Association of interpretable histomorphic features with molecular markers: A Computational Histology Artificial Intelligence (CHAI) biomarker development platform analysis

Background: Biomarkers are needed to guide precision oncology. Ideally, tools have rapid turnaround and integrate into existing workflows. Computational pathology analyzing features on routine hematoxylin and eosin (H&E) stained whole slide images (WSI) provide an accessible system for biomarker discovery. The Computational Histology Artificial Intelligence (CHAI) platform has been validated to predict clinical outcome endpoints across multiple solid tumor types. To explore the unknown overlap of histomorphic features with molecular markers, we assessed associations of CHAI features with markers from multiplex immunofluorescence (MIF). Methods: The CHAI platform was built on deep learning models trained on >25,000 pan cancer H&E WSI and incorporates >500,000 pathologist annotated nuclei and 100 million μm² tissue, with macro AUC 0.99 for nuclei and tissue segmentation. These models process H&E WSIs, segment comprehensive cancer-relevant cell and tissue types and quantify >30,000 histomorphologic features representing hallmarks of cancer biology (e.g. nuclei size and shape, spatial arrangement, immune infiltration, stromal density). On 41 colorectal cancer WSIs with matched MIF scans from the ORION dataset, CHAI cell/tissue-typing performance was evaluated against MIF by calculating Pearson correlation coefficient between the densities of CHAI's predicted target and matched MIF markers. Results: Across 289,619 200 x 200 μm² tissue patches, cell segmentation correlation comparing CHAI-segmented nuclei vs MIF DAPI was 0.899 (95% CI 0.898, 0.900). Cell typing correlation was 0.642 (0.640, 0.644) for CHAI-predicted epithelial cells vs MIF cytokeratin (CK) and 0.587 (0.584, 0.590) for CHAI pan-leukocyte vs MIF CD45. Tissue typing correlation was 0.656 (0.653, 0.658) for CHAI tumor-epithelial regions vs MIF CK and 0.543 (0.541, 0.546) for CHAI stromal regions vs MIF smooth muscle actin. All correlations were statistically significant (p<0.001). Conclusion: The CHAI platform measures histomorphic features from H&E WSI at high accuracy; it captures facets of the tumor microenvironment that showed significant overlaps with molecular markers captured by MIF, while also identifying areas to further explore complementarity in these orthogonal modalities. This work underscores the biologic basis of the CHAI system as a novel modality for biomarker development with potential for biomedical research and clinical applications.