Differential gene profiling in acute lung injury identifies injury-specific gene expression

Critical Care Medicine

Volumn 36, Issue 3, 2008, Pages 855-865

  Dos Santos, Claudia C ^a,b   Okutani, Daisuke ^a   Hu, Pingzhao ^c   Han, Bing ^a   Crimi, Ettore ^b   He, Xiaolin ^a   Keshavjee, Shaf ^a   Greenwood, Celia ^c   Slutsky, Author S ^b   Zhang, Haibo ^b   Liu, Mingyao ^a  

^a UNIVERSITY HEALTH NETWORK   (Canada)

^b ST MICHAEL'S HOSPITAL   (Canada)

^c HOSPITAL FOR SICK CHILDREN   (Canada)

Author keywords

Acute respiratory distress syndrome; Bioinformatics; Sepsis; Shock; Transcriptional profiling; Ventilator induced lung injury

Indexed keywords

LIPOPOLYSACCHARIDE;

ACUTE LUNG INJURY; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; ARTIFICIAL VENTILATION; CELL CYCLE; CELL DEATH; CELL DIFFERENTIATION; CELL MIGRATION; CELL PROLIFERATION; CONTROLLED STUDY; FUNCTIONAL GENOMICS; GENE ACTIVATION; GENE CONTROL; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; HEMORRHAGIC SHOCK; IMMUNOCOMPETENT CELL; MALE; MORPHOGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; ORGANOGENESIS; PREDICTION; PRIORITY JOURNAL; RAT; RESUSCITATION; RNA HYBRIDIZATION; TIDAL VOLUME; UNINDEXED SEQUENCE; ADULT RESPIRATORY DISTRESS SYNDROME; ANIMAL; GENE EXPRESSION; GENETICS; SPRAGUE DAWLEY RAT;

ANIMALS; GENE EXPRESSION; GENE EXPRESSION PROFILING; MALE; RATS; RATS, SPRAGUE-DAWLEY; RESPIRATORY DISTRESS SYNDROME, ADULT;

EID: 44449098334     PISSN: 00903493     EISSN: 15300293     Source Type: Journal    
DOI: 10.1097/CCM.0B013E3181659333     Document Type: Article

References (41)

