Decoding the complexity of intestinal immunity with spatial transcriptomics

The intestine integrates nutrient digestion and absorption with immune surveillance, being continuously challenged by dietary antigens, commensal microbiota, and pathogens. Its highly regionalized structure requires the immune system to balance tolerance to food and commensal organisms with protective responses against pathogens, generating substantial heterogeneity and complexity across multiple spatial scales that make it inherently difficult to study. Conventional techniques such as flow cytometry, immunohistochemistry, and RNA-sequencing can characterize immune cell location, composition, and transcriptional state, but do not enable simultaneous and unbiased interrogation of cellular state and spatial context. Over the last decade, spatial transcriptomics has allowed researchers to unbiasedly profile gene expression in situ for the first time. In this review, we discuss the suitability of spatial transcriptomics for profiling the intestinal immune system, key discoveries made using this technology, complementary techniques, current challenges, and future opportunities for its application in gut immunology research and beyond.