Cover: Biomarkers in Drug Discovery and Development, Second Edition by Ramin Rahbari, Jonathan Van Niewaal, Michael R. Bleavins

Biomarkers in Drug Discovery and Development

A Handbook of Practice, Application, and Strategy

 

 

Edited by

Ramin Rahbari, MS, MBA

Innovative Scientific Management

New York, New York

Jonathan Van Niewaal, MBA

Innovative Scientific Management

Woodbury, Minnesota

Michael R. Bleavins, PhD, DABT

White Crow Innovation

Dexter, Michigan

 

 

 

Second Edition

 

 

 

 

 

Wiley Logo

List of Contributors

  • Salvatore Alesci
  • Takeda Pharmaceuticals
  • Cambridge, MA
  • USA
  • Sara Assadian
  • PROOF Centre of Excellence
  • Vancouver, BC
  • Canada
  • and
  • University of British Columbia
  • Vancouver, British Columbia
  • Canada
  • Robert Balshaw
  • PROOF Centre of Excellence and Biomarkers in Transplantation Team
  • Vancouver, BC
  • Canada
  • Mats Bergstrom
  • Independent Consultant
  • Uppsala
  • Sweden
  • Sven A. Beushausen
  • Zoetic Pharmaceuticals
  • Amherst
  • New York, NY
  • USA
  • Michael R. Bleavins
  • White Crow Innovation
  • Dexter, MI
  • USA
  • Alan P. Brown
  • Novartis Institutes for Biomedical Research
  • Cambridge, MA
  • USA
  • Michael Burgess
  • University of British Columbia
  • Vancouver, BC
  • Canada
  • Bruce D. Car
  • Bristol-Myers Squibb Co.
  • Princeton, NJ
  • USA
  • Stephen Y. Chan
  • University of Pittsburgh Medical Center
  • Pittsburgh, PA
  • USA
  • Kay A. Criswell
  • Westbrook Biomarker & Pharmaceutical Consulting, LLC
  • Westbrook, CT
  • USA
  • Breanne Crouch
  • PROOF Centre of Excellence
  • Vancouver, BC
  • Canada
  • and
  • University of British Columbia
  • Vancouver, British Columbia
  • Canada
  • Miranda K. Culley
  • Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute
  • University of Pittsburgh School of Medicine
  • Pittsburgh, PA
  • USA
  • Ian Dews
  • Envestia Ltd.
  • Thame, Oxfordshire
  • UK
  • Andrew Dorner
  • Takeda Pharmaceuticals International Co.
  • Cambridge, MA
  • USA
  • Gregory J. Downing
  • Innovation Horizons, LLC
  • Washington, DC
  • USA
  • Robert W. Dunstan
  • Abbvie
  • Worcester, MA
  • USA
  • Giora Z. Feuerstein
  • United States Department of Defense
  • Defense Threat Reduction Agency
  • Fort Belvoir, VA
  • USA
  • Edward P. Ficaro
  • INVIA Medical Imaging Solutions
  • Ann Arbor, MI
  • USA
  • William R. Foster
  • Bristol-Myers Squibb Co.
  • Princeton, NJ
  • USA
  • Ross A. Fredenburg
  • Amathus Therapeutics, Inc.
  • Cambridge, MA
  • USA
  • Gregory P. Fusco
  • Epividian, Inc.
  • Chicago, IL
  • USA
  • Brian Gemzik
  • Bristol-Myers Squibb Co.
  • Princeton, NJ
  • USA
  • Federico Goodsaid
  • Regulatory Pathfinders
  • San Juan
  • PR USA
  • Michael Hehenberger
  • HM NanoMed
  • Westport, CT
  • USA
  • Nita Ichhpurani
  • Innovative Scientific Management
  • Toronto, ON
  • Canada
  • Malle Jurima-Romet
  • Celerion
  • Montreal, QC
  • Canada
  • Paul Keown
  • PROOF Centre of Excellence and Biomarkers in Transplantation Team
  • Vancouver, BC
  • Canada
  • Anthony A. Killeen
  • University of Minnesota
  • Minneapolis, MN
  • USA
  • Ji-Young V. Kim
  • PROOF Centre of Excellence and Biomarkers in Transplantation Team
  • Vancouver, BC
  • Canada
  • Lena King
  • Innovative Scientific Management
  • Guelph, ON
  • Canada
  • Lars Klareskog
  • Karolinska Institute
  • Stockholm
  • Sweden
  • Frank Kramer
  • Bayer AG
  • Wuppertal
  • Germany
  • Karen Lam
  • PROOF Centre of Excellence
  • Vancouver, BC
  • Canada
  • and
  • University of British Columbia
  • Vancouver, British Columbia
  • Canada
  • Jean W. Lee
  • BioQualQuan
  • Camarillo, CA
  • USA
  • Deanne Lister
  • Invicro, a KonicaMinolta Company, San Diego, CA and Department of Radiology
  • University of California, San Diego, Molecular Imaging Center, Sanford Consortium for Regenerative Medicine
  • Bin Li
  • Takeda Pharmaceuticals International Co.
  • Cambridge, MA
  • USA
  • Xiaowu Liang
  • ImmPORT Therapeutics
  • Irvine
  • California
  • Calvert Louden
  • Johnson & Johnson Pharmaceuticals
  • Raritan, NJ
  • USA
  • William B. Mattes
  • National Center for Toxicological Research
  • US FDA
  • Jefferson, AR
  • USA
  • Patrick McConville
  • Invicro, a KonicaMinolta Company, San Diego, CA and Department of Radiology
  • University of California, San Diego, Molecular Imaging Center, Sanford Consortium for Regenerative Medicine
  • Bruce McManus
  • PROOF Centre of Excellence
  • Vancouver, BC
  • Canada
  • and
  • University of British Columbia
  • Vancouver, British Columbia
  • Canada
  • Robert McMaster
  • PROOF Centre of Excellence and Biomarkers in Transplantation Team
  • Vancouver, BC
  • Canada
  • Jonathan B. Moody
  • INVIA Medical Imaging Solutions
  • Ann Arbor, MI
  • USA
  • Philip S. Murphy
  • GlaxoSmithKline Research and Development
  • Stevenage
  • UK
  • Raymond T. Ng
  • PROOF Centre of Excellence and Biomarkers in Transplantation Team
  • Vancouver, BC
  • Canada
  • Matthias Ocker
  • Bayer AG
  • Germany
  • Berlin

