Abstract PO-082: Automated tumor segmentation, grading, and analysis of tumor heterogeneity in preclinical models of lung adenocarcinoma
Authors: Lockhart John H. , Ackerman Hayley D. , Lee Kyubum , Abdalah Mahmoud , Davis Andrew , Montey Nicole , Boyle Theresa , Saller James , Keske Ayensur , Hänggi Kay , Ruffell Brian , Stringfield Olya , Tan Aik Choon , Flores Elsa R. 
Published: March 2021

Abstract
Preclinical mouse models of lung adenocarcinoma are invaluable for the discovery of molecular drivers of tumor formation, progression, and therapeutic resistance. Histological analyses of these preclinical models require significant investments of time and training to ensure accuracy and consistency. Analysis by a clinical pathologist is the gold standard in this approach, but may be difficult to obtain due to the cost and availability of their services. As an alternative we have developed a digital pathology tool to identify, segment, grade, and analyze tumors in mouse models of lung adenocarcinoma. This convolutional neural network (CNN) model, based on ResNet18, was trained to classify normal lung tissue, normal airways, and the different grades (1 – 4) of lung adenocarcinoma from 100,000 224 × 224 pixel image patches (~16,000 patches per class). Our training dataset was constructed from whole slide images of hematoxylin and eosin stained lung sections from 4 different mouse models of lung adenocarcinoma with oncogenic Kras (KrasG12D/+), in combination with oncogenic p53 mutations (KrasG12D/+; p53R172H/+ and KrasG12D/+;p53R270H/+), or with the loss of the tumor suppressive TAp73 (KrasG12D/+;TAp7fltd/fltd). Our CNN demonstrated a strong correspondence with human pathologists on our holdout dataset, achieving a micro-F1 score of 0.81 on a pixel-by-pixel basis. As a test of our CNN, we analyzed two mouse models to better understand the role of TAp73 in lung adenocarcinoma: KrasG12D/+ (“K”) and KrasG12D/+;TAp73fltd/fltd (“TK”). Both human raters and our CNN reported a significant increase in the tumor burden of the compound mutant “TK” mice compared to the single mutant “K” mice. According to our CNN, this increased tumor burden was driven primarily by an increase in tumor size and not an increased number of tumors in “TK” mice. Because our CNN can assign different grades to regions within the same image patch and tumor, we also uncovered a high degree of intratumor heterogeneity that was not reported by the human pathologists, who are trained to assign one grade to a single tumor with a bias for the highest grade present in a given tumor. The finer grading resolution allowed our CNN to uncover the increased tumor size observed in the “TK” mice was due to expansion of Grade 2 regions (characterized by enlarged nuclei without irregular shape) within tumors that would be considered a higher grade by pathologists. Our CNN also provides a detailed map of tumor grades overlaid on the H&E images used for analysis, allowing for precise targeting of regions within tumors with other assays. We are currently utilizing these outputs in conjunction with other assays, such as spatial transcriptomic analysis and immunohistochemistry, to investigate the molecular mechanisms that underlie the expansion of Grade 2 tumor regions in “TK” mice. Future work will expand this tool into a multidimensional digital pathology pipeline that can accelerate current investigations and reveal new therapeutic targets and prognostic markers.
Citation Format: John H. Lockhart, Hayley D. Ackerman, Kyubum Lee, Mahmoud Abdalah, Andrew Davis, Nicole Montey, Theresa Boyle, James Saller, Ayensur Keske, Kay Hänggi, Brian Ruffell, Olya Stringfield, Aik Choon Tan, Elsa R. Flores. Automated tumor segmentation, grading, and analysis of tumor heterogeneity in preclinical models of lung adenocarcinoma [abstract]. In: Proceedings of the AACR Virtual Special Conference on Artificial Intelligence, Diagnosis, and Imaging; 2021 Jan 13-14. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(5_Suppl):Abstract nr PO-082.