Cancer Genomics. From Bench to Personalized Medicine

472 Pages·2013·59.03 MB·English

by  Graham Dellaire, Jason N. Berman and Robert J. Arceci (Eds.)

Cancer Genomics
From Bench to Personalized Medicine
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Cancer Genomics: From Bench to Personalized Medicine
Graham Dellaire, Jason N. Berman and Robert J. Arceci, Editors
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Cancer Genomics
From Bench to Personalized Medicine
Edited by
Graham Dellaire, Ph.D.
Departments of Pathology and Biochemistry &
Molecular Biology Dalhousie University, Halifax, Canada
Jason. N. Berman, M.D., FRCPC, FAAP
IWK Health Centre, Departments of Pediatrics,
Pathology and Microbiology and Immunology
Dalhousie University, Halifax, Canada
Robert J. Arceci, M.D., Ph.D.
The Ron Matricaria Institute of Molecular Medicine at
Phoenix Childrens Hospital, Department of Child Health,
University of Arizona, College of Medicine,
Phoenix, USA
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This book is dedicated to the patients and their families past and future who have both inspired and will one day benefit
from the great advancements in cancer genomics and to our own families for their ongoing patience and support of
this project.
List of Contributors
Kenneth C. Anderson Department of Medical Hye-Jung E. Chun British Columbia Cancer Agency,
Oncology, Jerome Lipper Multiple Myeloma Center, Vancouver, BC, Canada; Canada’s Michael Smith
Dana-Farber Cancer Institute and Department of Genome Sciences Centre, Vancouver, BC, Canada
Medicine, Harvard Medical School, Boston, MA, USA
Francesca Cottini Department of Medical Oncology,
Samuel A. Aparicio British Columbia Cancer Agency, Jerome Lipper Multiple Myeloma Center, Dana-Farber
Vancouver, BC, Canada; Department of Pathology and Cancer Institute and Department of Medicine, Harvard
Laboratory Medicine, University of British Columbia, Medical School, Boston, MA, USA
Vancouver, BC, Canada; Molecular Oncology, British
Janet E. Dancey Ontario Institute for Cancer Research,
Columbia Cancer Research Centre, Vancouver, BC,
Toronto, ON; NCIC Clinical Trials Group, Queen’s
Canada
University, Kingston, ON, Canada
Robert J. Arceci Children’s Center for Cancer and Blood
Graham Dellaire Departments of Pathology and
Disorders, Hematology/Oncology and The Ron Matricaria
Biochemistry & Molecular Biology, Dalhousie
Institute of Molecular Medicine, Phoenix Children’s
University, Halifax, NS, Canada
Hospital, Department of Child Health, University of
Amal M. EL-Naggar Department of Molecular
Arizona, College of Medicine, Phoenix, AZ, USA
Oncology, BC Cancer Research Center, Vancouver, BC;
Alejandro Berlin Departments of Radiation Oncology
Department of Pathology and Laboratory Medicine,
and Medical Biophysics, University of Toronto,
University of British Columbia, Vancouver, BC, Canada
Toronto, ON, Canada; Ontario Cancer Institute and
Conrad V. Fernandez Departments of Pediatrics and
Princess Margaret Cancer Center (University Health
Bioethics, Head, Division of Pediatric Hematology/
Network), Toronto, ON, Canada
Oncology, Dalhousie University and IWK Health Centre,
Jason N. Berman Departments of Pediatrics,
Halifax, NS, Canada
Microbiology and Immunology, and Pathology,
Michael Fraser Ontario Cancer Institute and Princess
Dalhousie University and IWK Health Centre, Halifax,
Margaret Cancer Center (University Health Network),
NS, Canada
Toronto, ON, Canada
Maria Grazia Borrello Molecular Mechanisms Unit,
Daniel Gaston Department of Pathology, Dalhousie
Department of Experimental Oncology and Molecular
University, Halifax, NS, Canada
Medicine, Fondazione IRCCS Istituto Nazionale dei
Tumori, Milan, Italy Carman Giacomantonio Departments of Pathology and
Surgery, Dalhousie University, Halifax, NS, Canada
Robert G. Bristow Ontario Cancer Institute and
Princess Margaret Cancer Center (University Health Angela Greco Molecular Mechanisms Unit,
Network), Toronto, ON, Canada; Departments of Department of Experimental Oncology and Molecular
