Hybrid identity and distinct methylation profiles of incomplete intestinal metaplasia in the stomach

Abstract

Background: Gastric intestinal metaplasia (GIM), particularly the incomplete subtype (Inc IM), is strongly associated with increased gastric cancer (GC) risk. However, its role as a true precursor lesion remains uncertain. Objective: We aimed to delineate the molecular identity, differentiation potential and oncogenic relevance of Inc IM. Methods: Spatial transcriptomics using a custom lineage-enriched panel was applied to profile GIM and GC tissues. Subtype-specific GIM organoid models were developed for DNA methylation and chromatin accessibility profiling. Single-cell RNA sequencing was performed to evaluate differentiation capacity. Results: Spatial transcriptomics revealed that Inc IM potentially originates from the deep antral gland cells and harbours a hybrid transcriptomic signature incorporating gastric, small intestinal and large intestinal lineages across both differentiated and stem/progenitor compartments. DNA methylation profiling of subtype-specific organoids showed that Inc IM exhibits extensive intergenic hypermethylation, resembling native antral mucosa. In contrast, complete subtype was marked by promoter hypermethylation of tumour suppressor genes and displayed a more fully intestinalised epigenetic profile. Organoid models recapitulated subtype-specific traits and demonstrated lineage plasticity. Spatial mapping of GC samples revealed an enrichment of Inc IM-like cells, particularly within microsatellite stable tumours. Approximately 76% of the GCs analysed were linked to GIM, while the remaining (24%) appeared to be associated with deep antral differentiation. Conclusions: Inc IM represents a phenotypically unstable and epigenetically deregulated metaplastic state with dual-lineage potential and molecular resemblance to GC. These findings establish Inc IM as a true precursor to GC and underscore the importance of active surveillance and early intervention strategies.