Single-cell atlas of lineage states, tumor microenvironment and subtype-specific expression programs in gastric cancer.

Gastric cancer (GC) heterogeneity represents a barrier to disease management. We generated a comprehensive single-cell atlas of GC (>200,000 cells) comprising 48 samples from 31 patients across clinical stages and histological subtypes. We identified 34 distinct cell-lineage states including novel rare cell populations. Many lineage states exhibited distinct cancer-associated expression profiles, individually contributing to a combined tumor-wide molecular collage. We observed increased plasma cell proportions in diffuse-type tumors associated with epithelial-resident KLF2, and stage-wise accrual of cancer-associated fibroblast sub-populations marked by high INHBA and FAP co-expression. Single-cell comparisons between patient-derived organoids (PDOs) and primary tumors highlighted inter- and intra-lineage similarities and differences, demarcating molecular boundaries of PDOs as experimental models. We complemented these findings by spatial transcriptomics, orthogonal validation in independent bulk RNA-seq cohorts, and functional demonstration using in vitro and in vivo models. Our results provide a high-resolution molecular resource of intra- and inter-patient lineage-states across distinct GC subtypes.