Josip Blonder, M.D., senior research scientist and head of quantitative proteomics in the laboratory of proteomics and analytical technologies at the NCI, spoke at “Biomarker Assay Development” about cancer biomarker discovery in the context of personalized medicine. “The major goal of oncoproteomics is the discovery of clinically relevant molecular biomarkers. So far, the translation of proteomic assays to applicable diagnostic and/or prognostic tests in clinical oncology and personalized medicine has been disappointing. We developed an innovative proteomic platform for cancer biomarker discovery that is amenable to personalized medicine since all analyzed specimens were obtained from a single patient diagnosed with cancer.”
Recent advances in MS-based proteomics have raised expectations for the discovery of novel cancer biomarkers, Dr. Blonder observed. A protein or panel of proteins that can be detected in the patient’s blood or other easily obtainable body fluids in the early stages of cancer would represent a “prototypical cancer biomarker or biomarkers.” But the straightforward analysis of human plasma has proven to be a daunting challenge.
The complexity of plasma, Dr. Blonder notes, is exemplified by the large number of protein species exhibiting a wide dynamic range of concentrations. He cites findings reported by the Human Proteome Organization indicating that the dynamic range of plasma protein concentration is in the order of 1010, while the current state-of-the-art MS instrumentation can only measure over a dynamic range of approximately 104 to 106.
To overcome the analytical obstacles, Dr. Blonder’s group used “subtractive proteomics” coupled with protein depletion to remove the high- and mid-level proteins. The approach relies on concurrent profiling of peripheral plasma specimens obtained prior to surgery along with subtractive analysis of non-tumorous and tumorous tissue samples procured during the surgical intervention.
Multidimensional shotgun proteomic analysis and rigorous bioinformatics data processing were then employed to narrow the selection/panel of potential cancer biomarker proteins. The proteins derived from tumorous tissues that were detected in peripheral blood are currently under cross-validation using orthogonal analytical approaches to confirm that they can be used successfully as cancer biomarkers in personalized medicine.