Radiation Oncology and Medical Biophysics, Medicine, Fondazione IRCCS Istituto Nazionale dei
University of Toronto, Toronto, ON, Canada Tumori, Milan, Italy
Moamen Bydoun Department of Pathology, Dalhousie Erin Hedlund Computational Biology Department,
University, Halifax, NS, Canada St Jude Children’s Research Hospital Memphis, TN, USA
George A. Calin Department of Experimental Matthew Herder Health Law Institute, Faculties of
Therapeutics and Leukemia, The University of Texas Medicine and Law, Dalhousie University, Halifax, NS,
MD Anderson Cancer Center, Houston, TX, USA Canada
Priscilla P.L. Chiu Department of Surgery, The Peter Hohenstein The Roslin Institute, University of
Hospital for Sick Children, Toronto, ON, Canada Edinburgh, Easter Bush Campus, Midlothian, UK
xiii
xiv List of Contributors
Meredith S. Irwin Department of Paediatrics, Hospital Marco A. Marra British Columbia Cancer Agency,
for Sick Children and University of Toronto, Toronto, Vancouver, BC, Canada; Canada’s Michael Smith
ON, Canada Genome Sciences Centre, Vancouver, BC, Canada;
Department of Medical Genetics, University of British
Steven J.M. Jones Canada’s Michael Smith Genome
Columbia, Vancouver, BC, Canada
Sciences Centre, British Columbia Cancer Agency,
Vancouver, BC, Canada Anne-Marie Mes-Masson Universite´ de Montre´al,
Department of Medicine, Montreal, QC, Canada;
Katayoon Kasaian Canada’s Michael Smith Genome
Centre hospitalier de l’Universite´ de Montre´al, Institut
Sciences Centre, British Columbia Cancer Agency,
du Cancer de Montre´al, Montreal, QC, Canada
Vancouver, BC, Canada
Soheil Meshinchi Clinical Research Division, Fred
Javed Khan Oncogenomics Section, Pediatric
Hutchinson Cancer Research Center, Department of
Oncology Branch, Advanced Technology Center,
Pediatrics, University of Washington School of Medicine,
National Cancer Institute, Bethesda, MD, USA
Seattle, WA, USA
Jaswinder Khattra British Columbia Cancer Agency,
Claudia Miranda Molecular Mechanisms Unit,
Vancouver, BC, Canada; Department of Pathology and
Department of Experimental Oncology and Molecular
Laboratory Medicine, University of British Columbia,
Medicine, Fondazione IRCCS Istituto Nazionale dei
Vancouver, BC, Canada; Molecular Oncology, British
Tumori, Milan, Italy
Columbia Cancer Research Centre, Vancouver, BC,
Canada Stephen B. Montgomery Departments of Pathology
and Genetics, Stanford University, Stanford, CA, USA
Martin Krzywinski British Columbia Cancer Agency,
Vancouver, BC, Canada; Canada’s Michael Smith Daniel A. Morgenstern Department of Paediatrics,
Genome Sciences Centre, Vancouver, BC, Canada Hospital for Sick Children and University of Toronto,
Toronto, ON, Canada
Ce´cile Le Page Centre hospitalier de l’Universite´ de
Montre´al, Institut du Cancer de Montre´al, Montreal, Ryan D. Morin Department of Molecular Biology and
QC, Canada Biochemistry, Simon Fraser University, Burnaby, BC,
Canada
Gabriel Leprivier Department of Molecular Oncology,
BC Cancer Research Center, Vancouver, BC; Department Veronique Ouellet Centre de Recherche du Centre hos-
of Pathology and Laboratory Medicine, University of pitalier de l’Universite´ de Montre´al, Montreal, QC,
British Columbia, Vancouver, BC, Canada Canada
Yvonne Y. Li Canada’s Michael Smith Genome Louise Parker Departments of Medicine and
Sciences Centre, British Columbia Cancer Agency, Pediatrics, Dalhousie University, Halifax, NS, Canada
Vancouver, BC, Canada
Matthew Parker Computational Biology Department,
Hui Ling Department of Experimental Therapeutics St Jude Children’s Research Hospital Memphis, TN,
and Leukemia, The University of Texas MD Anderson USA
Cancer Center, Houston, TX, USA
Elizabeth J. Perlman Ann & Robert H. Lurie Children’s
Anthony M. Magliocco H. Lee Moffitt Cancer Center Hospital of Chicago, Northwestern University Feinberg
and Research Institute, Tampa, FL, USA School of Medicine, Chicago, IL, USA
David Malkin Division of Hematology/Oncology, Marco A. Pierotti Scientific Directorate, Fondazione
