Molecular Pathology of Lung Diseases PDF
Preview Molecular Pathology of Lung Diseases
Molecular Pathology of Lung Diseases MOLECULAR PATHOLOGY LIBRARY SERIES Philip T. Cagle, MD, Series Editor 1. D.S. Zander, H.H. Popper, J. Jagirdar, A.K. Haque, P.T. Cagle, R. Barrios: ISBN 978-0-387-72429-4 Molecular Pathology of Lung Diseases. 2008 Molecular Pathology of Lung Diseases Edited by Dani S. Zander, MD Penn State Milton S. Hershey Medical Center, Hershey, Pennsylvania Helmut H. Popper, MD Institute of Pathology, Laboratories for Molecular Cytogenetics, Environmental and Respiratory Pathology, Medical University of Graz, Graz, Austria Jaishree Jagirdar, MD University of Texas Health Science Center at San Antonio, San Antonio, Texas Abida K. Haque, MD Weill Medical College of Cornell University, New York; San Jacinto Methodist Hospital, Baytown, Texas Philip T. Cagle, MD Weill Medical College of Cornell University, New York; The Methodist Hospital, Houston, Texas Roberto Barrios, MD Weill Medical College of Cornell University, New York; The Methodist Hospital, Houston, Texas Dani S. Zander, MD Helmut H. Popper, MD Department of Pathology Institute of Pathology Penn State Milton S. Hershey Medical Center Laboratories for Molecular Cytogenetics Hershey, PA Medical University of Graz USA Graz, Austria Jaishree Jagirdar, MD Abida K. Haque, MD Department of Pathology Weill Medical College of Cornell University University of Texas Health Science Center New York, NY San Antonio, TX San Jacinto Methodist Hospital USA Department of Pathology Baytown, TX USA Philip T. Cagle, MD Roberto Barrios, MD Pathology and Laboratory Medicine Pathology and Laboratory Medicine Weill Medical College of Cornell University Weill Medical College of Cornell University New York, NY New York, NY The Methodist Hospital The Methodist Hospital Houston, TX Houston, TX USA USA Series Editor: Philip T. Cagle, MD Pathology and Laboratory Medicine Weill Medical College of Cornell University New York, NY The Methodist Hospital Houston, Texas USA Library of Congress Control Number: 2007928822 ISBN: 978-0-387-72429-4 e-ISBN: 978-0-387-72430-0 Printed on acid-free paper. © 2008 Springer Science+Business Media, LLC. All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC., 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connec- tion with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identifi ed as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. While the advice and information in this book are believed to be true and accurate at the date of going to press, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. 9 8 7 6 5 4 3 2 1 springer.com Series Preface The past two decades have seen an ever-accelerating growth in knowledge about molecular pathology of human diseases, which received a large boost with the sequencing of the human genome in 2003. Molecular diagnostics, molecular tar- geted therapy, and genetic therapy are now routine in many medical centers. The molecular fi eld now impacts every fi eld in medicine, whether clinical research or routine patient care. There is a great need for basic researchers to understand the potential clinical implications of their research, whereas private practice clinicians of all types (general internal medicine and internal medicine specialists, medical oncologists, radiation oncologists, surgeons, pediatricians, and family practitio- ners), clinical investigators, pathologists, and medical laboratory directors and radi- ologists require a basic understanding of the fundamentals of molecular pathogenesis, diagnosis, and treatment for their patients. Traditional textbooks in molecular biology deal with basic science and are not readily applicable to the medical setting. Most medical textbooks that include a mention of molecular pathology in the clinical setting are limited in scope and assume that the reader already has a working knowledge of the basic science of molecular biology. Other texts emphasize technology and testing procedures without integrating the clinical perspective. There is an urgent need for a text that fi lls the gap between basic science books and clinical practice. In the Molecular Pathology Library Series the basic science and the technology is integrated with the medical perspective and clinical application. Each book in the series is divided according to neoplastic and nonneoplastic diseases for each of the organ systems traditionally associated with medical subspecialties. Each book in the series is organized to provide (1) a succinct background of the essential terminology, concepts; and technology of molecular biology; (2) an overview of the broad application of molecular biology principles to disease; and (3) specifi c application of molecular pathology to the pathogenesis, diag- nosis, and treatment of neoplastic and nonneoplastic diseases specifi c to each organ system. These broad section topics are broken down into succinct chap- ters, averaging about 15 to 20 pages each, to cover a very specifi c disease entity. The chapters are written by established authorities on the specifi c topic from academic centers around the world. In one book, diverse subjects are included that the reader would have to pursue from multiple sources in order to have a clear understanding of the molecular pathogenesis, diagnosis, and treatment of specifi c diseases. Attempting to hunt for the full information from basic concept to specifi c applications for a disease from the varied sources is time consuming and frustrating. By providing this quick and user-friendly ref- erence, understanding and application of this rapidly growing fi eld are made more accessible to both expert and generalist alike. v vi Series Preface As books that bridge the gap between basic science and clinical understanding and practice, the Molecular Pathology Library Series serves the basic scientist, the clinical researcher, and the practicing physician or other health care provider who require more understanding of the application of basic research to patient care, from “bench to bedside.” This series is