Comprehensive Plasma Profiling in NSCLC Patients Undergoing IO- and Chemotherapy Identifies Potential Proteomic Signatures for Progression-Free Survival

In NSCLC, the identification of circulating predictive biomarkers is critical to improve patient stratification. Circulating biomarkers have the advantage of accessibility of samples but challenges arise in detecting disease-relevant biomarkers in plasma, where low-abundance circulating analytes are often obscured by highly abundant proteins. This underlines the need for highly sensitive, reproducible assays to detect subtle changes. Therefore, developing a sensitive, reproducible method for biomarker discovery in plasma could significantly enhance clinical outcomes for patients with NSCLC.

To address this need, we developed a novel workflow combining particle enrichment (P2) and quantitative mass spectrometry (DIA-MS). We deployed this method on plasma samples from a multicentric phase II clinical trial (SAKK17/18) in patients with NSCLC (Fig. 1). Longitudinal plasma samples were collected at baseline (n=33) and at two post-dose time points (C1D8, n=31 and C2D1, n=31). The samples were subjected to the developed P2 workflow and unbiased mass spectrometry analysis (Fig. 2), leading to the quantification of 9283 proteins across all 95 samples. With this depth at plasma proteome profiling, we could cover up to 12 orders of magnitude, detecting low-abundance tissue/cell proteins from leakage events as well as proteins from extracellular vesicles.