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28 Using AI to predict molecular subtype from histopathology slides in endometrial cancer

Published online by Cambridge University Press:  11 April 2025

Vincent Wagner
Affiliation:
University of Iowa
Jesus Gonzalez
Affiliation:
University of Iowa
Bosquet
Affiliation:
Division of Gynecologic Oncology, University of Iowa
Michael Goodheart
Affiliation:
Division of Gynecologic Oncology, University of Iowa
Xiaodong Wu
Affiliation:
Department of Electrical and Computer Engineering, University of Iowa
Megan Samuelson
Affiliation:
Department of Surgical Pathology, University of Iowa
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Abstract

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Objectives/Goals: Endometrial cancer is one of the few cancers that has both a rising incidence and mortality rate. Molecular classification is becoming more important for the management of endometrial cancer but the ability to translate this into clinical practice remains constrained. Our goal is to use AI to predict the molecular subtype from histopathology slides. Methods/Study Population: We utilized the open source endometrial cancer datasets from The Cancer Genome Atlas (TCGA) (N = 387) and Cancer Proteomics Transcriptomic Tumor Analysis Consortium (CPTAC) (N = 135) to develop and train a vision transformer AI model. We used a proprietary cohort of patients (N = 548) for external validation. Whole slide images (WSI) and molecular subtype data were collected. Subtypes include POLE ultramutated (POLE), microsatellite instability (MSI-H), copy-number low (CNV-L), and copy-number high (CNV-H). WSI were preprocessed, and features were extracted. Modified STAMP protocol was used in training, utilizing a pretrained foundation transformer model (Virchow2). Cross-validation of the TCGA was used for initial training, followed by testing on the CPTAC dataset and validation on our proprietary cohort. Results/Anticipated Results: Fivefold cross-validation of the TCGA database (60% training, 20% testing, and 20% validation) developed a best overall model with a mean AUC of 0.74 (POLE 0.78, MSI-H 0.76, CNV-H 0.86, CNV-L 0.77). Overall precision 0.58, recall 0.55. CNV-H was the subtype with the most accurate prediction. CPTAC holdout testing revealed moderately high AUC (POLE 0.63, MSI-H 0.62, CNV-H 0.98, and CNV-L 0.76). Overall precision 0.54 and recall 0.58. Again, CNV-H was the most accurate prediction. Validation on our proprietary cohort revealed a drop in performance with overall mixed results by AUC (POLE 0.50, MSI-H 0.69, CNV-H 0.78, and CNV-L 0.61). Overall precision 0.57, recall 0.45. Again, CNV-H with the most accurate prediction but F1 score dropped from 0.77 in the CPTAC to 0.47 on validation. POLE was the least accurate prediction subtype. Discussion/Significance of Impact: The CNV-H subtype demonstrated robust performance, suggesting the model effectively captures the features associated with this subtype. CNV-L had moderate performance. MSI-H and POLE were notably lower. WSI-based AI models show translational potential for subtype prediction in the management of endometrial cancer but more work is necessary.

Information

Type
Informatics, AI and Data Science
Creative Commons
Creative Common License - CCCreative Common License - BYCreative Common License - NCCreative Common License - ND
This is an Open Access article, distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives licence (https://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is unaltered and is properly cited. The written permission of Cambridge University Press must be obtained for commercial re-use or in order to create a derivative work.
Copyright
© The Author(s), 2025. The Association for Clinical and Translational Science