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28 Using AI to predict molecular subtype from histopathology slides in endometrial cancer
Abstract   Open access   Peer reviewed

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

Vincent Wagner, Jesus Gonzalez Bosquet, Michael Goodheart, Xiaodong Wu and Megan Samuelson
Journal of clinical and translational science, Vol.9(s1), pp.10-11
04/01/2025
DOI: 10.1017/cts.2024.719
PMCID: PMC12050797
url
https://doi.org/10.1017/cts.2024.719View
Published (Version of record) Open Access

Abstract

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.
 Endometrial Cancer Proteomics Uterine Cancer Endometrium Histopathology Microsatellite instability Population studies Predictions Transcriptomics

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