CDK8 regulates definitive endoderm commitment through cAMP-lysosomal homeostasis and neuroectodermal suppression [CUT&Tag]

Here, we identify cyclin-dependent kinase 8 (CDK8) as a decisive regulator of human DE commitment. Profiling CDK8 expression during pluripotent stem cell differentiation revealed stage-specific upregulation, while pharmacological inhibition or genetic ablation of CDK8 severely compromised DE formation and hepatic competency.

Mechanistically, CDK8 directly represses neuroectoderm programs while concurrently activating endoderm-lysosomal transcriptional networks. CDK8 deficiency triggered convergent dysregulation of EPAC-dependent cAMP signaling hyperactivation and lysosomal dysfunction, underpinning the DE defect. Integrative multi-omics (RNA-seq, CUT&Tag) demonstrated that CDK8 licenses lineage commitment by directly suppressing neural differentiation genes and enhancing endoderm-TGFβ pathways through recruitment to promoter-proximal regulatory elements.