Circadian-rhythm-based dynamics of the secretome in molecular subtypes of pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) lacks a reliable diagnostic biomarker, largely due to its asymptomatic onset and frequent late-stage detection, resulting in a poor 5-year survival rate. Identifying biomarkers for timely diagnosis is critical. Cancer cells display distinct protein regulation changes that drive disease hallmarks, and characterizing these across PDAC subtypes may provide insights into disease progression. In this study, a label-free quantitative (LFQ) proteomics approach using mass spectrometry (MS) was employed to profile circadian rhythm-regulated proteins in the secretome of PDAC cell lines. LFQ analysis revealed rhythmic protein regulation patterns, reflecting temporal control of biological processes in PDAC. Upregulated pathways included signal transduction, glycolysis, angiogenesis, and protein synthesis, indicating enhanced metabolic and proliferative activity. Downregulated immune pathways suggested potential immune modulation. Comparative analysis revealed subtype-specific patterns: the quasi-mesenchymal subtype exhibited higher levels of metabolic and extracellular matrix (ECM) remodeling proteins, while the classical subtype showed higher levels of ECM-degrading proteins, consistent with known phenotypic differences. These findings highlight rhythmically regulated proteins as potential subtype-specific markers in PDAC and provide a basis for future validation studies. Mass spectrometry proteomics data are available via the ProteomeXchange Consortium (PRIDE: PXD054693).