Integrated DIA proteomics of tissue and exudate reveals screening markers for early detection of ulcerative colitis and colorectal cancer.

BACKGROUND

Early detection biomarkers are needed to support the timely detection and monitoring of ulcerative colitis (UC) and its potential association with colorectal cancer (CRC). We used Data-Independent Acquisition (DIA) proteomics on paired colorectal tissue and exudate samples to define the pathway changes and identify serum-accessible markers.

METHODS

We employed DIA-based mass spectrometry to profile the proteomes of paired tissue and exudate samples from patients with UC and CRC. Differentially expressed proteins (DEPs) were analyzed using Gene Ontology (GO), KEGG, and Gene Set Enrichment Analysis (GSEA). Four candidate biomarkers, CDA, REG4, LCN2, and TNS1, were validated in serum samples using ELISA and receiver operating characteristic (ROC) curve analysis.

RESULTS

DIA proteomic analysis of colorectal tissues and exudates identified >7000 proteins and revealed profound microenvironmental remodeling associated with UC and CRC. Heatmap clustering of the top 50 features showed consistent change patterns across comparisons, supporting the robustness of the differential signatures. DEPs in the UC group were enriched in crucial biological processes (BPs), including oxidative phosphorylation, the TCA cycle, autophagy, lysosomes, and immune dysregulation. The DEPs ih the CRC group were clustered into many vital BPs, such as glycolysis, focal adhesion, ECM remodeling, suppressed antigen presentation, N-glycan biosynthesis and p53 pathway inhibition. Exudate profiling uniquely revealed complement and coagulation activation, consistent with a systemic prothrombotic and immunosuppressive state. Compared with the control group, the AUC values for CDA, REG4, LCN2, and TNS1 were 0.841, 0.878, 0.922, and 0.800 in the UC group, and 0.880, 0.752, 0.887, and 0.718 in the CRC group, respectively.

CONCLUSIONS

UC and CRC are primarily driven by a metabolic shift from oxidative phosphorylation to glycolysis, progressive immune silencing, and extracellular matrix remodeling. These findings indicate that CDA, REG4, LCN2, and TNS1 have strong potential as serum biomarkers for the early detection of UC and CRC.