Deep Learning for Molecular and Genomic Characterization of Lung Cancer in Never-Smokers Using Hematoxylin and Eosin-Stained Images

Abstract

Despite promising results in using deep learning to infer genetic features from histological whole-slide images (WSIs), no prior studies have specifically applied these methods to lung adenocarcinomas from subjects who have never smoked tobacco (NS-LUAD) - a molecularly and histologically distinct subset of lung cancer. Existing models have focused on LUAD from predominantly smoker populations, with limited molecular scope and variable performance. Here, we propose a customized deep convolutional neural network based on ResNet50 architecture, optimized for multilabel classification for NS-LUAD, enabling simultaneous prediction of 16 molecular alterations from a single H&E-stained WSI. Key architectural modifications included a simplified two-layer residual block without bottleneck layers, selective shortcut connections, and a sigmoid-based classification head for independent prediction of each alteration, designed to reduce computational complexity while maintaining predictive accuracy. The model was trained and evaluated on 495 WSIs from the Sherlock-Lung study (70% training with 10% internal test set for 10-fold cross-validation, and 30% held-out validation set for final evaluation). For the held-out validation data, our model achieved high areas under the receiver operating characteristic curve [AUROC] values =0.84-0.93 for detecting 11 features: EGFR, KRAS, TP53, RBM10 mutations, MDM2 amplification, kataegis, CDKN2A deletion, ALK fusion, whole-genome doubling, and EGFR hotspot mutations (p.L858R and p.E746_A750del). Performance was low to moderate for tumor mutational burden (AUROC=0.67), APOBEC mutational signature (AUROC=0.57), and KRAS hotspot mutations (p.G12C: AUROC=0.74, p.G12V: AUROC=0.55, p.G12D: AUROC=0.43). Compared to results from established architectures such as Inception-v3 on the same WSIs, our model demonstrated significantly improved performance for most features. With further optimization, our model could support triaging for molecular testing and inform precision treatment strategies for NS-LUAD patients.