Single-cell atlas of the esophageal squamous cell carcinoma immune ecosystem to predict immunotherapy response

Abstract Esophageal squamous cell carcinoma (ESCC) evolves within a highly interactive tumor microenvironment (TME) that shapes therapeutic response. We utilized mass cytometry to analyze over 10 million cells from 25 ESCC tumors, 24 adjacent nontumor tissues, and 23 peripheral blood samples, employing an extensive panel of 42 immune markers. The resulting atlas reveals a compartmentalized landscape with a reproducible paucity of CD4⁺ and CD8⁺ central memory T cells (TCM) in tumor sites. Reintroduction of patient-derived TCMs restored antitumor immunity in coculture assays, demonstrating their cytotoxic capacity in vitro and suggesting their potential relevance for future therapeutic exploration. Myeloid profiling identified PD-L1⁺ tumor-associated macrophages (TAMs) as correlates of clinical benefit; ex vivo PD-L1 blockade reprogrammed TAMs toward proinflammatory states, indicating pharmacological malleability. Notably, CD39⁺ tumor-infiltrating T cells were consistently associated with favorable prognosis and increased responsiveness to PD-1 blockade across cancer types. The functional inhibition of CD39 impaired cytotoxic T-cell activity, underscoring its dual role as a marker of immune dysfunction and a promising therapeutic target. Collectively, our findings provide a comprehensive immune landscape of ESCC, highlighting key immunological deficits and opportunities for targeted interventions. The insights gained underscore the potential of tailoring immunotherapies to the specific immune profiles of the TME, potentially revolutionizing treatment paradigms for ESCC patients. This study sets the stage for a more nuanced understanding and manipulation of the immune elements critical for optimizing cancer immunotherapy.