D108-24 A Canonical Role of Smad4 in Safeguarding Three-dimensional (3d) Genome Architecture to Suppress Lung Tumorigenesis

Rationale

Dysregulation of three-dimensional (3D) genome architecture is a hallmark of cancer, yet the mechanisms by which its disruption drives tumorigenesis remain incompletely understood. Here, we demonstrated that SMAD family member 4 (SMAD4) regulated 3D genome organization through its canonical transcription factor activity by directly binding chromatin, thereby suppressing lung tumorigenesis.

Methods

Hi-C analyses of human lung tumors identify SMAD4 as a potential regulator of 3D genome integrity. Using PTEN-deficient human bronchial epithelial cells and genetically engineered mouse models,

Results

we showed that SMAD4 loss induced widespread reorganization of chromatin compartments, topologically associating domain (TAD) boundaries, and chromatin loops, leading to oncogenic transcriptional rewiring during early tumorigenesis. Mechanistically, SMAD4 directly bound chromatin loops and spatially connected gene promoters with active or repressive regulatory elements to control transcription. Upon SMAD4 ablation, enhancer-promoter rewiring dysregulated critical oncogenic drivers, including E74 like ETS transcription factor 3 (ELF3). Functional manipulation of an SMAD4-regulated ELF3-associated chromatin loop altered ELF3 expression and cell survival both in vitro and in vivo.

Conclusion

Collectively, our findings establish SMAD4 as a direct regulator of 3D genome architecture through classical transcription factor binding to chromatin loops and reveal enhancer-promoter rewiring as a key mechanism driving lung tumorigenesis and a potential therapeutic vulnerability in SMAD4-deficient lung cancer.

This abstract is funded by: Natural Science Foundation (NSF) of China (General Grant: 82172899 and 82472637), the NSF of Zhejiang Province (Continuation Grant of Distinguished Young Scholars: LRG26H160001), Noncommunicable Chronic Diseases-National Science and Technology Major Project (2023ZD0502900/2023ZD0502902 and 2023ZD0507500/2023ZD0507501), Dr. Li Dak Sum & Yip Yio Chin Development Fund for Regenerative Medicine, Zhejiang University, the Open Fund of Zhejiang Provincial Key Laboratory of Pulmonology (KF202302), ZJE seed funding, ZJE 2024 International Campus Talent Special Funding Program, ZJE-UoE Joint Research Project, and Startup Funding of Tenure-track Assistant Professor of Zhejiang University. This work was also supported by the Zhejiang Province Pioneer Research and Development Project (No.2025C02091).