Molecular Pathology in Cancer Research PDF
Preview Molecular Pathology in Cancer Research
Sunil R. Lakhani · Stephen B. Fox Editors Molecular Pathology in Cancer Research Molecular Pathology in Cancer Research Sunil R. Lakhani • Stephen B. Fox Editors Molecular Pathology in Cancer Research Editors Sunil R. Lakhani Stephen B. Fox UQ Centre for Clinical Research Director of Pathology The Royal Brisbane and Women’s Hospital Peter MacCallum Cancer Centre University of Queensland and Pathology Professorial Fellow Queensland University of Melbourne Brisbane, QLD, Australia Melbourne, VIC, Australia ISBN 978-1-4939-6641-7 ISBN 978-1-4939-6643-1 (eBook) DOI 10.1007/978-1-4939-6643-1 Library of Congress Control Number: 2016958971 © Springer Science+Business Media LLC 2016 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer Science+Business Media LLC The registered company address is: 233 Spring Street, New York, NY 10013, U.S.A. Introduction: Setting the Scene, Morphology to Molecular Revolution and/or evolution is a constant theme in pathology, but never has it been more pertinent than today with the adoption by diagnostic laboratories of a number of new key technologies. Borne out of the research environment, these have driven significant changes in laboratory practice and changes in workforce especially in the field of cancer diagnostics. The increase in our understanding underlying the biology of cancer has spawned a new generation of tests using previously unused “tissue” sources with levels of detection that only a few years ago would have seen inconceivable. Thus, we are now able to identify DNA sequence mutations using whole-genome approaches in single cells isolated from peripheral blood, assess the underlying aetiology of tumours from their mutational signatures and perform methylation and expression analysis with profiles that give prognostic and/or pre- dictive information. Much of our increased knowledge have been underpinned by platform enablers such as autopsy and tissue banking which have become disciplines of their own, with the emergence of speciality expertise that is needed to provide appropriately col- lected, processed and stored samples for molecular interrogation in cancer research. The changes in the use of new methods and applications in the pathology of cancer are in many ways analogous to the introduction of the microscope in Paris in the 1840s when morphology challenged conventional wisdom and the use of clini- cal classification of tumours. Thus, the applications from the technologies and tech- niques outlined in this book in a similar manner raise fundamental questions on tumour classification, biology and therapeutics. Indeed for the classification of tumours, there is a similar discourse around whether tumours should be genomi- cally “binned” or whether conventional morphology should continue to be used. There is emerging data to demonstrate close similarities between tumours of vastly different origins but look, behave and respond to therapeutic targets in the same manner. This discussion will continue over the coming decade, but it is likely that a combination of conventional and innovative technologies will be used to go from a v vi Introduction: Setting the Scene, Morphology to Molecular standard classification system to more of an ontology definition of tumours with all the ancillary information that this provides. A highly thought-provoking and pro- vocative “future scoping” further explores how pathology and the revolution in technology and platform enablers may change the face of pathology across not only the neoplastic diseases but throughout all pathology. Melbourne, VIC, Australia Stephen B. Fox Brisbane, QLD, Australia Sunil R. Lakhani Contents Molecular Diagnostics: Translation from Discovery to Clinical Practice .......................................................................................... 1 Fares Al-Ejeh and Andrew V. Biankin Biobanking in Cancer Research .................................................................... 27 Lisa Devereux, Heather Thorne, and Stephen B. Fox Cytogenetics: Methodologies .......................................................................... 51 Chiyan Lau Cytogenetics: Applications ............................................................................. 67 Chiyan Lau Genomic Analysis ............................................................................................ 83 Sally M. Hunter, Amy E. McCart Reed, Ian G. Campbell, and Kylie L. Gorringe Gene Expression Analysis: Current Methods .............................................. 107 Zhi Ling Teo, Peter Savas, and Sherene Loi Gene Expression Analysis: Applications ....................................................... 137 Peter Savas, Zhi Ling Teo, and Sherene Loi Methods Used for Noncoding RNAs Analysis .............................................. 151 Marjan E. Askarian-Amiri, Darren J. Korbie, Debina Sarkar, and Graeme Finlay Applications of Non-coding RNA in the Molecular Pathology of Cancer .......................................................................................................... 177 Keerthana Krishnan and Nicole Cloonan Proteomics Methods ........................................................................................ 