    and

  • Charite University Medicine
  • Berlin
  • Germany
  • Damian O'Connell
  • Experimental Drug Development Centre A*STAR
  • Singapore
  • J. Fred Pritchard
  • Celerion
  • Lincoln Nebraska, NE
  • USA
  • M. Lynn Pritchard
  • Branta Bioscience, LLC
  • Littleton, NC
  • USA
  • Ramin Rahbari
  • Innovative Scientific Management
  • New York, NY
  • USA
  • Ruth A. Roberts
  • Apconix
  • Alderley Edge, Cheshire
  • UK
  • Robert R. Ruffolo
  • Ruffolo Consulting
  • Spring City, PA
  • USA
  • J. Lynn Rutkowski
  • Ossianix
  • Philadelphia, PA
  • USA
  • David Adler
  • Bayer AG
  • Germany
  • Berlin
  • Hyunjin Shin
  • Takeda Pharmaceuticals International Co.
  • Cambridge, MA
  • USA
  • Frank D. Sistare
  • Merck Research Laboratories
  • West Point, PA
  • USA
  • Scott J. Tebbutt
  • PROOF Centre of Excellence and Biomarkers in Transplantation Team
  • Vancouver, BC
  • Canada
  • William L. Trepicchio
  • Takeda Pharmaceuticals International Co.
  • Cambridge, MA
  • USA
  • Christina Trollmo
  • Roche Pharmaceuticals
  • Stockholm
  • Sweden
  • Jin Wang
  • Amgen, Inc.
  • Thousand Oaks, CA
  • USA
  • Frank L. Walsh
  • Wyeth Research
  • Collegeville, PA
  • USA
  • Yuling Wu
  • MedImmune
  • Gaithersburg, MD
  • USA
  • Mary Zacour
  • BioZac Consulting
  • Montreal, QC
  • Canada

