Differential Gene Expression in Coiled versus Flow-Diverter-Treated Aneurysms: RNA Sequencing Analysis in a Rabbit Aneurysm Model

References

1. 1.↵
   2. Brinjikji W,
   3. Murad MH,
   4. Lanzino G, et al

   . Endovascular treatment of intracranial aneurysms with flow diverters: a meta-analysis. Stroke 2013;44:442–47 doi:10.1161/STROKEAHA.112.678151 pmid:23321438

   Abstract/FREE Full Text
2. 2.↵
   2. Cebral JR,
   3. Mut F,
   4. Raschi M, et al

   . Aneurysm rupture following treatment with flow-diverting stents: computational hemodynamics analysis of treatment. AJNR Am J Neuroradiol 2011;32:27–33 doi:10.3174/ajnr.A2398 pmid:21071533

   Abstract/FREE Full Text
3. 3.↵
   2. Kulcsár Z,
   3. Houdart E,
   4. Bonafé A, et al

   . Intra-aneurysmal thrombosis as a possible cause of delayed aneurysm rupture after flow-diversion treatment. AJNR Am J Neuroradiol 2011;32:20–25 doi:10.3174/ajnr.A2370 pmid:21071538

   Abstract/FREE Full Text
4. 4.↵
   2. Kulcsár Z,
   3. Szikora I

   . The ESMINT Retrospective Analysis of Delayed Aneurysm Ruptures after flow diversion (RADAR) study. The eJournal of the European Society of Minimally Invasive Neurological Therapy 2012. http://www.ejmint.org/original-article/1244000088. Accessed December 15, 2015.
5. 5.↵
   2. Brinjikji W,
   3. Kallmes DF,
   4. Kadirvel R

   . Mechanisms of healing in coiled intracranial aneurysms: a review of the literature. AJNR Am J Neuroradiol 2015;36:1216–22 doi:10.3174/ajnr.A4175 pmid:25430855

   Abstract/FREE Full Text
6. 6.↵
   2. Kadirvel R,
   3. Ding YH,
   4. Dai D, et al

   . Cellular mechanisms of aneurysm occlusion after treatment with a flow diverter. Radiology 2014;270:394–99 doi:10.1148/radiol.13130796 pmid:24086073

   CrossRefPubMedWeb of Science
7. 7.↵
   2. Rouchaud A,
   3. Journé C,
   4. Louedec L, et al

   . Autologous mesenchymal stem cell endografting in experimental cerebrovascular aneurysms. Neuroradiology 2013;55:741–49 doi:10.1007/s00234-013-1167-4 pmid:23515660

   CrossRefPubMed
8. 8.↵
   2. Kallmes DF,
   3. Helm GA,
   4. Hudson SB, et al

   . Histologic evaluation of platinum coil embolization in an aneurysm model in rabbits. Radiology 1999;213:217–22 doi:10.1148/radiology.213.1.r99oc16217 pmid:10540665

   CrossRefPubMedWeb of Science
9. 9.↵
   2. Crobeddu E,
   3. Lanzino G,
   4. Kallmes DF, et al

   . Review of 2 decades of aneurysm-recurrence literature, part 1: reducing recurrence after endovascular coiling. AJNR Am J Neuroradiol 2013;34:266–70 doi:10.3174/ajnr.A3032 pmid:22422180

   Abstract/FREE Full Text
10. 10.↵
    2. Raymond J,
    3. Guilbert F,
    4. Weill A, et al

    . Long-term angiographic recurrences after selective endovascular treatment of aneurysms with detachable coils. Stroke 2003;34:1398–403 doi:10.1161/01.STR.0000073841.88563.E9 pmid:12775880

    Abstract/FREE Full Text
11. 11.↵
    2. Li ZF,
    3. Fang XG,
    4. Yang PF, et al

    . Endothelial progenitor cells contribute to neointima formation in rabbit elastase-induced aneurysm after flow diverter treatment. CNS Neurosci Ther 2013;19:352–57 doi:10.1111/cns.12086 pmid:23528070

    CrossRefPubMedWeb of Science
12. 12.↵
    2. Kadirvel R,
    3. Ding YH,
    4. Dai D, et al

