Identifying Cellular Neighborhood Phenotypes Differentiating Normal and Quiescent Crohn's Disease via MxIF

Crohn's disease (CD) is a chronic inflammatory condition of the gastrointestinal tract characterized by alternating periods of activity and remission. This study investigates whether the cellular environments of quiescent (inactive disease) and normal tissues show similarities or differences, exploring potential residual effects from disease and tissue recovery patterns. While active CD can typically be characterized by high neutrophil density, whereas quiescent tissues present less pronounced inflammatory markers. This study leverages multiplexed immunofluorescence (MxIF) data to examine the distributions and patterns of various nuclei subtypes in quiescent versus normal tissues, aiming to determine how similar or different these tissues are in the absence of active inflammation. In our study, we analyze four tissue samples labeled as normal and five as quiescent from CD patients, as determined by a pathologist. We use rigid and deformable registration of MxIF images to analyze these tissues in a unified space and classify the nuclei into 13 subtypes. Using a KD tree, we identify the 10 nearest neighbors for each nucleus, building a combined distance-weighted neighborhood matrix representing both normal and quiescent tissues. We projected these neighborhoods into 2 dimensions using t-distributed stochastic nearest neighbor(t-SNE), clustered them, and calculated the enrichment for each subtype between normal and quiescent states within each of 20 and 40 clusters. In the 20-cluster analysis, we find monocytes enrich in one cluster and leukocytes enrich in two clusters for normal and quiescent tissues respectively. For the 40-cluster analysis, we observe monocytes, macrophages, and leukocytes enrich in one cluster each in normal tissues, and in the quiescent condition, one cluster enriched with enteroendocrine cells, and two clusters enriched with leukocytes. The results were statistically significant as determined by a chi-squared test (𝑝 < 0.01). These differences suggest a possible association with the tissue state and its microenvironment dynamics between normal and quiescent CD.