Abstract 1140: A spatially mapped gene expression signature for intestinal stem-like cells identifies high-risk precursors of gastric cancer
Authors: Wichmann Ignacio A. , Huang Robert J. , Su Andrew , Sathe Anuja , Shum Miranda V. , Grimes Susan M. , Meka Rithika , Almeda Alison , Bai Xiangqi , Shen Jeanne , Nguyen Quan , Amieva Manuel , Hwang Joo Ha , Ji Hanlee P. 
Published: March 2024

Abstract
Gastric intestinal metaplasia (GIM) is a precursor lesion for the intestinal subtype of gastric cancer (GC). A risk stratification tool is the Operative Link on GIM (OLGIM), a system that relies on histopathologic annotation of gastric biopsies. Advanced OLGIM (stages III and IV) have the highest risk of progression to GC. Molecular biomarkers for advanced OLGIM are lacking. We explored transcriptomics biomarkers for advanced OLGIM to aid risk assessment efforts among GC precursors.We used clinical and genomic data from four cohorts: 1) GAPS, a cohort of OLGIM-staged patients (N=303); 2) a subset of confirmed intestinal-type GC from The Cancer Genome Atlas (TCGA, N=198); 3) a compilation of scRNA-seq data (N=40), and 4) a spatial transcriptomics cohort (N=5) with annotated H&E-stained histopathology slides from GC or OLGIM-staged patients.We separated the GAPS bulk RNAseq gene expression dataset into independent discovery (N=88) and validation (N=215) sets. Through a combination of differential expression analysis and co-expression analysis, we identified a discrete set of 100 significantly upregulated genes characterizing advanced OLGIM that were confirmed in the validation set. Importantly, these genes were overexpressed both in the corpus and antrum of the stomach. We leveraged spatial transcriptomics assays to refine this signature to genes overexpressed specifically in GIM foci. We interrogated the TCGA dataset and confirmed these genes to be also expressed in gastric tumors. The final high-risk signature included 26 genes. Single-cell RNAseq analysis revealed these genes to be expressed by aberrant intestinal-like lineages. Further, reference-mapping identified cells resembling mature enterocytes and goblet cells that expressed 16 of these genes, whereas 10 genes from the high-risk signature pinpoint immature intestinal stem-like cells at varying stages of differentiation (duodenum stem cells, duodenum differentiating stem cells, and duodenum transit amplifying cells). Finally, we confirmed expression of 12 of these genes by single-molecule fluorescence in situ hybridization (smFISH), that distinguish differentiated from stem-like lineages in metaplasia and are absent in normal gastric glands in intact tissue sections from GC precursors.Our study identified as signature of 26 genes that are: i) characteristically over-expressed in advanced OLGIM stages, ii) localize specifically to metaplasia, iii) are expressed in gastric tumors, and iv) distinguish differentiated from stem-like cells in GIM. These results provide transcriptomics biomarkers that indicate the establishment and expansion of intestinal stem-like cells in advanced OLGIM, with profound translational implications, as these cells may harbor and expand mutations that predispose advanced OLGIM patients to GC.
Citation Format: Ignacio A. Wichmann, Robert J. Huang, Andrew Su, Anuja Sathe, Miranda V. Shum, Susan M. Grimes, Rithika Meka, Alison Almeda, Xiangqi Bai, Jeanne Shen, Quan Nguyen, Manuel Amieva, Joo Ha Hwang, Hanlee P. Ji. A spatially mapped gene expression signature for intestinal stem-like cells identifies high-risk precursors of gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1140.