Predicting protein cascade expression from H&E images

Protein expression within oncogenic or suppressive pathways is a hallmark indicator of oncogenesis. While traditional AI models in digital pathology attempt to predict singular proteins, there is a need to predict the downstream expression of proteins to indicate the propagation of signals. RNA expression provides novel information, but does not provide information about the downstream propagation of protein signals or whether those signals are functional. Using Reverse Phase Protein Array (RPPA) data with whole-slide images (WSIs) from the publicly available Cancer Genome Atlas Breast Adenocarcinoma dataset (TCGA-BRCA), we predict the expression of five key proteins identified from the apoptosis cascade, using DNA damage and repair (DDR) cascades as a biological control. Furthermore, we examine the performance of patch- level Vision Transformers (ViT) on the regression task, which was tested against the designed cellular-level ViT, CellRPPA. Our results demonstrate that patch-level vision transformers were unable to obtain statistically significant predictive results, achieving R-squared values < 0.1 for all folds. In addition, CellViT obtained R-squared values >0.1 in all five test folds. We also show that morphologically indicative cascades, such as the apoptosis cascade, provide significantly higher performance compared to the DDR cascade.