Towards systems biology of human pulmonary fibrosis

Proceedings of the American Thoracic Society

Volumn 4, Issue 1, 2007, Pages 85-91

  Studer, Sean M ^a   Kaminski, Naftali ^a  

^a UNIVERSITY OF PITTSBURGH MEDICAL CENTER   (United States)

Author keywords

Cancer Biomedical Informatics Grid, caBIG; Idiopathic pulmonary fibrosis; Interstitial lung disease; Microarrays

Indexed keywords

ALLERGIC PNEUMONITIS; CELL ISOLATION; FIBROSING ALVEOLITIS; GENE FUNCTION; GENE MAPPING; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENOTYPE; HAPLOTYPE; HEALTH PRACTITIONER; HEREDITY; HUMAN; MEDICAL EDUCATION; MEDICAL INFORMATION; MEDICAL LITERATURE; MEDICAL RESEARCH; MOLECULAR BIOLOGY; NONHUMAN; PHENOTYPE; REVIEW;

ANIMALS; DISEASE MODELS, ANIMAL; GENOME; HAPLOTYPES; HUMANS; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; PULMONARY FIBROSIS; RATS; SYSTEMS BIOLOGY;

EID: 33846127093     PISSN: 15463222     EISSN: None     Source Type: Journal    
DOI: 10.1513/pats.200607-139JG     Document Type: Review

References (39)

