Genetics, genomics and proteomics in atherosclerosis research

References

• Ross R. Atherosclerosis is an inflammatory disease. Am Heart J 1999; 138: S419–20
   PubMed Web of Science ®Google Scholar
• Lusis A. J., Fogelman A. M., Fonarow G. C. Genetic basis of atherosclerosis: part I: new genes and pathways. Circulation 2004; 110: 1868–73
   PubMed Web of Science ®Google Scholar
• Lusis A. J., Mar R., Pajukanta P. Genetics of atherosclerosis. Annu Rev Genomics Hum Genet 2004; 5: 189–218
   PubMed Web of Science ®Google Scholar
• Humphries S. E., Talmud P. J., Hawe E., Bolla M., Day I. N., Miller G. J. Apolipoprotein E4 and coronary heart disease in middle‐aged men who smoke: a prospective study. Lancet 2001; 358: 115–9
   PubMed Web of Science ®Google Scholar
• Chiodini B. D., Lewis C. M. Meta‐analysis of 4 coronary heart disease genome‐wide linkage studies confirms a susceptibility locus on chromosome 3q. Arterioscler Thromb Vasc Biol 2003; 23: 1863–8
   Google Scholar
• Suh Y., Vijg J. SNP discovery in associating genetic variation with human disease phenotypes. Mutat Res 2005; 573: 41–53
   PubMed Web of Science ®Google Scholar
• Ozaki K., Ohnishi Y., Iida A., Sekine A., Yamada R., Tsunoda T., et al. Functional SNPs in the lymphotoxin‐alpha gene that are associated with susceptibility to myocardial infarction. Nat Genet 2002; 32: 650–4
   PubMed Web of Science ®Google Scholar
• Stevenson M. Dissecting HIV‐1 through RNA interference. Nat Rev Immunol 2003; 3: 851–8
   PubMed Web of Science ®Google Scholar
• Egger G., Liang G., Aparicio A., Jones P. A. Epigenetics in human disease and prospects for epigenetic therapy. Nature 2004; 429: 457–63
   PubMed Web of Science ®Google Scholar
• Hiltunen M. O., Yla‐Herttuala S. DNA methylation, smooth muscle cells, and atherogenesis. Arterioscler Thromb Vasc Biol 2003; 23: 1750–3
   PubMed Web of Science ®Google Scholar
• Shi H., Maier S., Nimmrich I., Yan P. S., Caldwell C. W., Olek A., et al. Oligonucleotide‐based microarray for DNA methylation analysis: principles and applications. J Cell Biochem 2003; 88: 138–43
   PubMed Web of Science ®Google Scholar
• Austin M. A., Hutter C. M., Zimmern R. L., Humphries S. E. Genetic causes of monogenic heterozygous familial hypercholesterolemia: a HuGE prevalence review. Am J Epidemiol 2004; 160: 407–20
   PubMed Web of Science ®Google Scholar
• Marks D., Wonderling D., Thorogood M., Lambert H., Humphries S. E., Neil H. A. Cost effectiveness analysis of different approaches of screening for familial hypercholesterolaemia. BMJ 2002; 324: 1303
   PubMed Web of Science ®Google Scholar
• Puddu D., Cravero E., Puddu G., Muscari A. Genes and atherosclerosis: at the origin of the predisposition. Int J Clin Pract 2005; 59: 462–72
   PubMed Web of Science ®Google Scholar
• Franco R. F., Reitsma P. H. Gene polymorphisms of the haemostatic system and the risk of arterial thrombotic disease. Br J Haematol 2001; 115: 491–506
   Google Scholar
• Juhan‐Vague I., Morange P. E., Frere C., Aillaud M. F., Alessi M. C., Hawe E., et al. The plasminogen activator inhibitor‐1 ‐675 4G/5G genotype influences the risk of myocardial infarction associated with elevated plasma proinsulin and insulin concentrations in men from Europe: the HIFMECH study. J Thromb Haemost 2003; 1: 2322–9
   Google Scholar
• Lijnen H. R. Pleiotropic functions of plasminogen activator inhibitor‐1. J Thromb Haemost 2005; 3: 35–45
   PubMed Web of Science ®Google Scholar
• Binder B. R., Christ G., Gruber F., Grubic N., Hufnagl P., Krebs M., et al. Plasminogen activator inhibitor 1: physiological and pathophysiological roles. News Physiol Sci 2002; 17: 56–61
   PubMedGoogle Scholar
