Molecular Histopathology and Tissue Biomarkers in Drug and Diagnostic Development

384 Pages·2015·9.38 MB·English

by  Steven J. Potts, David A. Eberhard, Keith A. Wharton, Jr. (eds.)

Methods in Pharmacology
and Toxicology
Steven J. Potts
David A. Eberhard
Keith A. Wharton, Jr. Editors
Molecular
Histopathology and
Tissue Biomarkers in
Drug and Diagnostic
Development
M E T H O D S I N P H A R M A C O L O G Y
A N D T O X I C O L O G Y
Series Editor
Y. James Kang
Department of Medicine
University of Louisville School of Medicine
Prospect, Kentucky, USA
For further volumes: http://www.springer.com/series/7653
Molecular Histopathology
and Tissue Biomarkers
in Drug and Diagnostic
Development
Edited by
Steven J. Potts
Flagship Biosciences, LLC, Westminster, CO, USA
David A. Eberhard
University of North Carolina, Chapel Hill, NC, USA
Keith A. Wharton, Jr.
Novartis Institutes for BioMedical Research, Cambridge, MA, USA
Editors David A. Eberhard
Steven J. Potts University of North Carolina
Flagship Biosciences, LLC Chapel Hill, NC, USA
Westminster, CO, USA
Keith A. Wharton, Jr.
Novartis Institutes for BioMedical Research
Cambridge, MA, USA
ISSN 1557-2153 ISSN 1940-6053 (electronic)
Methods in Pharmacology and Toxicology
ISBN 978-1-4939-2680-0 ISBN 978-1-4939-2681-7 (eBook)
DOI 10.1007/978-1-4939-2681-7
Library of Congress Control Number: 2015939268
Springer New York Heidelberg Dordrecht London
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Dedication
Chris Callahan, M.D., Ph.D.
This book is dedicated to the memory of our dear friend and esteemed colleague, Chris
Callahan, M.D., Ph.D., who suffered an untimely death from a progressive brain tumor in
2011. Already recognized as a leader early in his career, Chris held the position of Scientist
and Investigative Pathologist at Genentech/Roche at the time of his passing at the young
age of 46. Chris’s professional contributions pervade this book’s themes of molecular
histopathology and tissue-based biomarkers, and several of its contributors trained with or
worked alongside Chris at various stages of his career. More importantly, Chris represented
a generation of visionary physician-scientists who began their training in the 1980s, the last
“pre-genome” decade of human history, with the belief that the discovery of molecules and
pathways governing normal development would provide key insights into human disease.
While now considered dogma, at that time only scattered yet tantalizing hints existed to
indicate that alterations of these same handful of pathways, deeply conserved during our
evolution, caused (and were druggable targets of) diverse human diseases.
Chris completed his B.S. at Brown University in 1987, and earned his M.D. and Ph.D.
degrees as a graduate student in John Thomas’s lab at UC San Diego and Salk Institute
performing groundbreaking work in Drosophila neurobiology. His accomplishments
include the molecular cloning of derailed, a receptor tyrosine kinase crucial for axon
guidance [1]. Recognizing the central role of pathology in identifying molecular and
cellular mechanisms of disease, Chris moved to Stanford University to pursue residency
training in anatomic pathology, ultimately serving as Attending Physician and Acting
Assistant Professor of Pathology while engaged in postdoctoral research in Dermatology
with Tony Oro (also a former fellow M.D./Ph.D. student with Chris at UC San Diego).
Extending Tony’s postdoctoral work with Matthew Scott that implicated aberrant Hedge-
hog signaling in the most common human tumor, basal cell carcinoma [4], Chris went on
to discover a critical role for a Hedgehog pathway target gene Mtss1 (Missing in Metasta-
sis) in the regulation of signaling and cancer progression [3].
Tragically, Chris’s cancer diagnosis came at a most inopportune time—just as he
sought to start his own lab. Following aggressive surgery and chemotherapy, he returned
to the bench within days to continue his passion. By this time, Hedgehog pathway
v
vi
inhibitors were being developed for oncology indications, and Chris felt the best opportu-
nity to apply his skills and talents to directly benefit cancer patients was to continue his
career as a pathologist in biopharma. Chris joined Genentech, supporting drug develop-
ment projects while directing several research projects aimed at understanding the mechan-
isms of Hedgehog pathway activation and therapy resistance in human cancer. Chris was a
key contributor to the R&D team efforts that led to the FDA approval of vismodegib, the
first-in-class Hedgehog pathway inhibitor for clinical use in advanced basal cell carcinoma.
