GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE306nnn/GSE306077/primaryOK200GenomicsHomo sapiensGenome binding/occupancy profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE306077GEOGSEfalseCDK8 regulates definitive endoderm commitment through cAMP-lysosomal homeostasis and neuroectodermal suppression [CUT&Tag]Definitive endoderm (DE) specification is critical for generating gastrointestinal and respiratory organs, yet upstream molecular checkpoints integrating transcriptional control with metabolic regulation remain incompletely defined. 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. Our work establishes the CDK8 as a metabolic-epigenetic checkpoint for endoderm specification, offering novel mechanistic insights into cell fate determination and therapeutic strategies for developmental disorders of endoderm-derived organs.2026/09/14GSE306077GSM9192831GSM9192832GSM9192833GSM9192834GSM9192830GSM9192828GSM9192829GSM9192835GSM9192824GSM9192825GSM9192826GSM919282724676306077Homo sapiens