    . Differential gene expression in well-healed and poorly healed experimental aneurysms after coil treatment. Radiology 2010;257:418–26 doi:10.1148/radiol.10100362 pmid:20829543

    CrossRefPubMedWeb of Science
13. 13.↵
    2. Mangrum WI,
    3. Farassati F,
    4. Kadirvel R, et al

    . mRNA expression in rabbit experimental aneurysms: a study using gene chip microarrays. AJNR Am J Neuroradiol 2007;28:864–69 pmid:17494658

    Abstract/FREE Full Text
14. 14.↵
    2. Kadirvel R,
    3. Ding YH,
    4. Dai D, et al

    . Gene expression profiling of experimental saccular aneurysms using deoxyribonucleic acid microarrays. AJNR Am J Neuroradiol 2008;29:1566–69 doi:10.3174/ajnr.A1125 pmid:18599579

    Abstract/FREE Full Text
15. 15.↵
    2. Puffer C,
    3. Dai D,
    4. Ding YH, et al

    . Gene expression comparison of flow diversion and coiling in an experimental aneurysm model. J Neurointerv Surg 2015;7:926–30 doi:10.1136/neurintsurg-2014-011452 pmid:25332413

    Abstract/FREE Full Text
16. 16.↵
    2. Holcomb M,
    3. Ding YH,
    4. Dai D, et al

    . RNA-sequencing analysis of messenger RNA/microRNA in a rabbit aneurysm model identifies pathways and genes of interest. AJNR Am J Neuroradiol 2015;36:1710–15 doi:10.3174/ajnr.A4390 pmid:26228879

    Abstract/FREE Full Text
17. 17.↵
    2. Nakaoka H,
    3. Tajima A,
    4. Yoneyama T, et al

    . Gene expression profiling reveals distinct molecular signatures associated with the rupture of intracranial aneurysm. Stroke 2014;45:2239–45 doi:10.1161/STROKEAHA.114.005851 pmid:24938844

    Abstract/FREE Full Text
18. 18.↵
    2. Roder C,
    3. Kasuya H,
    4. Harati A, et al

    . Meta-analysis of microarray gene expression studies on intracranial aneurysms. Neuroscience 2012;201:105–13 doi:10.1016/j.neuroscience.2011.10.033 pmid:22079572

    CrossRefPubMed
19. 19.↵
    2. Altes TA,
    3. Cloft HJ,
    4. Short JG, et al

    . 1999 ARRS Executive Council Award: creation of saccular aneurysms in the rabbit: a model suitable for testing endovascular devices—American Roentgen Ray Society. AJR Am J Roentgenol 2000;174:349–54 doi:10.2214/ajr.174.2.1740349 pmid:10658703

    CrossRefPubMedWeb of Science
20. 20.↵
    2. Kallmes DF,
    3. Ding YH,
    4. Dai D, et al

    . A new endoluminal, flow-disrupting device for treatment of saccular aneurysms. Stroke 2007;38:2346–52 doi:10.1161/STROKEAHA.106.479576 pmid:17615366

    Abstract/FREE Full Text
21. 21.↵
    2. Kalari KR,
    3. Nair AA,
    4. Bhavsar JD, et al

    . MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing. BMC Bioinformatics 2014;15:224 doi:10.1186/1471-2105-15-224 pmid:24972667

    CrossRefPubMed
22. 22.↵
    2. Wang L,
    3. Wang S,
    4. Li W

    . RSeQC: quality control of RNA-seq experiments. Bioinformatics 2012;28:2184–85 doi:10.1093/bioinformatics/bts356 pmid:22743226

    Abstract/FREE Full Text
23. 23.↵
    2. Trapnell C,
    3. Pachter L,
    4. Salzberg SL

    . TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009;25:1105–11 doi:10.1093/bioinformatics/btp120 pmid:19289445

    Abstract/FREE Full Text
24. 24.↵
    2. Langmead B,
    3. Trapnell C,
    4. Pop M, et al

    . Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009;10:R25 doi:10.1186/gb-2009-10-3-r25 pmid:19261174

