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Systematic characterization of BAF mutations explains intra-complex synthetic lethalities

ABSTRACT: Aberrations in genes coding for subunits of the BAF chromatin remodeling complex are highly abundant in human cancers. Currently, it is not understood how these loss-of-function mutations contribute to cancer development and how they can be targeted therapeutically. The cancer type specific occurrence patterns of certain subunit mutations suggest subunit-specific effects on BAF complex function, possibly by the formation of aberrant residual complexes. Here, we systematically characterize the effects of individual subunit loss on complex composition, chromatin accessibility and gene expression in a panel of knock-out cell lines deficient for 22 targetable BAF subunits. We observe strong, specific and often discordant alterations dependent on the targeted subunit and show that these explain intra-complex co-dependencies, including the novel synthetic lethal interactions SMARCA4-ARID2, SMARCA4-ACTB and SMARCC1-SMARCC2. These data provide insights into the role of different BAF subcomplexes in genome-wide chromatin organization and suggest novel approaches to therapeutically target BAF mutant cancers.

INSTRUMENT(S): Orbitrap Fusion Lumos, LTQ Orbitrap Velos, Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Peter Májek

LAB HEAD: Stefan Kubicek

PROVIDER: PXD013102 | Pride | 2019-08-01

REPOSITORIES: Pride

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			Action	DRS
	CC50-M568-C08-C09-CSKu-P8519-P8520-nonNorm-nonmerged - Copy for PD2.3.pride.mgf.gz	Mgf
	CC50-M568-C08-C09-CSKu-P8519-P8520-nonNorm-nonmerged-CopyforPD2.3.mzML	Mzml
	CC50-M568-C08-C09-CSKu-P8519-P8520-nonNorm-nonmerged_PD2.3.mzid.gz	Mzid
	CC50-M568-C08-C09-CSKu-P8519-P8520-nonNorm-nonmerged_PD2.3.pride.mztab.gz	Mztab
	CC50_Set1-3_A1A-IP_Arid-Norm_NonMerged-TMT - Copy for PD2.3.pride.mgf.gz	Mgf

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