CRISPR-Induced NUT Suppression Promotes Differentiation and Enhances Trop2-Targeted Immunocytokine Response in NUT Carcinoma

Juyoung Choi , Daesik Kim , Joo Youn Oh , Hee Geon Park , Hwa Lin Yi , Yurimi Lee , Hoyeon Jeong , Jiyoung Song , Minjung Sung , Eun Sol Chang , Kyungsoo Jung , Saehyung Lee , Young Kee Shin , Se‐Hoon Lee , Christopher A. French , Mi-Sook Lee , Yoon–La Choi ·

YOU? · · 2025 · Open Access · · DOI: https://doi.org/10.1101/2025.10.28.685224

NUT carcinoma (NC) is an aggressive malignancy driven by NUTM1 gene rearrangements with limited therapeutic options. Here, we show that direct suppression of NUTM1 using CRISPR/Cas9 induces squamous-like differentiation and upregulates TROP2 expression in NC cells. Building on this finding, we developed a TROP2–interferon beta (IFN-β) mutein immunocytokine that selectively targets TROP2-expressing tumors. Combined NUTM1 suppression and TROP2-targeted immunotherapy synergistically enhanced cytotoxic and immune-mediated responses in vitro . Transcriptomic and spatial analyses of NC patient tumors revealed that differentiation status correlates with TROP2 expression, upregulated immune pathways, and favorable clinical outcomes. Our results suggest that overcoming differentiation blockade not only alters tumor phenotype but also creates a more immune-permissive microenvironment. These findings highlight the therapeutic potential of sequential tumor reprogramming followed by targeted immunotherapy in treating NC and propose a broader strategy for overcoming differentiation blockade in fusion-driven cancers.