    CrossRefPubMed
25. 25.↵
    2. Anders S,
    3. Pyl PT,
    4. Huber W

    . HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics 2015;31:166–69 doi:10.1093/bioinformatics/btu638 pmid:25260700

    Abstract/FREE Full Text
26. 26.↵
    2. Khoo AA,
    3. Ogrizek-Tomas M,
    4. Bulovic A, et al

    . ExoLocator–an online view into genetic makeup of vertebrate proteins. Nucleic Acids Res 2014;42:D879–81 doi:10.1093/nar/gkt1164 pmid:24271393

    Abstract/FREE Full Text
27. 27.↵
    2. Krämer A,
    3. Green J,
    4. Pollard J Jr., et al

    . Causal analysis approaches in Ingenuity Pathway Analysis. Bioinformatics 2014;30:523–30 doi:10.1093/bioinformatics/btt703 pmid:24336805

    Abstract/FREE Full Text
28. 28.↵
    2. Reiner A,
    3. Yekutieli D,
    4. Benjamini Y

    . Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 2003;19:368–75 doi:10.1093/bioinformatics/btf877 pmid:12584122

    Abstract/FREE Full Text
29. 29.↵
    2. Obermajer N,
    3. Doljak B,
    4. Kos J

    . Cytokeratin 8 ectoplasmic domain binds urokinase-type plasminogen activator to breast tumor cells and modulates their adhesion, growth and invasiveness. Mol Cancer 2009;8:88 doi:10.1186/1476-4598-8-88 pmid:19845941

    CrossRefPubMed
30. 30.↵
    2. Didiasova M,
    3. Wujak L,
    4. Wygrecka M, et al

    . From plasminogen to plasmin: role of plasminogen receptors in human cancer. Int J Mol Sci 2014;15:21229–52 doi:10.3390/ijms151121229 pmid:25407528

    CrossRefPubMed
31. 31.↵
    2. Syrovets T,
    3. Lunov O,
    4. Simmet T

    . Plasmin as a proinflammatory cell activator. J Leukoc Biol 2012;92:509–19 doi:10.1189/jlb.0212056 pmid:22561604

    Abstract/FREE Full Text
32. 32.↵
    2. Lijnen HR

    . Plasmin and matrix metalloproteinases in vascular remodeling. Thromb Haemost 2001;86:324–33 pmid:11487021

    PubMedWeb of Science
33. 33.↵
    2. Carmeliet P,
    3. Moons L,
    4. Lijnen R, et al

    . Urokinase-generated plasmin activates matrix metalloproteinases during aneurysm formation. Nat Genet 1997;17:439–44 doi:10.1038/ng1297-439 pmid:9398846

    CrossRefPubMedWeb of Science
34. 34.↵
    2. Leeper NJ,
    3. Tedesco MM,
    4. Kojima Y, et al

    . Apelin prevents aortic aneurysm formation by inhibiting macrophage inflammation. Am J Physiol Heart Circ Physiol 2009;296:H1329–35 doi:10.1152/ajpheart.01341.2008 pmid:19304942

    Abstract/FREE Full Text
35. 35.↵
    2. Zhou Y,
    3. Wang Y,
    4. Qiao S

    . Apelin: a potential marker of coronary artery stenosis and atherosclerotic plaque stability in ACS patients. Int Heart J 2014;55:204–12 doi:10.1536/ihj.13-234 pmid:24806385

    CrossRefPubMed
36. 36.↵
    2. Masri B,
    3. Morin N,
    4. Cornu M, et al

    . Apelin (65–77) activates p70 S6 kinase and is mitogenic for umbilical endothelial cells. FASEB J 2004;18:1909–11 pmid:15385434

    Abstract/FREE Full Text
37. 37.↵
    2. Du X,
    3. Kang JP,
    4. Wu JH, et al

    . Elevated high sensitive C-reactive protein and apelin levels after percutaneous coronary intervention and drug-eluting stent implantation. J Zhejiang Univ Sci B 2010;11:548–52 doi:10.1631/jzus.B1001004 pmid:20669343