unique and an invaluable resource to those who need to know about molecular pathology from a clinical, disease-oriented perspective. These books will be indispensable to physicians and health care provid- ers in multiple disciplines as noted above, to residents and fellows in these multiple disciplines as well as their teaching institutions, and to researchers who increasingly must justify the clinical implications of their research. Philip T. Cagle, MD Series Editor Preface Molecular Pathology of Lung Diseases is the fi rst volume in the Molecular Pathol- ogy Library Series by Springer Science+Business Media. Molecular pathology is rapidly becoming part of everyday medical practice from targeted molecular therapy to molecular imaging, and it is no longer limited to the basic research bench. Knowl- edge in this fi eld is increasingly essential to those who provide patient care, and they are unlikely to fi nd the perspective they need in traditional basic science text- books. Because the goal of Molecular Pathology of Lung Diseases is to provide a bridge between clinical pulmonary pathology and basic molecular science, selection of chapter topics and approaches to the material were based largely on the needs of the practicing pathologist or other health care provider. As a result, this book has a very unique perspective compared with the more traditional molecular genet- ics textbooks or molecular laboratory procedure manuals. This alternative perspec- tive is also valuable to the clinical and translational researchers who must think in terms of clinical objectives for their investigations. Clinical pulmonary pathology is extensive and complex, including an intimidating list of environmental, hereditary, immunologic, and idiopathic diseases, both neo- plastic and nonneoplastic. The fi rst two sections of Molecular Pathology of Lung Diseases briefl y familiarize the reader with general concepts, terminology, and pro- cedures in molecular pathology. Subsequent to the introductory sections, this book is broadly subdivided into neoplastic and nonneoplastic lung diseases. Following discussion of general molecular pathologic principles of lung and pleural diseases under each of these two broad categories, separate chapters detail the current molecular pathologies of specifi c diseases. This design approximates the approach to lung disease that is most familiar to pathologists, pulmonologists, thoracic sur- geons, and other health care providers; to medical students, residents, and fellows; and to those involved in clinical investigations or translational research. The unique format of this book results in multiple relatively short chapters that can serve as a ready reference to specifi c medical topics. No other book currently provides the practical disease-based overview that is found in Molecular Pathology of Lung Diseases. Philip T. Cagle, MD vii Contents Series Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv Section 1 Basic Concepts of Molecular Pathology Chapter 1 Genes, Gene Products, and Transcription Factors . . . . . . . . 3 Philip T. Cagle Chapter 2 Receptors, Signaling Pathways, Cell Cycle, and DNA Damage Repair . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 Philip T. Cagle Chapter 3 Cell Adhesion Molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 Timothy Craig Allen and Philip T. Cagle Chapter 4 Apoptosis and Cell Death: Relevance to Lung . . . . . . . . . . 40 Pothana Saikumar and Rekha Kar Chapter 5 Roles of Mutation and Epimutation in the Development of Lung Disease . . . . . . . . . . . . . . . . . . . . . 53 William B. Coleman Section 2 Techniques and Experimental Systems in Molecular Pathology Chapter 6 Bioinformatics and Omics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 Timothy Craig Allen and Philip T. Cagle Chapter 7 General Approach to Molecular Pathology . . . . . . . . . . . . . 70 Gregory L. Blakey and Daniel H. Farkas Chapter 8 Applications of Molecular Tests in Anatomic Pathology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78 Jennifer L. Hunt and Sanja Dacic ix x Contents Chapter 9 Polymerase Chain Reaction and Reverse Transcription–Polymerase Chain Reaction . . . . . . . . . . . . . . 83 Dwight Oliver Chapter 10 Array Comparative Genomic Hybridization in Pathology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97 Reinhard Ullmann Chapter 11 Loss of Heterozygosity in Lung Diseases . . . . . . . . . . . . . . . 108 Sharon C. Presnell Chapter 12 In Situ Hybridization: Principles and Applications for Pulmonary Medicine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 Kevin C. Halling and Amy J. Wendel Chapter 13 Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130 Larry Fowler and Wieslaw Furmaga Chapter 14 Animal Models of Lung Disease . . . . . . . . . . . . . . . . . . . . . . 144 Roberto Barrios Chapter 15 Tissue Culture Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150 R oger A. Vertrees, Thomas Goodwin, Jeffrey M. Jordan, and Joseph B. Zwischenberger Section 3 Molecular Pathology of Pulmonary and Pleural Neoplasms: General Principles Chapter 16 Molecular Oncogenesis of Lung Cancer . . . . . . . . . . . . . . . . 169 Arwen A. Stelter and Jingwu Xie Chapter 17 Genetic Susceptibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176 Philip T. Cagle and Timothy Craig Allen Chapter 18 Prognostic Markers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193 A nna Sienko, Timothy Craig Allen, and Philip T. Cagle Chapter 19 Pulmonary Angiogenesis in Neoplastic and Nonneoplastic Disorders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200 Michael P. Keane and Robert M. Strieter Chapter 20 Lung Cancer Stem Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213 Timothy Craig Allen and Philip T. Cagle Chapter 21 Gene Therapy Approaches for Lung Cancer . . . . . . . . . . . . 219 Jack A. Roth Chapter 22 Response to Conventional Therapy and Targeted Molecular Therapy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226 T imothy Craig Allen, Anna Sienko, and Philip T. Cagle
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