Morphological diversity of cancer cells predicts prognosis across tumor types

Intratumor heterogeneity drives disease progression and treatment resistance, which can lead to poor patient outcomes. Here, we present a computational approach for quantification of cancer cell diversity in routine hematoxylin-eosin-stained histopathology images. We analyzed publicly available digitized whole-slide hematoxylin-eosin images for 2000 patients. Four tumor types were included: lung, head and neck, colon, and rectal cancers, representing major histology subtypes (adenocarcinomas and squamous cell carcinomas). We performed single-cell analysis on hematoxylin-eosin images and trained a deep convolutional autoencoder to automatically learn feature representations of individual cancer nuclei. We then computed features of intranuclear variability and internuclear diversity to quantify tumor heterogeneity. Finally, we used these features to build a machine-learning model to predict patient prognosis. A total of 68 million cancer cells were segmented and analyzed for nuclear image features. We discovered multiple morphological subtypes of cancer cells (range = 15-20) that co-exist within the same tumor, each with distinct phenotypic characteristics. Moreover, we showed that a higher morphological diversity is associated with chromosome instability and genomic aneuploidy. A machine-learning model based on morphological diversity demonstrated independent prognostic values across tumor types (hazard ratio range = 1.62-3.23, P