Plasma proteomic and metabolomic profiling reveals molecular features relevant to neoadjuvant therapy response in locally advanced esophageal squamous cell carcinoma

Neoadjuvant therapy (NAT) followed by radical surgery is the standard treatment for locally advanced esophageal squamous cell carcinoma (LA-ESCC), yet many patients fail to achieve pathologic complete response (pCR). Predictive biomarkers and biological mechanisms underlying NAT resistance remain elusive. We aimed to address this challenge through longitudinal multi-omics profiling of patient plasma during NAT. We performed longitudinal plasma proteomic and metabolomic analyses in a discovery cohort of patients with LA-ESCC ( n = 40) receiving neoadjuvant chemotherapy (nCT) or neoadjuvant immunochemotherapy (nICT) to reveal molecular features relevant to treatment response. Predictive biomarkers for pCR were assessed in plasma samples from an independent validation cohort ( n = 93) by ELISA. Mechanistic studies were conducted through in vitro cell co-culture, in vivo mouse experiments, and analysis of ESCC tissue samples from another validation cohort ( n = 33). Multi-omics analysis revealed distinct molecular profiles between treatment responders and non-responders. Metabolomic profiling revealed dynamic treatment-associated changes in amino acid and lipid metabolism during NAT, and proteomic profiling highlighted baseline differences related to neutrophil activity and inflammatory responses. DEFA1 was validated as an unfavorable predictive biomarker for achieving pCR after nICT. Mechanistic studies demonstrated that DEFA1 fosters an immunosuppressive microenvironment by promoting myeloid-derived suppressor cell (MDSC) differentiation and impairing CD8 + T cell cytotoxicity. This study delineates the longitudinal plasma multi-omic landscape associated with NAT response in LA-ESCC and identifies DEFA1 as a predictive biomarker and potential therapeutic target for overcoming immunotherapy resistance.