The peptidome should be a fertile field for isolation of new biomarkers, but progress has been slow in this area. This situation may now be changing, according to Paul Tempst, Ph.D., professor and director of the Protein Center at the Memorial Sloan-Kettering Cancer Center.
“By correlating the proteolytic patterns with disease groups and controls, we have shown that exopeptidase activities contribute to the generation of not only cancer-specific but also cancer type specific serum peptides. So there is a direct link between peptide marker profiles of disease and differential protease activity.” For this reason Dr. Tempst argues that “the patterns we describe may have value as surrogate markers for detection and classification of cancer.”
To investigate this avenue, Dr. Tempst and his colleagues have followed the relationship between exopeptidase activities and metastatic disease.
“We monitored controlled, de novo peptide breakdown in large numbers of biological samples using mass spectrometry, with relative quantitation of the metabolites,” Dr. Tempst explains. This entailed the use of magnetic, reverse-phase beads for analyte capture and a MALDI-TOF MS read-out.
“In biomarker discovery programs, functional proteomics is usually not pursued,” says Dr. Tempst. “For putative biomarkers, one may observe no difference in quantitative levels of proteins, while at the same time, there may be substantial differences in enzymatic activity.”
In a preliminary prostate cancer study, the team found a significant difference in activity levels of exopeptidases in serum from patients with metastatic prostate cancer as compared to primary tumor-bearing individuals and normal healthy controls. However, there were no differences in amounts of the target protein, and this potential biomarker would have been missed if quantitative levels of protein had been the only criterion of selection.
Ironically, many studies of correlations of enzyme activity and cancerous states were carried out long ago, in the 1950s and 1960s. Acidic phosphatase activity was used as a blood-based marker for prostate cancer long before the PSA test was put into general use in the 1980s.
“These older observations on enzymes, including aminopeptidases caught our attention and convinced us that we were on solid ground,” Dr. Tempst states.
It is frequently stated that “practical fusion energy is 30 years in the future and always will be.” The same might be said of functional, practical biomarkers that can pass muster with the FDA. But splice variation represents a new handle on this vexing problem. It appears that we are seeing the emergence of a new approach that may finally yield definitive diagnostic tests, detectable in serum and urine samples.