Preface

Since the first edition of Biomarkers in Drug Development: A Handbook of Practice, Application, and Strategy was published in 2010, biomarkers have become even more significant, valuable, and important in the decision-making multiple criteria for the development of new drugs. In particular, previously novel biomarkers in nonclinical studies have transitioned into clinical trials. Companies and regulatory agencies have become more comfortable with the inclusion of biomarkers in ex vivo experiments with human tissues/biofluids or Phase I trials, with many early clinical trials now including patients after an additional single ascending dose study in human volunteers.

The use of biomarker technologies and strategies in pharmaceutical development remains the basis for translational medicine, improved patient stratification, and identification of underlying causes of diseases once lumped together based primarily on symptomatology. The approval rates for new drugs have also increased relative to 2010, at least partially due to judicious use of biomarkers to identify the best compounds, as well as answering the regulators' questions more specifically. Patients, regulatory reviewers, and the pharmaceutical industry are seeing safer, more efficacious, and better understood drugs to treat complex diseases. The challenges of escalating drug development costs, increasing duration of clinical development times, high rates of compound failure in Phase II and III clinical trials, blockbuster drugs coming off patent, and novel but unproven targets emerging from discovery all continue to modify the arena. These factors have pressured pharmaceutical research divisions to look for ways to reduce development costs, make better and more informed decisions earlier, reassess traditional testing strategies, and implement new technologies to improve the drug discovery and development processes. Biomarkers remain an important tool for getting new medicines to patients and helping identify molecules with unacceptable liabilities earlier in the process.

Biomarkers have proven to be valuable drug development tools that enhance target validation, thereby helping better understand mechanisms of action and enabling earlier identification of compounds with the highest potential for efficacy in humans. In gene therapy, use of animal models of disease in toxicology studies frequently allows very early monitoring of disease-related biomarkers that are known to be important in disease cause and progression, with the same biomarkers measured in the clinical trials. The biomarker endpoints can be essential for eliminating compounds with unacceptable safety risks or lack of target engagement, enabling the concept of “fail fast, fail early,” and providing more accurate or complete information regarding drug performance and disease progression. At the same time that pharmaceutical scientists are focusing on biomarkers in drug discovery and development, and clinical investigators and health care practitioners are using biomarkers increasingly in medical decision-making and diagnosis. Similarly, regulatory agencies have recognized and embraced the value of biomarkers to guide regulatory decision-making about targeting, drug safety, and efficacy. Regulatory agencies in the United States, Europe, Great Britain, Japan, and China have taken leadership roles in encouraging biomarker innovation in the industry and collaboration to identify, evaluate, and qualify novel biomarkers. Moreover, a biomarker strategy facilitates the choice of a critical path to differentiate products in a competitive marketplace.

