Abstract 6233: A deep learning pipeline to capture the prognostic immune responses in lymph nodes of breast cancer patients
Authors: Verghese Gregory , Li Mengyuan , Lohan Amit , Cherian Nikhil , Rane Swapnil , Liu Fangfang , Shah Aekta , Gazinska Pat , Thavaraj Selvam , Sethi Amit , Grigoriadis Anita 
Published: June 2022

Abstract
Capturing tumor infiltrating leucocytes (TILS) and systemic immune responses in breast cancer informs disease progression and optimal treatment management. We have previously shown that morphological alterations in axillary lymph nodes (LNs), namely the formation of germinal centers in cancer-free LNs, adds prognostic value to TILs in triple negative breast cancer patients (TNBC) for the development of distant metastasis. Extending manual assessment of LNs beyond the detection of cancer requires the integration of robust deep learning pipelines into the digital pathology workflow. In this retrospective study, we used 1,100 Haematoxylin & Eosin-stained (H&E) Whole Slide Images (WSI) from Guy’s Hospital (London, UK) of metastatic and cancer-free LNs from 151 patients (100 N+) enriched for triple-negative or HER2-positive breast cancer to implement a supervised deep learning pipeline. A subset of 114 WSI, along with 5 breast cancer LN WSIs from each of Barts Hospital (London, UK) and Tianjin University Hospital (Tianjin, China), and 5 head and neck squamous cell carcinomas LN WSI (Guy’s Hospital) were used to develop, train and evaluate the segmentation task. For training Fully Convolutional Networks (FCNs), WSIs manually annotated for both germinal centers and sinuses formed a ground-truth set. Three FCNs were implemented: (i) a standard U-Net architecture; (ii) a U-Net model with an attention gate mechanism; and (iii) a multiscale-U-Net network (MSA-U-Net) that encodes, in parallel, a feature representation of the image at multiple resolutions. The MSA-U-Net achieved the best performance with an average dice score of 0.85 for germinal centers and 0.75 for sinuses. In comparison, the average dice score amongst 4 pathologists assessing 25 LN WSI for germinal centers and sinuses, was 0.67 and 0.61 respectively, demonstrating the robustness of the MSA-U-Net model. To quantify germinal centers and sinuses in LNs across the entire cohort, the trained MSA-U-Net was used in an inference step on all 1,100 WSI. The detected morphological features were initially localized within LNs using image thresholding and contouring techniques, and quantitatively assessed based on their number, area, shape, and Shannon diversity. We found significant morphological differences in metastatic and cancer-free LNs between N0 and N+ patients, with the latter displaying larger germinal centers with more irregular shapes especially in their metastatic LNs. In addition, we found differences in the Sinus area between LNs containing GCs and those without. Here, we propose a robust deep learning pipeline based on a multiscale FCN framework to automatically detect, localize and quantify histopathological immune features in WSI of LNs. By applying our pipeline to LNs of cancer patients, such as breast or head and neck, in prospective studies or clinical trials, we will further evaluate their prognostic and predictive values.
Citation Format: Gregory Verghese, Mengyuan Li, Amit Lohan, Nikhil Cherian, Swapnil Rane, Fangfang Liu, Aekta Shah, Pat Gazinska, Selvam Thavaraj, Amit Sethi, Anita Grigoriadis. A deep learning pipeline to capture the prognostic immune responses in lymph nodes of breast cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6233.