Abstract 5136: Unraveling SMARCA1’s role in cancer progression, drug resistance, and muscle differentiation through EMT-related signaling, TGF-β pathway, and key transcription factors SNAI1 and EGR1

SMARCA1, a member of the ISWI family of ATP-dependent chromatin remodelers, plays a crucial role in organizing DNA structure and regulating gene expression. The role of SMARCA1 in either normal skeletal muscle or rhabdomyosarcoma (RMS) development has not previously been explored. RMS, an aggressive soft tissue cancer, arises from cells resembling skeletal muscle precursor cells and exhibits invasive behavior. In this study, we conducted an integrated analysis of RNA-seq, ATAC-seq, and CUT&RUN data from RH30 cells, a PAX fusion-positive alveolar RMS line, with and without SMARCA1. This comprehensive data integration revealed that SMARCA1 knockout (KO) cells showed significant changes in gene expression and chromatin accessibility. Key genes such as TGFBR1, MYOG, and SMARCD3, critical for muscle differentiation, were highly active in normal RH30 cells but markedly reduced in SMARCA1 KO cells, underscoring SMARCA1’s role in supporting genetic pathways essential for muscle growth, survival, and differentiation. Additionally, SMARCA1 influenced regulatory factors, including SNAI1, EGR1, PTEN, TBX2, and P53. Interestingly, SMARCA1 appears to interact with HDAC2, and combined inhibition of SMARCA1 and HDAC2 has shown promise in overcoming drug resistance in these models. Further cell survival assays revealed that SMARCA1 KO cells are particularly sensitive to the HDAC2 inhibitor Mocetinostat and the MEK inhibitor Trametinib, proposing that targeting SMARCA1 in combination with HDAC2 or MEK inhibition could be an effective therapeutic approach for RMS. Our integrated analysis also links SMARCA1 to regulatory genes and transcription factors such as SNAI1, EMC1, PPP2R5C, EGR1, EYA2, SMARCA4, MYCN, CDK4, and NFKB2, with SMARCA1 enriched on the DNA of these genes. These factors are essential for EMT, cell adhesion, and key cancer-related pathways, including MAPK, WNT, PI3K, and TGF-β. Additionally, SMARCA1 KO cells responded differently to both canonical and non-canonical TGF-β pathway inhibitors, including SB505124 (TGFBR1 inhibitor), the PI3K-mTOR inhibitor Dactolisib, and Withaferin A (NF-κB inhibitor). Notably, these TGF-β pathway inhibitors effectively overcame resistance in ARMS cells with SMARCA1 expression, exposing specific vulnerabilities in these otherwise resistant cells. Together, our findings suggest that targeting both canonical and non-canonical TGF-β pathways, alongside SMARCA1, presents promising therapeutic strategies for overcoming drug resistance and potentially limiting RMS progression. Citation Format: Ashwaq K. Aljabri, Yuliya Kriga, Juan Manuel Caravaca, Jyoti Shetty, Bao Tran, Matthew Geisler, Judith K. Davie, Marielle E. Yohe. Unraveling SMARCA1’s role in cancer progression, drug resistance, and muscle differentiation through EMT-related signaling, TGF-β pathway, and key transcription factors SNAI1 and EGR1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5136.