Biomarkers continue to be a significant focus of specialized scientific meetings and extensive media coverage. The targeted use of biomarkers also is more prominent in scientific society meeting presentations to highlight new therapeutic targets, upstream and downstream applications relevant to a given disease, and as case studies describing how decision-making and compound selection were influenced. We, the coeditors, felt that updating the first edition of Biomarkers in Drug Development: A Handbook of Practice, Application, and Strategy was timely, as was the continued emphasis on practical aspects of biomarker identification and use, as well as their strategic implementation, and essential application in improving drug development approaches. We each have experience working with biomarkers in drug development, but we recognized that the specialized knowledge of a diverse group of experts was necessary to create the type of comprehensive book that is needed. Therefore, contributions were invited from authors writing chapters in the first edition, and others who are equally renowned experts in their respective fields. The contributors include scientists from academia, research hospitals, biotechnology and pharmaceutical companies, contract research organizations, and consulting firms and those from the FDA. This second edition also has included more coverage on information technology and computational influences in biomarker development and application. The result is a book that we believe will appeal broadly to pharmaceutical research scientists, clinical and academic investigators, regulatory scientists, managers, students, and all other professionals engaged in drug development who are interested in furthering their knowledge of biomarkers.

As discussed early in the book, biomarkers are not new, yet they also are continuously evolving. They have been used for hundreds of years to help physicians diagnose and treat disease. What is new is an expansion from outcome biomarkers to target and mechanistic biomarkers; the availability of “omics,” imaging, and other technologies that allow collection of large amounts of data at the molecular, tissue, and whole-organism levels; and the use of data-rich biomarker information for “translational research,” from the laboratory bench to the clinic and back. The potential and value from the clinical observations back to the bench should not be taken lightly. Improvements in data storage, computational tools, and modeling abilities provide us with the insight through the process and the ability to reverse mine even very large data sets. Later chapters are dedicated to highlighting several important technologies that affect drug discovery and development, the conduct of clinical trials, and the treatment of patients.

The book continues with invited leaders from industry and regulatory agencies to discuss the qualification of biomarker assays in the fit-for-purpose process, including perspectives on the development of diagnostics. The importance of statistics cannot be overlooked, and this topic is also profiled with a practical overview of concepts, common mistakes, and helpful tips to ensure credible biomarkers that can address their intended uses. Specific case studies are used to present information on concepts and examples of utilizing biomarkers in discovery, preclinical safety assessment, clinical trials, and translational medicine. Examples are drawn from a wide range of target-organ toxicities, therapeutic areas, and product types. It is hoped that by presenting a wide range of biomarker applications, discussed by knowledgeable and experienced scientists, readers will develop an appreciation of the scope and breadth of biomarker knowledge and find examples that will help them in their own work.

Lessons learned and the practical aspects of implementing biomarkers in drug development programs are perhaps the most critical message to convey. Many pharmaceutical companies have created translational research divisions, and increasingly, external partners, including academic and government institutions, contract research organizations, and specialty laboratories, are providing technologies and services to support biomarker programs. This is changing the traditional organizational models within industry and paving the way toward greater collaboration across sectors and even among companies within a competitive industry. Perspectives from contributing authors representing several of these different sectors are presented.

The book concludes with a perspective on future trends and outlooks on development, including increasing capabilities in data integration, privacy concerns, the reality of personalized medicine, and the addressing of ethical concerns. The field of biomarkers in drug development is evolving rapidly, and this book presents a snapshot of some exciting new approaches. By utilizing the book as a source of new knowledge, or to reinforce or integrate existing knowledge, we hope that readers will gain a greater understanding and appreciation of the strategy and application of biomarkers in drug development and become more effective decision-makers and contributors in their own organizations.

We also note with regret the passing of Dr. Mallé Jurima-Romet, our coeditor for the first edition. Although Mallé was not able to be part of the second edition of the book, her spirit and commitment to the field of biomarkers resides throughout the book. She was a champion of biomarkers and influenced many during her career.

As he has for many years, Dr. Felix de la Iglesia also directed us with advice, commentary, and mentorship. His coaching to always work with sound science, pay attention to the literature, not being afraid to go somewhere just because no one else has ventured into that territory, and to push boundaries all resonate in work. The value of his experience and critical commentary have enhanced this book.

July 2019

Ramin Rahbari

Jon Van Niewaal

Michael R. Bleavins

Part I
Biomarkers and Their Role in Drug Development