title: Proteomics analysis of human coronary atherosclerotic plaque: a feasibility study of direct tissue proteomics by liquid chromatography and tandem mass spectrometry.
abstract: Cardiovascular disease presents significant variations in human populations with respect to the atherosclerotic plaque progression, inflammation, thrombosis, and rupture. To gain a more comprehensive picture of the pathogenic mechanism of atherosclerosis and the variations seen in patients, efficient methods to identify proteins from the normal and diseased arteries need to be developed. To accomplish this goal, we tested the feasibility and efficiency of protein identification by a recently developed method, termed direct tissue proteomics (DTP). We analyzed frozen and paraformaldehyde-fixed archival coronary arteries with the DTP method. We also validated the distinct expression of four proteins by immunohistochemistry. In addition, we demonstrated the compatibility of the DTP method with laser capture microdissection and the possibility of monitoring specific cytokines and growth factors by the absolute quantification of abundance method. Major findings from this feasibility study are that 1) DTP can be used to efficiently identify proteins from paraformaldehyde-fixed, paraffin-embedded, and frozen coronary arteries; 2) approximately twice the number of proteins were identified from the frozen sections when compared with the paraformaldehyde-fixed sections; 3) laser capture microdissection is compatible with DTP; and 4) detection of low abundance cytokines and growth factors in the coronary arteries required selective reaction monitoring experiments coupled to absolute quantification of abundance. The analysis of 35 human coronary atherosclerotic samples allowed identification of a total of 806 proteins. The present study provides the first large scale proteomics map of human coronary atherosclerotic plaques.
authors.affiliation: Department of Cell Biology, Center for Vascular Biology, University of Connecticut School of Medicine, Farmington, Connecticut 06030, USA.
authors.forename: Carolina
authors.initials: C
authors.lastname: Bagnato
authors.forename: Jaykumar
authors.initials: J
authors.lastname: Thumar
authors.forename: Viveka
authors.initials: V
authors.lastname: Mayya
authors.forename: Sun-Il
authors.initials: SI
authors.lastname: Hwang
authors.forename: Henry
authors.initials: H
authors.lastname: Zebroski
authors.forename: Kevin P
authors.initials: KP
authors.lastname: Claffey
authors.forename: Christian
authors.initials: C
authors.lastname: Haudenschild
authors.forename: Jimmy K
authors.initials: JK
authors.lastname: Eng
authors.forename: Deborah H
authors.initials: DH
authors.lastname: Lundgren
authors.forename: David K
authors.initials: DK
authors.lastname: Han
mesh_terms: D017305:Annexin A1 / Q000378:metabolism; D000954:Antigens, Surface / Q000378:metabolism; D050197:Atherosclerosis / Q000378:metabolism* / Q000473:pathology*; D015815:Cell Adhesion Molecules / Q000378:metabolism; D002853:Chromatography, Liquid; D003331:Coronary Vessels / Q000737:chemistry*; D016207:Cytokines / Q000032:analysis; D016326:Extracellular Matrix Proteins / Q000378:metabolism; D005136:Eye Proteins / Q000737:chemistry / Q000378:metabolism; D005240:Feasibility Studies; D006801:Humans; D018836:Inflammation Mediators / Q000378:metabolism; D036341:Intercellular Signaling Peptides and Proteins / Q000032:analysis; D008024:Ligands; D042282:Microdissection; D008894:Milk Proteins / Q000378:metabolism; D009414:Nerve Growth Factors / Q000737:chemistry / Q000378:metabolism; D010587:Phagocytosis; D020543:Proteome / Q000032:analysis*; D040901:Proteomics; D015203:Reproducibility of Results; D015843:Serpins / Q000737:chemistry / Q000378:metabolism; D053719:Tandem Mass Spectrometry; D000099174:Pigment Epithelium-Derived Factor
chemical_list: D017305:Annexin A1; D000954:Antigens, Surface; D015815:Cell Adhesion Molecules; D016207:Cytokines; D016326:Extracellular Matrix Proteins; D005136:Eye Proteins; D018836:Inflammation Mediators; D036341:Intercellular Signaling Peptides and Proteins; D008024:Ligands; D008894:Milk Proteins; D009414:Nerve Growth Factors; D020543:Proteome; D015843:Serpins; D000099174:Pigment Epithelium-Derived Factor; C098942:MFGE8 protein, human; C512835:POSTN protein, human