1. Bernard GR, Artigas A, Brigham KL, et al: The American-European Consensus Conference on ARDS: Definitions, mechanisms, relevant outcomes, and clinical trial coordination. Am J Respir Crit Care Med 1994;149(3 Pt 1):818-824 (Pubitemid 24082248)
2. Esteban A, Anzueto A, Alia I, et al: How is mechanical ventilation employed in the intensive care unit? An international utilization review. Am J Respir Crit Care Med 2000;161:1450-1458
3. Esteban A, Anzueto A, Frutos F, et al: Characteristics and outcomes in adult patients receiving mechanical ventilation: A 28-day international study. JAMA 2002;287:345-355
4. Ventilation with lower tidal volumes as compared with traditional tidal volumes for acute lung injury and the acute respiratory distress syndrome: The Acute Respiratory Distress Syndrome Network. N Engl J Med 2000;342:1301-1308
5. Marshall JC: Clinical trials of mediatordirected therapy in sepsis: What have we learned? Intensive Care Med 2000;26(Suppl 1): S75-S83
6. Liu M, Slutsky AS: Anti-inflammatory therapies: Application of molecular biology techniques in intensive care medicine. Intensive Care Med 1997;23:718-731
7. Liu M: Searching for acute respiratory distress syndrome genes: Aren't we there yet? Am J Respir Crit Care Med 2005;171:298-299
8. dos Santos CC, Han B, Andrade CF, et al: DNA microarray analysis of gene expression in alveolar epithelial cells in response to TNFα, LPS, and cyclic stretch. Physiol Genomics 2004;19:331-342
9. Kaminski N, Allard JD, Pittet JF, et al: Global analysis of gene expression in pulmonary fibrosis reveals distinct programs regulating lung inflammation and fibrosis. Proc Natl Acad Sci USA 2000;97:1778-1783
10. Leikauf GD, McDowell SA, Wesselkamper SC, et al: Acute lung injury: Functional genomics and genetic susceptibility. Chest 2002;121(3 Suppl):70S-75S
11. Okutani D, Han B, Mura M, et al: Highvolume ventilation induces pentraxin 3 expression in multiple acute lung injury models in rats. Am J Physiol Lung Cell Mol Physiol 2006;292: L144-L153
12. Yamane M, Liu M, Kaneda H, et al: Reperfusion-induced gene expression profiles in rat lung transplantation. Am J Transplant 2005;5:2160-2169
13. Smyth G: Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004;3: Article 3
14. Gentleman RC, Carey VJ, Bates DM, et al: Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol 2004;5: R80
15. Andrade CF, Kaneda H, der S, et al: Toll-like receptor and cytokine gene expression in the early phase of human lung transplantation. J Heart Lung Transplant 2006;25:1317-1323
16. Han B, Mura M, Andrade CF, et al: TNFα-induced long pentraxin PTX3 expression in human lung epithelial cells via JNK. J Immunol 2005;175:8303-8311
17. Benjamini Y, Drai D, Elmer G, et al: Controlling the false discovery rate in behavior genetics research. Behav Brain Res 2001;125:279-284
18. Altemeier WA, Matute-Bello G, Gharib SA, et al: Modulation of lipopolysaccharide-induced gene transcription and promotion of lung injury by mechanical ventilation. J Immunol 2005;175:3369-3376
19. Jeyaseelan S, Chu HW, Young SK, et al: Transcriptional profiling of lipopolysaccharide-induced acute lung injury. Infect Immun 2004;72:7247-7256
20. Draghici S, Khatri P, Bhavsar P, et al: Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate. Nucleic Acids Res 2003;31:3775-3781
21. Draghici S, Khatri P, Martins RP, et al: Global functional profiling of gene expression. Genomics 2003;81:98-104
22. Grigoryev DN, Ma SF, Irizarry RA, et al: Orthologous gene-expression profiling in multi-species models: Search for candidate genes. Genome Biol 2004;5: R34
23. Ma SF, Grigoryev DN, Taylor AD, et al: Bioinformatic identification of novel early stress response genes in rodent models of lung injury. Am J Physiol Lung Cell Mol Physiol 2005;289: L468-L477
24. He X, Han B, Liu M: Long pentraxin 3 in pulmonary infection and acute lung injury. Am J Physiol Lung Cell Mol Physiol 2007;292: L1039-L1049
25. Andrade CF, Waddell TK, Keshavjee S, et al: Innate immunity and organ transplantation: The potential role of toll-like receptors. Am J Transplant 2005;5:969-975
26. Severgnini M, Takahashi S, Tu P, et al: Inhibition of the Src and Jak kinases protects against lipopolysaccharide-induced acute lung injury. Am J Respir Crit Care Med 2005;171:858-867
27. Gharib SA, Liles WC, Matute-Bello G, et al: Computational identification of key biologic modules and transcription factors in acute lung injury. Am J Respir Crit Care Med 2006;173:653-658
28. Tang PS, Tsang ME, Lodyga M, et al: Lipopolysaccharide accelerates caspase-independent but cathepsin B-dependent death of human lung epithelial cells. J Cell Physiol 2006;209:457-467
29. Han B, Bai XH, Lodyga M, et al: Conversion of mechanical force into biochemical signaling. J Biol Chem 2004;279:54793-54801
30. Liu M, Tanswell AK, Post M: Mechanical force-induced signal transduction in lung cells. Am J Physiol 1999;277(4 Pt 1): L667-L683
31. Okutani D, Lodyga M, Han B, et al: Src protein tyrosine kinase family and acute inflammatory responses. Am J Physiol Lung Cell Mol Physiol 2006;291: L129-L141
32. Han B, Lodyga M, Liu M: Ventilator-induced lung injury: Role of protein-protein interaction in mechanosensation. Proc Am Thorac Soc 2005;2:181-187
33. Peng X, Hassoun PM, Sammani S, et al: Protective effects of sphingosine 1-phosphate in murine endotoxin-induced inflammatory lung injury. Am J Respir Crit Care Med 2004;169:1245-1251 (Pubitemid 38680403)
34. Gon Y, Wood MR, Kiosses WB, et al: S1P3 receptor-induced reorganization of epithelial tight junctions compromises lung barrier integrity and is potentiated by TNF. Proc Natl Acad Sci USA 2005;102:9270-9275
35. Shikata Y, Birukov KG, Birukova AA, et al: Involvement of site-specific FAK phosphorylation in sphingosine-1 phosphateand thrombin-induced focal adhesion remodeling: Role of Src and GIT. FASEB J 2003;17:2240-2249
36. Schaphorst KL, Chiang E, Jacobs KN, et al: Role of sphingosine-1 phosphate in the enhancement of endothelial barrier integrity by platelet-released products. Am J Physiol Lung Cell Mol Physiol 2003;285: L258-L267
37. Le Stunff H, Milstien S, Spiegel S: Generation and metabolism of bioactive sphingosine-1-phosphate. J Cell Biochem 2004;92:882-899
38. Beil M, Micoulet A, von Wichert G, et al: Sphingosylphosphorylcholine regulates keratin network architecture and visco-elastic properties of human cancer cells. Nat Cell Biol 2003;5:803-811
39. Soeda S, Honda O, Shimeno H, et al: Sphingomyelinase and cell-permeable ceramide analogs increase the release of plasminogen activator inhibitor-1 from cultured endothelial cells. Thromb Res 1995;80:509-518
40. Khadaroo RG, Parodo J, Powers KA, et al: Oxidant-induced priming of the macrophage involves activation of p38 mitogenactivated protein kinase through an Srcdependent pathway. Surgery 2003;134:242-246
41. Khadaroo RG, He R, Parodo J, et al: The role of the Src family of tyrosine kinases after oxidant-induced lung injury in vivo. Surgery 2004;136:483-488