Bioinformatics Approach to Evaluate Differential Gene Expression of M1/M2 Macrophage Phenotypes and Antioxidant Genes in Atherosclerosis

Cell Biochemistry and Biophysics

Volumn 70, Issue 2, 2014, Pages 831-839

  da Rocha, Ricardo Fagundes ^a,b   De Bastiani, Marco Antônio ^a,b   Klamt, Fábio ^a,b  

^a FEDERAL UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^b National Institute of Science and Technology in Translational Medicine (INCT TM)   (Brazil)

Author keywords

Antioxidants; Atherosclerosis; Bioinformatics; Gene expression; Macrophages polarization

Indexed keywords

ANTIOXIDANT; MESSENGER RNA;

ATHEROSCLEROTIC PLAQUE; BIOLOGY; CYTOLOGY; GENE EXPRESSION PROFILING; GENETICS; HUMAN; IMMUNOLOGY; MACROPHAGE; METABOLISM; PHENOTYPE;

ANTIOXIDANTS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; HUMANS; MACROPHAGES; PHENOTYPE; PLAQUE, ATHEROSCLEROTIC; RNA, MESSENGER;

EID: 84924082400     PISSN: 10859195     EISSN: 15590283     Source Type: Journal    
DOI: 10.1007/s12013-014-9987-3     Document Type: Article

References (60)