The several hats Chris wore in these efforts included basic research and medical scientist,
translational biomarker and companion diagnostics R&D investigator, and pathology
advisor to the development team. Chris investigated cancer mechanisms to the end of his
life, with his final senior author paper on the role of Hedgehog signaling in tumor-stroma
interactions published in the Proceedings of the National Academy of Sciences just a few
months before his death [4].
Chris’s approach to life inspired those around him, as these quotes from two of his
Genentech colleagues attest:
(I have) never met anyone with more selfless dedication, engagement, focus, and commitment to his work
and family than Chris. Chris loved his role as a pathologist at Genentech and immersed himself in it 100 %. He
knew that his work was helping to transform the lives of patients, and felt fortunate that he could do so by
engaging in professional activities he loved most—basic hypothesis-driven research and scientific collaboration.
Chris knew, more clearly than most of us do, that his time with his family, his friends, and his work was
limited. He relished that time, and he shared it generously with others. Chris had a selfless, collegial
enthusiasm for his work. He was absolutely committed to his colleagues and to the projects he supported; he
would do everything he could to maximize the chances for their success. He had a great appreciation of, and
loved sharing subtle details of biology—not to advertise his brilliance, but because he trusted you would find
them as satisfying and wonderful as he did. When he dropped off his sons at school in the morning he would tell
them, ‘Have fun, learn a lot, and be kind.’ He fully modeled that advice.
Beyond describing Chris to a tee, these reminiscences illustrate three qualities of a
successful anatomic pathologist in biopharma that emerge as themes throughout this
book: a focus on the biology of disease, a passionate curiosity, and a collaborative mindset.
Although new insights about disease emerge daily, and opportunities for new discoveries
have never been greater than the present time, some things haven’t changed: A century and
half ago, Rudolf Virchow, founder of cellular pathology, said “If we would serve science,
we must extend her limits, not only as far as our own knowledge is concerned, but in the
estimation of others.” [5]. Chris exemplified this Virchowian ideal.
Comprehending the biology of disease requires integration of knowledge from diverse
disciplines, of which we concede the histopathology “stock in trade” of fixed and stained
tissue is only one part. As a role model, Chris excelled at the challenges faced by anatomic
pathologists embedded in drug and diagnostic industries, chief among them to bridge the
power (and limitations) of histopathology methods and knowledge with those from a
growing number of technology-driven disciplines, including genomics, protein biochem-
istry, quantitative image analysis, and in vivo imaging of cells to whole animals. Chris saw
firsthand that delivering a diagnostic test or new therapy to patients requires diverse skills,
far beyond what any one individual could possibly master. Whether performed in industry
or research institutes, drug development requires coordinated efforts by multidisciplinary
teams, and so the pathologist on the team must persuasively communicate with members
from diverse backgrounds and viewpoints in order to foster collaboration, and ultimately,
progress. Rare talents like Chris, with curious and creative minds, able to integrate
emerging data and knowledge across disciplines, are poised to see old problems in new
vii
ways and develop novel, important hypotheses that demand investigation. As Virchow said,
the pathologist must push the science—“. . .extend her limits. . .”—for all to see. Chris
fearlessly pursued multidisciplinary investigations in fruit flies, mice, and human systems in
order to understand core biologies and their alterations in human disease. We don’t yet
know if flies or mice will benefit from the fruits of Chris’s research, but humanity has
already benefited, and for that we are most grateful.
Chris and his wife Andrea are the proud parents of two boys, Nathan and Ryan.
Acknowledgements
Special thanks to Tony Oro, Cary Austin, and UCSD, Stanford, and Genentech colleagues
for their contributions to this dedication.
Cambridge, MA, USA Keith A. Wharton, Jr.
