Molecular mechanisms and precision medicine in SMARCA4/BRG1-mutant lung cancers

Abstract

Mutations in subunits of the chromatin remodeling SWI/SNF complex are pervasive in cancer. Inactivation of SMARCA4/BRG1, the core ATPase subunit of mammalian SWI/SNF complexes, occurs at high frequency (15-20%) in non-small cell lung cancers. In this dissertation, two distinct lines of investigation were used to address the limited knowledge of the clinical and mechanistic implications of BRG1 loss in lung cancers. Using a combination of gain- and loss-of-function approaches, we demonstrated that deletion of BRG1 in lung cancers leads to increased activation of replication stress, genomic instability, and reduced chromatin accessibility. Gene expression profiles of BRG1-mutant lung cancers from patients revealed increased signatures related to replication stress responses (RSR) and pre-replication. Single-molecule assessment of replication fork dynamics in BRG1-deficient cells resulted in increased origin firing mediated by the pre-licensing protein CDC6. Quantitative mass spectrometry and co-immunoprecipitation assays showed that BRG1-containing SWI/SNF complexes interact with RPA complexes. BRG1-deficient lung cancers were sensitive to the pharmacological inhibition of ATR. These results suggest a role for BRG1 in promoting replication fork progression and preventing untimely origin firing. Our data implicate ATR signaling as a targetable synthetic lethal pathway in BRG1-deficient lung cancers. The consequences of Brg1 loss were also assessed in mouse models and in publicly available patient data sets. In vivo deletion of Brg1 in genetically engineered mouse models of lung adenocarcinoma increased tumor lesions and promoted high grade tumors. Heterozygous loss of Brg1 resulted in higher tumor burden compared to complete loss of Brg1, suggesting a haploinsufficient tumor suppressive role for BRG1. Loss of Brg1 in mouse tumors was associated with a significant increase in expression for the key immune evasion ligand Pd-l1, suggesting opportunities for immune checkpoint therapy for BRG1-mutant lung cancers. Analyses of synthetic lethality data from pan-cancer dependency maps confirmed that cancers in other tissues where BRG1 is frequently mutated are highly susceptible to ATR knockdown/ knockout. Overall, these studies provide novel mechanistic insight into the role of BRG1 in lung cancer and suggest that their dependency on ATR can be leveraged therapeutically and potentially expanded to BRG1-mutant cancers in other tissues.