1. Ignarro, L. J. (2002). Nitric oxide as a unique signaling molecule in the vascular system: a historical overview. Journal of Physiology and Pharmacology,53, 503–514.
2. Howell, K. W., Meng, X., Fullerton, D. A., et al. (2011). Toll-like receptor 4 mediates oxidized LDL-induced macrophage differentiation to foam cells. Journal of Surgical Research,171, e27–e31.
3. Park, Y. M., Febbraio, M., & Silverstein, R. L. (2009). CD36 modulates migration of mouse and human macrophages in response to oxidized LDL and may contribute to macrophage trapping in the arterial intima. The Journal of Clinical Investigation,119, 136–145.
4. Tontonoz, P., Nagy, L., Alvarez, J. G., Thomazy, V. A., & Evans, R. M. (1998). PPARgamma promotes monocyte/macrophage differentiation and uptake of oxidized LDL. Cell,93, 241–252.
5. Stocker, R., & Keaney, J. F, Jr. (2004). Role of oxidative modifications in atherosclerosis. Physiological Reviews,84, 1381–1478.
6. Chen, Y. L., Chang, Y. J., & Jiang, M. J. (1999). Monocyte chemotactic protein-1 gene and protein expression in atherogenesis of hypercholesterolemic rabbits. Atherosclerosis,143, 115–123.
7. Kim, J. H., Park, Y. M., Shin, J. S., et al. (2009). Fraxinellone inhibits lipopolysaccharide-induced I nducible nitric oxide synthase and cyclooxygenase-2 expression by negatively regulating nuclear factor-kappa B in RAW 264.7 macrophages cells. Biological &/and Pharmaceutical Bulletin,32, 1062–1068.
8. Padro, T., Lugano, R., Garcia-Arguinzonis, M., & Badimon, L. (2012). LDL-induced impairment of human vascular smooth muscle cells repair function is reversed by HMG-CoA reductase inhibition. PLoS One,7, e38935.
9. Taylor, A. M., Li, F., Thimmalapura, P., et al. (2006). Hyperlipemia and oxidation of LDL induce vascular smooth muscle cell growth: an effect mediated by the HLH factor Id3. Journal of Vascular Research,43, 123–130.
10. Stocker, R., Huang, A., Jeranian, E., et al. (2004). Hypochlorous acid impairs endothelium-derived nitric oxide bioactivity through a superoxide-dependent mechanism. Arteriosclerosis, Thrombosis, and Vascular Biology,24, 2028–2033.
11. Doronzo, G., Viretto, M., Russo, I., et al. (2011). Nitric oxide activates PI3-K and MAPK signalling pathways in human and rat vascular smooth muscle cells: influence of insulin resistance and oxidative stress. Atherosclerosis,216, 44–53.
12. Szilvassy, Z., Csont, T., Pali, T., Droy-Lefaix, M. T., & Ferdinandy, P. (2001). Nitric oxide, peroxynitrite and cGMP in atherosclerosis-induced hypertension in rabbits: beneficial effects of cicletanine. Journal of Vascular Research,38, 39–46.
13. White, C. R., Brock, T. A., Chang, L. Y., et al. (1994). Superoxide and peroxynitrite in atherosclerosis. Proceedings of the National Academy of Sciences of the USA,91, 1044–1048.
14. Violi, F., Pignatelli, P., Pignata, C., et al. (2013). Reduced atherosclerotic burden in subjects with genetically determined low oxidative stress. Arteriosclerosis, Thrombosis, and Vascular Biology,33, 406–412.
15. Zinellu, E., Lepedda, A. J., Cigliano, A., et al. (2012). Association between human plasma chondroitin sulfate isomers and carotid atherosclerotic plaques. Biochemistry Research International,2012, 281284.
16. Pashkow, F. J. (2011). Oxidative Stress and Inflammation in Heart Disease: do Antioxidants Have a Role in Treatment and/or Prevention? International Journal of Inflammation,2011, 514623.
17. Gordon, S. (1998). The role of the macrophage in immune regulation. Research in Immunology,149, 685–688.
18. Gordon, S. (2003). Alternative activation of macrophages. Nature Reviews Immunology,3, 23–35.
19. Gordon, S. (2003). Do macrophage innate immune receptors enhance atherogenesis? Developmental Cell,5, 666–668.
20. Butcher, M. J., & Galkina, E. V. (2012). Phenotypic and functional heterogeneity of macrophages and dendritic cell subsets in the healthy and atherosclerosis-prone aorta. Frontiers in Physiology,3, 44.
21. Devaraj, S., & Jialal, I. (2011). C-reactive protein polarizes human macrophages to an M1 phenotype and inhibits transformation to the M2 phenotype. Arteriosclerosis, Thrombosis, and Vascular Biology,31, 1397–1402.
22. Sindrilaru, A., Peters, T., Wieschalka, S., et al. (2011). An unrestrained proinflammatory M1 macrophage population induced by iron impairs wound healing in humans and mice. The Journal of Clinical Investigation,121, 985–997.
23. Liu, L., Ge, D., Ma, L., et al. (2012). Interleukin-17 and prostaglandin E2 are involved in formation of an M2 macrophage-dominant microenvironment in lung cancer. Journal of Thoracic Oncology,7, 1091–1100.
24. Becker, M., Muller, C. B., De Bastiani, M. A., & Klamt, F. (2013). The prognostic impact of tumor-associated macrophages and intra-tumoral apoptosis in non-small cell lung cancer. Histology and Histopathology,29(1), 21–31.
25. Radonjic, M., Wielinga, P. Y., Wopereis, S., et al. (2013). Differential effects of drug interventions and dietary lifestyle in developing type 2 diabetes and complications: a systems biology analysis in LDLr-/- mice. PLoS One,8, e56122.
26. Muller, C. B., De Barros, R. L., Castro, M. A., et al. (2011). Validation of cofilin-1 as a biomarker in non-small cell lung cancer: application of quantitative method in a retrospective cohort. Journal of Cancer Research and Clinical Oncology,137, 1309–1316.
27. Castro, M. A., Dal-Pizzol, F., Zdanov, S., et al. (2010). CFL1 expression levels as a prognostic and drug resistance marker in nonsmall cell lung cancer. Cancer,116, 3645–3655.
28. Mombach, J. C., Castro, M. A., Moreira, J. C., & De Almeida, R. M. (2008). On the absence of mutations in nucleotide excision repair genes in sporadic solid tumors. Genetics and Molecular Research,7, 152–160.
29. Martinez, F. O., Gordon, S., Locati, M., & Mantovani, A. (2006). Transcriptional profiling of the human monocyte-to-macrophage differentiation and polarization: new molecules and patterns of gene expression. Journal of Immunology,177, 7303–7311.
30. Baek, Y. S., Haas, S., Hackstein, H., et al. (2009). Identification of novel transcriptional regulators involved in macrophage differentiation and activation in U937 cells. BMC Immunol,10, 18.
