Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Esophageal Squamous Cell Carcinoma

Lymph node metastasis, the leading cause of mortality in esophageal squamous carcinoma (ESCC) with a highly complex tumor microenvironment, remains underexplored. Here, the transcriptomes of 85 263 single cells are analyzed from four ESCC patients with lymph node metastases. Strikingly, it is observed that the metastatic microenvironment undergoes the emergence or expansion of interferon induced IFIT3(+) T, B cells, and immunosuppressive cells such as APOC1(+)APOE(+) macrophages and myofibroblasts with highly expression of immunoglobulin genes (IGKC) and extracellular matrix component and matrix metallopeptidase genes. A poor-prognostic epithelial-immune dual expression program regulating immune effector processes, whose activity is significantly enhanced in metastatic malignant epithelial cells and enriched in CD74(+)CXCR4(+) and major histocompatibility complex (MHC) class II genes upregulated malignant epithelia cells is discovered. Comparing with primary tumor, differential intercellular communications of metastatic ESCC microenvironment are revealed and furtherly validated via multiplexed immunofluorescence and immunohistochemistry staining, which mainly rely on the crosstalk of APOC1(+)APOE(+) macrophages with tumor and stromal cell. The data highlight potential molecular mechanisms that shape the lymph-node metastatic microenvironment and may inform drug discovery and the development of new strategies to target these prometastatic nontumor components for inhibiting tumor growth and overcoming metastasis to improve clinical outcomes.

Automated summary

In this study, the authors analyzed the transcriptomes of 85,263 single cells from four ESCC patients with lymph node metastasis. They identified various cells and genes that play a role in the metastatic microenvironment, including IFIT3(+) T and B cells, APOC1(+)APOE(+) macrophages, myofibroblasts, and immunoglobulin genes. They also discovered an epithelial-immune dual expression program that regulates immune processes in metastatic cells. Additionally, they found differential intercellular communications in the metastatic ESCC microenvironment, mainly involving the interaction of APOC1(+)APOE(+) macrophages with tumor and stromal cells. These findings provide insights into the molecular mechanisms underlying lymph-node metastasis and offer potential targets for inhibiting tumor growth and improving clinical outcomes.