Chapel Hill, NC, USA David A. Eberhard
References
1. Callahan CA, Bonkovsky JL, Scully AL, Thomas JB (1996) derailed is required for muscle attachment
site selection in Drosophila. Development 122(9):2761–2767
2. Oro AE, Higgins KM, Hu Z, Bonifas JM, Epstein EH, Jr., Scott MP (1997) Basal cell carcinomas in
mice overexpressing sonic hedgehog. Science 276(5313):817–821
3. Callahan CA, Ofstad T, Horng L, Wang JK, Zhen HH, Coulombe PA, Oro AE (2004) MIM/BEG4,
a Sonic hedgehog-responsive gene that potentiates Gli-dependent transcription. Genes Dev 18
(22):2724-2729. doi:10.1101/gad.1221804
4. Chen W, Tang T, Eastham-Anderson J, Dunlap D, Alicke B, Nannini M, Gould S, Yauch R,
Modrusan Z, DuPree KJ, Darbonne WC, Plowman G, de Sauvage FJ, Callahan CA (2011) Canonical
hedgehog signaling augments tumor angiogenesis by induction of VEGF-A in stromal perivascular
cells. Proc Natl Acad Sci U S A 108 (23):9589-9594. doi:10.1073/pnas.1017945108
5. Virchow R (1858) Cellular pathology (trans: Chance F). Edwards Brothers, Inc., Ann Arbor, MI
Preface
I’ve just sucked one year of your life away. . . What did this do to you? Tell me.
And remember, this is for posterity so be honest. How do you feel?
–Count Rugen, antagonist in the 1987 movie The Princess Bride
In the movie The Princess Bride, the hero, Westley, has just been subjected to The
Machine, a torture device that sucks years of life out of the victim. Like Westley, who cries
andmoans in pain in response to Count Rugen’s query, anyone embarking on, or reflecting
upon, a multi-year project knows the pathologic feeling of time spent on a lengthy and
complex project, whether it is a book, a drug, or a film.
Feature films aspiring for blockbuster status can consume $100 million or more in
production costs and 3 years just to get to production stage—all to entertain people for a
mere 2 hours. Yet this amount of money pales in comparison to the economic realities of
producing a new therapeutic that might address an unmet medical need for thousands or
even millions of people. By most measures, developing a new drug in 2015 costs at least ten
times more than a blockbuster movie. Three years in production is feature film fiction
compared to the industry average of ~14 years for drug development.
The feature film and the pharmaceutical industries face similar challenges: years
between the initial idea and a revenue-generating product, huge multifaceted teams,
millions of dollars invested in multiple projects, only a few of which succeed, and the
hope of the occasional blockbuster that must finance the failures of the rest.
At each phase in drug development, from early discovery through IND (Initial New
Drug Application) to NDA (New Drug Application), the promise of efficacy is balanced
against the penalty of toxicity. While there are many ways that efficacy and toxicity can be
evaluated in animals and in people, the highest concentration of information relevant to
many diseases remains the lesional tissue sample, microscopic examination of which pro-
vides a foundation to understand disease and the effect of therapy. Increasingly, whole
microscopic slide imaging is used, providing at least an order of magnitude higher resolu-
tion of cellular context than current noninvasive in vivo radiological imaging techniques.
However, microscopic data requires many players to extract its maximum value: histology
(preparing the tissue sample) and pathology (interpreting the tissue sample), in addition to
experts in disease-specific biology. Tissue-based studies help to understand how candidate
therapies act in animals and humans, and this work is often performed by small biotech
companies, large pharmaceutical companies, academic medical centers, commercial refer-
ence laboratories, and government entities. Each actor has a critical role to play in the
process and in the development of the final product.
We anticipate those who will most benefit from reading this book will be embedded in
government-sponsored academic research, diagnostics, or biopharmaceuticals, but we have
strived to make the chapters accessible and interesting to a wide audience. Due to shrinking
government budgets for basic research, more academic researchers are responding to grant
announcements and pharmaceutical partnerships that drive them deeper into drug devel-
opment. With the growth of companion diagnostics, experts in disease diagnostics will find
useful information in this volume about co-development of diagnostic and therapeutic
products, though the nature and timelines of the diagnostic industry are very different
from those of drug development, creating some unanticipated but, on deeper
ix