Background: ARID1A and ARID1B are mutually exclusive subunits of the mSwi/Snf (BAF) complex implicated as a tumor suppressor in >20% of cancers. Programmed exchanges among subunits directs divergent cell fates, such as the transition between embryonic stem cell BAF composition (esBAF) to neural progenitor (npBAF) to neuron (nBAF). ARID1A/B mutations disrupt BAF structure and function and define an aggressive neuroblastoma subset.
Methods: Deep-genome sequencing identified BAF subunit mutations in neuroblastoma cell lines and primary tumors, and gene expression profiles (GEP) were correlated with BAF mutation status. BAF wild-type and mutant neuroblastomas were characterized by co-IP and MS/MS to define complex composition, ChIP-seq to identify genome binding sites, and synthetic-lethal screening to define specific vulnerabilities.
Results: Excluding common hemizygous deletion of ARID1A (1p35), mutually exclusive ARID1A (biallelic; n=6), ARID1B (n=9), ARID2 (n=2) and SMARCA4 (n=2) mutations were identified in 19/74 (26%) neuroblastoma cell lines. Target-capture sequencing of 476 primary neuroblastomas identified ARID1A or ARID1B mutation, excluding deletion (ongoing), in 2% (correlated with unfavorable features). mRNA expression of subunits unique to npBAF correlated directly with each other (r>0.3; p<0.001) and inversely with subunits unique to nBAF (r>-0.3; p<0.001). Similarly, BAF-driven neurogenesis genes correlated directly with nBAF and indirectly with npBAF, and high npBAF expression correlated with unfavorable outcome. Biochemical analyses of ARID1A/1B mutant complexes demonstrate a role for heterozygous and homozygous mutations on BAF complex abundancy and subunit and associated factor composition. ChIP-seq studies reveal differential BAF complex genomic localization and GEP in wild-type versus ARID1A/B mutant cell lines.
Conclusion: We identified BAF complex mutations (predominantly in ARID1A and ARID1B) in a large proportion of neuroblastoma cell lines and in aggressive primary tumors, underscoring their oncogenic relevance. Functional deregulation of BAF complexes may not be restricted to tumors with BAF-complex mutations as evidenced by strong correlations between npBAF subunit expression and poor outcome in neuroblastomas lacking ARID1A/B gene mutation.