Spatially interrogating immune cells and associated gene signatures in inflammatory bowel disease

Inflammatory Bowel Disease (IBD), encompassing Crohn’s disease (CD) and Ulcerative colitis (UC), is marked by chronic inflammation of the gastrointestinal tract and presents significant clinical challenges due to its complex immune-mediated pathology. The persistent inflammation observed in IBD is driven by dysregulated immune responses, with distinct immune cell populations and cytokine profiles contributing to disease onset and progression. Recent studies have highlighted the 
importance of characterizing these immune cell infiltrates and their activation states to understand disease mechanisms better and inform targeted therapeutic strategies. Traditional approaches to profiling immune cells in IBD have been limited by the inability to simultaneously visualize both RNA and protein markers within the same tissue context. 

The RNAscope™ assay has emerged as a robust platform for spatially mapping inflammatory biomarkers, enabling the detection of cytokines and their cellular origins directly within formalin-fixed, paraffin-embedded (FFPE) tissue samples. Building on this, the new protease-free RNAscope Multiomic LS assay allows concurrent detection of up to six RNA and protein targets on a single slide, leveraging a TSA-based amplification strategy to enhance signal strength and specificity.

In this study, we apply the RNAscope Multiomic LS assay to investigate immune cell populations and inflammatory gene signatures in Crohn’s disease tissue. By integrating pre-conjugated antibodies and RNA probes, we aim to provide a comprehensive spatial characterization of immune cell subsets and their activation markers in inflamed versus uninflamed intestinal regions. This approach offers valuable insights into IBD's cellular and molecular landscape, supporting the development of next-generation targeted therapies for affected patients.

This poster was presented at the AAI 2025 meeting.