Differential exoprotease activities confer tumor-specific serum peptidome patterns

TLDR

Mass spectrometry has revealed distinct serum polypeptide patterns that correlate with clinical outcomes, but broader biomarker use awaits detailed component sequencing and mechanistic understanding. The authors optimized peptide extraction and MALDI‑TOF MS to identify a limited serum peptide signature that accurately distinguishes three solid tumor types from non‑cancer controls. The 61 identified signature peptides, largely produced by exopeptidase activity, cluster into cancer‑specific patterns that enable highly accurate classification of tumor types and suggest a direct link between protease activity and peptide biomarkers, offering clinical utility and guiding future discovery.

Abstract

Recent studies have established distinctive serum polypeptide patterns through mass spectrometry (MS) that reportedly correlate with clinically relevant outcomes. Wider acceptance of these signatures as valid biomarkers for disease may follow sequence characterization of the components and elucidation of the mechanisms by which they are generated. Using a highly optimized peptide extraction and matrix-assisted laser desorption/ionization–time-of-flight (MALDI-TOF) MS–based approach, we now show that a limited subset of serum peptides (a signature) provides accurate class discrimination between patients with 3 types of solid tumors and controls without cancer. Targeted sequence identification of 61 signature peptides revealed that they fall into several tight clusters and that most are generated by exopeptidase activities that confer cancer type–specific differences superimposed on the proteolytic events of the ex vivo coagulation and complement degradation pathways. This small but robust set of marker peptides then enabled highly accurate class prediction for an external validation set of prostate cancer samples. In sum, this study provides a direct link between peptide marker profiles of disease and differential protease activity, and the patterns we describe may have clinical utility as surrogate markers for detection and classification of cancer. Our findings also have important implications for future peptide biomarker discovery efforts.