Deep learning-based approach for 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. As such, researchers have studied mouse models of colitis to further understand its pathogenesis and identify new treatment targets. Although bench methods like flow cytometry and RNA-sequencing can characterize immune responses with single-cell resolution, whole murine colon specimens are processed at once. Given the simultaneous presence of colonic regions that are involved or uninvolved with abnormal histology, processing whole colons may lead to a loss of spatial context. Detecting these regions in hematoxylin and eosin (H&E)-stained colonic tissues offers the downstream potential of quantifying immune populations in areas with and without disease involvement by immunohistochemistry on serially sectioned slides. This could provide a complementary, spatially-aware approach to further characterize populations identified by other methods. However, detection of such regions requires expert interpretation by pathologists and is a tedious process that may be difficult to perform consistently across experiments. To this end, we have trained a deep learning model to detect ‘Involved’ and ‘Uninvolved’ regions from H&E-stained colonic slides across controls and three mouse models of colitis – the dextran sodium sulfate (DSS) chemical induction model, the recently established intestinal epithelium-specific, inducible Klf5 Δ IND ( Villin-CreER T2 ;Klf5 fl/fl ) genetic model, and one that combines both induction methods. The trained classifier allows for extraction of ‘Involved’ colonic regions across mice to cluster and identify histological classes. Here, we show that quantification of ‘Involved’ and ‘Uninvolved’ image patch classes in swiss rolls of colonic specimens can be utilized to train a linear determinant analysis classifier to distinguish between mouse models. Such an approach has the potential for revealing histological links and improving synergy between various colitis mouse model studies to identify new therapeutic targets and pathophysiological mechanisms. ### Competing Interest Statement The authors have declared no competing interest.