Deep learning-based approach to the characterization and quantification of histopathology in mouse models of colitis

Inflammatory bowel disease (IBD) is a chronic immune-mediated disease of the gastrointestinal tract. While therapies exist, response can be limited within the patient population. Researchers have thus studied mouse models of colitis to further understand pathogenesis and identify new treatment targets. Flow cytometry and RNA-sequencing can phenotype immune populations with single-cell resolution but provide no spatial context. Spatial context may be particularly important in colitis mouse models, due to the simultaneous presence of colonic regions that are involved or uninvolved with disease. These regions can be identified on hematoxylin and eosin (H&E)-stained colonic tissue slides based on the presence of abnormal or normal histology. However, detection of such regions requires expert interpretation by pathologists. This can be a tedious process that may be difficult to perform consistently across experiments. To this end, we trained a deep learning model to detect ‘Involved’ and ‘Uninvolved’ regions from H&E-stained colonic tissue slides. Our model was trained on specimens from controls and three mouse models of colitis–the dextran sodium sulfate (DSS) chemical induction model, the recently established intestinal epithelium-specific, inducible Klf5^ΔIND (Villin-CreER^T2;Klf5^fl/fl) genetic model, and one that combines both induction methods. Image patches predicted to be ‘Involved’ and ‘Uninvolved’ were extracted across mice to cluster and identify histological classes. We quantified the proportion of ‘Uninvolved’ patches and ‘Involved’ patch classes in murine swiss-rolled colons. Furthermore, we trained linear determinant analysis classifiers on these patch proportions to predict mouse model and clinical score bins in a prospectively treated cohort of mice. Such a pipeline has the potential to reveal histological links and improve synergy between various colitis mouse model studies to identify new therapeutic targets and pathophysiological mechanisms.