Abstract Cancer and inflammation are associated with vascular diseases that affect endothelial cells (ECs) and alter gene expression. We aimed at understanding whether the site Y 685 in the cytoplasmic domain of VE-cadherin triggers epigenetic programming in vivo . Using our knock-in mice carrying the Y 685 F VE-cadherin mutation, RNA sequencing from lung ECs identified 884 differentially expressed genes (DEG) involved in processes such as cell-cell adhesion, vascular development, and angiogenesis. The 30 DEGs include 22 down-regulated genes (genes encoding cell signalling enzymes, anion transport and lipid metabolism) and 8 up-regulated genes, including the endothelial-specific S1PR1. Analysis of the VEGF/VEGFR2 signaling pathway shows a significant decrease in the expression of pY 1173 VEGFR2 whereas VEGF remains constant, this was consistent with impaired migration, proliferation and protrusive properties of ECs in vitro . Co-immunoprecipitation experiments showed that c-Src and Y 685 F-VE-cadherin association which was enhanced in KI compared to WT, resulting in increased in Y 685 F-VE-cadherin phosphorylation at site Y 731 . As a consequence, its partner β-catenin translocates to the nucleus. CHIPS assay showed that FOXF1 binds to the s1pr1 promoter, leading to increased expression of the S1PR1. In vivo, in the lung vasculature, this process was associated with increased vessel wall thickness and reduced fibrosis. Overall, our findings provide a novel transcriptomic profile triggered by Y 685 F-VE-cadherin ECs for potential insights into therapeutic targets to envisage normalisation of the tumor vasculature.