• Ordovas J. M., Mooser V. The APOE locus and the pharmacogenetics of lipid response. Curr Opin Lipidol 2002; 13: 113–7
   Google Scholar
• Kuivenhoven J. A., Jukema J. W., Zwinderman A. H., de Knijff P., McPherson R., Bruschke A. V., et al. The role of a common variant of the cholesteryl ester transfer protein gene in the progression of coronary atherosclerosis. The Regression Growth Evaluation Statin Study Group. N Engl J Med 1998; 338: 86–93
   PubMed Web of Science ®Google Scholar
• Lockhart D. J., Winzeler E. A. Genomics, gene expression and DNA arrays. Nature 2000; 405: 827–36
   PubMed Web of Science ®Google Scholar
• McCaffrey T. A. TGF‐betas and TGF‐beta receptors in atherosclerosis. Cytokine Growth Factor Rev 2000; 11: 103–14
   Google Scholar
• Hiltunen M. O., Tuomisto T. T., Niemi M., Brasen J. H., Rissanen T. T., Toronen P., et al. Changes in gene expression in atherosclerotic plaques analyzed using DNA array. Atherosclerosis 2002; 165: 23–32
   Google Scholar
• Tuomisto T. T., Korkeela A., Rutanen J., Viita H., Brasen J. H., Riekkinen M. S., et al. Gene expression in macrophage‐rich inflammatory cell infiltrates in human atherosclerotic lesions as studied by laser microdissection and DNA array: overexpression of HMG‐CoA reductase, colony stimulating factor receptors, CD11A/CD18 integrins, and interleukin receptors. Arterioscler Thromb Vasc Biol 2003; 23: 2235–40
   PubMedGoogle Scholar
• Napoli C., de Nigris F., Welch J. S., Calara F. B., Stuart R. O., Glass C. K., et al. Maternal hypercholesterolemia during pregnancy promotes early atherogenesis in LDL receptor‐deficient mice and alters aortic gene expression determined by microarray. Circulation 2002; 105: 1360–7
   PubMed Web of Science ®Google Scholar
• Wesselman J. P., Kuijs R., Hermans J. J., Janssen G. M., Fazzi G. E., van Essen H., et al. Role of the Rhoa/Rho kinase system in flow‐related remodeling of rat mesenteric small arteries in vivo. J Vasc Res 2004; 41: 277–90
   Google Scholar
• Dupuis M., Soubrier F., Brocheriou I., Raoux S., Haloui M., Louedec L., et al. Profiling of aortic smooth muscle cell gene expression in response to chronic inhibition of nitric oxide synthase in rats. Circulation 2004; 110: 867–73
   Google Scholar
• Smirnova I. V., Sawamura T., Goligorsky M. S. Upregulation of lectin‐like oxidized low‐density lipoprotein receptor‐1 (LOX‐1) in endothelial cells by nitric oxide deficiency. Am J Physiol Renal Physiol 2004; 287: F25–32
   Google Scholar
• Csiszar A., Ungvari Z., Koller A., Edwards J. G., Kaley G. Aging‐induced proinflammatory shift in cytokine expression profile in coronary arteries. FASEB J 2003; 17: 1183–5
   PubMed Web of Science ®Google Scholar
• Csiszar A., Ungvari Z., Koller A., Edwards J. G., Kaley G. Proinflammatory phenotype of coronary arteries promotes endothelial apoptosis in aging. Physiol Genomics 2004; 17: 21–30
   PubMed Web of Science ®Google Scholar
• Burnett M. S., Durrani S., Stabile E., Saji M., Lee C. W., Kinnaird T. D., et al. Murine cytomegalovirus infection increases aortic expression of proatherosclerotic genes. Circulation 2004; 109: 893–7
   Google Scholar
• Takahashi K., Mizuarai S., Araki H., Mashiko S., Ishihara A., Kanatani A., et al. Adiposity elevates plasma MCP‐1 levels leading to the increased CD11b‐positive monocytes in mice. J Biol Chem 2003; 278: 46654–60
   PubMed Web of Science ®Google Scholar
• Blaschke F., Bruemmer D., Yin F., Takata Y., Wang W., Fishbein M. C., et al. C‐reactive protein induces apoptosis in human coronary vascular smooth muscle cells. Circulation 2004; 110: 579–87
   PubMed Web of Science ®Google Scholar
• Wang Q., Zhu X., Xu Q., Ding X., Chen Y. E., Song Q. Effect of C‐Reactive Protein on Gene Expression in Vascular Endothelial Cells. Am J Physiol Heart Circ Physiol 2005; 288: H1539–45
