FET fusion oncoproteins enrich SWI/SNF complex subtypes and interaction partners

• Abstract: FET fusion oncoproteins, containing the N-terminal of a FET protein (FUS, EWSR1 and TAF15) together with a DNA-binding transcription factor partner, are characteristic for around 20 different sarcomas and leukemias, including myxoid liposarcoma (MLS) and Ewing sarcoma (EWS). FET oncoproteins interact with all three main subtypes of the SWI/SNF chromatin remodeling complexes cBAF, PBAF and GBAF, resulting in epigenetic changes and oncogenic gene expression patterns. We developed a comprehensive immunoprecipitation (IP) protocol followed by quantitative mass spectrometry (QMS) analysis using a global approach for relative quantification with chemical tandem mass tag (TMT) labels. We employed two immunoprecipitation strategies, by pulling down either all SWI/SNF complexes using BRG1 as a target or FET-FOP-bound SWI/SNF complexes using the fusion oncoproteins FUS-DDIT3 or EWSR1-FLI1 as a target. This approach allowed us to assess differences between SWI/SNF composition and interaction partners in MLS and EWS cells, as well as determine the composition and interactome of FET-FOP-bound SWI/SNF complexes.