Neoadjuvant chemotherapy (NAC) response prediction for triple negative breast
cancer (TNBC) patients is a challenging task clinically as it requires
understanding complex histology interactions within the tumor microenvironment
(TME). Digital whole slide images (WSIs) capture detailed tissue information,
but their giga-pixel size necessitates computational methods based on multiple
instance learning, which typically analyze small, isolated image tiles without
the spatial context of the TME. To address this limitation and incorporate TME
spatial histology interactions in predicting NAC response for TNBC patients, we
developed a histology context-aware transformer graph convolution network
(NACNet). Our deep learning method identifies the histopathological labels on
individual image tiles from WSIs, constructs a spatial TME graph, and
represents each node with features derived from tissue texture and social
network analysis. It predicts NAC response using a transformer graph
convolution network model enhanced with graph isomorphism network layers. We
evaluate our method with WSIs of a cohort of TNBC patient (N=105) and compared
its performance with multiple state-of-the-art machine learning and deep
learning models, including both graph and non-graph approaches. Our NACNet
achieves 90.0% accuracy, 96.0% sensitivity, 88.0% specificity, and an AUC of
0.82, through eight-fold cross-validation, outperforming baseline models. These
comprehensive experimental results suggest that NACNet holds strong potential
for stratifying TNBC patients by NAC response, thereby helping to prevent
overtreatment, improve patient quality of life, reduce treatment cost, and
enhance clinical outcomes, marking an important advancement toward personalized
breast cancer treatment.