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Committee on Cancer Biology

This is an archived copy of the 2012-13 catalog. To access the most recent version of the catalog, please visit http://catalogs.uchicago.edu.

Chair

  • Geoffrey Greene, Ben May Department for Cancer Research

Professors

  • Habibul Ahsan, Health Studies
  • Eric Beyer, Pediatrics
  • Douglas Bishop, Radiation and Cellular Oncology
  • Marcus Clark, Medicine
  • Susan Cohn, Pediatrics
  • Nancy Cox, Medicine
  • M. Eileen Dolan, Medicine
  • Richard Fehon, Molecular Genetics and Cell Biology
  • Edwin Ferguson, Molecular Genetics and Cell Biology
  • Yang-Xin Fu, Pathology
  • Thomas Gajewski, Medicine 
  • David Grdina, Radiation and Cellular Oncology
  • Gregory Karczmar, Radiation and Cellular Oncology
  • Bruce Lahn, Human Genetics
  • Michelle Le Beau, Medicine
  • Ernst Lengyel, Obstetrics and Gynecology
  • Maciej Lesniak, Surgery
  • Shutsung Liao, Ben May Department for Cancer Research
  • Anning Lin, Ben May Department for Cancer Research
  • Olufunmilayo Olopade, Medicine
  • Ilaria Rebay, Ben May Department for Cancer Research
  • Carrie Rinker-Schaeffer, Surgery
  • Marsha Rosner, Ben May Department for Cancer Research
  • Benoit Roux, Biochemistry and Molecular Biology
  • Janet Rowley, Medicine
  • Ravi Salgia, Medicine
  • Hans Schreiber, Pathology
  • Walter Stadler, Medicine
  • Ursula Storb, Molecular Genetics and Cell Biology
  • Wei-Jen Tang, Ben May Department for Cancer Research
  • Mitchel Villereal, Neurobiology, Pharmacology and Physiology
  • Ralph R. Weichselbaum, Radiation and Cellular Oncology

Associate Professors

  • Suzanne Conzen, Medicine
  • Wei Du, Ben May Department for Cancer Research
  • Tong Chuan He, Surgery
  • Lucy Godley, Medicine
  • Akira Imamoto, Ben May Department for Cancer Research
  • Barbara Kee, Pathology
  • Mark Lingen, Pathology
  • Kay Macleod, Ben May Department for Cancer Research
  • Kenan Onel, Pediatrics
  • Michael Thirman, Medicine
  • Amittha Wickrema, Medicine
  • Yingming Zhao, Ben May Department for Cancer Research

Assistant Professors

  • Jianjun Chen, Medicine
  • Kenneth Cohen, Medicine
  • Jill De Jong, Pediatrics
  • Nickolai Dulin, Medicine
  • Kathleen Goss, Surgery
  • Fotini Gounari, Medicine
  • Yu-Ying He, Medicine
  • Stephanie Huang, Medicine
  • Richard Jones, Ben May Department of Cancer Research
  • Deborah Lang, Medicine
  • Peter Savage, Pathology
  • Dorothy Sipkins, Medicine
  • Michael Spiotto, Radiation and Cellular Oncology
  • Donald Vander Griend, Surgery

The Committee on Cancer Biology offers a graduate program of study leading to the Doctor of Philosophy degree in Cancer Biology, and is supported by a National Cancer Institute sponsored training grant for predoctoral and postdoctoral trainees in cancer biology. The program provides multidisciplinary training for students interested in pursuing a research career in any aspect of Cancer Biology, focusing on mammalian (particularly human) biology as well as the study of genes and processes in other eukaryotic organisms. The program provides doctoral students with the most up to date knowledge and research training in molecular and cellular aspects of Cancer Biology and prepares the students for leadership positions in the academic community. The broad range of interests and expertise of the 67 faculty members of the Committee on Cancer Biology enables students to concentrate in multiple areas of cancer biology, including angiogenesis, animal models of cancer, apoptosis and cell survival, cancer genetics, cell cycle regulation, carcinogenesis, chromosome damage and repair, drug discovery/development, hormone action, metastatic progression, radiation biology, signal transduction, and tumor biology and immunology.

The Committee on Cancer Biology is a member of the Biomedical Sciences Cluster, which also includes graduate programs from the Committee on Immunology, the Committee on Microbiology, the Committee on Molecular Metabolism and Nutrition, and the Department of Pathology's Molecular Pathogenesis and Molecular Medicine Graduate Program. The five academic units share several common courses and additional common events for students and faculty within the cluster. The goal of the cluster system is to encourage interdisciplinary interactions among both trainees and faculty, and to allow students flexibility in designing their particular course of study.

