MicroRNA expression signature in human abdominal aortic aneurysms

BMC Medical Genomics

Helena Kuivaniemi¹  Gerard Tromp¹  David J Carey¹  John L Gray⁴  David P Franklin⁴  Thomas C Peeler⁵  Charles M Schworer¹  James R Elmore⁴  Irene Hinterseher²  Gabor Gäbel³  Kimberly Derr¹  Matthew C Pahl⁵ 

[1] The Sigfried and Janet Weis Center for Research, Geisinger Clinic, 100 North Academy Avenue, Pennsylvania, 17822-2610, USA;Department of General, Visceral, Vascular and Thoracic Surgery, Charité Universitätsmedizin, Charité Campus Mitte, Berlin, Germany;Department of Visceral, Thoracic and Vascular Surgery, Technical University of Dresden, Dresden, Germany;Department of Vascular and Endovascular Surgery, Geisinger Clinic, Danville, PA, USA;Department of Biology, Susquehanna University, Selinsgrove, PA, USA

关键词: Network analysis;    miRNA-mRNA analysis;    Vascular biology;    Microarray analysis;    Apoptosis;   

Others  :  1134837
DOI  :  10.1186/1755-8794-5-25

 received in 2012-02-23, accepted in 2012-05-31,  发布年份 2012

【 授权许可】

   
2012 Pahl et al.; licensee BioMed Central Ltd.

【 参考文献 】

• [1]Sakalihasan N, Limet R, Defawe OD: Abdominal aortic aneurysm. Lancet 2005, 365:1577-1589.
• [2]Boddy AM, Lenk GM, Lillvis JH, Nischan J, Kyo Y, Kuivaniemi H: Basic research studies to understand aneurysm disease. Drug News Perspect 2008, 21:142-148.
• [3]Vorp DA: Biomechanics of abdominal aortic aneurysm. J Biomech 2007, 40:1887-1902.
• [4]Hinterseher I, Tromp G, Kuivaniemi H: Genes and abdominal aortic aneurysm. Ann Vasc Surg 2011, 25:388-412.
• [5]Kuivaniemi H, Platsoucas CD, Tilson MD 3rd: Aortic aneurysms: an immune disease with a strong genetic component. Circulation 2008, 117:242-252.
• [6]Abdul-Hussien H, Hanemaaijer R, Kleemann R, Verhaaren BF, van Bockel JH, Lindeman JH: The pathophysiology of abdominal aortic aneurysm growth: corresponding and discordant inflammatory and proteolytic processes in abdominal aortic and popliteal artery aneurysms. J Vasc Surg 2010, 51:1479-1487.
• [7]Henderson EL, Geng YJ, Sukhova GK, Whittemore AD, Knox J, Libby P: Death of smooth muscle cells and expression of mediators of apoptosis by T lymphocytes in human abdominal aortic aneurysms. Circulation 1999, 99:96-104.
• [8]McCormick ML, Gavrila D, Weintraub NL: Role of oxidative stress in the pathogenesis of abdominal aortic aneurysms. Arterioscler Thromb Vasc Biol 2007, 27:461-469.
• [9]Lenk GM, Tromp G, Weinsheimer S, Gatalica Z, Berguer R, Kuivaniemi H: Whole genome expression profiling reveals a significant role for immune function in human abdominal aortic aneurysms. BMC Genomics 2007, 8:237. BioMed Central Full Text
• [10]Angaji SA, Hedayati SS, Poor RH, Madani S, Poor SS, Panahi S: Application of RNA interference in treating human diseases. J Genet 2010, 89:527-537.
• [11]Lewis BP, Burge CB, Bartel DP: Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:15-20.
• [12]Lynam-Lennon N, Maher SG, Reynolds JV: The roles of microRNA in cancer and apoptosis. Biol Rev Camb Philos Soc 2009, 84:55-71.
• [13]van Rooij E: The art of microRNA research. Circ Res 2011, 108:219-234.