31. Pello, O. M., De Pizzol, M., Mirolo, M., et al. (2011). Role of c-MYC in alternative activation of human macrophages and tumor-associated macrophage biology. Blood,119, 411–421.
32. Gelain, D. P., Dalmolin, R. J., Belau, V. L., et al. (2009). A systematic review of human antioxidant genes. Frontiers Bioscience,14, 4457–4463.
33. Castro, M. A., Mombach, J. C., De Almeida, R. M., & Moreira, J. C. (2007). Impaired expression of NER gene network in sporadic solid tumors. Nucleic Acids Research,35, 1859–1867.
34. Castro, M. A., Filho, J. L., Dalmolin, R. J., et al. (2009). ViaComplex: software for landscape analysis of gene expression networks in genomic context. Bioinformatics,25, 1468–1469.
35. Subramanian, A., Tamayo, P., Mootha, V. K., et al. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the USA,102, 15545–15550.
36. Gratchev, A., Sobenin, I., Orekhov, A., & Kzhyshkowska, J. (2012). Monocytes as a diagnostic marker of cardiovascular diseases. Immunobiology,217, 476–482.
37. Gratchev, A., Ovsiy, I., Manousaridis, I., et al. (2013). Novel Monocyte Biomarkers of Atherogenic Conditions. Current Pharmaceutical Design,19(33), 5859–5864.
38. Graham, A., Hogg, N., Kalyanaraman, B., et al. (1993). Peroxynitrite modification of low-density lipoprotein leads to recognition by the macrophage scavenger receptor. FEBS Letters,330, 181–185.
39. Noguchi, N., Gotoh, N., & Niki, E. (1994). Effects of ebselen and probucol on oxidative modifications of lipid and protein of low density lipoprotein induced by free radicals. Biochimica et Biophysica Acta,1213, 176–182.
40. Mahmood, D. F., Abderrazak, A., Couchie, D., et al. (2013). Truncated thioredoxin (Trx-80) promotes pro-inflammatory macrophages of the M1 phenotype and enhances atherosclerosis. Journal of Cellular Physiology,228(7), 1577–1583.
41. Stoger, J. L., Gijbels, M. J., Van Der Velden, S., et al. (2012). Distribution of macrophage polarization markers in human atherosclerosis. Atherosclerosis,225, 461–468.
42. Mantovani, A., Garlanda, C., & Locati, M. (2009). Macrophage diversity and polarization in atherosclerosis: a question of balance. Arteriosclerosis, Thrombosis, and Vascular Biology,29, 1419–1423.
43. Martinez, F. O., Sica, A., Mantovani, A., & Locati, M. (2008). Macrophage activation and polarization. Frontiers in Bioscience,13, 453–461.
44. Hirose, K., Iwabuchi, K., Shimada, K., et al. (2011). Different responses to oxidized low-density lipoproteins in human polarized macrophages. Lipids Health Dis,10, 1.
45. Gray, S. P., Di Marco, E., Okabe, J., et al. (2013). Nox1 plays a key role in diabetes accelerated atherosclerosis. Circulation,127, 1888–1902.
46. Blin, J., Ahmad, Z., Rampal, L. R., et al. (2013). Preliminary assessment of differential expression of candidate genes associated with atherosclerosis. Genes and Genetic Systems,88, 199–209.
47. Ye, S. (2006). Influence of matrix metalloproteinase genotype on cardiovascular disease susceptibility and outcome. Cardiovascular Research,69, 636–645.
48. Pollanen, P. J., Lehtimaki, T., Mikkelsson, J., et al. (2005). Matrix metalloproteinase3 and 9 gene promoter polymorphisms: joint action of two loci as a risk factor for coronary artery complicated plaques. Atherosclerosis,180, 73–78.
49. Pu, H., Yin, J., Wu, Y., et al. (2013). The association between CD14 gene C-260T polymorphism and coronary heart disease risk: a meta-analysis. Molecular Biology Reports,40, 4001–4008.
50. Zhou, M. S., Chadipiralla, K., Mendez, A. J., et al. (2013). Nicotine potentiates proatherogenic effects of oxLDL by stimulating and upregulating macrophage CD36 signaling. American Journal of Physiology Heart and Circulatory Physiology,305, H563–H574.
51. Hermann, M., Fischer, D., Hoffmann, M. M., et al. (2011). CRP and CD14 polymorphisms correlate with coronary plaque volume in patients with coronary artery disease–IVUS substudy of the ENCORE trials. Atherosclerosis,220, 172–176.
52. Poitou, C., Dalmas, E., Renovato, M., et al. (2011). CD14dimCD16+ and CD14+CD16+ monocytes in obesity and during weight loss: relationships with fat mass and subclinical atherosclerosis. Arteriosclerosis, Thrombosis, and Vascular Biology,31, 2322–2330.
53. Konii, H., Sato, K., Kikuchi, S., et al. (2013). Stimulatory effects of cardiotrophin 1 on atherosclerosis. Hypertension,62(5), 942–950.
54. Rogacev, K. S., Cremers, B., Zawada, A. M., et al. (2012). CD14++CD16+ monocytes independently predict cardiovascular events: a cohort study of 951 patients referred for elective coronary angiography. Journal of the American College of Cardiology,60, 1512–1520.
55. Lepedda, A. J., Zinellu, A., Nieddu, G., et al. (2013). Protein sulfhydryl group oxidation and mixed-disulfide modifications in stable and unstable human carotid plaques. Oxidative Medicine Cellular Longevity,2013, 403973.
56. Giacconi, R., Cipriano, C., Muti, E., et al. (2005). Novel -209A/G MT2A polymorphism in old patients with type 2 diabetes and atherosclerosis: relationship with inflammation (IL-6) and zinc. Biogerontology,6, 407–413.
57. Ponnuswamy, P., Schrottle, A., Ostermeier, E., et al. (2012). eNOS protects from atherosclerosis despite relevant superoxide production by the enzyme in apoE mice. PLoS One,7, e30193.
58. Perrotta, I., Perrotta, E., Sesti, S., Cassese, M., & Mazzulla, S. (2013). MnSOD expression in human atherosclerotic plaques: an immunohistochemical and ultrastructural study. Cardiovascular Pathology,22(6), 428–437.
59. Cloarec, M., Caillard, P., Provost, J. C., et al. (2007). GliSODin, a vegetal sod with gliadin, as preventative agent vs. atherosclerosis, as confirmed with carotid ultrasound-B imaging. European Annals of Allergy Clinical Immunology,39, 45–50.
60. Antoniades, C., Bakogiannis, C., Leeson, P., et al. (2011). Rapid, direct effects of statin treatment on arterial redox state and nitric oxide bioavailability in human atherosclerosis via tetrahydrobiopterin-mediated endothelial nitric oxide synthase coupling. Circulation,124, 335–345.