MECP2T203M mutation disrupts neurogenesis in human cerebral organoids by altering chromatin dynamics and transcriptional regulation.

Rett syndrome (RTT) is a severe, neurodevelopmental disorder caused primarily by loss-of-function mutations in the methyl-CpG-binding protein 2 (MECP2) gene. Although the regulatory role of MECP2 in neuronal development and postnatal functions has been thoroughly investigated, its mechanisms in prenatal human brain development remain elusive. Here, we successfully established a stable culture of cerebral organoids derived from human induced pluripotent stem cells (hiPSCs) to mimic the MECP2 mutant in the prenatal brain that causes RTT. We found that T203M, a human-specific MECP2 point mutation, disrupts neurogenesis. To systematically infer the molecular mechanisms underlying aberrant neurogenesis, we applied an integrative multi-omics approach to comprehensively characterize the associated chromatin dynamics and transcriptomic alterations. Our findings revealed a notably open chromatin state in the organoids with a mutated MECP2, particularly in the enhancer regions with a high proportion of adenine (A) and thymine (T) bases. This alteration induced the expression of genes related to proliferation but suppressed those associated with neuronal differentiation. Furthermore, through multi-omics, we uncovered a MECP2-mutation-driven, cell-type-specific, and disease-related multi-layered regulatory network contributing to development states with high pluripotency but low differentiation, and abnormal neurogenesis. Our study provides a comprehensive resource to elucidate the molecular mechanisms underlying the pathological processes of RTT during prenatal brain development.