Plasma proteomics reveals stage-specific EMT-linked signals: NAMPT in early and complement in advanced colorectal cancer

Epithelial–mesenchymal transition (EMT) plays a dual role in driving both metastatic progression and therapy resistance in colorectal cancer (CRC). To identify systemic EMT-related signals across disease stages, we performed stage-specific plasma proteomics in treatment-naïve CRC patients from an Asia–Pacific (APAC)-representative discovery cohort in India. EMT-associated proteins were curated using FANTOM5 and validated through MSigDB enrichment, with protein interaction networks constructed via STRING and GeneMANIA. We developed an EMT Progression and Resistance Index (EPRI) that integrates literature support, stage specificity, and clinical trial relevance to prioritize clinically meaningful effectors. EPRI identified NAMPT as a central hub enriched in Stage I plasma, consistent with metabolic priming via NAD + biosynthesis. A NAMPT-centered subnetwork revealed stage-dependent interactions spanning complement and metabolic pathways, implicating systemic redox remodeling and PI3K/Akt signaling in EMT-driven dissemination and 5-FU/FOLFOX resistance. In later stages (III–IV), plasma signatures consolidated into complement pathway activation (notably elevated C4A/B and CR1), reflecting immune remodeling and metastatic fixation. These stage-resolved plasma signatures—ranging from NAMPT-linked metabolic priming to complement-driven EMT stabilization—offer a noninvasive framework for monitoring EMT-associated resistance and metastasis. To our knowledge, NAMPT has not previously been examined within EMT-focused plasma proteomics in CRC, highlighting the novelty of this approach while aligning with recent reports linking NAMPT to EMT, stemness, and drug resistance across cancers. The rising incidence of early-onset CRC (EOCRC), particularly in APAC populations, underscores the urgency of validating these plasma signatures in larger, longitudinal, and molecularly stratified cohorts. Together, this discovery-phase study provides regionally grounded yet globally relevant insights into EMT-linked progression and therapeutic resistance, warranting validation in expanded, longitudinal cohorts. Schematic representation of epithelial-to-mesenchymal transition (EMT) initiation in colorectal cancer (CRC) highlighting NAMPT as an early-stage (Stage I) hub. NAMPT, upregulated in epithelial cells, promotes EMT through PI3K/Akt activation and redox signaling. Upstream inducers include SDF-1 (C4BPA) and NAD⁺ metabolism. Downstream, NAMPT engages IRS1, IGF1R, IFITM3, GRB10, and QPR1, converging on PI3K/Akt and redox modulation. Functional clusters—including ubiquitin regulators (USP49, CUL5), redox mediators (NOX4), and EMT effectors—facilitate mesenchymal transition. The model integrates stage-specific expression and functional modules relevant to CRC progression. • Stage-resolved plasma proteomics maps EMT progression and therapy resistance in CRC. • NAMPT was identified as an early metabolic priming hub linked to 5-FU/FOLFOX resistance. • Complement pathway (C4A/B–CR1 axis) dominates advanced-stage EMT fixation and metastasis. • EMT Progression and Resistance Index (EPRI) integrates literature, stage specificity, and clinical trial relevance. • Provides a discovery-phase, noninvasive roadmap to liquid-biopsy biomarkers, prioritizing EOCRC and multicenter validation.