May 15, 2005 (Vol. 25, No. 10)

The Definition of Biomarker Depends in Large Part on Who You’re Talking To

Scientists trying to improve the productivity and efficiency of their drug discovery efforts still face issues of escalating R&D costs and the lengthy time it takes to conduct clinical trials. As a result, biotech and pharma companies are looking at biomarkers as a possible answer to these obstacles.

“The clinical trials phase currently accounts for over 60% of drug discovery and development cost, and it may take up to $1.7 billion to get a drug to market,” explains Phil Webster, a research analyst at Frost & Sullivan ( “Using biomarkers to indicate drug efficacy and toxicity or to stratify patient populations has the potential to significantly reduce clinical trial costs and duration.”

The global biomarkers market is expected to grow at a compound annual growth rate of 28.5% from $0.63 billion in 2004 to $2.9 billion in 2008, according to Webster. Despite the early stages of market development, leading drug companies are already responding by investing in biomarker discovery programs, he adds.

“Failure of potential drugs to clear clinical trials is another factor driving research in biomarkers. Approximately 90 percent of compounds fail during clinical development,” continues Webster. “Over 60 percent of those failures are due to absorption, distribution, metabolism, and excretion (ADME) problems, as well as toxicology.

What exactly is a biomarker, in addition to being one of the hottest new terms in biotech? The concept itself is not novel; the term was defined at the 1999 NIH/FDA conference “Biomarkers and Surrogate Endpoints: Advancing Clinical Research and Applications.”

At that meeting, a biomarker was called a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention.

A clinical end point is a characteristic or variable that reflects how a patient feels, functions, or survives. A surrogate end point is a biomarker that is intended to substitute for a clinical end point.

“When companies say they are doing work in biomarker research, more often than not they are testing a limited number of hypothesized markers, often on the diagnostic side,” says Howard Schulman, vp, research and development at SurroMed (Menlo Park, CA).

His company’s platform for biological marker discovery incorporates proprietary technologies for profiling and analyzing thousands of immune cell populations, proteins, endogenous peptides, and low-molecular-weight organic molecules such as metabolites in small volumes of blood and/or other biological samples.

By capturing, integrating, and analyzing large amounts of clinical and biological information, at the level of the cell, gene, protein, and low-molecular-weight organic molecule, SurroMed is able to identify useful biological markers and provide a detailed picture, or “fingerprint,” of pathways involved in disease and therapeutic response.

SurroMed analyzes samples in its Biomarker Discovery Laboratory under quality control procedures designed to ensure sample accountability and data integrity. The firm’s core technologies include proteomics and metabolomics, a proprietary micro-volume laser scanning cytometry system, and informatics.

“SurroMed’s name was derived at its founding by surrogate markers in medicine,” Schulman says. “There is a paucity of good biomarkers for complex diseases and, in the rush to incorporate biomarkers for improved drug development, pharma often skip the discovery step and go with putative biomarkers that are best guesses.

“Our approach to proteomics and metabolomics includes mass spectrometry-based methods for differential analysis and broad profiling of proteins and low-molecular-weight organic molecules. It provides high-sensitivity, linear signal response, and high reproducibility, enabling detection and quantification of small biological changes.

“The work we are doing is part of the realization that abnormalities are going to exist and discovery of these changes is critical, an integral part of doing work in the biomarker field.”

Schulman also adds that the biomarker assets of SurroMed have been acquired by PPD (Morrisville, NC), a major clinical research organization. “The acquisition is a validation of the importance of biomarker discovery and implementation to the suite of existing drug development services and an indication that biomarkers have come of age,” Schulman says.

“The PPD parent adds stability to biomarker discovery services for the industry since the ultimate goal of biotechs doing proteomics or metabolomics is to eventually become a diagnostics company or a pharma, and thus such services terminate when the biotech goes under or successfully converts itself into a nonservice business.

PPD has a dual strategy in this acquisition. First, it can provide biomarker discovery, validation, and implementation services to pharma and biotech that have been asking for this to be included in clinical trials.

Second, PPD partners compounds from pharma and biotech, sharing the risk of their development, and is using its SurroMed unit as an internal biomarker discovery team that will help them better develop their partnered compounds.”

Computer-Assisted Drug Development

The pharmaceutical world agrees that better development decisions need to be made faster. Research and development departments are under continual pressure to produce rapid results in the form of marketable drugs.

To that end, many companies are integrating information collected in preclinical toxicokinetic, pharmacokinetic, pharmacodynamic, and metabolism studies to create a knowledge-based drug development framework in humans.

Xiao Feng, senior scientist, global preclinical development at Johnson & Johnson Pharamaceutical Research & Development (J&JPRD; Raritan, NJ), says, “The search for biomarkers has to be a large-scale collaborative effortno one group can get this done.”

