AIM: In heart failure (HF), pulmonary venous hypertension (PVH) produces pulmonary hypertension (PH) with remodeling of pulmonary veins (PV) and arteries (PA). In a porcine PVH model, we performed proteomic-based bioinformatics to investigate unique pathophysiologic mechanisms mediating PA and PV remodeling. METHODS: Large PV were banded (PVH, n= 10) or not (Sham, n=9) in piglets. At sacrifice, PV and PA were perfusion labeled for vessel specific histology and proteomics. The PA and PV were separately sampled with laser-capture micro-dissection for mass spectrometry. RESULTS: Pulmonary vascular resistance (Wood Units; 8.6 versus 2.0) and PA (19.9 versus 10.3) and PV (14.2 versus 7.6) wall thickness/external diameter (%) were increased in PVH (p<0.01 for all). Similar numbers of proteins were identified in PA (2093) and PV (2085) with 94% overlap, but biological processes differed. There were more differentially expressed proteins (287 versus 161), altered canonical pathways (17 versus 3) and predicted up-stream regulators (PUSR; 22 versus 6) in PV than PA. In PA and PV, bioinformatics indicated activation of the integrated stress response and mTOR signaling with dysregulated growth. In PV, there was also activation of Rho/Rho kinase signaling with decreased actin cytoskeletal signaling and altered tight and adherens junctions, ephrin B, and caveolar mediated endocytosis signaling; all indicating disrupted endothelial barrier function. Indeed, protein biomarkers and the top PUSR in PV (TGF-β) indicated endothelial mesenchymal transition (EndoMT) in PV. Findings were confirmed in human autopsy specimens. CONCLUSION: These findings provide new therapeutic targets to oppose pulmonary vascular remodeling in HF-related PH.