    CrossRefPubMed
38. 38.↵
    2. Tulamo R,
    3. Frösen J,
    4. Hernesniemi J, et al

    . Inflammatory changes in the aneurysm wall: a review. J Neurointerv Surg 2010;2:120–30 doi:10.1136/jnis.2009.002055 pmid:21990591

    Abstract/FREE Full Text
39. 39.↵
    2. Frösen J

    . Smooth muscle cells and the formation, degeneration, and rupture of saccular intracranial aneurysm wall: a review of current pathophysiological knowledge. Transl Stroke Res 2014;5:347–56 doi:10.1007/s12975-014-0340-3 pmid:24683005

    CrossRefPubMed
40. 40.↵
    2. Aoki T,
    3. Kataoka H,
    4. Morimoto M, et al

    . Macrophage-derived matrix metalloproteinase-2 and -9 promote the progression of cerebral aneurysms in rats. Stroke 2007;38:162–69 doi:10.1161/01.STR.0000252129.18605.c8 pmid:17122420

    Abstract/FREE Full Text
41. 41.↵
    2. Kadirvel R,
    3. Dai D,
    4. Ding YH, et al

    . Endovascular treatment of aneurysms: healing mechanisms in a swine model are associated with increased expression of matrix metalloproteinases, vascular cell adhesion molecule-1, and vascular endothelial growth factor, and decreased expression of tissue inhibitors of matrix metalloproteinases. AJNR Am J Neuroradiol 2007;28:849–56 pmid:17494655

    Abstract/FREE Full Text
42. 42.↵
    2. Courtois A,
    3. Nusgens BV,
    4. Hustinx R, et al

    . 18F-FDG uptake assessed by PET/CT in abdominal aortic aneurysms is associated with cellular and molecular alterations prefacing wall deterioration and rupture. J Nucl Med 2013;54:1740–47 doi:10.2967/jnumed.112.115873 pmid:24009278

    Abstract/FREE Full Text
43. 43.↵
    2. Morris DR,
    3. Biros E,
    4. Cronin O, et al

    . The association of genetic variants of matrix metalloproteinases with abdominal aortic aneurysm: a systematic review and meta-analysis. Heart 2014;100:295–302 doi:10.1136/heartjnl-2013-304129 pmid:23813847

    Abstract/FREE Full Text
44. 44.↵
    2. Saracini C,
    3. Bolli P,
    4. Sticchi E, et al

    . Polymorphisms of genes involved in extracellular matrix remodeling and abdominal aortic aneurysm. J Vasc Surg 2012;55:171–79 e2 doi:10.1016/j.jvs.2011.07.051 pmid:22094117

    CrossRefPubMed
45. 45.↵
    2. Wilson WR,
    3. Anderton M,
    4. Choke EC, et al

    . Elevated plasma MMP1 and MMP9 are associated with abdominal aortic aneurysm rupture. Eur J Vasc Endovasc Surg 2008;35:580–84 doi:10.1016/j.ejvs.2007.12.004 pmid:18226564

    CrossRefPubMedWeb of Science
46. 46.↵
    2. Chase AJ,
    3. Newby AC

    . Regulation of matrix metalloproteinase (matrixin) genes in blood vessels: a multi-step recruitment model for pathological remodelling. J Vasc Res 2003;40:329–43 doi:10.1159/000072697 pmid:12891002

    CrossRefPubMedWeb of Science
47. 47.↵
    2. Xiong W,
    3. Knispel R,
    4. MacTaggart J, et al

    . Membrane-type 1 matrix metalloproteinase regulates macrophage-dependent elastolytic activity and aneurysm formation in vivo. J Boil Chem 2009;284:1765–71 doi:10.1074/jbc.M806239200 pmid:19010778

    Abstract/FREE Full Text
48. 48.↵
    2. Dai X,
    3. Shen J,
    4. Annam NP, et al

    . SMAD3 deficiency promotes vessel wall remodeling, collagen fiber reorganization and leukocyte infiltration in an inflammatory abdominal aortic aneurysm mouse model. Sci Rep 2015;5:10180 doi:10.1038/srep10180 pmid:25985281

