Novel functional insights revealed by distinct protein-protein interactions of the residual SWI/SNF complex in SMARCA4-deficient small cell carcinoma of the ovary, hypercalcemic type

Abstract

Chromatin remodeling plays a critical role in tumor suppression as demonstrated by 20% of human cancers bearing inactivating mutations in SWI/SNF chromatin remodeling complex members. Mutations in different SWI/SNF subunits drive a variety of adult and pediatric tumor types, including non-small cell lung cancers, rhabdoid tumors, medulloblastomas, and ovarian cancers. Small cell carcinoma of the ovary hypercalcemic type (SCCOHT) is an aggressive subtype of ovarian cancer occurring in young women. Nearly all (>98%) SCCOHTs have inactivating mutations in SMARCA4, which encodes 1 of 2 mutually exclusive catalytic subunits of the SWI/SNF complex. Less than half of SCCOHT patients survive 5 years despite aggressive surgery and multimodal chemotherapy. Empirical support for effective SCCOHT treatments is scarce, in part because of the poor understanding of SCCOHT tumorigenesis. To gain insight into the functional consequences of SWI/SNF subunit loss, we defined SWI/SNF composition and its protein-protein interactions (PPIs) by immunoprecipitation and mass spectrometry (IP-MS) of SWI/SNF subunits in 3 SCCOHT cell lines. Comparing these results to a cell line containing a wild-type SWI/SNF complex, the interaction of most canonical core SWI/SNF subunits was observed in all SCCOHT cell lines at a lower abundance. The SCCOHT SWI/SNF also lacked ATPase module subunits and showed a drastic reduction in PBAF-specific subunit interactions. The wild-type and SCCOHT SWI/SNF subunits immunoprecipitated a shared set of 26 proteins, including core SWI/SNF subunits and RNA processing proteins. We observed 131 proteins exclusively interacting with the wild-type SWI/SNF complex including isoform-specific SWI/SNF subunits, members of the NuRD complex, and members of the MLL3/4 complex. We observed 60 PPIs exclusive to the SCCOHT residual SWI/SNF shared in at least 2 of the 3 SCCOHT cell lines, including many proteins involved in RNA processing. Differential interactions with the residual SWI/SNF complex in SCCOHT may further elucidate altered functional consequences of SMARCA4 mutations in these tumors as well as identify synthetic lethal targets that translate to other SWI/SNF-deficient tumors.Introduction:

Role of Specialized Composition of SWI/SNF Complexes in Prostate Cancer Lineage Plasticity

“…Moreover, we found several members of the NuRD chromatin remodeling complex, such as MTA1 and CHD4 This is in line with previous findings of a potential interaction of those two chromatin remodeling complexes ( Fig. 4a, 4b) 40,41 . A considerable amount of CRPC-NE specific SWI/SNF interactors were found to be involved in chromatin regulation or DNA-repair ( Fig.…”

Landscape of super-enhancers in small cell carcinoma of the ovary, hypercalcemic type and efficacy of targeting with natural product triptolide

“…However, in SCCOHT tumors, the SWI/SNF complex only exists in a residual form distinct and less abundant than ncBAF (33). Further, the rhabdoid tumor data did not show a corresponding loss of H3K27ac signal at SEs.…”

Proteomic analysis identifies plasma correlates of remote ischemic conditioning in the context of experimental traumatic brain injury

“…The trapped peptides were separated using an Acclaim PepMap RSLC C18 analytical column (Thermo Scientific, 50 µm, 15 cm, 2 µm particle size, 100 Å pore size) and a 95 min gradient (3% to 7% solvent B for 1 min, 7% to 25% solvent B for 72 min, 25% solvent B to 45% B for 10 min, 45% to 90% B for 0.5 min, 90% B for 1 min, 3% B in 0.5 min and re-equilibration at 3% B for 10 min) at 300 nL/minute flow rate. Data-dependent acquisition was performed in Top Speed mode with a duty cycle of 3 s and the following parameters: spray voltage of 2100 V, ion transfer tube temperature of 275 °C, survey scan in the Orbitrap at a resolution of 120 K at 200 m/z, scan range of 400–1,500 m/z, AGC target of 2E5 and maximum ion injection time of 50 ms. Parent scans were followed by a daughter scan using High Energy Collision (HCD) dissociation of top abundant peaks and detection in the ion-trap with the following settings: quadrupole isolation mode, isolation window at 1.4 m/z, AGC target of 5E3 with maximum ion injection time of 35 ms and 35% HCD collision energy 56 . Dynamic exclusion was set to 60 s. Peptide precursor ion intensities were used to calculate relative abundance.…”