• [14]MacDonald JW: Affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips. R package version 1.26.0; 2008.
• [15]Smyth GK, Michaud J, Scott HS: Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics 2005, 21:2067-2075.
• [16]Benjamini Y, Hochberg J: Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B 1995, 57:289-300.
• [17]Guo L, Lu Z: The fate of miRNA* strand through evolutionary analysis: implication for degradation as merely carrier strand or potential regulatory molecule? PLoS One 2010, 5:e11387.
• [18]Favero F: RmiR.hsa:Various databases of microRNA targets. R package version 1.0.4. 2009.
• [19]Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R: Fast and effective prediction of microRNA/target duplexes. RNA 2004, 10:1507-1517.
• [20]Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504.
• [21]Duncan DT, Prodduturi N, Zhang B: WebGestalt2: an updated and expanded version of the Web-based Gene Set Analysis Toolkit. BMC Bioinforma 2010, 11:P10. BioMed Central Full Text
• [22]Care A, Catalucci D, Felicetti F, Bonci D, Addario A, Gallo P, Bang ML, Segnalini P, Gu Y, Dalton ND, et al.: MicroRNA-133 controls cardiac hypertrophy. Nat Med 2007, 13:613-618.
• [23]Horie T, Ono K, Nishi H, Iwanaga Y, Nagao K, Kinoshita M, Kuwabara Y, Takanabe R, Hasegawa K, Kita T, et al.: MicroRNA-133 regulates the expression of GLUT4 by targeting KLF15 and is involved in metabolic control in cardiac myocytes. Biochem Biophys Res Commun 2009, 389:315-320.
• [24]Li Q, Lin X, Yang X, Chang J: NFATc4 is negatively regulated in miR-133a-mediated cardiomyocyte hypertrophic repression. Am J Physiol Heart Circ Physiol 2010, 298:H1340-1347.
• [25]Liu N, Bezprozvannaya S, Williams AH, Qi X, Richardson JA, Bassel-Duby R, Olson EN: microRNA-133a regulates cardiomyocyte proliferation and suppresses smooth muscle gene expression in the heart. Genes Dev 2008, 22:3242-3254.
• [26]Sun SG, Zheng B, Han M, Fang XM, Li HX, Miao SB, Su M, Han Y, Shi HJ, Wen JK: miR-146a and Kruppel-like factor 4 form a feedback loop to participate in vascular smooth muscle cell proliferation. EMBO Rep 2011, 12:56-62.
• [27]Torella D, Iaconetti C, Catalucci D, Ellison GM, Leone A, Waring CD, Bochicchio A, Vicinanza C, Aquila I, Curcio A, et al.: MicroRNA-133 controls vascular smooth muscle cell phenotypic switch in vitro and vascular remodeling in vivo. Circ Res 2011, 109:880-893.
• [28]Xiao J, Zhu X, He B, Zhang Y, Kang B, Wang Z, Ni X: MiR-204 regulates cardiomyocyte autophagy induced by ischemia-reperfusion through LC3-II. J Biomed Sci 2011, 18:35. BioMed Central Full Text
• [29]Liao M, Zou S, Weng J, Hou L, Yang L, Zhao Z, Bao J, Jing Z: A microRNA profile comparison between thoracic aortic dissection and normal thoracic aorta indicates the potential role of microRNAs in contributing to thoracic aortic dissection pathogenesis. J Vasc Surg 2011, 53:1341-1349.
• [30]Maegdefessel L, Azuma J, Toh R, Deng A, Merk DR, Raiesdana A, Leeper NJ, Raaz U, Schoelmerich AM, McConnell MV, et al.: MicroRNA-21 blocks abdominal aortic aneurysm development and nicotine-augmented expansion. Sci Transl Med 2012, 4:122.
