification, deafness-related proteins and cell death
Left: Three rows of outer hair cells showing prestin proteins (green). Right: location of marshalin (green) in the organ of Corti, the mammalian hearing organ. Microtubule bundles (red) are stained with anti-a-tubulin.
The goal of my lab is to identify and investigate molecules that play important roles in mammalian hearing, thus enriching our understanding of cochlear physiology and further developing a better strategy to prevent hearing loss. Deafness is commonly caused by defects in inner ear hair cells. In mammalian cochleae, inner hair cells (IHCs) function as sensory receptors conveying sound-related information to the central nervous system. Outer hair cells (OHCs) amplify the mechanical signals delivered to IHCs. The cooperation between IHCs and OHCs results in sensitive hearing and sharp tuning. Complex and sophisticated protein networks in hair cells facilitate their functions. Very often, genetic defects in a single protein can interfere with the entire network and cause deafness. Our research has been centered on several important proteins expressed in cochlea.
1. Molecular basis of cochlear amplification. OHCs undergo rapid somatic length changes when the voltage across their membrane is altered. This unique somatic electromotility provides the local mechanical amplification of the cochlear response to sound. Without OHCs, hearing threshold is elevated by 40-50 dB and frequency resolution deteriorates. Prestin is the motor protein of OHCs and is required for cochlear amplification (Zheng et al., Nature, 2000). Coincidently, prestin is only expressed in OHCs, which are also the most vulnerable cells in the organ of Corti. In the past, studying OHC amplification mechanisms and preventing OHC loss were considered two separate research fields. However, our recent data indicate a close connection between prestin's function and the vulnerability of OHCs to a variety of ototoxic exposures. To understand this link, we focus on investigating the molecular mechanism of the motor protein prestin using various cellular, biochemical and molecular biological methods.
2. Protein network of hair cells. We are focus on several deafness-related proteins: CDH23, CEACAM16 and Marshalin. Cadherin 23 is a tip-link protein of hair cells. CEACAM16 is an adhesive protein localized at the tectorial membrane (Zheng et al. PNAS, 2011). Marshalin is another newly identified microtubule minus-end binding protein that is expressed in the inner ear. Its expression is developmentally controlled (Zheng et al., Biology Open 2013). Very often, genetic defects in a single protein can interfere with the entire network and cause deafness. We are in the process of investigating interactions among these proteins and their physiological roles for normal hearing and deafness.
For more information, visit the faculty profile of Jing Zheng, PhD.
View Dr. Zheng's publications in PubMed