ViroLogic (www.virologic.com), which recently acquired Aclara Biosciences, is taking a different approach by identifying dimerization, which indicates downstream pathway activation, as a key biomarker for cancer activity.
According to Sharat Singh, Ph.D., CTO, the eTAG system correctly differentiates responders from non-responders to Herceptin treatment. Results from a 13-patient trial indicate it may be more accurate than DakoCytomation's Hercep-Test (which identifies the presence of the Her2 receptor) in predicting response to Herceptin treatments. A larger, confirmatory study is being planned.
Unlike phosphorylation, which companies initially considered promising, protein complexes are stable in paraffin-embedded tissues, allowing eTAG to identify dimerization and thereby identify activated signaling pathways in tumor tissues. The eTAG System is focusing on the HER and VEGF pathways.
More than 600 tags can be attached to various analytes and then separated and analyzed by capillary electrophoresis.
According to Dr. Singh, "The multi-label eTag System is an extremely sensitive assay method for identifying protein or pathway activation in FFPE samples. Along with identifying responders to Herceptin in breast cancer, the eTag System is being used to identify responders to targeted therapies in non-small cell lung cancer, head and neck cancer, and colorectal cancer. Results are extremely promising."
Agendia (www.agendia com) used the 20,000 samples and 20 years of research from the Netherlands Cancer Institute/ Antoni van Leeuwen-hoek Hospital in Amsterdam in developing the MammaPrint gene expression profiling service.
"We determined that 231 genes were linked to significant differences in expression related to metastasis," Bernhard Sixt, Ph.D., president and CEO, says. "Of those we looked at the best predictors a 70 gene set. It was an unbiased way to look at it as the analysis wasn't tethered to known function. In fact, half the genes had no known function at the time. Science doesn't really understand the complexity of tumors, and diagnostics should be hanged by it."
MammaPrint uses customized DNA microarray chips for gene expression profiling to determine the chance of recurrence of breast cancer in women under age 55 with lymph node negative tumors and either positive or negative estrogen receptor status. The chips include several hundred normalization genes, which are used to adjust the signal strength of the two fluorescent labels, and negative control genes to avoid artifacts. Because each chip contains three identical sets of 70 genes, one chip enables three independent measurements.
The prognostic test is for all breast cancer subtypes. It identifies not only high-risk patients who were undetected by conventional diagnostic tests, but can further identify "the very, very high-risk patients," Dr. Sixt says.
In drug development, Dr. Sixt notes that MammaPrint can identify the population subset for which particular drugs would elicit responses. "We have trials under way for high-risk groups for drug development, involving 5,000 patients," he says.
MammaPrint has been validated in more than 300 patients and is available globally. It became available in the U.S. in January, through the Molecular Profiling Institute in Phoenix.
AutoGenomics (www.autogenomics.com) is focusing on developing near-patient prognostic tests for breast and cervical cancers, the pharmacogenomics tests CYP 450, 2D6, 2C9, 2C19, and tests for cystic fibrosis, cardiovascular diseases, and bleeding disorders. The company also is developing tests for tumor suppressors, response modulators, apoptotic modulators, and angiogenesis and methylation markers. "Eventually, all these markers could go on one chip," according to Fareed Kureshy, CEO.
Using BioFilmChip microarrays, up to 48 tests can be performed simultaneously on the Infiniti genomic and proteomic analysis platform. Most proteomic tests can be performed in less than one hour, and genomic tests in less than two hours, Kureshy says.
"We envision a signature of markers that will include DNA, DNA methylation, and proteins and will provide a better profile for diagnosis, prognosis, and management of disease states."