    CrossRefPubMed
49. 49.↵
    2. Didangelos A,
    3. Yin X,
    4. Mandal K, et al

    . Extracellular matrix composition and remodeling in human abdominal aortic aneurysms: a proteomics approach. Mol Cell Proteomics 2011;10:M111.008128 doi:10.1074/mcp.M111.008128 pmid:21593211

    Abstract/FREE Full Text
50. 50.↵
    2. Zhang B,
    3. Dhillon S,
    4. Geary I, et al

    . Polymorphisms in matrix metalloproteinase-1, -3, -9, and -12 genes in relation to subarachnoid hemorrhage. Stroke 2001;32:2198–202 doi:10.1161/hs0901.095382 pmid:11546917

    Abstract/FREE Full Text
51. 51.↵
    2. Curci JA,
    3. Liao S,
    4. Huffman MD, et al

    . Expression and localization of macrophage elastase (matrix metalloproteinase-12) in abdominal aortic aneurysms. J Clin Invest 1998;102:1900–10 doi:10.1172/JCI2182 pmid:9835614

    CrossRefPubMedWeb of Science
52. 52.↵
    2. Tromp G,
    3. Gatalica Z,
    4. Skunca M, et al

    . Elevated expression of matrix metalloproteinase-13 in abdominal aortic aneurysms. Ann Vasc Surg 2004;18:414–20 doi:10.1007/s10016-004-0050-5 pmid:15156361

    CrossRefPubMedWeb of Science
53. 53.↵
    2. Bouzeghrane F,
    3. Darsaut T,
    4. Salazkin I, et al

    . Matrix metalloproteinase-9 may play a role in recanalization and recurrence after therapeutic embolization of aneurysms or arteries. J Vasc Interv Radiol 2007;18:1271–79 doi:10.1016/j.jvir.2007.06.034 pmid:17911518

    CrossRefPubMedWeb of Science
54. 54.↵
    2. Chen XF,
    3. Wang JA,
    4. Hou J, et al

    . Extracellular matrix metalloproteinase inducer (EMMPRIN) is present in smooth muscle cells of human aneurysmal aorta and is induced by angiotensin II in vitro. Clin Sci (Lond) 2009;116:819–26 doi:10.1042/CS20080235 pmid:19086920

    CrossRefPubMed
55. 55.↵
    2. Lizarbe TR,
    3. Tarín C,
    4. Gómez M, et al

    . Nitric oxide induces the progression of abdominal aortic aneurysms through the matrix metalloproteinase inducer EMMPRIN. Am J Pathol 2009;175:1421–30 doi:10.2353/ajpath.2009.080845 pmid:19779140

    CrossRefPubMedWeb of Science
56. 56.↵
    2. Kazi M,
    3. Zhu C,
    4. Roy J, et al

    . Difference in matrix-degrading protease expression and activity between thrombus-free and thrombus-covered wall of abdominal aortic aneurysm. Arterioscler Thromb Vasc Boil 2005;25:1341–46 doi:10.1161/01.ATV.0000166601.49954.21 pmid:15845912

    Abstract/FREE Full Text
57. 57.↵
    2. Fontaine V,
    3. Jacob MP,
    4. Houard X, et al

    . Involvement of the mural thrombus as a site of protease release and activation in human aortic aneurysms. Am J Pathol 2002;161:1701–10 doi:10.1016/S0002-9440(10)64447-1 pmid:12414517

    CrossRefPubMedWeb of Science
58. 58.↵
    2. Li Q,
    3. Laumonnier Y,
    4. Syrovets T, et al

    . Plasmin triggers cytokine induction in human monocyte-derived macrophages. Arterioscler Thromb Vasc Biol 2007;27:1383–89 doi:10.1161/ATVBAHA.107.142901 pmid:17413040

    Abstract/FREE Full Text
59. 59.↵
    2. Burysek L,
    3. Syrovets T,
    4. Simmet T

    . The serine protease plasmin triggers expression of MCP-1 and CD40 in human primary monocytes via activation of p38 MAPK and janus kinase (JAK)/STAT signaling pathways. J Biol Chem 2002;277:33509–17 doi:10.1074/jbc.M201941200 pmid:12093796

