Targeted Proteomics Pipeline Reveals Potential Biomarkers for the Diagnosis of Metastatic Lung Cancer in Pleural Effusion

The ability to discriminate lung
cancer malignant pleural effusion
(LC-MPE) from benign pleural effusion has profound implications for
the therapy and prognosis of lung cancer. Here, we established a pipeline
to verify potential biomarkers for this purpose. In the discovery
phase, label-free quantification was performed for the proteome profiling
of exudative pleural effusion in order to select 34 candidate biomarkers
with significantly elevated levels in LC-MPE. In the verification
phase, signature peptides for 34 candidates were first confirmed by
accurate inclusion mass screening (AIMS). To quantify the candidates
in PEs, multiple reaction monitoring mass spectrometry (MRM–MS)
with stable isotope-labeled standards (SIS) peptides was performed
for the 34 candidate biomarkers using the QconCAT approach for the
generation of the SIS peptides. The results of the MRM assay were
used to prioritize candidates based on their discriminatory power
in 82 exudative PE samples. The five potential biomarkers (ALCAM,
CDH1, MUC1, SPINT1, and THBS4; AUC > 0.7) and one three-marker
panel
(SPINT1/SVEP1/THBS4; AUC = 0.95) were able to effectively differentiate
LC-MPE from benign PE. Collectively, these results demonstrate that
our pipeline is a feasible platform for verifying potential biomarkers
for human diseases.