Single-cell transcriptomic analysis reveals seed cells and microenvironmental crosstalk in gastric cancer peritoneal metastasis

Abstract Peritoneal metastasis is the most frequent and lethal metastatic pattern in gastric cancer, yet the identity of metastatic seed cells and the accompanying microenvironmental remodeling remain poorly defined. Integrated single-cell RNA sequencing analysis of cells derived from primary gastric tumors and peritoneal metastases revealed markedly distinct cellular compositions. Copy number variation and clonality analyses indicated that peritoneal metastases originate from primary tumor subclones with chromosome 12 amplification. Trajectory analysis identified epithelial cell cluster 2 as a transitional population exhibiting bifurcating cell fates, marked cellular plasticity, and metabolic adaptability. These cells were defined as peritoneal metastasis–associated epithelial cells (PMAECs) and proposed as a putative metastatic seed-cell population. Integrated machine learning identified five PMAEC marker genes, and a nomogram for predicting peritoneal dissemination risk was constructed and validated in an independent cohort, demonstrating robust predictive and prognostic performance. Single-cell dissection of the tumor microenvironment revealed extensive remodeling of macrophage, fibroblast, T cell, and B cell subpopulations, along with aberrantly activated signaling networks between PMAECs and multiple microenvironmental components in peritoneal metastases. This study provides a comprehensive single-cell atlas of gastric cancer peritoneal metastasis and delineates the coordinated evolution of metastatic seed cells and microenvironmental crosstalk, thereby offering potential biomarkers and therapeutic targets.