Characterization of the immune infiltrate and the chromatin 3D structure of gastric tumors from Mexican patients.

Abstract

e16145 Background: Identifying cellular populations within tumors and theirmicroenvironment, along with genome structure characterization in human samples,is crucial for understanding the extensive heterogeneity observed in clinical settingsand for gaining mechanistic insights into cellular transformation. These analyses aremade possible by technologies such as single-cell RNA sequencing (scRNA-seq)and genome conformation capture (Hi-C). We characterized the cellular compositionand the three-dimensional genome organization of gastric cancer samples andadjacent tissues from Mexican patients. Methods: Gastric and esophagogastric junction biopsies were obtained from twohistological subtypes: diffuse and intestinal. After quality control, we analyzedapproximately 80,000 cells using scRNA-seq and Hi-C. By applying canonicalmarkers and automated cell classifiers, we identified a diverse set of cellpopulations, including T cells, B cells, myeloid cells, epithelial cells, endothelial cells,mesenchymal cells, and fibroblasts. Results: Tumor samples showed a higher proportion of immune cells compared toadjacent tissues. Notably, a subset of NKT/T cells expressed FOXP3, a markercharacteristic of regulatory T cells. Other immune subsets exhibited increasedexpression of exhaustion-associated markers such as CTLA4, ICOS, LAIR2, andTIGIT, suggesting an exhausted phenotype and supporting the potential use ofimmunotherapeutic strategies. Hi-C revealed a total of 791 structural variants, whichwere visually confirmed in interaction matrices. Regarding their distribution, 83% ofthe variants identified in diffuse-type gastric tumors corresponded to deletions,whereas 50% of the variants detected in intestinal-type gastric tumors wereduplications. In samples from the esophagogastric junction, 42% and 62% of thevariants corresponded to translocations in the diffuse and intestinal subtypes,respectively. Hi-C identified a series of neo-topologically associating domains(neoTADs), with 234 out of 423 including at least one gene with differentialexpression, indicating potential functional implications of these genomicrearrangements. Among structural variants, translocations were the maincontributors to neoTAD formation, generating 121 neoTADs, corresponding to approximately 60% of the total, and exhibited the highest proportion of neoTADsassociated with differential gene expression. Conclusions: The integrative characterization of tumor samples using scRNA-seqand Hi-C provides valuable insights into the molecular mechanisms underlyinggastric cancer in an underrepresented population, such as individuals of Mexicandescent, and may contribute to the identification of novel biomarkers.