Chicago Region Physical Science Oncology Center
List of Collaborating Institutions:
- University of Chicago
- University of Illinois at Chicago
- Massachusetts Institute of Technology
- Memorial Sloan Kettering Cancer Center
- University of Massachusetts Medical Center
The Chicago Region-Physical Science Oncology Center (CR-PSOC) is organized around the conceptual framework that addresses the spatio-temporal organization of chromatin and information transfer in cancer. This organizing framework integrates the strengths of chemistry, genetics, and physics to address chromatin dynamics in cancer. Through the use of shared model systems Center investigators are able to integrate data from across projects to develop a new conceptual understanding of the mechanisms underlying physical rearrangement of chromatin in cancer and how that controls gene expression.
The Center is composed of three interrelated project areas, each focused on different aspects of chromatin structure and function. Each project integrates emerging physical science approaches and molecular and cancer cell biology tools, as well as theory and modeling methods from the physical sciences, to achieve a quantitative and predictive understanding of the of deregulation of chromatin mechanics, epigenetic regulatory pathways, gene expression, and the nuclear environment in cancer. The Center’s projects maintain a clear cancer focus rooted in understanding the molecular mechanism behind genetic alterations in chromatin regulators in cancer, particularly hematological malignancy. The scientific activities of the CR-PSOC are supported by two shared resource cores: the Nanocytometry Core and the PDX Human Tumor Model Core.
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Thomas V. O’Halloran, Ph.D.: Dr. O’Halloran is the Charles and Emma Morrison Professor of Chemistry and Professor of Molecular Biosciences at Northwestern University. He is widely known for his transdisciplinary research program spanning chemical synthesis, analytical chemistry, biochemistry, molecular biology and cell biology. In his role as the Director of the Chemistry of Life Processes Institute, Professor O’Halloran administers and leads teams of interdisciplinary biomedical researchers. This Institute brings together researchers from the fields of chemistry, biology, physics, engineering, medicine, proteomics, molecular therapeutics and biological molecular imaging. He also serves as the Associate Director for the Basic Sciences Research Division of the Robert H. Lurie Comprehensive Cancer Center of Northwestern University.
Professor O’Halloran received his BS and MA degrees in Chemistry from the University of Missouri, and a Ph.D. in 1985 from Columbia University in Bioinorganic Chemistry. Dr. O'Halloran joined the faculty of Northwestern University in 1986 after postdoctoral training at MIT. Dr. O'Halloran is the Morrison Professor in the Department of Chemistry and in the Department of Molecular Biosciences at Northwestern. In his tenure at Northwestern University he has supervised over 40 Ph.D. theses and more than 25 postdoctoral fellows. Professor O'Halloran's scientific recognitions include a National Science Foundation Presidential Young Investigator Award, a National Searle Scholars Award, an Alfred P. Sloan Research Fellowship, the Camille and Henry Dreyfus Foundation Teacher-Scholar Award, the Bioinorganic Award from the Royal Society of Chemistry and the American Society of Biochemistry and Molecular Biology Schering-Plough Scientific Achievement Award. He is a Fellow of the Royal Society of Chemistry, the Japanese Society for the Promotion of Science and the American Association for the Advancement of Science and a John Simon Guggenheim Fellow. Professor O'Halloran received a MERIT award from the National Institutes of Health.
Dr. Jonathan Licht, MD: Jonathan D. Licht, M.D. is the Johanna Dobe Professor of Medicine at Northwestern University and has served as Director of the Division of Hematology/Oncology and Associate Director for Clinical Sciences Research of the Robert H. Lurie Comprehensive Cancer Center since the spring of 2006. Dr. Licht sees patients with hematological malignancies including leukemia, lymphoma myeloma while directing a laboratory based translational research program. In addition he has served as Senior Scientific Investigator for the Northwestern University PS-OC (5U54CA143869-05). Dr. Licht, a graduate of Columbia University College of Physicians and Surgeons, trained in medical oncology and molecular biology at the Dana-Farber Cancer Institute of Harvard Medical School. On the faculty of the Mount Sinai School of Medicine for 15 years, he rose to the rank of Professor of Medicine and Associate Dean for Cancer Programs before his recruitment to Northwestern in 2006. Since that time he has built a robust basic research group within the Division of Hematology/ Oncology. Dr. Licht' s laboratory studies aberrant gene regulation repression as a cause of hematologic malignancy, including acute promyelocytic leukemia, multiple myeloma and myeloproliferative neoplasms, and developing small molecules and peptides strategies to revert abnormal gene regulation and treat disease. Dr. Licht is currently the Principal Investigator of a Leukemia and Lymphoma Society Specialized Center of Excellence grant, studying gene regulation mechanisms in hematological malignancy. He is a member of the Board of Scientific Councilors of the National Cancer Institute, is a Senior Editor of Clinical Cancer Research and serves on the editorial board of Oncogene. He also served as a Councilor of the American Society for Clinical Investigation and is a member of the Association of American Physicians. Dr. Licht is a charter member of the NIH Cancer Molecular Pathology Study section and has served on American Cancer Society and Leukemia and Lymphoma Society review panels.
