Abstract PO4-07-04: Breast Cancer HER2 Status Prediction from Hematoxylin-Eosin Stained Images Using Point Cloud Transformer
Authors: Li Bao , Liu Zhenyu , Du Yang , Tian Jie 
Published: May 2024

Background: Human epidermal growth factor receptor-2 (HER2) status is a key factor in determining the treatment strategy for breast cancer patients. Patients with HER2-positive status are more likely to benefit from HER2-targeted therapy, leading to improved prognosis. In current routine diagnostic practice, pathologists utilize Hematoxylin-Eosin (HE) stained tumor tissues for histopathological assessment. Subsequently, IHC assessment and/or FISH test are performed to evaluate the HER2 status. However, manual assessment results may be affected by tissue usability and observer-subjectivity. Therefore, there is a necessity to predict the HER2 status directly from HE images to minimize time and cost while ensuring enhanced consistency.

Methods: We identified 608 HE diagnostic slides with HER2 status from The Cancer Genome Atlas in breast cancer (TCGA-BRCA). It contains 474 HER2-positive slides (IHC 3+, IHC 2+ and FISH positive) and 134 HER2-negative slides (IHC 0, IHC 1+, IHC 2+ and FISH negative). To analyze these slides, we first tiled the HE images into patches with a fixed size of 256 × 256 at 20 × magnification. Then the patch-level feature was derived from a self-supervised pretrained transformer. Meanwhile, artificial intelligence (AI) methods are adopted to predict HER2 status from HE images. To capture the long-distance patch relations within a slide, we represented the patches as distinct points and utilized the Point Cloud Transformer model for HER2 status prediction. Specifically, 1024 patches (points) in each slide were randomly selected and input into the Point Cloud Transformer. This process yielded a slide-level prediction result for the HER2 status. Furthermore, Graph Attention Network (GAT), Graph Sample and Aggregate Network (Graph SAGE), and hierarchical Point Cloud Network (PointNet++) were adopted to compare the effectiveness of HER2 status prediction using Point Cloud Transformer. Of note that Point Cloud Transformer incorporated attention mechanisms for point aggregation compared to PointNet++.

Results: The Point Cloud Transformer was trained with 5-fold cross-validation, and the area under the curve (AUC) of the receiver operating characteristic (ROC) curve was reported. The performance of point-based models outperformed the graph-based models. And the Point Cloud Transformer achieved the highest AUC of 0.7496 among all AI models. The detailed AUC for each AI model was shown in Table 1.

Conclusion: Our study revealed that the HER2 status can be predicted directly from HE images without using IHC images. Furthermore, point-based models have demonstrated the ability to capture long-distance relations among patches, surpassing graph-based models in terms of prediction performance. To further enhance performance, we adopted a better point aggregation method, such as the Point Cloud Transformer, which held promise for further improving the accuracy of predictions in the future.

Table 1: AUC of HER2 status prediction from HE images in the TCGA-BRCA dataset Method GAT Graph SAGE PointNet++ Point Cloud Transformer AUC 0.6640 0.6737 0.7201 0.7496

Citation Format: Bao Li, Zhenyu Liu, Yang Du, Jie Tian. Breast Cancer HER2 Status Prediction from Hematoxylin-Eosin Stained Images Using Point Cloud Transformer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-07-04.