Microarray studies in pulmonary arterial hypertension

International Journal of Clinical Practice

Volumn 65, Issue SUPPL. 169, 2011, Pages 19-28

  Menon, S ^a   Fessel, J ^b   West, J ^a,b  

^a JAWAHARLAL NEHRU UNIVERSITY   (India)

^b VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ANGIOGENESIS; COMPUTER PROGRAM; CONFERENCE PAPER; FALSE POSITIVE RESULT; GENE EXPRESSION; GENETICS; HISTOPATHOLOGY; HUMAN; HUMAN CELL CULTURE; INFLAMMATION; LUNG ARTERY; LUNG BIOPSY; LUNG ENDOTHELIUM; LUNG PARENCHYMA; MACHINE LEARNING; MICROARRAY ANALYSIS; NONHUMAN; PERIPHERAL BLOOD MONONUCLEAR CELL; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; PULMONARY HYPERTENSION; SMOOTH MUSCLE FIBER; STANDARDIZATION; VALIDATION PROCESS; ANIMAL; DNA MICROARRAY; GENE EXPRESSION REGULATION; IDIOPATHIC PULMONARY HYPERTENSION; LUNG; METABOLISM; MONONUCLEAR CELL; REVIEW;

ANIMALS; GENE EXPRESSION REGULATION; HUMANS; HYPERTENSION, PULMONARY; LEUKOCYTES, MONONUCLEAR; LUNG; MICROARRAY ANALYSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 78650831606     PISSN: 13685031     EISSN: 17421241     Source Type: Journal    
DOI: 10.1111/j.1742-1241.2010.02604.x     Document Type: Conference Paper

References (48)