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Project 1: Ionic Modulation of Chromatin in Cancer
Project Co-Leaders: Thomas V. O'Halloran, Chemistry, Northwestern University; Andrew P. Mazar, Pharmacology, Northwestern University
Team Members: Jack Kaplan, Biochemistry and Molecular Genetics, University of Illinois-Chicago; Vadim Backman, Biomedical Engineering, Northwestern University; Igal Szleifer, Biomedical Engineering, Northwestern University; Ming Zhao, Medicine, Feinberg School of Medicine, Northwestern University; John Marko, Molecular Biosciences, Northwestern University; Navdeep Chandel, Medicine, Feinberg School of Medicine, Northwestern University
Project Summary: Project 1 focuses on theionic composition of nuclei in cancer and its role in modulating chromatin conformation and nuclear shape and ultimately, its impact on gene expression and the emergence of cancer phenotypes. The proposed experiments test the proposition that a massive ion imbalance is a significant contributor to the transformed phenotype of metastatic breast cancer, glioblastoma and multiple myeloma cancer cells. This central hypothesis will be tested in whole cells, as well as animal models of cancer, using an array of physical methods including vital imaging probes, Partial Wave Spectroscopy (Nanocytometry Core), x-ray fluorescence microscopy, nuclear nanomechanics and EDS-STEM ultrastructure studies. The overarching goal of this project is to translate these physical science insights into the role of the intracellular ion concentrations in modulating tumor cell behavior into the development of new targets for therapeutic intervention in metastatic disease.
Project 2: Molecular Modulation of Chromatin and Nuclear Structure in Cancer
Project Co-Leaders: Jonathan Licht, Hematology-Oncology, Feinberg School of Medicine, Northwestern University; Chuan He, Chemistry, University of Chicago
Project Investigators: Ross Levine, Medicine, Memorial Sloan Kettering Cancer Center; Job Dekker, Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School; Lucy Godley, Medicine, University of Chicago
Project Summary: This project seeks to elucidate the role of enhancer dysfunction in modulating the spatio-temporal organization of chromatin and information transfer in cancer. These experiments will test the hypothesis that enhancer dysfunction leads to an altered physical state of chromatin, including an abnormal state of 3-D looping, leading to aberrant formation of transcriptional initiating and elongating complexes, destroying the normal balance of gene expression in the cell. The sequelae of these events are ineffective hematopoiesis and clonal expansion of MDS and AML precursors. Emerging CRISPR technology, sophisticated chromatin confirmation capture and genome wide chromatin surveys and the nanocytometry and animal cores will be used to elucidate the aberrant structure and function of chromatin.
