Blood-based protein biomarkers would make a significant difference in clinical practice. Even though proteomics is expected to play a leading role in clinical biomarker discovery, translation of MS-based assays into clinical diagnostic tests has been lagging.
The human proteome content varies significantly even within a single individual based on food intake, rest, and other physiological factors. Finding differences between blood proteomes of healthy individuals and cancer patients that could indicate the presence of cancer rather than merely a physiological bias has been problematic.
The strategy proposed by Josip Blonder, M.D., head of clinical proteomics at the National Cancer Institute, utilizes combined plasma/tissue proteome analysis from a single patient. This strategy relies on the assumption that salient proteins present in the tumor are detectable in blood. A three-way comparison of plasma, tumor, and normal tissue would help to narrow down the selection of relevant biomarker candidates.
Comparison of samples from the same patient minimizes the effect of normal biological variances. First, Dr. Blonder’s team identified tumor-specific proteins by discounting common proteins found in renal cell carcinoma (RCC) and adjacent normal tissue. Next, the tumor-specific proteins were compared with the plasma, looking for overlapping sets.
“This strategy is not devoid of typical proteomics deficiencies, such as the mismatch between the dynamic ranges of MS instrumentation and the human proteome. This issue is significantly alleviated, however, by the use of shotgun proteomics coupled with high-resolution and high-accuracy mass measurements,” says Dr. Blonder.
“Analysis resulted in the identification of 202 proteins that belong only to the tumor. This set was compared with 179 proteins from plasma, revealing 8 overlapping proteins, whose spectral count was higher in the tumor than in the plasma.” All eight proteins were specific to the tumor tissue, and four of these proteins were cross-validated in the blood of this patient and in the blood of four additional patients diagnosed with RCC.
“This pilot study was a proof of concept demonstrating that the comparative analysis of blood and tissue may result in the identification of tumor proteins in blood and may yield a realistic biomarker panel,” continues Dr. Blonder. “We hope this schema will be adopted and popularized by other laboratories.
“I do believe that current state-of-the-art clinical proteomics has matured enough for comprehensive and coordinated effort focused on creation of the cancer proteome atlas by relying on shotgun proteomics to sequence human cancers individually. The resulting atlas will be used as a complement to the cancer genome atlas and accelerate our understanding of the molecular basis of cancer.”