• [31]Maegdefessel L, Azuma J, Toh R, Merk DR, Deng A, Chin JT, Raaz U, Schoelmerich AM, Raiesdana A, Leeper NJ, et al.: Inhibition of microRNA-29b reduces murine abdominal aortic aneurysm development. J Clin Invest 2012, 122:497-506.
• [32]Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, Epstein EJ, MacMenamin P, da Piedade I, Gunsalus KC, Stoffel M, et al.: Combinatorial microRNA target predictions. Nat Genet 2005, 37:495-500.
• [33]Wang X, El Naqa IM: Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics 2008, 24:325-332.
• [34]Van Rechem C, Boulay G, Pinte S, Stankovic-Valentin N, Guerardel C, Leprince D: Differential regulation of HIC1 target genes by CtBP and NuRD, via an acetylation/SUMOylation switch, in quiescent versus proliferating cells. Mol Cell Biol 2010, 30:4045-4059.
• [35]Courboulin A, Paulin R, Giguere NJ, Saksouk N, Perreault T, Meloche J, Paquet ER, Biardel S, Provencher S, Cote J, et al.: Role for miR-204 in human pulmonary arterial hypertension. J Exp Med 2011, 208:535-548.
• [36]Sun SY: Understanding the Role of the Death Receptor 5/FADD/caspase-8 Death Signaling in Cancer Metastasis. Mol Cell Pharmacol 2011, 3:31-34.
• [37]Aizawa S, Nakano H, Ishida T, Horie R, Nagai M, Ito K, Yagita H, Okumura K, Inoue J, Watanabe T: Tumor necrosis factor receptor-associated factor (TRAF) 5 and TRAF2 are involved in CD30-mediated NFkappaB activation. J Biol Chem 1997, 272:2042-2045.
• [38]Cano CE, Gommeaux J, Pietri S, Culcasi M, Garcia S, Seux M, Barelier S, Vasseur S, Spoto RP, Pebusque MJ, et al.: Tumor protein 53-induced nuclear protein 1 is a major mediator of p53 antioxidant function. Cancer Res 2009, 69:219-226.
• [39]Pober JS, Tellides G: Participation of blood vessel cells in human adaptive immune responses. Trends Immunol 2012, 33:49-57.
• [40]Krummel MF, Allison JP: Pillars article: CD28 and CTLA-4 have opposing effects on the response of T cells to stimulation. The journal of experimental medicine. 1995. 182: 459–465. J Immunol 2011, 187:3459-3465.
• [41]Collins M, Ling V, Carreno BM: The B7 family of immune-regulatory ligands. Genome Biol 2005, 6:223. BioMed Central Full Text
• [42]Sakthivel P, Shively V, Kakoulidou M, Pearce W, Lefvert AK: The soluble forms of CD28, CD86 and CTLA-4 constitute possible immunological markers in patients with abdominal aortic aneurysm. J Intern Med 2007, 261:399-407.
• [43]Al-Mutairi MS, Cadalbert LC, McGachy HA, Shweash M, Schroeder J, Kurnik M, Sloss CM, Bryant CE, Alexander J, Plevin R: MAP kinase phosphatase-2 plays a critical role in response to infection by Leishmania mexicana. PLoS Pathog 2010, 6:e1001192.
• [44]Colli ML, Moore F, Gurzov EN, Ortis F, Eizirik DL: MDA5 and PTPN2, two candidate genes for type 1 diabetes, modify pancreatic beta-cell responses to the viral by-product double-stranded RNA. Hum Mol Genet 2010, 19:135-146.
• [45]Dimayuga PC, Li H, Chyu KY, Fredrikson GN, Nilsson J, Fishbein MC, Shah PK, Cercek B: T cell modulation of intimal thickening after vascular injury: the bimodal role of IFN-gamma in immune deficiency. Arterioscler Thromb Vasc Biol 2005, 25:2528-2534.