    Abstract/FREE Full Text
60. 60.↵
    2. Reilly JM

    . Plasminogen activators in abdominal aortic aneurysmal disease. Ann N Y Acad Sci 1996;800:151–56 doi:10.1111/j.1749-6632.1996.tb33306.x pmid:8958990

    CrossRefPubMed
61. 61.↵
    2. Coutard M,
    3. Touat Z,
    4. Houard X, et al

    . Thrombus versus wall biological activities in experimental aortic aneurysms. J Vasc Res 2010;47:355–66 doi:10.1159/000265569 pmid:20016209

    CrossRefPubMed
62. 62.↵
    2. Killer M,
    3. Plenk H,
    4. Minnich B, et al

    . Histological demonstration of healing in experimental aneurysms. Minim Invasive Neurosurg 2009;52:170–75 doi:10.1055/s-0029-1237366 pmid:19838970

    CrossRefPubMedWeb of Science
63. 63.↵
    2. Daley JM,
    3. Brancato SK,
    4. Thomay AA, et al

    . The phenotype of murine wound macrophages. J Leukoc Biol 2010;87:59–67 doi:10.1189/jlb.0409236 pmid:20052800

    Abstract/FREE Full Text
64. 64.↵
    2. van den Berg LM,
    3. Zijlstra-Willems EM,
    4. Richters CD, et al

    . Dectin-1 activation induces proliferation and migration of human keratinocytes enhancing wound re-epithelialization. Cell Immunol 2014;289:49–54 doi:10.1016/j.cellimm.2014.03.007 pmid:24721111

    CrossRefPubMed
65. 65.↵
    2. Roy S,
    3. Dickerson R,
    4. Khanna S, et al

    . Particulate β-glucan induces TNF-α production in wound macrophages via a redox-sensitive NF-κβ-dependent pathway. Wound Repair Regen 2011;19:411–19 doi:10.1111/j.1524-475X.2011.00688.x pmid:21518092

    CrossRefPubMed
66. 66.↵
    2. Beer HD,
    3. Bittner M,
    4. Niklaus G, et al

    . The fibroblast growth factor binding protein is a novel interaction partner of FGF-7, FGF-10 and FGF-22 and regulates FGF activity: implications for epithelial repair. Oncogene 2005;24:5269–77 doi:10.1038/sj.onc.1208560 pmid:15806171

    CrossRefPubMedWeb of Science
67. 67.↵
    2. Tassi E,
    3. McDonnell K,
    4. Gibby KA, et al

    . Impact of fibroblast growth factor-binding protein-1 expression on angiogenesis and wound healing. Am J Pathol 2011;179:2220–32 doi:10.1016/j.ajpath.2011.07.043 pmid:21945411

    CrossRefPubMedWeb of Science
68. 68.↵
    2. Olsen CL,
    3. Hsu PP,
    4. Glienke J, et al

    . Hedgehog-interacting protein is highly expressed in endothelial cells but down-regulated during angiogenesis and in several human tumors. BMC Cancer 2004;4:43 doi:10.1186/1471-2407-4-43 pmid:15294024

    CrossRefPubMed
69. 69.↵
    2. Wong VW,
    3. Crawford JD

    . Vasculogenic cytokines in wound healing. Biomed Res Int 2013;2013:190486 doi:10.1155/2013/190486 pmid:23555076

    CrossRefPubMed
70. 70.↵
    2. Gounis MJ,
    3. van der Bom IM,
    4. Wakhloo AK, et al

    . MR imaging of myeloperoxidase activity in a model of the inflamed aneurysm wall. AJNR Am J Neuroradiol 2015;36:146–52 doi:10.3174/ajnr.A4135 pmid:25273534

    Abstract/FREE Full Text
71. 71.↵
    2. Delbosc S,
    3. Alsac JM,
    4. Journe C, et al

    . Porphyromonas gingivalis participates in pathogenesis of human abdominal aortic aneurysm by neutrophil activation: proof of concept in rats. PLoS One 2011;6:e18679 doi:10.1371/journal.pone.0018679 pmid:21533243

    CrossRefPubMed