RNF2 Missense Variants Disrupt Polycomb Repression and Enable Ectopic Mesenchymal Lineage Conversion During Human Neural Differentiation

Polycomb Repressive Complex 1 (PRC1) catalyzes H2AK119ub1 to facilitate transcriptional repression during development. De novo dominant missense variants in RNF2, the principal E3 ligase of PRC1, are the genetic basis of Luo-Schoch-Yamamoto syndrome. To investigate the developmental impact of catalytically impaired RNF2 alleles, we engineered hESC lines harboring homozygous hypomorphic RNF2 missense alleles (RNF2MS/MS) that stably expresses RNF2 but results in reduced H2AK119ub1. Upon directed neural differentiation, RNF2MS/MS cells exhibited asynchronous neural differentiation and ectopic emergence of mesenchymal fated lineages. Single-cell transcriptomic analyses revealed a fate bifurcation characterized by derepression of TWIST1 and other epithelial-to-mesenchymal transition (EMT) gene-network components, coinciding with focal loss of H2AK119ub1 and H3K27me3. These findings demonstrate that RNF2-mediated H2AK119ub1 is required to constrain lineage fidelity by repressing context-inappropriate developmental programs during early human neural differentiation and reveal a shared chromatin-based mechanism linking RNF2 missense variants to both neurodevelopmental pathology and oncogenic plasticity.