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Selective Sensitivity of Ph-like B-ALL to BRG1 Inhibition Reveals a Novel Targeted Therapy Strategy

V. A. Ayyadevara,Shikha Gaur,Ashley Paik,Ria Perencsik,Monika M. Toma,Gerald Wertheim,H. Geng,Tomasz Skorski,Srividya Swaminathan,C. Hurtz

Published 2025 in bioRxiv

ABSTRACT

Despite therapeutic advances, high-risk subtypes of B-cell acute lymphoblastic leukemia (B-ALL) such as Philadelphia chromosome-like (Ph-like) and KMT2A-rearranged (KMT2A-R) remain a formidable clinical challenge. BRG1 (gene name SMARCA4), the ATPase subunit of the SWI/SNF chromatin-remodeling complex, has been extensively studied in solid tumors, where inactivating mutations are linked to aggressive disease and poor prognosis. Although BRG1 is known to be essential for early B cell development, its role in B-ALL remains poorly understood. Therefore, we investigated the therapeutic relevance of BRG1 in high-risk B-ALL. Meta-analysis of gene expression data revealed that BRG1-inactivating mutations are exceedingly rare (0.35%) in B-ALL, suggesting that intact BRG1 function may be critical for leukemogenesis. Subtype-specific analyses revealed that elevated BRG1 expression is associated with significantly shorter overall survival in children with Ph-like B-ALL, while the opposite trend was observed in KMT2A-R B-ALL. We confirmed higher BRG1 expressions in Ph-like compared to KMT2A-R B-ALL via gene expression analysis, RT-PCR, and Western blotting. The pharmacologic inhibition of BRG1 using two selective inhibitors, BRM014 and FHD-286, revealed marked sensitivity in Ph-like B-ALL cell lines, whereas KMT2A-R B-ALL was resistant. Mechanistically, we found that BRG1 inhibition results in cell cycle arrest via downregulation of cell cycle regulators (CCND3, CDK4, CDK6, E2F1, and MYC) and upregulation of the cell cycle inhibitor CDKN1B (p27). Importantly, treatment with FHD-286 significantly prolonged the survival of NSG mice engrafted with Ph-like B-ALL cells. Taken together, these findings establish BRG1 as a critical, subtype-specific dependency in Ph-like B-ALL and demonstrate that its pharmacologic inhibition effectively suppresses leukemic cell proliferation through induction of cell cycle arrest. The pronounced in vitro sensitivity and improved in vivo survival upon BRG1 inhibition provide compelling preclinical evidence for its therapeutic targeting. These results support the advancement of BRG1-directed strategies as a viable treatment approach for patients with Ph-like B-ALL, with the potential to improve outcomes in this high-risk population. Highlights Higher levels of BRG1 correlate to poor clinical outcomes in Ph-like but KMT2A-R B-ALL Inhibition of BRG1 induces cell cycle arrest in Ph-like cells in vitro and extends the survival of mice in pre-clinical in vivo studies Graphical Abstract

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