Abstract Body: Obstructive sleep apnea (OSA) is characterized by recurrent airway obstruction, leading to intermittent hypoxia (IH) and sleep fragmentation. OSA is highly prevalent, affecting approximately 1 billion people worldwide and has been associated with increased cardiovascular risk. However, the underlying mechanisms remain largely unknown. With the recent discovery of venous endothelial cells (vECs) in human atherosclerotic plaque, we hypothesized that unbiased profiling of vECs from healthy controls and patients with OSA would provide novel insights into mechanisms of OSA-mediated cardiovascular risk. Brachial vein ECs were harvested from 14 otherwise healthy patients with OSA (6F; mean±SD age 44±9y, body mass index [BMI] 35±7kg/m², apnea-hypopnea index [AHI] 33 ±18/h) and 13 healthy controls (6F; mean±SD age 41±16y, BMI 28±4kg/m², AHI 1.8 ±1.3/h) and subjected to single-nucleus RNA sequencing. Contactin-associated protein-like 3 (CNTNAP3), a transmembrane protein involved in cell adhesion and intercellular communication, was downregulated in vECs from OSA patients compared with controls (log₂FC=-0.89,P_adj=5.76x10^-14). Notably, an inverse relationship between CNTNAP3 and AHI during non-rapid eye movement sleep has been found in GWAS, suggesting enrichment for reduced expression CNTNAP3 variants in blood vessels in OSA. Gene Set Enrichment Analysis reveals that patients with OSA have reduced cell junction assembly (NES=-1.6,P_adj=3.5x10^-5) and organization (NES=-1.44,P_adj=6.9x10^-5), blood vessel morphogenesis (NES=-1.40,P_adj=0.001), and nitric oxide metabolic process (NES=-1.68,P_adj=0.013). Venous-specific genes - FLRT2 (log₂FC=-1.34,P_adj=2.09x10^-15) and ARHGAP6 (log₂FC=-0.71,P_adj=4.99x10^-9) were downregulated in OSA patients compared with controls. Reduced expression of FLRT2, which has a key role in EC junction formation, was confirmed by qPCR in patients with OSA. Compared with normoxia, IH reduced FLRT2 expression by 40% in cultured vECs, suggesting that IH associated with transient airway obstructions in OSA impairs EC junction integrity in these patients. Consistently, we observed a vEC cluster enriched with these venous-specific genes in publicly available single-cell RNA sequencing datasets from human carotid atherosclerotic plaques. Our finding suggests that dysfunctional vECs that fail to maintain blood vessel integrity could play a role in IH-mediated atherosclerotic plaque instability, leading to increased cardiovascular risk in patients with OSA.