1. Simonneau G, Robbins IM, Beghetti M, et al. Updated clinical classification of pulmonary hypertension. J Am Coll Cardiol 2009; 54 (1 Suppl.): S43 - 54.
2. Chen JJ,. Key aspects of analyzing microarray gene-expression data. Pharmacogenomics 2007; 8: 473 - 82.
3. Kauffmann A, Huber W,. Microarray data quality control improves the detection of differentially expressed genes. Genomics 2010; 95: 138 - 42.
4. Owzar K, Barry WT, Jung SH, et al. Statistical challenges in preprocessing in microarray experiments in cancer. Clin Cancer Res 2008; 14: 5959 - 66.
5. Hackstadt AJ, Hess AM,. Filtering for increased power for microarray data analysis. BMC Bioinformatics 2009; 10: 11.
6. Murie C, Woody O, Lee AY, Nadon R,. Comparison of small n statistical tests of differential expression applied to microarrays. BMC Bioinformatics 2009; 10: 45.
7. Hochberg Y, Benjamini Y,. More powerful procedures for multiple significance testing. Stat Med 1990; 9: 811 - 8.
8. Leonard MO, Howell K, Madden SF, et al. Hypoxia selectively activates the CREB family of transcription factors in the in vivo lung. Am J Respir Crit Care Med 2008; 178: 977 - 83.
9. Shi L, Campbell G, Jones WD, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol 2010; 28: 827 - 38.
10. Choe SE, Boutros M, Michelson AM, et al. Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol 2005; 6: R16.
11. Irizarry RA, Wu Z, Jaffee HA,. Comparison of Affymetrix GeneChip expression measures. Bioinformatics 2006; 22: 789 - 94.
12. Allison DB, Cui X, Page GP, Sabripour M,. Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 2006; 7: 55 - 65.
13. Bull TM, Coldren CD, Moore M, et al. Gene microarray analysis of peripheral blood cells in pulmonary arterial hypertension. Am J Respir Crit Care Med 2004; 170: 911 - 9.
14. West J, Cogan J, Geraci M, et al. Gene expression in BMPR2 mutation carriers with and without evidence of pulmonary arterial hypertension suggests pathways relevant to disease penetrance. BMC Med Genomics 2008; 1: 45.
15. Geraci MW, Moore M, Gesell T, et al. Gene expression patterns in the lungs of patients with primary pulmonary hypertension: a gene microarray analysis. Circ Res 2001; 88: 555 - 62.
16. Ulrich S, Taraseviciene-Stewart L, Huber LC, et al. Peripheral blood B lymphocytes derived from patients with idiopathic pulmonary arterial hypertension express a different RNA pattern compared with healthy controls: a cross sectional study. Respir Res 2008; 9: 20.
17. Gharib SA, Luchtel DL, Madtes DK, Glenny RW,. Global gene annotation analysis and transcriptional profiling identify key biological modules in hypoxic pulmonary hypertension. Physiol Genomics 2005; 22: 14 - 23.
18. Grigoryev DN, Mathai SC, Fisher MR, et al. Identification of candidate genes in scleroderma-related pulmonary arterial hypertension. Transl Res 2008; 151: 197 - 207.
19. Moreno-Vinasco L, Gomberg-Maitland M, Maitland ML, et al. Genomic assessment of a multikinase inhibitor, sorafenib, in a rodent model of pulmonary hypertension. Physiol Genomics 2008; 33: 278 - 91.
20. Pendergrass SA, Hayes E, Farina G, et al. Limited systemic sclerosis patients with pulmonary arterial hypertension show biomarkers of inflammation and vascular injury. PLoS ONE 2010; 5.
21. Rajkumar R, Konishi K, Richards TJ, et al. Genomewide RNA expression profiling in lung identifies distinct signatures in idiopathic pulmonary arterial hypertension and secondary pulmonary hypertension. Am J Physiol Heart Circ Physiol 2010; 298: H1235 - 48.
22. Vaszar LT, Nishimura T, Storey JD, et al. Longitudinal transcriptional analysis of developing neointimal vascular occlusion and pulmonary hypertension in rats. Physiol Genomics 2004; 17: 150 - 6.
23. Wu W, Dave NB, Yu G, et al. Network analysis of temporal effects of intermittent and sustained hypoxia on rat lungs. Physiol Genomics 2008; 36: 24 - 34.
24. Laumanns IP, Fink L, Wilhelm J, et al. The noncanonical WNT pathway is operative in idiopathic pulmonary arterial hypertension. Am J Respir Cell Mol Biol 2009; 40: 683 - 91.
25. Bull TM, Coldren CD, Geraci MW, Voelkel NF,. Gene expression profiling in pulmonary hypertension. Proc Am Thorac Soc 2007; 4: 117 - 20.
26. Fantozzi I, Huang W, Zhang J, et al. Divergent effects of BMP-2 on gene expression in pulmonary artery smooth muscle cells from normal subjects and patients with idiopathic pulmonary arterial hypertension. Exp Lung Res 2005; 31: 783 - 806.
27. Lane K, Talati M, Blackwell T, et al. Oxidative injury is a common consequence of BMPR2 mutation. Am J Respir Crit Care Med 2010; 181: A2286.
28. Rehman J, Archer SL,. A proposed mitochondrial-metabolic mechanism for initiation and maintenance of pulmonary arterial hypertension in fawn-hooded rats: the Warburg model of pulmonary arterial hypertension. Adv Exp Med Biol 2010; 661: 171 - 85.
29. de Jesus Perez VA, Alastalo TP, Wu JC, et al. Bone morphogenetic protein 2 induces pulmonary angiogenesis via Wnt-beta-catenin and Wnt-RhoA-Rac1 pathways. J Cell Biol 2009; 184: 83 - 99.
30. Johnson JA, Hemnes AR, Lane KB, et al. ACE2 reverses established pulmonary arterial hypertension in BMPR2R899X mice. Am J Respir Crit Care Med 2010; 181: A6327.
31. Rudarakanchana N, Flanagan JA, Chen H, et al. Functional analysis of bone morphogenetic protein type II receptor mutations underlying primary pulmonary hypertension. Hum Mol Genet 2002; 11: 1517 - 25.
32. West J,. Cross talk between Smad, MAPK, and actin in the etiology of pulmonary arterial hypertension. Adv Exp Med Biol 2010; 661: 265 - 78.
33. Wertz JW, Bauer PM,. Caveolin-1 regulates BMPRII localization and signaling in vascular smooth muscle cells. Biochem Biophys Res Commun 2008; 375: 557 - 61.
34. Glynne R, Akkaraju S, Healy JI, et al. How self-tolerance and the immunosuppressive drug FK506 prevent B-cell mitogenesis. Nature 2000; 403: 672 - 6.
35. Austin ED, Cogan JD, West JD, et al. Alterations in oestrogen metabolism: implications for higher penetrance of familial pulmonary arterial hypertension in females. Eur Respir J 2009; 34: 1093 - 9.
36. Caruso P, MacLean MR, Khanin R, et al. Dynamic changes in lung microRNA profiles during the development of pulmonary hypertension due to chronic hypoxia and monocrotaline. Arterioscler Thromb Vasc Biol 2010; 30: 716 - 23.
37. Hoshikawa Y, Nana-Sinkam P, Moore MD, et al. Hypoxia induces different genes in the lungs of rats compared with mice. Physiol Genomics 2003; 12: 209 - 19.
38. Kwapiszewska G, Wilhelm J, Wolff S, et al. Expression profiling of laser-microdissected intrapulmonary arteries in hypoxia-induced pulmonary hypertension. Respir Res 2005; 6: 109.
39. Laudi S, Trump S, Schmitz V, et al. Serotonin transporter protein in pulmonary hypertensive rats treated with atorvastatin. Am J Physiol Lung Cell Mol Physiol 2007; 293: L630 - 8.
40. Tada Y, Laudi S, Harral J, et al. Murine pulmonary response to chronic hypoxia is strain specific. Exp Lung Res 2008; 34: 313 - 23.
41. van Albada ME, Bartelds B, Wijnberg H, et al. Gene expression profile in flow-associated pulmonary arterial hypertension with neointimal lesions. Am J Physiol Lung Cell Mol Physiol 2010; 298: L483 - 91.
42. Crona D, Harral J, Adnot S, et al. Gene expression in lungs of mice lacking the 5-hydroxytryptamine transporter gene. BMC Pulm Med 2009; 9: 19.
43. Hamidi SA, Prabhakar S, Said SI,. Enhancement of pulmonary vascular remodelling and inflammatory genes with VIP gene deletion. Eur Respir J 2008; 31: 135 - 9.
44. Tada Y, Majka S, Carr M, et al. Molecular effects of loss of BMPR2 signaling in smooth muscle in a transgenic mouse model of PAH. Am J Physiol Lung Cell Mol Physiol 2007; 292: L1556 - 63.
45. West J, Harral J, Lane K, et al. Mice expressing BMPR2R899X transgene in smooth muscle develop pulmonary vascular lesions. Am J Physiol Lung Cell Mol Physiol 2008; 295: L744 - 55.
46. Kugathasan L, Ray JB, Deng Y, et al. The angiopietin-1-Tie2 pathway prevents rather than promotes pulmonary arterial hypertension in transgenic mice. J Exp Med 2009; 206: 2221 - 34.
47. Steiner MK, Syrkina OL, Kolliputi N, et al. Interleukin-6 overexpression induces pulmonary hypertension. Circ Res 2009; 104: 236 - 44. 28p following 44.
48. Young KA, Ivester C, West J, et al. BMP signaling controls PASMC KV channel expression in vitro and in vivo. Am J Physiol Lung Cell Mol Physiol 2006; 290: L841 - 8.