Inflammation is a somewhat generic sign of something gone wrong, and its markers are often picked up when looking for more specific indicators of disease.
Samir Hanash, M.D., Ph.D., searches for biomarkers that can be used to identify solid tumors from blood. To do this, the program head of molecular diagnosis at Fred Hutchinson Cancer Research Center starts with a host of different samples including mouse models, human tumor cell lines, and patient blood collected prior to and at diagnosis.
Samples are fragmented into a hundred separate fractions, which are then separately analyzed by mass spectrometry. Cases and controls are isotopically labeled and mixed together to determine the ratio of case to control, Dr. Hanash explained. “It’s the combination of isotopic labeling, extensive fractionation, the use of high-resolution MS that is allowing us to dig very deep into the plasma proteome to pull out markers.” He added that it’s “not unlike deep genome sequencing in terms of strategy but applied to proteins.”
Doing such analyses reveals different levels of specificity for biomarkers. There are markers of an acute-phase response (inflammation) and those common to epithelial tumors that don’t distinguish lung from breast, Dr. Hanash pointed out. “Then there are markers that are more restricted on an organ-type basis, and then markers that are more restricted based on molecular subtypes within that organ type,” such as the EGFR mutation found in some lung cancers.
One of the strategies Dr. Hanash and his team use is to turn on an oncogene in a transgenic mouse and periodically sample its blood for the appearance of proteomic markers that can be used to identify early- and advanced-stage disease. These can then be used to identify candidate human homologues that may appear prior to any clinical symptoms.
Once candidate biomarkers are found, the researchers try to establish a mechanistic link between what they are seeing and the tumor that they’re looking for markers for: “Is this a something that the tumor cell is producing? And if the tumor cell is producing it, why is it producing it? What’s regulating it, and how it is related to the pathogenesis of the cancer that we’re finding markers for?” Dr. Hanash asked.
Although Dr. Hanash’s discovery of the biomarkers is done by sorting through terabytes of MS data, the ultimate goal is to see these as part of a routine check-up—a blood test for common cancers using standard lab assays. That may be pretty far down the road for an average patient, he admitted.
The Social Network
A little closer to the horizon, Avantra Biosciences recently established a pair of collaborations aimed at allowing clinicians to use a rapid assessment of biomarkers to make treatment decisions for their patients. While these are currently for research use only, the goal is ultimately to obtain regulatory approval to move the strategies to the clinic.
In the first of these, Avantra’s self-contained, automated combination Q400 Biomarker Workstation and Angio Qx Biochip Immunoassay—which the firm says can provide quantitative protein biomarker results for ten analytes in less than an hour with minimal preparation time—has been paired with TGen Drug Development’s suite of molecular analysis tools.
In the second, Avantra teamed up with TGen spin-off MedTrust Online, a professional online social network-like community of cancer doctors. The collaboration will allow MedTrust’s users early access to the list of genes and gene products that Avantra has developed as potential biomarkers.
“MedTrust will encourage discussion by specific users within our 11,000+ oncologist user base and help determine whether or not there is strong interest for utilizing those biomarkers from a clinical perspective,” says Christopher Yoo, Ph.D., MedTrust’s CEO.
“And from those discussions we can further understand how aware doctors are that these markers are important, whether there’s good understanding of how to assess those markers, and whether there is a strong market need for those markers to be assessed clinically.”