Divergent lineage trajectories and genetic landscapes in human gastric intestinal metaplasia organoids associated with early neoplastic progression

Objective: Gastric intestinal metaplasia (IM) is a pre-cancerous stage spanning a morphological spectrum that is poorly represented by human cell line models. We aim to establish and characterize human IM cell models to better understand IM progression along the cancer spectrum. Design: A large human gastric IM organoid (IMO) cohort (n=28) was established, along with normal gastric organoids (n=42) for comparison, and comprehensive multi-omics profiling and functional characterization were performed. Results: Single-cell transcriptomes revealed IMO cells spanning a spectrum from hybrid gastric/intestinal to advanced intestinal differentiation, and unveiled lineage trajectories that connected different cycling and quiescent stem and progenitors, highlighting their differences in gastric to IM transition. The hybrid IMO cells showed impaired differentiation potential, high lineage plasticity beyond gastric or intestinal fates, and reactivation of a fetal gene program. Cell populations in gastric IM and cancer tissues were found to be highly similar to those derived from IMOs and exhibited fetal signature. Genomically, IMOs showed an elevated mutation burden, frequent chromosome 20 gain, and epigenetic de-regulation of many intestinal and gastric genes. Functionally, IMOs downregulated FGFR2 and became independent of FGF10 for survival. Several IMOs exhibited a cell-matrix adhesion independent (CMi) subpopulation that displayed chromosome 20 gain but lacked key cancer driver mutations, which could represent the earliest neoplastic precursor of IM-induced gastric cancer. Conclusions: Overall, our IM organoid biobank captured the heterogeneous nature of IM, revealing mechanistic insights on IM pathogenesis and its neoplastic progression, offering an ideal platform for studying early gastric neoplastic transformation and chemoprevention. ### Competing Interest Statement SYL and STY have received research sponsorships from Pfizer, Merck, Servier. HC is inventor on patents related to organoid research. His full disclosure: www.uu.nl/staff/JCClevers/Additional functions. The other authors declare no competing interests.