Hans Winkler, head of functional genomics at J&JPRD in Beerse, Belgium, adds, “We tend to do global profiling for biomarkers using a combination of higher throughput technology and bioinformatics. We’re set to cover the whole spectrum from lead optimization to pharmacokinetics and pharmacodynamics.”

The team at J&JPRD in Beerse conducted an MTB mode of action study for their tuberculosis (TB) compound (R207910). J&JPRD sought the new antituberculosis compounds by selecting prototypes of different chemical series and testing them for inhibition of growth of mycobacterium smegmatis, which was used for experimentation because of safety issues.

R207910 is active against Mycobacterium tuberculosis and other species of Mycobacteria, including multidrug resistant strains. However, it is not active against a range of other bacteria. The mode of action of this investigational drug was discovered by comparative genomics.

The experimental approaches to discover the mode of action of R207910 included drug cross-resistance and growth inhibition studies with radioactively labeled metabolites.

The genomics approaches included: comparing the common genes of the sensitive bacteria with the common genes of the resistant bacteria; examining gene expression of sensitive Mycobacterium species to resistant mutants in the presence of the drug; and sequencing complete genomes of sensitive and resistant Mycobacterium species and identify resistance-conferring mutations.

“I think one thing we can all agree on is that the heightened attention being given to biomarkers is driven by the confluence of new technology and resources, and the drive by pharmaceutical companies to make better decisions, sooner,” says Christopher J. Godfrey, senior pharmacometrician, clinical pharmacology at Vertex Pharmaceuticals (Cambridge, MA).

Vertex has a broad-based drug discovery effort targeting the human protein kinase family, which consists of approximately 500 members. Protein kinases are enzymes that play a key role in transmitting signals between and within cells.

Kinases exert their effect by phosphorylating other proteins, which then become activated and perform a specific function. Kinase activity has been implicated in most major diseases, including cancer and autoimmune, inflammatory, cardiovascular, metabolic, and neurological diseases. Thus, kinases can be ideal targets for therapeutic intervention.

In November, Novartis Pharma selected Vertex’ small molecule protein kinase inhibitor, VX-322, for clinical development. VX-322 is a novel compound targeting the key mechanisms implicated in leukemia and other cancers. Vertex and Novartis collaborate on the discovery, development, and commercialization of small molecule drugs directed at protein kinases.

In June 2004, Vertex and Merck entered a global collaboration to develop and commercialize VX-680, a small molecule inhibitor of Aurora kinases, for the treatment of cancer. Aurora kinases are three closely-related proteins required in rapidly dividing cells.

Inhibition of Aurora kinase activity with a small molecule may provide a means of slowing or reversing the uncontrolled cell growth observed in cancer. VX-680 is currently being evaluated in cancer patients as part of a Phase I study initiated in January 2005.

Vertex has advanced drug discovery efforts targeting several other kinase targets, including targets that play a role in the development and progression of cancer, inflammation, and autoimmune disease.

Vertex is also conducting a broad-based drug discovery program targeting the ion channel family. Ion channels are a gene family of more than 650 proteins that act as cellular gatekeepers, controlling the flow of ions across cell membranes.

The ion channel target family contains numerous druggable targets representing potential intervention paths for indications including cystic fibrosis, pain, and inflammatory, cardiovascular, and metabolic diseases.

Existing therapies such as amlodipine and nifedipine, calcium channel blockers for the treatment of hypertension, and lamotrigine and carbamezepine, sodium channel inhibitors for the treatment of epilepsy, provide a strong basis for developing drugs targeting ion channels.

Vertex’ ion channel research extends across several ion channel subfamilies, including sodium and calcium channels, and is principally focused on the design and development of small molecule drugs for the treatment of pain and cystic fibrosis. Specific sodium channels in peripheral nerves are particularly attractive targets for novel pain treatments.

In 2004, Vertex advanced a novel drug candidate, VX-409, a selective sodium channel inhibitor, into preclinical development for the treatment of pain. Ion channel modulators also could be important therapeutic agents for cystic fibrosis, since the primary genetic defect responsible results in a defective ion channel.

Vertex is collaborating with the Cystic Fibrosis Foundation in targeting this ion channel, the cystic fibrosis regulator protein (CFTR). The hope is that a drug that increases the activity of CFTR will be beneficial in lessening the buildup of mucous in the airways that otherwise leads to chronic infection and inflammation and progressive lung deterioration.

“We can generate significant amounts of biomarker data, which is very useful, but researchers need to be able to integrate this information into a coherent package to best inform decisions,” Godfrey says.

“Developing appropriate models for biomarker responses allows us to interpret that data and create knowledge, which is then converted to understanding when individual models can be integrated into one system. The integrated model can put responses into context and help us see higher-level implications.”

Godfrey adds, “Simulation is the critical tool that converts our understanding of the system into wisdom. It enables us to ask the What if?’ questions to test our system and see the results of our decisions. This is the role our research plays in capitalizing on biomarkers.”