• [46]Loitto VM, Forslund T, Sundqvist T, Magnusson KE, Gustafsson M: Neutrophil leukocyte motility requires directed water influx. J Leukoc Biol 2002, 71:212-222.
• [47]Lee K, Ahn TH, Kang WC, Han SH, Choi IS, Shin EK: The effects of statin and niacin on plaque stability, plaque regression, inflammation and oxidative stress in patients with mild to moderate coronary artery stenosis. Korean Circ J 2011, 41:641-648.
• [48]Boden WE, Probstfield JL, Anderson T, Chaitman BR, Desvignes-Nickens P, Koprowicz K, McBride R, Teo K, Weintraub W: Niacin in patients with low HDL cholesterol levels receiving intensive statin therapy. N Engl J Med 2011, 365:2255-2267.
• [49]Lee Y, Yang X, Huang Y, Fan H, Zhang Q, Wu Y, Li J, Hasina R, Cheng C, Lingen MW, et al.: Network modeling identifies molecular functions targeted by miR-204 to suppress head and neck tumor metastasis. PLoS Comput Biol 2010, 6:e1000730.
• [50]Freestone T, Turner RJ, Coady A, Higman DJ, Greenhalgh RM, Powell JT: Inflammation and matrix metalloproteinases in the enlarging abdominal aortic aneurysm. Arterioscler Thromb Vasc Biol 1995, 15:1145-1151.
• [51]Ferrell CM, Dorsam ST, Ohta H, Humphries RK, Derynck MK, Haqq C, Largman C, Lawrence HJ: Activation of stem-cell specific genes by HOXA9 and HOXA10 homeodomain proteins in CD34+ human cord blood cells. Stem Cells 2005, 23:644-655.
• [52]Li C, Li J, Cai X, Sun H, Jiao J, Bai T, Zhou XW, Chen X, Gill DL, Tang XD: Protein kinase D3 is a pivotal activator of pathological cardiac hypertrophy by selectively increasing the expression of hypertrophic transcription factors. J Biol Chem 2011, 286:40782-40791.
• [53]Lillvis JH, Erdman R, Schworer CM, Golden A, Derr K, Gatalica Z, Cox LA, Shen J, Vander Heide RS, Lenk GM, et al.: Regional expression of HOXA4 along the aorta and its potential role in human abdominal aortic aneurysms. BMC Physiol 2011, 11:9. BioMed Central Full Text
• [54]Berridge MJ, Bootman MD, Roderick HL: Calcium signalling: dynamics, homeostasis and remodelling. Nat Rev Mol Cell Biol 2003, 4:517-529.
• [55]Haldar SM, Lu Y, Jeyaraj D, Kawanami D, Cui Y, Eapen SJ, Hao C, Li Y, Doughman YQ, Watanabe M, et al.: Klf15 deficiency is a molecular link between heart failure and aortic aneurysm formation. Sci Transl Med 2010, 2:26.
• [56]Curci JA, Liao S, Huffman MD, Shapiro SD, Thompson RW: Expression and localization of macrophage elastase (matrix metalloproteinase-12) in abdominal aortic aneurysms. J Clin Invest 1998, 102:1900-1910.
• [57]Yoshimura K, Ikeda Y, Aoki H: Innocent bystander? Intraluminal thrombus in abdominal aortic aneurysm. Atherosclerosis 2011, 218:285-286.
• [58]Hinterseher I, Erdman R, Donoso LA, Vrabec TR, Schworer CM, Lillvis JH, Boddy AM, Derr K, Golden A, Bowen WD, et al.: Role of complement cascade in abdominal aortic aneurysms. Arterioscler Thromb Vasc Biol 2011, 31:1653-1660.
• [59]Hinterseher I, Erdman R, Elmore JR, Stahl E, Pahl MC, Derr K, Golden A, Lillvis JH, KJ , Cindric MC, et al.: Novel pathways in the pathobiology of human abdominal aortic aneurysms. Pathobiology 2013, 80(1):1-10.