Biomarkers as Companion Diagnostics Tools to Determine Therapy/Drug Efficacy

Biomarker discovery has been a major by-product of genomic sequencing since the completion of the Human Genome Project. For cancer disease, development of biomarkers for early detection and screening has been the highest priority at Early Detection Research Network (EDRN) in the National Cancer Institute (NCI).

Diagnostic measurement of cancer disease progression is essential to successful cancer disease management. The importance of biomarker to drug development has recently gained momentum, with the realization that integration of biomarkers through the different phases of drug development can yield safer drugs with enhanced therapeutic efficacy in a cost-effective manner. Good biomarker development potentially can help pharmaceutical companies to find targets in discovery much faster and to design clinical trials in a more effective and efficient way.

Meanwhile, personalized healthcare (PHC) is being driven by scientific and technological innovation and better understanding of disease heterogeneity. PHC is seen as the future of medicine, especially in oncology. Laboratory test that predicts individual response to therapy is now available, permitting the choice of the right drug for the right patient. The trial and error approach is being eliminated. Thus PHC will increasingly drive drug development strategy but strong industry buy-in is necessary. Unfortunately, the process involved in identifying and validating biomarkers, which are integral tools in the development of PHC and developing a commercial diagnostic test is lengthy with a low success rate. Examples of commercial biomarker tests include Oncotype DX biomarker test and MammaPrint test for breast cancer.

PHC means drugs and drug doses are made safer and more effective because they are chosen according to an individual’s genetic makeup. Targeted therapy is a familiar component of PHC. Examples of the five US FDA approved anti-cancer drugs that target mutation genes include:

1. Herceptin, which is a humanized antibody approved for treatment of HER2-positive metastatic breast cancer,

2. Gleevec, a protein tyrosine kinase inhibitor that is intended for patients with Philadelphia chromosome-positive chronic myeloid leukemia (CML),

3. Erbitux, an epidermal growth factor receptor (EGFR) inhibitor for colorectal cancer patients and Iressa which is an EGFR inhibitor indicated for patients diagnosed with non-small cell lung cancer, and

4. Tarcevas, which is also an EGFR inhibitor, is currently indicated for the treatment of patients with advanced or metastatic non-small cell lung cancer.

Targeted dosing is also a component of PHC. Examples include irinotecan, a chemotherapeutic drug for colorectal cancer and warfarin. Dosing could be guided by knowledge of CYP2C9 and VKORC1 genotypes, and 6-mercaptopurine (6-MP), a chemotherapeutic drug used in acute lymphoblastic leukemia where dosing should be based upon the thiopurine methyltransferase (TPMT) genotype of the patient.

Much of the inter-individual variability in drug response is attributable to the presence of single nucleotide polymorphisms (SNPs) in genes encoding drug-metabolizing enzymes and drug transporters. The pharmacogenetics of these drug-metabolizing enzymes in the Asian populations is different from those in the Caucasian and African populations. Conceptually dose requirements of certain drugs may not be optimal for Asian populations.

Companion diagnostics Recent therapeutic advances are based on agents that specifically target the products of the genes mutated in cancer cells. Development of companion diagnostics tests for these agents can simplify the drug discovery process, make clinical trials more efficient and informative, and be used to individualize the therapy of cancer patients. Three requirements for effective companion diagnostic tests are: 1. Availability of patient sample material suitable for testing, 2. A set of mutations that are predictive of a therapeutic response, and 3. An accurate and cost-effective technique for identifying mutations. Current methods used in companion diagnostics include: Immunohistochemistry to detect target protein expression, Cytogenetics to detect translocations and amplifications in mitotic cells, Fluorescent in situ hybridization (FISH) to detect translocations and amplifications, quantitative PCR (qPCR) to detect gene translocations or amplifications, DNA sequencing to sequence the entire PCR product, indirect mutation analysis methods, which include single-stranded conformation analysis, high-performance liquid chromatography, denaturing gradient gel electrophoresis or mismatch cleavage, mutation-specific assays which are hybridization-based methods and include allele specific amplification, single base extension, oligonucleotide ligation, and microarrays with labeled DNA or RNA from clinical specimens which are hybridized to thousands of genes. Method selection for companion diagnostics depends on type of mutations to be detected, type of samples and cost effectiveness. Direct or indirect sequencing methods are for target gene with multiple mutations. Mutation-specific method is for identification of predefined mutations. FISH or qPCR is for increased copy number of the target gene, direct sequencing is for primary or micro-dissected tumor. Mutation-specific assays or indirect mutation analysis methods are for clinical samples containing non-neoplastic cells. Cost effectiveness is also an issue, although companion diagnostic testing will generally constitute only a small fraction of the total cost of treatment with a mutation targeted agent. Companion diagnostics are now an essential component of the management of CML patients. The Gleevac test is a companion diagnostic test used to identify specific gastrointestinal stromal tumors (GIST) and chronic myeloid leukemia (CML). After the test confirms a positive result, the drug is given to the patient. Gleevec has provided the prototypical example of the principle that a targeted therapy should be gene specific rather than disease specific. Although Gleevec is the prototype for targeted therapy with small molecules, Herceptin is actually the first clinically approved drug directed against a mutated target. Herceptin is a humanized monoclonal antibody (mAb) generated from a mouse mAb reactive with HER-2. The agent was developed after it was recognized that HER-2 gene amplification was both a prognostic marker for breast cancer and a target for therapy. Approximately 25% of breast cancer patients harbor HER-2 amplification and this is associated with poor prognosis. With the use of Herceptin and the availability of companion diagnostic tests, this genetic alteration has allowed certain patients with HER-2 amplification to have better prognoses than patients without amplification. For measuring amplification of HER-2, the US FDA has approved both immunohistochemistry (IHC) and in situ hybridization (ISH)-based tests to determine the status of HER-2. Herceptin is a model for the importance of pharmacogenomics. It was not initially developed using genetic testing but it has come to achieve exciting survival benefits via the utilization of genetic testing. Herceptin is effective in the 20-30% of breast cancer patients who over-express HER2/neu, a protein that makes breast cancer cells grow quickly. Herceptin has high efficacy when patients are screened for the presence of HER2/neu. In April 2007, the European Union approved for Herceptin in combination with hormonal therapy (aromatase inhibitor) for the treatment of patients with advanced breast cancer that is both HER2-positive and hormone receptor-positive. This is the first combination of targeted therapies to be approved for the treatment of breast cancer.