In addition to formal course work, the program sponsors a student led journal club, a Student/Postdoctorate Research Presentation group, and an annual cluster retreat in which students and trainees present their research findings. In addition, the program co-sponsors the Ben May Symposium with the Ben May Department for Cancer Research. This symposium brings speakers of international renown to campus. Students and trainees also have the opportunity to attend national meetings and cancer biology workshops off campus. Through the auspices of the Ben May Department for Cancer Research, the Section of Hematology/Oncology, and the University of Chicago Cancer Research Center (an NCI designated Cancer Center), there are several additional seminar series and a Clinical Cancer Research/Basic Science Research Translational conference. Thus, there is a thriving, interactive community of cancer researchers.

Admission

Students interested in obtaining the Ph.D. in Cancer Biology should submit an application to the Biological Sciences Division by December 1st of each year; indicate their cluster of interest as Biomedical Sciences and select Cancer Biology as their proposed degree program.

 

The Degree of Doctor of Philosophy

Ph.D. requirements include:

  • Completion of 9.5 course credits consisting of basic science, cancer biology and elective courses
  • A preliminary examination in the form of a mock NIH-style grant proposal
  • A dissertation based on original research
  • A final thesis examination

Cancer Biology Courses

CABI 30800. Cancer Biology 1: Introduction to Cancer Biology. 100 Units.

 Overview of cancer biology, including epidemiology, pathology, diagnosis and staging, and the basis for various therapeutic strategies. Also covered are experimental models for cancer, including the generation and validation of animal models. The course will emphasize several tumor models, such as breast cancer, hematological malignancies, cervical carcinoma, colon carcinoma, and sarcomas.

Instructor(s): M. Lingen     Terms Offered: Autumn

CABI 30900. Cancer Biology 2: Molecular Mechanisms in Cancer Biology. 100 Units.

 This course provides students with an in-depth understanding of how key cellular processes are deregulated in cancer and the molecular mechanisms underpinning these defects. The course covers cell cycle checkpoint control, cell death, tumor suppressor and oncogene function, DNA repair mechanisms, epigenetics of cancer, nuclear hormone receptor activity in cancer, tumor metabolism, hypoxia responses, angiogenesis and metastasis. In addition to material covered in formal lectures, discussion sessions cover tumor stem cells, "oncogene addiction," inflammatory responses, cancer therapeutics, mouse models of human cancer and other topical subjects relevant to understanding tumor initiation and progression, as well as how current research may facilitate cancer treatment.

Instructor(s): K. Macleod     Terms Offered: Winter
Equivalent Course(s): MPMM 30900

CABI 31200. Cancer Biology 3: Signal Transduction and Model Organisms. 100 Units.

 The aim of this course is to familiarize students with the guiding principles of cellular signal transduction that include regulated protein interactions, complex signaling network architecture, and the interplay between signaling and associated systems such as metabolism. These principles will be illustrated by detailed examination of various signaling pathways and viewed through the lens of applying our understanding of signal transduction to progress in cancer prevention and therapy.

Instructor(s): D. Vander Griend     Terms Offered: Spring
Equivalent Course(s): NPHP 31200

CABI 31500. Cancer Biology 4: Frontiers in Cancer Research. 100 Units.

 This is a lecture-discussion course focused on developing and testing a hypothesis, building a scientific plan to support this hypothesis, and obtaining experience in the grant-writing process as well as responding to criticisms and presenting one's grant in a formal and concise manner. This workshop-style course will focus on a variety of topics in the field of cancer biology.

Instructor(s): D. Lang     Terms Offered: Spring

CABI 31800. Cancer Genomics and Systems Biology. 100 Units.

Cancer is a genetic disease characterized by the complex actions and interactions of environmental factors, multiple inherited and acquired genetic factors, networks, and cells.  Together, they predispose some individuals to develop cancer, protect others against it despite lifelong exposures to carcinogens, and determine the likelihood of response to therapy.  This inherent complexity presents constant challenges for diagnosing and treating patients with cancer.  Until recently, it has not been possible to explore the myriad genetic and biological factors varying among individuals that may account for the differences in susceptibility to cancer, the response to treatment, and the trajectory of disease.  With the advent of new genome-wide and high-throughput technologies, we are now beginning to unravel the genetic underpinnings of cancer.  A systems biology approach towards cancer examines the many components of the disease simultaneously.  It is hoped that findings resulting from systems biology studies will form the foundation for “personalized medicine.” The goal of this course is to teach students to manipulate and analyze the enormous datasets generated by genome-wide platforms.  The course is divided into four modules, each of which is dedicated to an in depth exploration of a single platform: 1) genome-wide association studies (GWAS); 2) next-generation sequencing 3) systems analysis of proteins; and 4) integrated data analysis.  Modules are comprised of both lectures and labs, and for each module, there is a student-led presentation of seminal papers demonstrating the translational potential of each technology to the investigation of human disease.   Although the focus of the course is cancer, the course has relevance to students interested in using systems biology strategies to investigate a variety of complex diseases. The course is complementary and non-overlapping with material covered by other Cancer Biology courses. 

