Leveraging SMARCA4 Dependency of Mantle Cell Lymphomas to Overcome BTK Inhibitor Resistance

Mantle cell lymphoma (MCL) is an uncommon lymphoid malignancy, accounting for 2.5–6% of all non-Hodgkin lymphomas. Covalent Bruton tyrosine kinase inhibitors (cBTKi), such as ibrutinib, zanubrutinib, and acalabrutinib, are mainstays of treatment relapsed MCL, and their use is emerging in the front-line setting. However, progression on cBTKi treatment is common, and these patients often experience more aggressive disease and a poor clinical outcome. Management of cBTKi-refractory MCL is non-standard and challenging. Pirtobrutinib, a highly selective, first-in-class reversible BTKi, has demonstrated clinical activity in relapsed/refractory (R/R) MCL, but responses only occur in about half of patients and the response duration is limited. Identifying relapse-prone features in MCL patients and improving BTKi-based therapeutic approaches is a critical area of research with significant unmet need.

In this context, through an unbiased CRISPR/Cas9 screening approach, we discovered a significant dependency of cBTKi-resistant, both TP53 wild type and mutant MCL cells, on SMARCA4, the common catalytic subunit of the mammalian BAF nucleosome remodeling complex. Notably, components of the BAF complex are mutated in at least 10% of MCL cases, with SMARCA4 mutations implicated in resistance to cBTKi combination treatment. Stable expression of SMARCA4 T910M mutant, a recurrent mutation in MCL, led to increased resistance to cBTKi in various MCL cell lines, highlighting the importance of SMARCA4 in MCL maintenance. We found that pharmacological inhibition of SMARCA4 by FHD-286, an allosteric SMARCA2/4 ATPase inhibitor, which is a clinical stage asset owned by Foghorn Therapeutics and currently under investigation in AML in combination with decitabine and cytarabine, potently induced cytotoxicity in MCL cells at low nanomolar ranges. Remarkably, MCL cells expressing the SMARCA4 T910M mutation exhibited even greater sensitivity to FHD-286 compared to those expressing wild-type SMARCA4. These findings suggest that targeting SMARCA4 may represent a novel therapeutic vulnerability in cBTKi-resistant MCL.

Mechanistically, our precision run-on (PRO)-seq combined with CUT&RUN analysis of cBTKi-resistant MCL cells revealed that SMARCA4 inhibition suppresses the transcription of a set of genes in the B cell receptor (BCR) signaling pathway (i.e., CD79A/B, SYK, BTK, RAC2, CARD11). We investigated whether maintaining active BCR signaling is a mechanism through which SMARCA4 supports the survival of MCL cells. By comparing cBTKi-resistant and sensitive isogenic MCL cell line pairs, we identified NR4A1 gene expression as a marker of activated BCR signaling, reflecting resistance to cBTKi. Both genetic and pharmacological targeting of SMARCA4 transcriptionally suppressed NR4A1 expression in cBTKi-resistant MCL cells, supporting its role in BCR signaling. Consistently, combining FHD-286 with pirtobrutinib led to a substantial synergistic cytotoxic effect in MCL cell lines and primary MCL cells. Altogether, our findings suggest that SMARCA4 plays a tumor maintenance role in MCL. Targeting SMARCA4 can be further exploited as a therapeutic strategy in cBTKi-resistant MCL and may be even more effective in SMARCA4-mutated MCL.