219 Keith Ashman, Greg Rice, and Murray Mitchell vii viii Contents The Clinical Application of Proteomics ........................................................ 239 Keith Ashman, Murray Mitchell, and Gregory Rice Analysis of DNA Methylation in Clinical Samples: Methods and Applications .............................................................................................. 261 Alexander Dobrovic Clinical Flow Cytometry for Hematopoietic Neoplasms ............................. 279 David Wu, Brent L. Wood, and Jonathan R. Fromm Bioinformatics Analysis of Sequence Data ................................................... 317 Anthony T. Papenfuss, Daniel Cameron, Jan Schroeder, and Ismael Vergara Forgotten Resources – The Autopsy .............................................................. 335 Deborah Smith, Amy McCart Reed, and Sunil R. Lakhani The Future of Molecular Pathology .............................................................. 349 John S. Mattick Index ................................................................................................................. 359 Molecular Diagnostics: Translation from Discovery to Clinical Practice Fares Al-Ejeh and Andrew V. Biankin Over the past decade, there has been broad publicity and discussions over the potential of “personalized medicine” to transform clinical practice in oncology. In its broad definition, personalized medicine in oncology refers to the use of biomark- ers to make decisions such as the type of therapies, prognosis, and extent of moni- toring of disease progression. As such, oncologists have been practicing personalized medicine throughout modern medicine where patients are treated according to clini- cal staging and the current understanding of specific cancer behaviors. It may be argued that even chemotherapy is personalized, not only in terms of using different chemotherapeutics for different cancer types but also for the concept of using anti- proliferation cytotoxic drugs against highly, uncontrolled proliferative cancers. Recent examples of personalized targeted therapies include trastuzumab and crizotinib. Diagnostic tests for Erbb2 amplification for Herceptin in breast cancer and ALK-gene fusion for crizotinib in non-small cell lung cancer are required to identify the patients who would benefit from these treatments. More recently, genome-wide molecular profiling has accelerated deeper understanding of the architecture of cancers in general and their heterogeneity in their response to thera- pies specifically. Transcriptome and genome profiling, and proteome profiling to some extent, have expounded the heterogeneity of cancers even of similar origins which has been recognized by clinicians and pathologists for decades. The rapid growth of molecular profiling has been paralleled with an exponential growth in the use of the term “personalized medicine” (Fig. 1). The promise made is that such F. Al-Ejeh (*) Personalised Medicine, QIMR Berghofer Medical Research Institute, Bancroft Building, 300 Herston Road, Herston, QLD 4006, Australia e-mail: [email protected] A.V. Biankin (*) Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland G61 1BD, UK e-mail: [email protected] © Springer Science+Business Media LLC 2016 1 S.R. Lakhani, S.B. Fox (eds.), Molecular Pathology in Cancer Research, DOI 10.1007/978-1-4939-6643-1_1 2 F. Al-Ejeh and A.V. Biankin Fig. 1 PubMed search of “personalized medicine” (http://www.ncbi.nlm.nih.gov/pubmed/?term= personalized+medicine) advances in the field would deliver sophisticated diagnostic tests and precise therapies beyond the “one marker-one drug” model of the past. Accordingly, it may be more suitable to refer to the new model as “precision medicine” or “precision oncology” to distinguish from personalized medicine although both terms may be related. In this chapter, we will discuss the advances of “omics” technologies particularly their translation into multiplexed molecular pathological tests, which are central for personalized/precision oncology. The pathways towards clinical development of such tests will also be discussed within the current and future regulatory landscapes, and the perspective of clinical utility and impact on patient management and benefit. New Technologies and Their Promise Cancer molecular diagnostics are based on the analysis of biomarkers such DNA, RNA, or protein to identify risk or incidence of disease, determine disease progres- sion (prognostic tests), determine therapy, and/or predict response (predictive or companion diagnostic tests). Microarrays enable high throughput measurements of DNA, RNA, or protein and have contributed vastly to our current research practice. One of the earliest descriptions of the use of “DNA microarrays” or “DNA chips” is probably the study by Augenlicht et al. in 1987 which measured the relative expres- sion of each of 4000 complementary DNA (cDNA) sequences from biopsies of human colonic tissue and in colonic carcinoma cells [1]. A follow-up study focused on 30 cDNA clones in an attempt to compare the expression profiles between two genetic groups from patients at high risk for developing colorectal cancer and
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