   Google Scholar
• Nakahashi T. K., Hoshina K., Tsao P. S., Sho E., Sho M., Karwowski J. K., et al. Flow loading induces macrophage antioxidative gene expression in experimental aneurysms. Arterioscler Thromb Vasc Biol 2002; 22: 2017–22
   PubMed Web of Science ®Google Scholar
• Kalish J. A., Willis D. J., Li C., Link J. J., Deutsch E. R., Contreras M. A., et al. Temporal genomics of vein bypass grafting through oligonucleotide microarray analysis. J Vasc Surg 2004; 39: 645–54
   Google Scholar
• Willis D. J., Kalish J. A., Li C., Deutsch E. R., Contreras M. A., LoGerfo F. W., et al. Temporal gene expression following prosthetic arterial grafting. J Surg Res 2004; 120: 27–36
   Google Scholar
• Llaverias G., Noe V., Penuelas S., Vazquez‐Carrera M., Sanchez R. M., Laguna J. C., et al. Atorvastatin reduces CD68, FABP4, and HBP expression in oxLDL‐treated human macrophages. Biochem Biophys Res Commun 2004; 318: 265–74
   PubMedGoogle Scholar
• Morikawa S., Takabe W., Mataki C., Wada Y., Izumi A., Saito Y., et al. Global analysis of RNA expression profile in human vascular cells treated with statins. J Atheroscler Thromb 2004; 11: 62–72
   PubMedGoogle Scholar
• Furnkranz A., Schober A., Bochkov V. N., Bashtrykov P., Kronke G., Kadl A., et al. Oxidized phospholipids trigger atherogenic inflammation in murine arteries. Arterioscler Thromb Vasc Biol 2005; 25: 633–8
   PubMed Web of Science ®Google Scholar
• Waehre T., Yndestad A., Smith C., Haug T., Tunheim S. H., Gullestad L., et al. Increased expression of interleukin‐1 in coronary artery disease with downregulatory effects of HMG‐CoA reductase inhibitors. Circulation 2004; 109: 1966–72
   PubMed Web of Science ®Google Scholar
• Nguyen K. T., Shaikh N., Shukla K. P., Su S. H., Eberhart R. C., Tang L. Molecular responses of vascular smooth muscle cells and phagocytes to curcumin‐eluting bioresorbable stent materials. Biomaterials 2004; 25: 5333–46
   PubMedGoogle Scholar
• Nguyen K. T., Shaikh N., Wawro D., Zhang S., Schwade N. D., Eberhart R. C., et al. Molecular responses of vascular smooth muscle cells to paclitaxel‐eluting bioresorbable stent materials. J Biomed Mater Res 2004; 69A: 513–24
   Google Scholar
• Hishikawa K., Nakaki T., Fujita T. Oral Flavonoid Supplementation Attenuates Atherosclerosis Development in Apolipoprotein E‐Deficient Mice. Arterioscler Thromb Vasc Biol 2005; 25: 442–6
   PubMed Web of Science ®Google Scholar
• Tamayo P., Slonim D., Mesirov J., Zhu Q., Kitareewan S., Dmitrovsky E., et al. Interpreting patterns of gene expression with self‐organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A 1999; 96: 2907–12
   PubMed Web of Science ®Google Scholar
• Shiffman D., Mikita T., Tai J. T., Wade D. P., Porter J. G., Seilhamer J. J., et al. Large scale gene expression analysis of cholesterol‐loaded macrophages. J Biol Chem 2000; 275: 37324–32
   PubMed Web of Science ®Google Scholar
• Tuomisto T. T., Riekkinen M. S., Viita H., Levonen A. L., Yla‐Herttuala S. Analysis of gene and protein expression during monocyte‐macrophage differentiation and cholesterol loading‐cDNA and protein array study. Atherosclerosis 2005; 180: 283–91
   PubMed Web of Science ®Google Scholar
• Mootha V. K., Lindgren C. M., Eriksson K. F., Subramanian A., Sihag S., Lehar J., et al. PGC‐1alpha‐responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 2003; 34: 267–73
   PubMed Web of Science ®Google Scholar
• Kohro T., Tanaka T., Murakami T., Wada Y., Aburatani H., Hamakubo T., et al. A comparison of differences in the gene expression profiles of phorbol 12‐myristate 13‐acetate differentiated THP‐1 cells and human monocyte‐derived macrophage. J Atheroscler Thromb 2004; 11: 88–97
   PubMedGoogle Scholar
