Esco2 restrains pathological endothelial-mesenchymal transition through hidden isoform regulation in a Roberts syndrome model

Roberts syndrome is caused by biallelic ESCO2 pathogenic variants, but the mechanisms linking ESCO2 loss to embryonic endothelial failure remain poorly defined. Endothelial cells must maintain identity and resist endothelial-mesenchymal transition (EndMT), yet conventional transcriptomics measures gene abundance rather than isoform composition. Here, using endothelial-specific Esco2 deletion in a mouse model relevant to Roberts syndrome, we show that Esco2 loss causes yolk sac vascular remodeling failure, pathological EndMT, diversion from hemogenic endothelial fate, hemogenic endothelial depletion, impaired hematopoietic output, and embryonic lethality. Short-read single-cell RNA-seq revealed broad endothelial reprogramming, whereas single-cell long-read isoform sequencing uncovered a hidden layer of isoform dysregulation that conventional gene-level analysis failed to resolve. Esco2-deficient endothelium exhibited transcriptome-wide isoform switching, disruption of a multi-tier splicing-factor network, and predicted broad loss or rewiring of protein-coding output. Chromatin occupancy profiling localized Esco2 to exonic regions near alternatively spliced loci, supporting a cotranscriptional route to spliceopathy. Whole-genome sequencing showed that local DNA variation was insufficient to explain these changes, supporting a predominantly posttranscriptional mechanism. These findings identify isoform control as a disease-relevant layer of endothelial identity maintenance in Roberts syndrome.