Single-cell transcriptomic profiling uncovers cellular complexity and microenvironment in gastric tumorigenesis associated with Helicobacter pylori

Graphical summary of cellular heterogeneity and microenvironment along the consecutive gastric carcinogenesis associated with H. pylori. (A) Cellular heterogeneity along the histological cascade of gastric carcinogenesis with or without H. pylori infection. (B) The DEGs between H. pylori −positive and −negative cell types. GS, gastritis; IM, intestinal metaplasia; GC, gastric cancer. • ScRNA-seq data revealed cellular heterogeneity in gastric tumorigenesis. • Enterocytes, was overwhelmingly abundant in gastric intestinal metaplasia lesion. HNF4G was predicted as the specific transcription factor. • ScRNA-seq unveiled the transcriptional features of distinct cell subtypes in GC. • The differentia expressed genes (DEGs) in epithelial, fibroblasts and myeolid cells associated with H. pylori infection have been identified. • H. pylori -positive specimens exhibited enriched cell-cell communication, with significant active TNF signaling network. Helicobacter pylori ( H. pylori ) infection is the main risk for gastric cancer (GC). However, the cellular heterogeneity and underlying molecular mechanisms in H. pylori -driven gastric tumorigenesis are poorly understood. Here, we generated a single-cell atlas of gastric tumorigenesis comprising 18 specimens of gastritis, gastric intestinal metaplasia (IM) and GC with or without H. pylori infection. Single-cell RNA sequencing (scRNA-seq) was performed. Immunofluorescence, immunohistochemistry and qRT-PCR analysis were applied in a second human gastric tissues cohort for validation. Bioinformatics analyses of public TCGA and GEO datasets were applied. Single-cell RNA profile highlights cellular heterogeneity and alterations in tissue ecology throughout the progression of gastric carcinoma. Various cell lineages exhibited unique cancer-associated expression profiles, such as tumor-like epithelial cell subset (EPC), inflammatory cancer-associated fibroblasts (iCAFs) and Tumor-associated macrophage (TAM). Notably, we revealed that the specific epithelial subset enterocytes from the precancerous lesion GIM, exhibited elevated expression of genes related to lipid metabolism, and HNF4G was predicted as its specific transcription factor. Furthermore, we identified differentially expressed genes in H. pylori -positive and negative epithelial cells, fibroblasts and myeloid cells were identified. Futhermore, H. pylori -positive specimens exhibited enriched cell–cell communication, characterized by significantly active TNF, SPP1, and THY1 signaling networks. Our study provides a comprehensive landscape of the gastric carcinogenesis ecosystem and novel insights into the molecular mechanisms of different cell types in H. pylori -induced GC.