1. Selman M, Thannickal VJ, Pardo A, Zisman DA, Martinez FJ, Lynch JP. Idiopathic pulmonary fibrosis: pathogenesis and therapeutic approaches. Drugs 2004;64:405-430.
2. Kelly M, Kolb M, Bonniaud P, Gauldie J. Re-evaluation of fibrogenic cytokines in lung fibrosis. Curr Pharm Des 2003;9:39-49.
3. Sheppard D. Transforming growth factor β: a central modulator of pulmonary and airway inflammation and fibrosis. Proc Am Thorac Soc 2006;3:413-417.
4. Agostini C, Gurrieri C. Chemokine/cytokine cocktail in idiopathic pulmonary fibrosis. Proc Am Thorac Soc 2006;3:357-363.
5. Chambers RC. Role of coagulation cascade proteases in lung repair and fibrosis. Eur Respir J Suppl 2003;44:33s-35s.
6. Thannickal VJ, Horowitz JC. Evolving concepts of apoptosis in idiopathic pulmonary fibrosis. Proc Am Thorac Soc 2006;3:350-356.
7. Charbeneau RP, Peters-Golden M. Eicosanoids: mediators and therapeutic targets in fibrotic lung disease. Clin Sci (Lond) 2005;108:479-491.
8. Selman M, Pardo A. Role of epithelial cells in idiopathic pulmonary fibrosis: from innocent targets to serial killers. Proc Am Thorac Soc 2006;3:364-372.
9. Huaux F, Liu T, McGarry B, Ullenbruch M, Xing Z, Phan SH. Eosinophils and T lymphocytes possess distinct roles in bleomycin-induced lung injury and fibrosis. J Immunol 2003;171:5470-5481.
10. Lama VN, Phan SH. The extrapulmonary origin of fibroblasts: stem/progenitor cells and beyond. Proc Am Thorac Soc 2006;3:373-376.
11. Kurosawa A. Rashômon. Japan: Janus Films; 1950.
12. Kaminski N, Rosas IO. Gene expression profiling as a window into idiopathic pulmonary fibrosis pathogenesis: can we identify the right target genes? Proc Am Thorac Soc 2006;3:339-344.
13. Aderem A. Systems biology: its practice and challenges. Cell 2005;121:511-513.
14. Martinez FJ, Safrin S, Weycker D, Starko KM, Bradford WZ, King TE Jr, Flaherty KR, Schwartz DA, Noble PW, Raghu G, et al. The clinical course of patients with idiopathic pulmonary fibrosis. Ann Intern Med 2005;142:963-967.
15. Segal E, Friedman N, Kaminski N, Regev A, Koller D. From signatures to models: understanding cancer using microarrays. Nat Genet 2005;37:S38-S45.
16. Kaminski N. Microarray analysis of idiopathic pulmonary fibrosis. Am J Respir Cell Mol Biol 2003;29:S32-S36.
17. Liu T, Dhanasekaran SM, Jin H, Hu B, Tomlins SA, Chinnaiyan AM, Phan SH. FIZZ1 stimulation of myofibroblast differentiation. Am J Pathol 2004;164:1315-1326.
18. Kaminski N, Allard JD, Pittet JF, Zuo F, Griffiths MJ, Morris D, Huang X, Sheppard D, Heller RA. 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.
19. Du M, Irani RA, Stivers DN, Lee SJ, Travis EL. H2-Ea deficiency is a risk factor for bleomycin-induced lung fibrosis in mice. Cancer Res 2004;64:6835-6839.
20. Haston CK, Wang M, Dejournett RE, Zhou X, Ni D, Gu X, King TM, Weil MM, Newman RA, Amos CI, et al. Bleomycin hydrolase and a genetic locus within the MHC affect risk for pulmonary fibrosis in mice. Hum Mol Genet 2002;11:1855-1863.
21. Haston CK, Tomko TG, Godin N, Kerckhoff L, Hallett MT. Murine candidate bleomycin induced pulmonary fibrosis susceptibility genes identified by gene expression and sequence analysis of linkage regions. J Med Genet 2005;42:464-473.
22. Lemay AM, Haston CK. Bleomycin-induced pulmonary fibrosis susceptibility genes in AcB/BcA recombinant congenic mice. Physiol Genomics 2005;23:54-61.
23. Choi ES, Jakubzick C, Carpenter KJ, Kunkel SL, Evanoff H, Martinez FJ, Flaherty KR, Toews GB, Colby TV, Kazerooni EA, et al. Enhanced monocyte chemoattractant protein-3/CC chemokine ligand-7 in usual interstitial pneumonia. Am J Respir Crit Care Med 2004;170:508-515.
24. Renzoni EA, Abraham DJ, Howat S, Shi-Wen X, Sestini P, Bou-Gharios G, Wells AU, Veeraraghavan S, Nicholson AG, Denton CP, et al. Gene expression profiling reveals novel TGFbeta targets in adult lung fibroblasts. Respir Res 2004;5:24.
25. Cosgrove GP, Schwarz MI, Geraci MW, Brown KK, Worthen GS. Over-expression of matrix metalloproteinase-7 in pulmonary fibrosis. Chest 2002;121:25S-26S.
26. Zuo F, Kaminski N, Eugui E, Allard J, Yakhini Z, Ben-Dor A, Lollini L, Morris D, Kim Y, DeLustro B, et al. Gene expression analysis reveals matrilysin as a key regulator of pulmonary fibrosis in mice and humans. Proc Natl Acad Sci USA 2002;99:6292-6297.
27. Cosgrove GP, Brown KK, Schiemann WP, Serls AE, Parr JE, Geraci MW, Schwarz MI, Cool CD, Worthen GS. Pigment epithelium-derived factor in idiopathic pulmonary fibrosis: a role in aberrant angiogenesis. Am J Respir Crit Care Med 2004;170:242-251.
28. Berman JS, Serlin D, Li X, Whitley G, Hayes J, Rishikof DC, Ricupero DA, Liaw L, Goetschkes M, O'Regan AW. Altered bleomycin-induced lung fibrosis in osteopontin-deficient mice. Am J Physiol Lung Cell Mol Physiol 2004;286:L1311-L1318.
29. Takahashi T, Ebihara Y, Manabe A, Tsuji K, Nakamura T, Nakahata T, Iwamoto A. Surfactant protein D and KL-6 as serologic indicators of Pneumocystis carinii pneumonia in a child with acute lymphoblastic leukemia. J Med 2001;32:41-51.
30. Pardo A, Gibson K, Cisneros J, Richards TJ, Yang Y, Becerril C, Yousem S, Herrera I, Ruiz V, Selman M, et al. Up-regulation and profibrotic role of osteopontin in human idiopathic pulmonary fibrosis. PLoS Med 2005;2:e251.
31. Selman M, Pardo A, Barrera L, Estrada A, Watson SR, Wilson K, Aziz N, Kaminski N, Zlotnik A. Gene expression profiles distinguish idiopathic pulmonary fibrosis from hypersensitivity pneumonitis. Am J Respir Crit Care Med 2006;173:188-198.
32. Dave NB, Kaminski N. Analysis of microarray experiments for pulmonary fibrosis. Methods Mol Med 2005;117:333-358.
33. Cary MP, Bader GD, Sander C. Pathway information for systems biology. FEBS Lett 2005;579:1815-1820.
34. Lindell KO, Erlen JA, Kaminski N. Lessons from our patients: development of a warm autopsy program. PLoS Med 2006;3:e234.
35. Lawson WE, Loyd JE. The genetic approach in pulmonary fibrosis: can it provide clues to this complex disease? Proc Am Thorac Soc 2006;3:345-349.
36. Perez AT, Coxson HO, Hogg JC, Gibson K, Thompson PF, Rogers RM. Use of CT morphometry to detect changes in lung weight and gas volume. Chest 2005;128(4):2471-2477.
37. Strange K. The end of "naive reductionism": rise of systems biology or renaissance of physiology? Am J Physiol Cell Physiol 2005;288:C968-C974.
38. Saltz J, Oster S, Hastings S, Langella S, Kurc T, Sanchez W, Kher M, Manisundaram A, Shanbhag K, Covitz P. caGrid: design and implementation of the core architecture of the cancer Biomedical Informatics Grid. Bioinformatics 2006;22:1910-1916. Epub 2006 Jun 9.
39. Katsuma S, Nishi K, Tanigawara K, Ikawa H, Shiojima S, Takagaki K, Kaminishi Y, Suzuki Y, Hirasawa A, Ohgi T, et al. Molecular monitoring of bleomycin-induced pulmonary fibrosis by cDNA microarray-based gene expression profiling. Biochem Biophys Res Commun 2001;288:747-751.