• Kerr M. K., Churchill G. A. Experimental design for gene expression microarrays. Biostatistics 2001; 2: 183–201
   PubMedGoogle Scholar
• Butte A. The use and analysis of microarray data. Nat Rev Drug Discov 2002; 1: 951–60
   PubMed Web of Science ®Google Scholar
• Li J., Pankratz M., Johnson J. A. Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays. Toxicol Sci 2002; 69: 383–90
   PubMed Web of Science ®Google Scholar
• Zubay G. L., Parson W. W., Vance D. E. Regulation of Gene Expression in Eukaryotes. Principles of Biochemistry, G. L Zubay, W. W Parson, D. E Vance. Wm. C. Brown, DubuqueU S A 1995; 800–29
   Google Scholar
• Gygi S. P., Rochon Y., Franza B. R., Aebersold R. Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 1999; 19: 1720–30
   PubMed Web of Science ®Google Scholar
• Greenbaum D., Jansen R., Gerstein M. Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. Bioinformatics 2002; 18: 585–96
   PubMed Web of Science ®Google Scholar
• Mayer H., Bilban M., Kurtev V., Gruber F., Wagner O., Binder B. R., et al. Deciphering regulatory patterns of inflammatory gene expression from interleukin‐1‐stimulated human endothelial cells. Arterioscler Thromb Vasc Biol 2004; 24: 1192–8
   PubMed Web of Science ®Google Scholar
• Stoeckert C. J, Jr., Causton H. C., Ball C. A. Microarray databases: standards and ontologies. Nat Genet 2002; 32 Suppl: 469–73
   PubMed Web of Science ®Google Scholar
• Zhu H., Snyder M. Protein chip technology. Curr Opin Chem Biol 2003; 7: 55–63
   PubMed Web of Science ®Google Scholar
• Huang L., Zhao A., Wong F., Ayala J. M., Struthers M., Ujjainwalla F., et al. Leukotriene B4 strongly increases monocyte chemoattractant protein‐1 in human monocytes. Arterioscler Thromb Vasc Biol 2004; 24: 1783–8
   PubMed Web of Science ®Google Scholar
• Martinet W., Schrijvers D. M., De Meyer G. R., Herman A. G., Kockx M. M. Western array analysis of human atherosclerotic plaques: downregulation of apoptosis‐linked gene 2. Cardiovasc Res 2003; 60: 259–67
   PubMed Web of Science ®Google Scholar
• Kallioniemi O. P., Wagner U., Kononen J., Sauter G. Tissue microarray technology for high‐throughput molecular profiling of cancer. Hum Mol Genet 2001; 10: 657–62
   PubMed Web of Science ®Google Scholar
• Koullias G. J., Ravichandran P., Korkolis D. P., Rimm D. L., Elefteriades J. A. Increased tissue microarray matrix metalloproteinase expression favors proteolysis in thoracic aortic aneurysms and dissections. Ann Thorac Surg 2004; 78: 2106–10
   PubMed Web of Science ®Google Scholar
• Fleiner M., Kummer M., Mirlacher M., Sauter G., Cathomas G., Krapf R., et al. Arterial neovascularization and inflammation in vulnerable patients: early and late signs of symptomatic atherosclerosis. Circulation 2004; 110: 2843–50
   PubMed Web of Science ®Google Scholar
• Cheung V. G., Spielman R. S. The genetics of variation in gene expression. Nat.Genet 2002; 32 Suppl: 522–5
   Google Scholar
• Ganesh S. K., Skelding K. A., Mehta L., O'Neill K., Joo J., Zheng G., et al. Rationale and study design of the CardioGene Study: genomics of in‐stent restenosis. Pharmacogenomics 2004; 5: 952–1004
   Google Scholar
• Martinet W., Schrijvers D. M., De Meyer G. R., Thielemans J., Knaapen M. W., Herman A. G., et al. Gene expression profiling of apoptosis‐related genes in human atherosclerosis: upregulation of death‐associated protein kinase. Arterioscler Thromb Vasc Biol 2002; 22: 2023–9
   PubMedGoogle Scholar
• Woodside K. J., Hernandez A., Smith F. W., Xue X. Y., Hu M., Daller J. A., et al. Differential gene expression in primary and recurrent carotid stenosis. Biochem Biophys Res Commun 2003; 302: 509–14
   Google Scholar