Biosite (San Diego) has developed a proprietary process utilizing phage display of antibodies that enables the selection and production of antibodies more rapidly and efficiently than is possible using hybridoma technology. The technology enables the high throughput generation of custom Omniclonal antibody libraries containing genes encoding antibodies specific to the target analyte.

Omniclonal antibodies produced from such libraries can contain thousands of different antibodies that bind to a target analyte with high affinity.

Monoclonal antibody candidates can be rapidly selected from an Omniclonal antibody library and produced in quantities sufficient for product development. During the course of product development, unexpected antibody cross reactivities often require additional selection of antibodies to improve the assay specificity.

Unlike hybridoma technology, Omniclonal antibody libraries can rapidly provide additional antibody candidates in these circumstances.

Biosite Discovery was launched as a research institute within the company in 1999. It seeks to discover whether or not protein levels correlate to diseases or disease states. The institute’s marker mining effort is a process by which analysis is conducted on both known disease markers and potential markers in order to determine their utility for diagnostic applications.

If the diagnostic utility of a protein marker is confirmed, it will then be reviewed for commercial potential. Through their internal research program, Biosite actively accumulates targets with suspected association to targeted disease states.

“Our stroke marker research project, which was conducted in conjunction with Duke University, was the first program for Biosite Discovery,” says Gunars Valkirs, vp, Biosite Discovery and co-founder of Biosite.

“Another aspect of our Discovery program is external discovery, which includes partnerships with pharmaceutical companies. In exchange for providing high affinity human or murine antibodies, we gain certain diagnostic rights to partners’ drug targets.

“In addition, we are also seeking to acquire diagnostic rights to targets. Under normal circumstances, it might cost $500,000 to go after one marker. But we can actively pursue 70 markers through this program at literally 1/20 of the cost.”

“We think we’ve discovered a panel of multiple markers we seem to need to aid in the assessment and diagnosis of stroke,” says Valkirs. “We have a device platform, antibody platform, and the MultiMarker Index, which is a proprietary algorithm that measures each analyte and calculates a single index result.”

Biosite’s molecular biology capabilities include the cloning and identification of specific proteins useful in the development of immunoassays. They developed proprietary expression vectors that enable the production and purification of these proteins for the development of antibodies and for use as calibrators and controls in their immunoassay products.

Database Mining

“Strictly speaking, we are neither a diagnostics nor a discovery company,” says Eric Kaldjian, M.D., senior scientific director of pharmacogenomics and oncology at Gene Logic (Gaithersburg, MD).

“But what we do is provide gene expression information that can be used for not only drug discovery, but for diagnostics and identification of biomarkers.” Gene Logic has created gene expression databases with over 30,000 human and animal tissue samples for investigation of both disease and toxicity.

“When implementing an efficacy biomarker in the clinic, you must ask whether the result will be meaningful,” Dr. Kaldjian adds. “A phenotypic biomarker, such as the expression level of a target, marks the presence of baseline characteristics that may predict clinical response.

Dynamic biomarkers, ones that demonstrate change after exposure to a therapeutic, can give information on appropriateness of dosing and, perhaps even more importantly, on whether hitting the target is having a meaningful downstream effect. Target interruption is necessary, but may not be sufficient, for biological response.”

Clinical context validation of biomarkers is a critical step. “We offer a set of tools that allow you to more effectively develop your drug therapy,” says Dr. Kaldjian.

“In exploratory development, you want to have confidence early on that your compound is doing what it’s designed to do. Discovery and development scientists have the mandate to understand how the science works, how the compound works, and to make sure that both work.”

Gene Logic’s human disease database allows rapid and early investigation of molecular differences between disease states for biomarker discovery. In addition, it provides an assessment of the prevalence and expression level of biomarkers within specific human populations and across normal tissues. This guides how a biomarker can be used for patient selection in clinical studies.

Gene Logic’s toxicogenomic database contains data from a variety of treatments with known toxicants in cell and tissue samples from various species, which include human, rat, and dog. They provide a resource to aid the process of finding safety biomarkers. The genomic data can be mined to provide toxicological guidance to how in vivo studies are to be carried out.

“Of course safety is the first consideration when looking at any treatment,” adds William Mattes, senior scientific director of toxicogenomics. “Efficacy is important, but that doesn’t matter if the product isn’t safe.”

The goal in safety biomarker discovery is an end point that can be measured noninvasively or in accessible tissue, before actual damage occurs, is specific to the tissue or injury, can be applied preclinically and clinically, and is not confounded by normal variation in the human population.

Again, knowledge of human population expression characteristics is essential. “I’ve presented this idea at a number of conferences,” Mattes says. “Am I setting the bar too high? By some opinions I am, but ideally this is the kind of information you need to see if the biomarker is going to fly.”

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