Abstract 7475: A comprehensive single-cell atlas of gastric cancer reveals malignant cell state dynamics and plasticity in tumor progression and metastasis

Abstract Background: Gastric cancer exhibits diverse malignant cell states that contribute to intratumor heterogeneity (ITH), a fundamental factor that drive tumor progression, metastasis, and treatment resistance. While previous single-cell RNA sequencing (scRNA-seq) studies have provided novel insights into ITH in gastric cancer, they are often constrained by small sample sizes and limited transcriptional coverage. Methods: In this study, we curated, annotated, and integrated scRNA-seq datasets from 21 studies, comprising 626 samples from 316 individuals, including healthy donors and patients with precancerous lesions and gastric cancer. Within the epithelial compartment, malignant and non-malignant cells were distinguished using three complementary computational methods. To refine malignant cell subclustering, we developed a novel approach that incorporates patient-specific copy number variations, minimizing the impact of inter-patient heterogeneity on clustering analysis. Results: Following rigorous quality control and data integration, unsupervised clustering analysis classified 2, 088, 266 high-quality cells into six major cell types or compartments: B cells, T cells, innate lymphoid cells, myeloid cells, stromal cells, and epithelial cells. Within the epithelial cell compartment, we identified 12 distinct malignant cell states characterized by unique expression profiles and phenotypic characteristics, such as cell proliferation capacity and lineage-specific plasticity. These cancer cell states exhibited substantial variation in the activity of hallmark cancer signaling pathways, with their presence and composition closely linked to tumor aggressiveness and clinical outcomes. Proliferative cancer cells and translationally active cancer cells predominated in intermediate tumor stages, dormant cells were prevalent in advanced stages, and epithelial-mesenchymal transition (EMT) states were enriched in metastatic tumors. Additionally, we identified a malignant cell population with high expression of intestinal lineage markers in patients with signet ring cell carcinoma, and these findings were validated using spatial transcriptomic. Conclusions: This study presents a comprehensive single-cell transcriptomic atlas of gastric cancer epithelial cells, providing valuable insights into transcriptional ITH. Our findings define distinct malignant cell states, elucidate their dynamics, and highlight their clinical significance, establishing a framework for understanding how these states contribute to disease progression and metastasis. Citation Format: Enyu Dai, Yanshuo Chu, Yang Liu, Ruiping Wang, Yibo Dai, Jaffer A. Ajani, Linghua Wang. A comprehensive single-cell atlas of gastric cancer reveals malignant cell state dynamics and plasticity in tumor progression and metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7475.