Inability to switch from ARID1A-BAF to ARID1B-BAF impairs exit from pluripotency and commitment towards neural crest differentiation in ARID1B-related neurodevelopmental disorders

The BAF complex modulates genome-wide chromatin accessibility. Specific BAF configurations have been shown to have functional consequences, and subunit switches are essential for cell differentiation. ARID1B and its paralog ARID1A encode for mutually exclusive BAF subunits. De novo ARID1B haploinsufficient mutations cause a neurodevelopmental disorder spectrum, including Coffin-Siris syndrome, which is characterized by neurological and craniofacial features. Here, we reprogrammed ARID1B+/- Coffin-Siris patient-derived skin fibroblasts into iPSCs, and investigated cranial neural crest cell (CNCC) differentiation. We discovered a novel BAF configuration (ARID1B-BAF), which includes ARID1B, SMARCA4, and eight additional subunits. This novel version of BAF acts as a gate-keeper which ensures exit from pluripotency and commitment towards neural crest differentiation, by attenuating pluripotency enhancers of the SOX2 network. At the iPSC stage, these enhancers are maintained in active state by an ARID1A-containing BAF. At the onset of differentiation, cells transition from ARID1A-BAF to ARID1B-BAF, eliciting attenuation of SOX2 enhancers and pluripotency exit. Coffin-Siris patient cells fail to perform the ARID1A/ARID1B switch, and maintain ARID1A-BAF at pluripotency enhancers throughout CNCC differentiation. This correlates with aberrant SOX2 binding at pluripotency enhancers, and failure to reposition SOX2 at developmental enhancers. SOX2 dysregulation promotes upregulation of the NANOG network, impairing CNCC differentiation. ARID1B-BAF directly modulates NANOG expression upon differentiation cues. Intriguingly, the cells with the most prominent molecular phenotype in multiple experimental assays are derived from a patient with a more severe clinical impairment. These findings suggest a direct connection between ARID1B mutations, CNCC differentiation, and a pathogenic mechanism for Coffin-Siris syndrome.