Crohn's disease (CD) is a chronic inflammatory disorder that affects all layers of the bowel wall, characterized by transmural and patchy inflammation with skip lesions. While the exact cause remains unclear, it is widely accepted that T cells play a pivotal role in the pathogenesis of CD, positioning them as a significant target for therapeutic interventions aimed at reducing gut inflammation by inhibiting T cell recruitment to the gut [1]. However, the presence of tissue-resident memory T (Trm) cells within the gut poses challenges to such therapies, as these cells establish local pro-inflammatory populations that are not influenced by trafficking inhibitors.

Trm cells serve as essential immune sentinels in the gut [2,3], with demonstrated longevity in the intestinal mucosa independent of circulating T cells [4]. They contribute to sustaining chronic immune responses and local inflammation [[5], [6], [7]], playing a significant role in CD pathogenesis [1,3,8,9]. Furthermore, their ability to migrate across bowel layers implies the potential for vertical cellular crosstalk [10], thus potentially influencing the transmural characteristics of CD. Experimental evidence confirms the involvement of Trm cells in disease flares [3,11], while their depletion has shown protective effects against experimental colitis [3,11]. However, their precise role in modulating the inflammatory response in CD, especially within different gut compartments, remains poorly understood [1].

To address this gap in knowledge, we comprehensively profiled a single-cell transcriptional and T cell receptor (TCR) profile using immune cells isolated from the small bowel of CD. Our objective was to characterize the distribution of Trm cells and identify their transcriptional profiles in the gut and to investigate their potential interactions with other immune cells. By assessing the clonal expansion of Trm cells and studying their migration properties, we aimed to gain insights into the dynamics of these cells within the gut microenvironment.