The Hospital for Sick Children and Department of IRCCS Istituto Nazionale dei Tumori, Milan, Italy
Pediatrics, University of Toronto, Toronto, ON,
Shahrad Rod Rassekh Child and Family Research
Canada
Institute, British Columbia’s Children’s Hospital,
Branavan Manoranjan McMaster Stem Cell and Vancouver, BC, Canada; Department of Pediatrics,
Cancer Research Institute, McMaster University, Division of Pediatric Hematology/Oncology/BMT,
Hamilton, ON, Canada; Michael G. DeGroote School University of British Columbia, Vancouver, BC,
of Medicine, McMaster University, Hamilton, ON, Canada
Canada
Colin J.D. Ross Child and Family Research Institute,
Paola Marcato Department of Pathology, Dalhousie British Columbia’s Children’s Hospital, Vancouver,
University, Halifax, NS, Canada BC, Canada; Department of Pediatrics, Division of
List of Contributors xv
Translational Therapeutics, University of British Chitra Venugopal McMaster Stem Cell and Cancer
Columbia, Vancouver, BC, Canada; Centre for Research Institute, McMaster University, Hamilton,
Molecular Medicine and Therapeutics, University of ON, Canada
British Columbia, Vancouver, BC, Canada
Parvez Vora McMaster Stem Cell and Cancer
Fred Saad Department of Surgery, Centre hospitalier Research Institute, McMaster University, Hamilton,
de l’Universite´ de Montre´al, Montreal, QC, Canada; ON, Canada
Montreal Cancer Institute, Montreal, QC, Canada
Jun S. Wei Oncogenomics Section, Pediatric Oncology
Sheila K. Singh McMaster Stem Cell and Cancer Branch, Advanced Technology Center, National
Research Institute, McMaster University, Hamilton, Cancer Institute, Bethesda, MD, USA
ON, Canada; Michael G. DeGroote School of
Zhaolin Xu Department of Pathology, Dalhousie
Medicine, McMaster University, Hamilton, ON,
University and Queen Elizabeth II Health Sciences
Canada; Surgery, Faculty of Health Sciences,
Centre, Halifax, NS, Canada
McMaster University, Hamilton, ON, Canada
Jinghui Zhang Computational Biology Department,
Poul H. Sorensen Department of Molecular Oncology,
St Jude Children’s Research Hospital Memphis, TN,
BC Cancer Research Center, Vancouver, BC; Department
USA
of Pathology and Laboratory Medicine, University of
Shile Zhang Oncogenomics Section, Pediatric
British Columbia, Vancouver, BC, Canada
Oncology Branch, Advanced Technology Center,
Giovanni Tonon Division of Molecular Oncology,
National Cancer Institute, Bethesda, MD, USA;
Functional Genomics of Cancer Unit, San Raffaele
Program in Bioinformatics, Boston University, Boston,
Scientific Institute, Milan, Italy
MA, USA
Chapter 1
Cancer Genomics
Historical Perspective and Current
Challenges of Cancer Genomics
Graham Dellaire1 1Departments of Pathology and Biochemistry & Molecular Biology,
Robert J. Arceci2 2D
Cahlhiloduresine’sUnCiveenrtseirty,foHraliCfaaxn,cNerS, aCnadnaBdalood Disorders, Hematology/
Oncology and The Ron Matricaria Institute of Molecular Medicine,
Phoenix Children’s Hospital, Department of Child Health, University of
Arizona, College of Medicine, Phoenix, AZ, USA
Contents
A Historical Perspective on the Development of
Cancer Genomics 4
Current and Future Challenges 7
Glossary 8
Abbreviations 8
References 8
Cancer Genomics. DOI: http://dx.doi.org/10.1016/B978-0-12-396967-5.00001-3
© 2014 Elsevier Inc. All rights reserved. 3
4 PART | 1 Introduction
the 20th century was ushered in by a set of remarkable
Key Concepts observations in cancer biology that were made before the
● Advances in nucleic acid sequencing technology have discovery of DNA. These included the theories of Rous
had a profound impact on the field of cancer genomics regarding the potential viral origin of some cancers in
and have enabled the interrogation of the genetic basis 1910, derived from his work on avian sarcomas, and the
of cancer at the single nucleotide level concept of the somatic mutation theory of cancer by
● Cancer genomics has provided a detailed view of the
Boveri in 1914 that stemmed from his work on polysper-
complexity of the cancer genome, including the
mic development in invertebrates [5,6].
