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).

胰腺导管腺癌（Pancreatic ductal adenocarcinoma, PDAC）缺乏可靠的诊断生物标志物，其主要原因为该病起病隐匿且常于晚期才被检出，进而导致患者5年生存率极低。及时筛选可用于早期诊断的生物标志物至关重要。癌细胞会呈现出驱动疾病特征的独特蛋白质调控变化，对胰腺导管腺癌各亚型的这类特征进行表征，或可为疾病进展研究提供新的见解。

本研究采用基于质谱法（mass spectrometry, MS）的无标记定量（label-free quantitative, LFQ）蛋白质组学方法，对胰腺导管腺癌细胞系分泌组（secretome）中的节律调控蛋白进行了图谱分析。

无标记定量分析揭示了节律性的蛋白质调控模式，反映了胰腺导管腺癌细胞内生物学过程的时序调控特性。上调通路涵盖信号转导、糖酵解、血管生成与蛋白质合成，提示肿瘤细胞的代谢与增殖活性增强；下调的免疫通路则提示存在潜在的免疫调节作用。比较分析还发现了亚型特异性的调控模式：拟间质亚型的代谢与细胞外基质（extracellular matrix, ECM）重塑相关蛋白水平更高，而经典亚型的细胞外基质降解蛋白水平更高，这与已知的表型差异相符。

本研究结果证实，节律调控蛋白可作为胰腺导管腺癌潜在的亚型特异性标志物，为后续验证研究奠定了基础。该质谱蛋白质组学数据可通过蛋白质组交换联盟（ProteomeXchange Consortium）获取（PRIDE: PXD054693）。