Project 3: Mechanics of Nuclei, Chromosomes and Chromatin in Cancer
Project Co-Leaders : John F. Marko, Molecular Biosciences/Physics & Astronomy, Northwestern University; John Crispino, Hematology-Oncology, Feinberg School of Medicine, Northwestern University
Team Members: Vadim Backman, Biomedical Engineering, Northwestern University; Robert Goldman, Cell and Molecular Biology, Northwestern University; Leonid Mirny, Health Sciences Technology/Physics, MIT; Adilson Motter, Physics and Astronomy, Northwestern University; Igal Szleifer, Biomedical Engineering, Northwestern University
Project Summary: Project 3 seeks to analyze the variation in chromatin structure – from the fiber level to chromosomes to the whole cell nucleus – using physical tools in combination with state-of-the-art cell biological approaches. Aim 1 of the project is based on the hypothesis, supported by an array of preliminary data, that the physical organization and mechanics of chromosomes and nuclei are altered in cancer cells. This will be tested using micromechanical studies of nuclei and chromosomes, combined fluorescence imaging of major chromosome- and nucleus-organizing proteins, and partial-wave spectroscopy measurements of nuclear disorder. Aim 2 will test how removal of specific chromosome-organizing proteins affects chromosome and nuclear structure. The results of both Aim 1 and Aim 2, in combination with Hi-C data, will then be used to develop mathematical models of metaphase chromosome and interphase nucleus organization, and in combination with gene regulation network modeling, to predict effects of drug and genetic interventions for further experiments. Aim 3 will focus on how chromatin fibers themselves are physically altered in different cell types in single-chromatin-fiber assembly and mechanics experiments. The result of Project 3 will be a comprehensive study of how chromatin and chromosomes are remodeled in cancer cells relative to normal cells, and how this remodeling affects gene expression.
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Core Leader: Vadim Backman, Biomedical Engineering, Northwestern University
Summary: The Nanocytometry Core will provide support for a broad range of photonics studies deploying two novel super-high resolution microscopy methods: Stochastic Optical Reconstruction Microscopy (STORM) and Partial Wave Spectroscopy (PWS) microscopy. PWS is a novel spectroscopic microscopy technique, developed by the Backman lab that is capable of quantification of intracellular structure at subdiffractional length scales. PWS can image modifications of higher order chromatin structure in the pre-initiation of transcription associated with a shift in genomic homeostasis to a globally more transcriptionally active state. STORM is an established super resolution technique that is capable of providing resolution down to sub 10-nm range for biological specimens. The CR-PSOC will depend on this core facility for PWS and STORM analyses of cells, nuclei and metaphase chromosomes.
PDX Human Tumor Model Core
Core Leader: Andrew P. Mazar, Pharmacology, Northwestern University
The Core will create and maintain carefully delineated, in vivo human
tumormodels from a broad range of histologies that retain the characteristics of fresh human tumors. These PDX models are passaged continuously in vivo
and are never exposed to tissue culture plastic and the limitations imposed by tissue culture selection of certain tumor cell clones. The PDX tumors retain histological characteristics that are similar to the patient tumors from which they were derived. Thus, these models are thought to be closer to the clinical situation than traditional xenograft models. Models will be available to investigators across the PS-ON. The Core will build on an already established PDX repository infrastructure that currently maintains sixty-two models covering ten different tumor histologies, with 2-3 new models are created each week. Early passage cell lines are created in parallel from these in vivo
PDX models and they will also be available to the CR-PSOC investigators, as well as potentially to investigators in the PS-ON.
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Education and Outreach Activities
The Northwestern University (NU) PS-OC has been sponsoring its own undergraduate summer research program since its inception in 2015 and for the prior five years as well, b/c our Center was also part of the Phase I Network. The summer program has two arms, one for students from NU and other institutions that are part of the NU PS-OC, and another for minority students from outside institutions. Typically, 5-7 undergraduates participate annually. In addition to the research component, participants write research proposals and attend weekly tumor biology seminars and a PS-OC-sponsored summer workshop. Since the NCI inaugurated its own summer program, our students have attended the NCI undergraduate conference in Bethesda and have also participated in the mini-Dream challenge organized by Sage Bionetworks. Our annual Summer Workshop on Cancer Fundamentals is another event that we have carried over from our Phase I Center. We hold this half-day workshop on NU’s Evanston campus and tailor it to students, trainees, and faculty on this campus who seek an introduction to basic principles of cancer biology and clinical oncology. Presentations are typically given by cancer researchers and cancer clinicians associated with NU’s Feinberg School of Medicine; they center on a theme that changes annually. The presentations are recorded, and the videos are posted on the PS-OC website. Because this is the only education event of its type on the Evanston campus, the workshop has proven very popular. Our Center typically holds one large symposium annually that attracts faculty and trainees from a number of Chicago-area institutions. In terms of outreach, our Center has sponsored public forums featuring roundtable discussions by clinicians associated with our center as well as talks by authors of popular books on cancer. Dr. Theodora Ross, author of “A Cancer in the Family,” will be giving talks on both the Evanston and downtown campuses in April, 2019.
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