extraordinary ability to sustain and thrive on alterations
While not necessarily providing a deeper understand-
of DNA
ing of the mechanisms of carcinogenesis, the first half of
● Translating cancer genomics into clinically real time
the 20th century in many ways broke open the gates of
and actionable personalized medicine is beginning to
cancer treatment. After being commissioned by the US
be tested, although significant advances in the speed of
providing molecular data, analysis, utilizing government to understand the physiological consequences
combination targeted agents and understanding clinical of nitrogen mustard gas used in warfare, Louis Goodman
response or no response will require new generations of and Alfred Gilman recognized the key bone marrow tox-
technology and bioinformatic tools icity of this agent and subsequently introduced its intrave-
nous use for the treatment of lymphoid malignancies in
1946 [7]. Soon afterward in 1948, the antimetabolite ami-
nopterin was used to treat several children with acute
lymphoblastic leukemia by Farber and colleagues, a treat-
ment built on the work of the chemist Subbarao [8].
A HISTORICAL PERSPECTIVE ON THE
A decade later, in 1958, Hertz, Li and colleagues reported
DEVELOPMENT OF CANCER GENOMICS
the first cure of a metastatic tumor, namely a gestational-
Several hundred years BC, Hippocrates is attributed with related choriocarcinoma, with another antimetabolite,
providing us with the term “carcinoma” and thus “can- methotrexate [9].
cer”, originating possibly from the image of finger-like However, despite such encouraging forays into treat-
extensions (veins) from a tumorous (main body of the ing patients, few cures were achievable with surgery,
tumor) breast lesion that shared resemblance to the shape radiation therapy and chemotherapy. In this regard, the
of a crab. Around 400 years later, the Roman physician extraordinary efforts of Ms Mary Lasker following her
Celsus translated the Greek (karkinos) into the Latin word husband’s death from cancer should not go unmentioned.
for crab, which led to the term “cancer” [1,2]. A relative Through her efforts and the Citizens Committee for the
late-comer to this nomenclature narrative, in 168 BC, Conquest of Cancer through the 1960s, they challenged
Galen introduced the terms “oncos”, meaning “swelling” government, physicians and scientists to push forth with a
to describe tumors, leading to the term defining the field “War on Cancer” [10 12]. And this was in spite of a sig-
of oncology [3,4]. nificant number of naysayers who had concluded in vari-
The next 2000 years witnessed several key events that ous publications that we knew enough to cure cancer and
helped to refine further the still ongoing main areas of all that was needed was to translate the knowledge that
cancer investigation and treatment. Maimonides in AD was available at the time. Such a lack of vision was
1190 appears to have been the first to document surgi- thankfully thwarted by those who propitiously concluded
cally removing tumors [3]. The recognition of cancer that only through scientific discovery and its ongoing
clustering in distinct populations was introduced in 1713 application would improvements in cancer outcomes
with Razmazzini’s observation of the low cervical but occur. In 1971, the US National Cancer Act was passed
high breast cancer incidence in nuns [2]. The observation by Congress and then President Nixon signed it into law
that environmental and occupational exposures can be within 2 weeks, an astonishingly rapid accomplishment
associated with increased incidence of specific cancers on the part of government and one that should inform cur-
also became evident. In the first half of the 1800s, rent, often stalled efforts [10 13]. The consequences of
Recmier appears to have reignited the flare for nomencla- the above investment, along with other efforts across the
ture by writing about “metastasis” in 1829 to describe the globe [14], led to an infusion of intellectual engagement
movement of some cancers to different parts of the body and financial support for conquering cancer. The results
[3]. Muller’s notes on the cellular origin of cancer also in included the establishment of clinical trial groups, com-
1838, and Paget’s subsequent “seed and soil” hypothesis prehensive cancer centers, an explosion of new antican-
over 50 years later in 1889, established the cognitive par- cer agents from the lab and from nature, and the
adigm for the cell biological basis for cancer and the con- beginning of work focused on the biological understand-
cept of microenvironmental niches [2,3]. The first half of ing of cancer. This latter work built of course on the