Multiplexed Immunofluorescence Profiling of the Pretreatment Tumor Microenvironment in Esophageal Adenocarcinoma-part1

Esophageal adenocarcinoma (EAC) has a poor prognosis, with only 30% of patients achieving a complete response to neoadjuvant chemotherapy (nCT). To identify features associated with response, we performed integrative spatial multi-omic profiling of treatment-naïve EAC biopsies from two independent cohorts (n = 73). Complete responders (CRs) exhibited extracellular matrix-remodeling programs and an organized tumor microenvironment characterized by immune–stromal niches enriched in dendritic cells, lymphocytes, granulocytes, and fibroblasts, together with effector T-cell populations and an IgG-associated B-cell phenotype. By contrast, non-responders (NRs) showed angiogenesis-, hypoxia-, epithelial-to-mesenchymal transition-, and keratin-associated programs, accompanied by lipid-associated macrophages, TIP-like endothelial cells, myofibroblastic cancer-associated fibroblasts, and reduced tumor–immune proximity. Integrating response-associated programs across modalities yielded a model capable of distinguishing CRs from NRs (cross-validation, AUC = 0.851). These findings reveal distinct pretreatment molecular and spatial architectures associated with nCT response and provide a framework for biomarker development and therapeutic targeting of the resistant EAC microenvironment.