RECENT PROGRESS IN HORMONE RESEARCH Edited by ANTHONY R. MEANS VOLUME 58 The Human Genome and Endocrinology “Recent Progress in Hormone Research” is an annual publication of The Endocrine Society that is published under the editorial auspices of Endocrine Reviews. The Endocrine Society 8401 Connecticut Avenue, Suite 900 Chevy Chase, Maryland 20815 Copyright 2003 by The Endocrine Society All Rights Reserved The reproduction or utilization of this work in any form or in any electronic, mechanical, or other means, now known or hereafter invented, including photocopying or recording and in any information storage or retrieval system, is forbidden, except as may be expressly permitted by the 1976 Copyright Act or by permission of the publisher. ISBN 0–879225-48-4 CONTENTS Senior Author Correspondence Information v 1. A Functional Proteomics Approach to Signal Transduction 1 Paul R. Graves and Timothy A.J. Haystead 2. The Use of DNA Microarrays to Assess Clinical Samples: The Transition from Bedside to Bench to Bedside 25 John A. Copland, Peter J. Davies, Gregory L. Shipley, Christopher G. Wood, Bruce A. Luxon, and Randall J. Urban 3. Gene Expression Profiling for Prediction of Clinical Characteristics of Breast Cancer 55 Erich Huang, Mike West, and Joseph R. Nevins 4. Statistical Approach to DNA Chip Analysis 75 N.M. Svrakic, O. Nesic, M.R.K. Dasu, D. Herndon, and J.R. Perez-Polo 5. Identification of a Nuclear Factor Kappa B-dependent Gene Network 95 Bing Tian and Allan R. Brasier 6. Role of Defective Apoptosis in Type 1 Diabetes and Other Autoimmune Diseases 131 Takuma Hayashi and Denise L. Faustman 7. Genomic Analysis of Glucocorticoid-regulated Promoters in Murine T-lymphoma Cells 155 Lu Chen, Celeste Finnerty, William C. Gustafson, Craig R. Bush, Ping Chi, Huiping Guo, Bruce Luxon, Alan P. Fields, and E. Aubrey Thompson 8. Regulation of a Distinctive Set of Genes in Glucocorticoid-evoked Apoptosis in CEM Human Lymphoid Cells 175 E. Brad Thompson and Betty H. Johnson 9. Overlapping but Distinct Profiles of Gene Expression Elicited by Glucocorticoids and Progestins 199 Yihong Wan and Steven K. Nordeen 10. Analysis of Gene Expression in the Normal and Malignant Cerebellum 227 Robert J. Wechsler-Reya 11. Paired-like Repression/Activation in Pituitary Development 249 Lorin E. Olson, Jeremy S. Dasen, Bong Gun Ju, Jessica Tollkuhn, and Michael G. Rosenfeld iii iv CONTENTS 12. Dynamic Changes in Gene Expression During Human Trophoblast Differentiation 263 Stuart Handwerger and Bruce Aronow 13. Regulation of Hematopoietic Stem Cell Self-Renewal 283 Tannishtha Reya 14. Investigation of the Transcriptional Changes Underlying Functional Defects in the Mammary Glands of Prolactin Receptor Knockout Mice 297 Christopher J. Ormandy, Matthew Naylor, Jessica Harris, Fiona Robertson, Nelson D. Horseman, Geoffrey J. Lindeman, Jane Visvader, and Paul A. Kelly 15. Microarray Analysis and Identification of Novel Molecules Involved in Insulin-like Growth Factor-1 Receptor Signaling and Gene Expression 325 Joelle Dupont, Sandra E. Dunn, J. Carl Barrett, and Derek LeRoith 16. Consequences of Elevated Luteinizing Hormone on Diverse Physiological Systems: Use of the LH␤CTP Transgenic Mouse as a Model of Ovarian Hyperstimulation-induced Pathophysiology 343 Rachel J. Mann, Ruth A. Keri, and John H. Nilson Author Index 377 Subject Index 379 Senior Author Correspondence Information Allan R. Brasier Timothy A.J. Haystead Department of Internal Medicine Department of Pharmacology and Cancer University of Texas Medical Branch Biology Room MRB 8.138, Route 1060 Duke University Medical Center 301 University Boulevard Levine Science Research Center, Room C118 Galveston, TX 77555-1060 Durham, NC 27710-3686 Phone: 409-772-2824 Phone: 919-613-8606 Fax: 409-772-8709 Fax: 919-668-0977 E-mail: [email protected] E-mail: [email protected] Denise L. Faustman Derek LeRoith Immunobiology Laboratory Clinical Endocrinology Branch Massachusetts General Hospital/Harvard National Cancer Institute Medical School National Institutes of Health MGH-East, Building 149 Room 8D12, Building 10 13th Street MSC 1758 Charlestown, MA 02129 Bethesda, MD 20892-1758 Phone: 617-726-4084 Phone: 301-496-8090 Fax: 617-726-4095 Fax: 301-480-4386 E-mail: [email protected] E-mail: [email protected] Stuart Handwerger Joseph R. Nevins Division of Endocrinology Department of Molecular Genetics and Children’s Hospital Medical Center Microbiology 3333 Burnet Avenue Howard Hughes Medical Institute Cincinnati, OH 45229-3039 Duke University Medical Center Phone: 513-636-4209 366 Clinical and Research Laboratories Fax: 513-636-7486 Durham, NC 27710 E-mail: [email protected] Phone: 919-684-2746 Fax: 919-681-8973 E-mail: [email protected] v vi CORRESPONDENCE INFORMATION