Machine learning on MRI radiomic features: identification of molecular subtype alteration in breast cancer after neoadjuvant therapy

Objectives Recent studies have revealed the change of molecular subtypes in breast cancer (BC) after neoadjuvant therapy (NAT). This study aims to construct a non-invasive model for predicting molecular subtype alteration in breast cancer after NAT. Methods Eighty-two estrogen receptor (ER)–negative/ human epidermal growth factor receptor 2 (HER2)–negative or ER-low-positive/HER2-negative breast cancer patients who underwent NAT and completed baseline MRI were retrospectively recruited between July 2010 and November 2020. Subtype alteration was observed in 21 cases after NAT. A 2D-DenseUNet machine-learning model was built to perform automatic segmentation of breast cancer. 851 radiomic features were extracted from each MRI sequence (T2-weighted imaging, ADC, DCE, and contrast-enhanced T1-weighted imaging), both in the manual and auto-segmentation masks. All samples were divided into a training set ( n = 66) and a test set ( n = 16). XGBoost model with 5-fold cross-validation was performed to predict molecular subtype alterations in breast cancer patients after NAT. The predictive ability of these models was subsequently evaluated by the AUC of the ROC curve, sensitivity, and specificity. Results A model consisting of three radiomics features from the manual segmentation of multi-sequence MRI achieved favorable predictive efficacy in identifying molecular subtype alteration in BC after NAT (cross-validation set: AUC = 0.908, independent test set: AUC = 0.864); whereas an automatic segmentation approach of BC lesions on the DCE sequence produced good segmentation results (Dice similarity coefficient = 0.720). Conclusions A machine learning model based on baseline MRI is proven useful for predicting molecular subtype alterations in breast cancer after NAT. Key Points • Machine learning models using MRI-based radiomics signature have the ability to predict molecular subtype alterations in breast cancer after neoadjuvant therapy, which subsequently affect treatment protocols. • The application of deep learning in the automatic segmentation of breast cancer lesions from MRI images shows the potential to replace manual segmentation..