Instructor(s): K. Onel, A. Skol, R. Jones     Terms Offered: Autumn
Equivalent Course(s): ECEV 31800

CABI 39000. Cancer Biology 5: Introduction to Experimental Cancer Biology. 050 Units.

 This course is related to a seminar series sponsored by the Committee on Cancer Biology and also incorporates seminars of interest from other Cluster programs. Typically, students meet to discuss research papers published by the following week's seminar speaker, attend the seminar, and then meet with the speaker afterward. The goal of the course is to broaden the students' exposure to current research and encourage discussion of scientific ideas among peers.

Instructor(s): K. Onel, K. Goss     Terms Offered: Autumn, Winter, Spring

CABI 40300. Systems Analysis of Proteins and Post-Translational Modifications. 100 Units.

Proteins play a major role in all cellular processes and their modification represents a major vehicle for expanding the genetic code of the cellular proteome (the inventory of all protein species in a cell). Given the crucial roles in the major cellular pathways and diseases such as cancer, proteins and PTM studies are a critical aspect of most biological projects. This course will cover concepts (including biochemistry, proteomics/systems biology, molecular biology, and bioinformatics), and practical techniques for identifying and quantifying proteins and PTMs. Topics include, but are not limited to quantification of protein interactions, abundances, modifications including phosphorylation, ubiquitination, and lysine acetylation, and subsequent discussion of biochemical and functional roles of proteins and PTMs in regulating biological networks.

Instructor(s): R. Jones, Y. Zhao, P. Nash     Terms Offered: Spring
Prerequisite(s): BIOS 20200
Equivalent Course(s): BIOS 21346,IMMU 40300,MOMN 40300

CABI 40700. From Structure Coordinates to Protein Function. 100 Units.

The course uses the atomic coordinate of proteins to explore how molecular machinery work in the context of physiological functions (vision, fight or flight) and human diseases (cancer). We begin by exploring protein components that make up the signal transduction pathway and how these components are assembled for the various physiological functions of humans. We then proceed to consider the physical properties of proteins. We conclude by discussing the protein-targeted therapeutics of human diseases. Computer graphic exercises and in-class student presentations complement the lecture topics.

Instructor(s): W.-J. Tang     Terms Offered: Winter. L.
Prerequisite(s): Completion of a Biological Sciences Fundamentals sequence. Biochemistry strongly recommended. Recommended for AP5 students.
Equivalent Course(s): BIOS 21339,NURB 40700

CABI 47300. Genomics and Systems Biology. 100 Units.

This lecture course explores the technologies that enable high-throughput collection of genomic-scale data, including sequencing, genotyping, gene expression profiling, assays of copy number variation, protein expression and protein-protein interaction. We also cover study design and statistical analysis of large data sets, as well as how data from different sources can be used to understand regulatory networks (i.e., systems). Statistical tools introduced include linear models, likelihood-based inference, supervised and unsupervised learning techniques, methods for assessing quality of data, hidden Markov models, and controlling for false discovery rates in large data sets. Readings are drawn from the primary literature.

Instructor(s): Y. Gilad, D. Nicolae     Terms Offered: Spring
Prerequisite(s): STAT 23400 or Statistics in the Biomath Sequence
Equivalent Course(s): BIOS 28407,BPHS 47300,HGEN 47300,IMMU 47300

CABI 47500. Pharmacogenomics. 100 Units.

 This class is aimed at advancing our knowledge of the genetic basis for variable drug response. The study of pharmacogenomics is complicated by the fact that response and toxicity are multigenic traits and are often confounded by nongenetic factors (e.g., age, co-morbidities, drug-drug interactions, environment, diet, etc). Using knowledge of an individual's DNA sequence as an integral determinant of drug therapy has not yet become standard clinical practice; however, several genetics-guided recommendations for physicians have been developed and will be highlighted.

Instructor(s): E. Dolan, H. Huang     Terms Offered: Spring
Equivalent Course(s): CCTS 40001