John H. Nilson Michael G. Rosenfeld Department of Pharmacology Howard Hughes Medical Institute School of Medicine University of California, San Diego Case Western Reserve University School of Medicine 10900 Euclid Avenue, W319 9500 Gilman Drive Cleveland, OH 44106 CMM-West, Room 345 Phone: 216-368-4497 La Jolla, CA 92093-0648 Fax: 216-368-3395 Phone: 858-534-5858 E-mail: [email protected] Fax: 858-534-8180 E-mail: [email protected] Steven K. Nordeen Department of Pathology B216 Nenad M. Svrakic University of Colorado Health Sciences Department of Psychiatry Center Washington University School of Medicine 4200 East Ninth Avenue 660 South Euclid Avenue Denver, CO 80262 St. Louis, MO 63110 Phone: 303-315-5463 Phone: 314-362-7041 Fax: 303-315-6721 Fax: 314-362-5594 E-mail: [email protected] E-mail: [email protected] Christopher J. Ormandy E. Aubrey Thompson Cancer Research Program Department of Human Biological Chemistry Garvan Institute of Medical Research and Genetics 384 Victoria Street University of Texas Medical Branch Darlinghurst, Sydney NSW 2010 9.104 Blocker MRB Australia Galveston, TX 77555-1048 Phone: 011-61-2-9295-8329 Phone: 409-772-3361 Fax: 011-61-2-9295-8321 Fax: 409-747-1938 E-mail: [email protected] E-mail: [email protected] Tannishtha Reya E. Brad Thompson Department of Pharmacology and Cancer Department of Human Biological Chemistry Biology and Genetics Duke University Medical Center University of Texas Medical Branch C333 LSRC 6.601 Basic Science Building Research Drive 301 University Boulevard Durham, NC 27710 Galveston, TX 77555-0645 Phone: 919-613-8756 Phone: 409-772-2271 Fax: 919-668-3556 Fax: 409-772-5159 E-mail: [email protected] E-mail: [email protected] CORRESPONDENCE INFORMATION vii Randall J. Urban Robert J. Wechsler-Reya Division of Endocrinology Department of Pharmacology and Cancer University of Texas Medical Branch Biology 8.138 Medical Research Building Duke University Medical Center Galveston, TX 77555-1060 LSRC Building, Room C303, Box 3813 Phone: 409-772-1176 Research Drive Fax: 409-772-8709 Durham, NC 27710 E-mail: [email protected] E-mail: [email protected] A Functional Proteomics Approach to Signal Transduction † PAUL R. GRAVES* AND TIMOTHY A.J. HAYSTEAD* *Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710-3686; †Serenex Inc., 323 Foster Street, Durham, North Carolina 27710 ABSTRACT The purpose of this review is to highlight how proteomics techniques can be used to answer specific questions related to signal transduction in a wide variety of systems. In our laboratory, we utilize proteomic technologies to elucidate signal transduction pathways involved in smooth muscle contraction and relaxation, cell growth and tumorigenesis, and the pathogenesis of malaria. We see the real application of this technology as a tool to enhance the power of existing approaches such as classical yeast and mouse genetics, tissue culture, protein expression systems, and site-directed mutagenesis. Our basic approach is to examine only those proteins that differ by some variable from the control sample. In this way, the number of proteins to be processed by electrophoresis, Edman degradation, or mass spectrometry is greatly reduced. In addition, since only those proteins that change in response to a given biological treatment are analyzed, the experimental outcome provides information about specific signaling pathways. Examples of typical experiments in our laboratory are measurement of changes in protein phosphorylation in response to treatment of cells with growth factors or specific drugs, characterization of proteins associated with a bait protein in a “pull-down” experiment, or measurement of changes in protein expression. Frequently, in these experiments, it is necessary to define complex protein mixtures. To achieve this goal, we utilize a variety of techniques to isolate specific types of proteins or “subproteomes” for further analysis. In this review, we discuss strategies used in our laboratory for studying signaling pathways, including subproteome isolation, proteome mining, and analysis of the phosphoproteome. I. Introduction Functional proteomics can be defined as a method to identify specific proteins in a cell, tissue, or organism that undergo changes in abundance, localization, or modification in response to a specific biological condition. In functional proteomics, the aim is not to identify or characterize every protein in the cell but rather to provide information about a small number of proteins that are directly relevant to the biological question being studied. To achieve this goal, functional proteomics often is combined with complementary techniques such as protein biochemistry, molecular biology, and cell physiology. In our laboratory,