Proteomics 2012, 12, 2547–2555 2547 DOI 10.1002/pmic.201200060 RESEARCH ARTICLE Proteomes of umbilical vein and microvascular endothelial cells reflect distinct biological properties and influence immune recognition Hanadi Dib 1,2,3 , Philippe Chafey 1,2,3 , Guilhem Clary 1,2,3 , Christian Federici 1,2,3 , Morgane Le Gall 1,2,3 , Julie Dwyer 1,2,3 , Julie Gavard 1,2,3 , Nicolas Tamas 1,2,3 , Guillaume Bussone 1,2,3,4 , C´ edric Broussard 1,2,3 , Luc Camoin 1,2,3 ,V´ eronique Witko-Sarsat 1,2,3 , Mathieu C. Tamby 1,2,3∗ and Luc Mouthon 1,2,3,4∗ 1 INSERM U1016, Institut Cochin, Paris, France 2 CNRS UMR 8104, Paris 3 Universit ´ e Paris Descartes, Paris 4 Facult ´ e de M ´ edecine, p ˆ ole de M ´ edecine Interne et centre de r ´ ef ´ erence pour les vascularites n ´ ecrosantes et la scl ´ erodermie syst ´ emique, Universit ´ e Paris Descartes, h ˆ opital Cochin, Assistance Publique-H ˆ opitaux de Paris, Paris Human umbilical vein endothelial cells (HUVEC) are widely used as a source of endothelial cells (EC). However, HUVEC characteristics cannot be extrapolated to other types of EC, particularly microvascular ECs. Our objective was to compare the proteomes of microvascular ECs and HUVEC. Proteomes of HUVEC and human microvascular pulmonary EC (HMVEC- P) and dermal EC (HMVEC-D) from healthy Caucasian donors were compared by 2D DIGE and MS. Fatty acid binding proteins 4 and 5 were among the 159 and 30 proteins spots found to have at least twofold change in expression between HUVEC and HMVEC-D and between HUVEC and HMVEC-P samples, respectively. Eight protein spots showed twofold changed expression between HMVEC-D and HMVEC-P samples. Ingenuity R  analysis revealed that proteins differentially expressed between HUVEC and HMVEC-D samples interact with retinoic acid. In vitro tubulogenesis assays showed a differential effect of retinoic acid between HUVEC and HMVEC. Moreover, serum IgG from patients with a rare vascular disease, systemic sclerosis, showed distinct reactivity profiles in HUVEC and HMVEC-D protein extracts. The proteome profiles of HUVEC and microvascular EC differ noticeably, which reflects distinct biological properties and influence immune recognition. Keywords: Cell biology / Endothelial cells / Human umbilical vein endothelial cells / Microvas- cular / Retinoic acid Received: February 15, 2012 Revised: April 26, 2012 Accepted: May 30, 2012 Correspondence: Dr. Luc Mouthon, Institut Cochin, Pavillon Gus- tave Roussy, 4` eme ´ etage, H ˆ opital Cochin, 8 rue M´ echain, 75014, Paris, France E-mail: luc.mouthon@cch.aphp.fr Fax: +33 (0) 1 44 41 25 46 Abbreviations: EC, endothelial cells; FABP4, fatty acid binding protein 4; FABP5, fatty acid binding protein 5; FGF, fibroblast growth factor; HMVEC-D, human microvascular dermal endothe- lial cells; HMVEC-P, human microvascular pulmonary endothe- lial cells; HUVEC, human umbilical vein endothelial cells; IPA, ingenuity pathway analysis; PAH, pulmonary arterial hyperten- 1 Introduction The endothelium constitutes a highly specialized organ that lines a complex network of arteries, veins, and mi- crovessels differing in size, structure, and function. Because sion; PDGF, platelet-derived growth factor; SSc, systemic scle- rosis; TGF-, transforming growth factor beta; VEGF, vascular endothelial growth factor ∗ These authors contributed equally to this study. Colour Online: See the article online to view Figs. 2 and 4 in colour. C  2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com