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

Area of Science:

• Gastroenterology
• Immunology
• Computational Biology

Background:

• Crohn's disease (CD) is a chronic gastrointestinal inflammatory condition with active and remission phases.
• Quiescent CD tissues, despite lacking active inflammation, may retain cellular microenvironment differences compared to normal tissues.
• Understanding these differences is crucial for assessing tissue recovery and potential residual disease effects.

Purpose of the Study:

• To investigate the cellular and microenvironmental similarities and differences between quiescent CD tissues and normal tissues.
• To identify distinct nuclei subtype distributions and patterns in quiescent versus normal tissues using multiplexed immunofluorescence (MxIF).
• To explore the impact of disease on tissue recovery and microenvironment dynamics.

Main Methods:

• Analysis of MxIF data from normal (n=4) and quiescent CD (n=5) patient tissues.
• Rigid and deformable image registration to unify tissues in a common space.
• Nuclei classification into 13 subtypes and KD tree analysis to determine nearest neighbors.
• Dimensionality reduction using t-distributed stochastic nearest neighbor (t-SNE) for clustering.
• Chi-squared tests to assess statistical significance of subtype enrichment.

Main Results:

• In a 20-cluster analysis, monocytes and leukocytes showed differential enrichment between normal and quiescent tissues.
• A 40-cluster analysis revealed distinct enrichments: normal tissues showed monocytes, macrophages, and leukocytes, while quiescent tissues showed enteroendocrine cells and leukocytes.
• Statistical significance (p < 0.01) was observed for these subtype differences.

Conclusions:

• Quiescent Crohn's disease tissues exhibit unique cellular microenvironment compositions compared to normal tissues.
• These cellular differences persist even in the absence of active inflammation, indicating potential long-term tissue alterations.
• The findings suggest that microenvironment dynamics play a role in the tissue state of quiescent CD.