Spatial transcriptomics reveals unique inflammatory signatures across all anatomic locations in post-operative crohn’s disease

Background and Aims Most patients with Crohn’s disease (CD) who have undergone ileocolonic resection experience recurrent inflammation within one year after surgery. We examined the molecular basis underlying gastrointestinal inflammation in post-operative CD across 3 common anatomic locations of recurrence. Methods To characterise spatial transcriptomic signatures, this study utilised biopsies from the colon, neo-terminal ileum, and anastomosis of patients with post-operative CD in the PREDICT-OR study. Sample analyses were performed with 10X Genomics Visium CytAssist system V2.0, and data analyses with R. Results Histologically inflamed biopsies from all locations shared transcriptional signatures across 3 cellular niches (myeloid, B, T cells) and a specialised epithelial cell type expressing inflammation-associated genes. Differentially expressed genes overexpressed inflammatory pathway activity across the 3 locations, whereas hypoxic pathways were less apparent. In addition to genes for known treatment targets, epidermal growth factor receptor and mitogen-activated protein kinase pathways were upregulated. Cellular niches shaped inflammatory microenvironments through endoplasmic reticulum stress and extracellular matrix remodelling signalling. Conclusions Application of spatial transcriptomics revealed a common disease signature for post-operative CD across the colon, neo-terminal ileum, and anastomosis. Inflamed biopsies from all locations demonstrated similar immune cell and inflammatory gene expression patterns as opposed to hypoxic pathways, and unique inflammatory pathways were revealed.