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ArticleCancer medicine2026

TFE3-DualNet: An Interpretable Foundation Model-Based Deep Learning Ensemble for Diagnosing TFE3-Rearranged Renal Cell Carcinoma From Whole-Slide Images in a Two-Center Cohort.

Yu-Hang Chen, Quan-Hui Xu, Hao-Hua Yao, Ke-Zhi Liu, Cheng-Peng Gui, Liang-Min Fu, Ying-Han Wang, Jiang-Quan Zhu, Jun-Cai Li, Min-Yu Chen and 8 more

Abstract readMulticenter Study
In one paragraph

Article in Cancer medicine, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

18 authors.

Yu-Hang ChenDepartment of Genitourinary Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China.ORCID https://orcid.org/0000-0002-2931-9934
Quan-Hui XuDepartment of Pathology, New York University Grossman School of Medicine, New York, New York, USA.ORCID https://orcid.org/0000-0001-5560-0861
Hao-Hua YaoDepartment of Urology, Guangdong Provincial People's Hospital, Guangzhou, Guangdong, China.ORCID https://orcid.org/0000-0003-0970-1295
Ke-Zhi LiuDepartment of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.ORCID https://orcid.org/0000-0003-4894-3713
Cheng-Peng GuiDepartment of Urology, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China.
Liang-Min FuDepartment of Urology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.ORCID https://orcid.org/0000-0001-8038-4742
Ying-Han WangDepartment of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
Jiang-Quan ZhuDepartment of Urology, Guangzhou Women and Children's Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Guangzhou, Guangdong, China.ORCID https://orcid.org/0000-0001-9502-7721
Jun-Cai LiFirst Clinical Medical College, Tianjin Medical University, Tianjin, China.ORCID https://orcid.org/0009-0005-1458-2106
Min-Yu ChenDepartment of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
Kang-Bo HuangDepartment of Urology, Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, China.
Han-Sen LinDepartment of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
Bing LiaoDepartment of Pathology, Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, China.ORCID https://orcid.org/0000-0003-4613-7929
Yun CaoDepartment of Pathology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
Jin-Huan WeiDepartment of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.ORCID https://orcid.org/0000-0003-0179-6250
Peng-Ju LiDepartment of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
Jun-Hang LuoDepartment of Urology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.ORCID https://orcid.org/0000-0002-5706-0990
Jia-Zheng CaoDepartment of Urology, Jiangmen Central Hospital, Jiangmen, Guangdong, China.ORCID https://orcid.org/0000-0002-6916-5503

Funding

Guangdong Basic and Applied Basic Research Foundation (Guangdong-Jiangmen Joint Fund) 2025A1515140247Guangzhou Science and Technology Program (Key Research and Development Project) 2025B03J0091National Natural Science Foundation of China 82373433National Natural Science Foundation of China 82573729Tianjin Health Science and Technology Project TJWJ2026QN015Tianjin Key Medical Discipline Construction Project TJYXZDXK-3-003A
6 · The paper itself

Abstract

backgroundTFE3-rearranged renal cell carcinoma (TFE3-rRCC) is a rare, aggressive subtype that predominantly affects adolescents and young adults. Its marked morphologic heterogeneity can delay recognition and downstream confirmatory testing.

methodsWe assembled a two-center retrospective cohort of patients < 30 years with renal cell carcinoma (n = 228; 59 TFE3-rRCC), using fluorescence in situ hybridization (FISH) as the reference standard. Model development was performed in a development cohort (n = 129), followed by independent external validation (n = 99). We developed TFE3-DualNet, an ensemble of weakly supervised CLAM models trained on routine hematoxylin and eosin (H&E) whole-slide images (WSIs) using patch embeddings extracted from two pathology foundation models (UNI and CHIEF). We compared performance with three immunohistochemistry (IHC) scoring methods and a feature-fusion CLAM baseline using concatenated H&E-derived UNI and CHIEF features, and assessed interpretability by attention mapping.

resultsIn the external validation cohort, TFE3-DualNet achieved an area under the receiver operating characteristic curve (AUROC) of 0.932, with accuracy 0.879, sensitivity 0.893, and specificity 0.873. The model outperformed IHC scoring methods (AUROC 0.793-0.819; all p < 0.05) and exceeded the feature-fusion baseline (AUROC 0.906). Attention hotspots localized to diagnostically relevant tumor regions and showed concordance with TFE3 IHC patterns.

conclusionsTFE3-DualNet showed encouraging performance as an interpretable H&E WSI-based screening model for TFE3-rRCC in young patients, supporting its potential use to prioritize confirmatory testing and pathologist review in routine diagnostic workflows.

Indexed as

Basic Helix-Loop-Helix Leucine Zipper Transcription FactorsCarcinoma, Renal CellDeep LearningGene RearrangementKidney NeoplasmsAdolescentAdultFemaleHumansImmunohistochemistryIn Situ Hybridization, FluorescenceMaleRetrospective StudiesYoung AdultBasic Helix-Loop-Helix Leucine Zipper Transcription FactorsTFE3 protein, humancomputational pathologyfoundation modelTFE3‐rearranged renal cell carcinomawhole‐slide image

Identifiers

PMID42543505
PMCPMC13429883

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.