Interpretable deep learning model to predict the molecular classification of endometrial cancer from haematoxylin and eosin-stained whole-slide images: a combined analysis of the PORTEC randomised trials and clinical cohorts

Fremond, S; Andani, S; Barkey Wolf, J; Dijkstra, J; Melsbach, S; Jobsen, JJ; Brinkhuis, M; Roothaan, S; Jurgenliemk-Schulz, I; Lutgens, LCHW; Nout, RA; van der Steen-Banasik, EM; de Boer, SM; Powell, ME; Singh, N; Mileshkin, LR; Mackay, HJ; Leary, A; Nijman, HW; Smit, VTHBM; Creutzberg, CL; Horeweg, N; Koelzer, VH; Bosse, T

Author(s): Fremond, S; Andani, S; Barkey Wolf, J; Dijkstra, J; Melsbach, S; Jobsen, JJ; Brinkhuis, M; Roothaan, S; Jurgenliemk-Schulz, I; Lutgens, LCHW; Nout, RA; van der Steen-Banasik, EM; de Boer, SM; Powell, ME; Singh, N; Mileshkin, LR; Mackay, HJ; Leary, A; Nijman, HW; Smit, VTHBM; Creutzberg, CL; Horeweg, N; Koelzer, VH; Bosse, T;
Details: Publication Year 2023-02,Volume 5,Issue #2,Page e71-e82
Journal Title: Lancet Digital Health
Publication Type: Research article
Abstract: BACKGROUND: Endometrial cancer can be molecularly classified into POLE(mut), mismatch repair deficient (MMRd), p53 abnormal (p53abn), and no specific molecular profile (NSMP) subgroups. We aimed to develop an interpretable deep learning pipeline for whole-slide-image-based prediction of the four molecular classes in endometrial cancer (im4MEC), to identify morpho-molecular correlates, and to refine prognostication. METHODS: This combined analysis included diagnostic haematoxylin and eosin-stained slides and molecular and clinicopathological data from 2028 patients with intermediate-to-high-risk endometrial cancer from the PORTEC-1 (n=466), PORTEC-2 (n=375), and PORTEC-3 (n=393) randomised trials and the TransPORTEC pilot study (n=110), the Medisch Spectrum Twente cohort (n=242), a case series of patients with POLE(mut) endometrial cancer in the Leiden Endometrial Cancer Repository (n=47), and The Cancer Genome Atlas-Uterine Corpus Endometrial Carcinoma cohort (n=395). PORTEC-3 was held out as an independent test set and a four-fold cross validation was performed. Performance was measured with the macro and class-wise area under the receiver operating characteristic curve (AUROC). Whole-slide images were segmented into tiles of 360 mum resized to 224 x 224 pixels. im4MEC was trained to learn tile-level morphological features with self-supervised learning and to molecularly classify whole-slide images with an attention mechanism. The top 20 tiles with the highest attention scores were reviewed to identify morpho-molecular correlates. Predictions of a nuclear classification deep learning model serve to derive interpretable morphological features. We analysed 5-year recurrence-free survival and explored prognostic refinement by molecular class using the Kaplan-Meier method. FINDINGS: im4MEC attained macro-average AUROCs of 0.874 (95% CI 0.856-0.893) on four-fold cross-validation and 0.876 on the independent test set. The class-wise AUROCs were 0.849 for POLE(mut) (n=51), 0.844 for MMRd (n=134), 0.883 for NSMP (n=120), and 0.928 for p53abn (n=88). POLE(mut) and MMRd tiles had a high density of lymphocytes, p53abn tiles had strong nuclear atypia, and the morphology of POLE(mut) and MMRd endometrial cancer overlapped. im4MEC highlighted a low tumour-to-stroma ratio as a potentially novel characteristic feature of the NSMP class. 5-year recurrence-free survival was significantly different between im4MEC predicted molecular classes in PORTEC-3 (log-rank p<0.0001). The ten patients with aggressive p53abn endometrial cancer that was predicted as MMRd showed inflammatory morphology and appeared to have a better prognosis than patients with correctly predicted p53abn endometrial cancer (p=0.30). The four patients with NSMP endometrial cancer that was predicted as p53abn showed higher nuclear atypia and appeared to have a worse prognosis than patients with correctly predicted NSMP (p=0.13). Patients with MMRd endometrial cancer predicted as POLE(mut) had an excellent prognosis, as do those with true POLE(mut) endometrial cancer. INTERPRETATION: We present the first interpretable deep learning model, im4MEC, for haematoxylin and eosin-based prediction of molecular endometrial cancer classification. im4MEC robustly identified morpho-molecular correlates and could enable further prognostic refinement of patients with endometrial cancer. FUNDING: The Hanarth Foundation, the Promedica Foundation, and the Swiss Federal Institutes of Technology.
Publisher: Elsevier
Keywords: Female; Humans; Eosine Yellowish-(YS); Hematoxylin; *Deep Learning; Pilot Projects; *Endometrial Neoplasms/diagnosis/genetics/pathology
Department(s): Medical Oncology
PubMed ID: 36496303
Publisher's Version: https://doi.org/10.1016/S2589-7500(22)00210-2
Open Access at Publisher's Site: https://doi.org/10.1016/s2589-7500(22)00210-2
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2023-04-06 06:53:48

Last Modified: 2023-04-17 11:52:08