• Randi A. M., Biguzzi E., Falciani F., Merlini P., Blakemore S., Bramucci E., et al. Identification of differentially expressed genes in coronary atherosclerotic plaques from patients with stable or unstable angina by cDNA array analysis. J Thromb Haemost 2003; 1: 829–35
   Google Scholar
• Ungvari Z., Csiszar A., Edwards J. G., Kaminski P. M., Wolin M. S., Kaley G., et al. Increased superoxide production in coronary arteries in hyperhomocysteinemia: role of tumor necrosis factor‐alpha, NAD(P)H oxidase, and inducible nitric oxide synthase. Arterioscler Thromb Vasc Biol 2003; 23: 418–24
   PubMed Web of Science ®Google Scholar
• Andersson T., Borang S., Larsson M., Wirta V., Wennborg A., Lundeberg J., et al. Novel candidate genes for atherosclerosis are identified by representational difference analysis‐based transcript profiling of cholesterol‐loaded macrophages. Pathobiology 2001; 69: 304–14
   Google Scholar
• Virgili F., Ambra R., Muratori F., Natella F., Majewicz J., Minihane A. M., et al. Effect of oxidized low‐density lipoprotein on differential gene expression in primary human endothelial cells. Antioxid Redox Signal 2003; 5: 237–47
   PubMed Web of Science ®Google Scholar
• Takabe W., Kanai Y., Chairoungdua A., Shibata N., Toi S., Kobayashi M., et al. Lysophosphatidylcholine enhances cytokine production of endothelial cells via induction of L‐type amino acid transporter 1 and cell surface antigen 4F2. Arterioscler Thromb Vasc Biol 2004; 24: 1640–5
   Google Scholar
• Sukhanov S., Hua S. Y., Delafontaine P. Global analysis of differentially expressed genes in oxidized LDL‐treated human aortic smooth muscle cells. Biochem Biophys Res Commun 2003; 306: 443–9
   Google Scholar
• Norata G. D., Pirillo A., Callegari E., Hamsten A., Catapano A. L., Eriksson P. Gene expression and intracellular pathways involved in endothelial dysfunction induced by VLDL and oxidised VLDL. Cardiovasc Res 2003; 59: 169–80
   PubMed Web of Science ®Google Scholar
• Haley K. J., Lilly C. M., Yang J. H., Feng Y., Kennedy S. P., Turi T. G., et al. Overexpression of eotaxin and the CCR3 receptor in human atherosclerosis: using genomic technology to identify a potential novel pathway of vascular inflammation. Circulation 2000; 102: 2185–9
   PubMed Web of Science ®Google Scholar
• Jang W. G., Kim H. S., Park K. G., Park Y. B., Yoon K. H., Han S. W., et al. Analysis of proteome and transcriptome of tumor necrosis factor alpha stimulated vascular smooth muscle cells with or without alpha lipoic acid. Proteomics 2004
   Google Scholar
• Lee Y. W., Eum S. Y., Chen K. C., Hennig B., Toborek M. Gene expression profile in interleukin‐4‐stimulated human vascular endothelial cells. Mol Med 2004; 10: 19–27
   PubMedGoogle Scholar
• Mikita T., Porter G., Lawn R. M., Shiffman D. Oxidized low density lipoprotein exposure alters the transcriptional response of macrophages to inflammatory stimulus. J Biol Chem 2001; 276: 45729–39
   PubMed Web of Science ®Google Scholar
• McCormick S. M., Eskin S. G., McIntire L. V., Teng C. L., Lu C. M., Russell C. G., et al. DNA microarray reveals changes in gene expression of shear stressed human umbilical vein endothelial cells. Proc Natl Acad Sci U S A 2001; 98: 8955–60
   PubMed Web of Science ®Google Scholar
• Ohura N., Yamamoto K., Ichioka S., Sokabe T., Nakatsuka H., Baba A., et al. Global analysis of shear stress‐responsive genes in vascular endothelial cells. J Atheroscler Thromb 2003; 10: 304–13
   Google Scholar
• Warabi E., Wada Y., Kajiwara H., Kobayashi M., Koshiba N., Hisada T., et al. Effect on endothelial cell gene expression of shear stress, oxygen concentration, and low‐density lipoprotein as studied by a novel flow cell culture system. Free Radic Biol Med 2004; 37: 682–94
   PubMedGoogle Scholar