SWI/SNF-associated DPF1 is a Unique Transcriptional Regulator of Malignant Peripheral Nerve Sheath Tumors

Background: Malignant peripheral nerve sheath tumors (MPNST) are rare soft tissue sarcomas that are typically therapy resistant and associated with a poor prognosis. Genetic aberrations of the polycomb repressive complex 2 (PRC2) occur in up to 75% of MPNST cases. PRC2 functions antagonistically to SWI/SNF protein complexes, regulating expression of target loci in a dynamic relationship that is critical to normal cellular development and maintenance of cell identity. The consequences of PRC2 loss on chromatin state maintained by SWI/SNF in MPNST is unexplored. Therefore, this study used functional genomics to elucidate the role of SWI/SNF in MPNST. Methods: To define the transcriptional regulatory role of SWI/SNF complexes in MPNST, SWI/SNF components were targeted via a CRISPR knock-out (KO) screen combined with a single cell RNA sequencing (RNAseq) readout. Genes of interest highlighted by this screen were further investigated using bulk CRISPR RNAseq. Phenotypic effects of the expression of these genes were studied using loss-of-function assays coupled with colony formation assays. SWI/SNF complex heterogeneity was characterized using glycerol gradient sedimentation, co-immunoprecipitation (co-IP), and mass spectrometry experiments. Results: The investigation of SWI/SNF transcriptional regulation in MPNST highlighted the Double PHD Finger family proteins (DPF1,2,3) as regulating distinct downstream targets. Notably, DPF1 had a unique transcriptional profile compared to other SWI/SNF components. Bulk CRISPR KO RNAseq confirmed these findings and highlighted a specific set of DPF1 target genes including many long non-coding RNAs. The phenotypic role of DPF1 in MPNST was investigated using in vitro siRNA and CRISPR experiments, where DPF1 KO reduced proliferation and viability of MPNST cells in both 2D and 3D cell culture assays. Further, DPF1 was found contribute to anchorage independent cell growth of MPNST cells using soft agar assays. Glycerol gradient sedimentation assays demonstrated that DPF1 co-migrated with core components of a SWI/SNF complex known as canonical BAF (cBAF) and not the alternate GBAF and PBAF SWI/SNF complexes. These findings were further validated using co-immunoprecipitation assays where core the SWI/SNF ATPase, SMARCA4, pulled down DPF1, while components unique to the GBAF and PBAF complexes did not. An ATPase directed proteolysis targeting chimers (PROTAC) was used to therapeutically target cBAF in MPNST cells, reducing their growth and viability. Combination treatment with standard of care chemotherapy synergistically increased the efficacy of this drug. Conclusions: DPF1 was identified as a unique transcriptional regulator of MPNST cells and acts as a member of the cBAF SWI/SNF complex to play important phenotypic roles in this cancer type. Citation Format: Bega Murray, Xiyuan Zhang, Shahroze Abbas, Haiyan Lei, Hilda Jafarah, Jack F. Shern. SWI/SNF-associated DPF1 is a unique transcriptional regulator of malignant peripheral nerve sheath tumors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3563.