Using mouse genomics to understand idiopathic interstitial fibrosis

Proceedings of the American Thoracic Society

Volumn 4, Issue 1, 2007, Pages 92-100

  Brass, David M ^a   Tomfohr, John ^a   Yang, Ivana V ^a   Schwartz, David A ^a  

^a NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

Fibrosis; Genomics; Microarray; QTL

Indexed keywords

BLEOMYCIN; LIPOPOLYSACCHARIDE;

CLINICAL FEATURE; DISEASE COURSE; FIBROSING ALVEOLITIS; GENE CLUSTER; GENE EXPRESSION; GENE IDENTIFICATION; HISTOPATHOLOGY; HUMAN; MICROARRAY ANALYSIS; NONHUMAN; OBSERVATIONAL STUDY; REVIEW; SEQUENCE HOMOLOGY;

ANIMALS; DISEASE MODELS, ANIMAL; GENE EXPRESSION; GENOMICS; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PULMONARY FIBROSIS; QUANTITATIVE TRAIT LOCI;

EID: 33846096491     PISSN: 15463222     EISSN: None     Source Type: Journal    
DOI: 10.1513/pats.200607-147JG     Document Type: Review

References (67)

1. Gal AA, Staton GW Jr. Current concepts in the classification of interstitial lung disease. Am J Clin Pathol 2005;123(Suppl):S67-S81.
2. American Thoracic Society; European Respiratory Society. American Thoracic Society/European Respiratory Society international multidisciplinary consensus classification of the idiopathic interstitial pneumonias. Am J Respir Crit Care Med 2002;165:277-304.
3. Selman M, King TE, Pardo A. Idiopathic pulmonary fibrosis: prevailing and evolving hypotheses about its pathogenesis and implications for therapy. Ann Intern Med 2001;134:136-151.
4. Noble PW, Homer RJ. Back to the future: historical perspective on the pathogenesis of idiopathic pulmonary fibrosis. Am J Respir Cell Mol Biol 2005;33:113-120.
5. Martin WJ II, Iannuzzi MC, Gail DB, Peavy HH. Future directions in sarcoidosis research: summary of an NHLBI working group. Am J Respir Crit Care Med 2004;170:567-571.
6. Fink JN, Ortega HG, Reynolds HY, Cormier YF, Fan LL, Franks TJ, Kreiss K, Kunkel S, Lynch D, Quirce S, et al. Needs and opportunities for research in hypersensitivity pneumonitis. Am J Respir Crit Care Med 2005;171:792-798.
7. Mestas J, Hughes CC. Of mice and not men: differences between mouse and human immunology. J Immunol 2004;172:2731-2738.
8. Lander ES, Botstein D. Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 1989;121:185-199.
9. Flint J, Valdar W, Shifman S, Mott R. Strategies for mapping and cloning quantitative trait genes in rodents. Nat Rev Genet 2005;6:271-286.
10. NIEHS Center for Rodent Genetics Mouse Genome Resequencing and SNP Discovery Project. Available from: http://mouse.perlegen.com/mouse/index.html (accessed July 14, 2006).
11. Austin CP, Battey JF, Bradley A, Bucan M, Capecchi M, Collins FS, Dove WF, Duyk G, Dymecki S, Eppig JT, et al. The knockout mouse project. Nat Genet 2004;36:921-924.
12. Grupe A, Germer S, Usuka J, Aud D, Belknap JK, Klein RF, Ahluwalia MK, Higuchi R, Peltz G. In silico mapping of complex disease-related traits in mice. Science 2001;292:1915-1918.
13. Pletcher MT, McClurg P, Batalov S, Su AI, Barnes SW, Lagler E, Korstanje R, Wang X, Nusskern D, Bogue MA, et al. Use of a dense single nucleotide polymorphism map for in silico mapping in the mouse. PLoS Biol 2004;2:e393.
14. Haston CK, Travis EL. Murine susceptibility to radiation-induced pulmonary fibrosis is influenced by a genetic factor implicated in susceptibility to bleomycin-induced pulmonary fibrosis. Cancer Res 1997;57:5286-5291.
15. Franko AJ, Sharplin J, Ward WF, Hinz JM. The genetic basis of strain-dependent differences in the early phase of radiation injury in mouse lung. Radiat Res 1991;126:349-356.
16. Franko AJ, Sharplin J, Ward WF, Taylor JM. Evidence for two patterns of inheritance of sensitivity to induction of lung fibrosis in mice by radiation, one of which involves two genes. Radiat Res 1996;146:68-74.
17. Sharplin J, Franko AJ. A quantitative histological study of strain-dependent differences in the effects of irradiation on mouse lung during the intermediate and late phases. Radiat Res 1989;119:15-31.
18. Sharplin J, Franko AJ. A quantitative histological study of strain-dependent differences in the effects of irradiation on mouse lung during the early phase. Radiat Res 1989;119:1-14.
19. Haston CK, Amos CI, King TM, Travis EL. Inheritance of susceptibility to bleomycin-induced pulmonary fibrosis in the mouse. Cancer Res 1996;56:2596-2601.
20. Haston CK, Zhou X, Gumbiner-Russo L, Irani R, Dejournett R, Gu X, Weil M, Amos CI, Travis EL. Universal and radiation-specific loci influence murine susceptibility to radiation-induced pulmonary fibrosis. Cancer Res 2002;62:3782-3788.
21. 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.
22. Kleeberger SR, Levitt RC, Zhang LY, Longphre M, Harkema J, Jedlicka A, Eleff SM, DiSilvestre D, Holroyd KJ. Linkage analysis of susceptibility to ozone-induced lung inflammation in inbred mice. Nat Genet 1997;17:475-478.
23. Ohtsuka Y, Brunson KJ, Jedlicka AE, Mitzner W, Clarke RW, Zhang LY, Eleff SM, Kleeberger SR. Genetic linkage analysis of susceptibility to particle exposure in mice. Am J Respir Cell Mol Biol 2000;22:574-581.
24. Zhang Y, Lefort J, Kearsey V, Lapa e Silva JR, Cookson WO, Vargaftig BB. A genome-wide screen for asthma-associated quantitative trait loci in a mouse model of allergic asthma. Hum Mol Genet 1999;8:601-605.
25. De Sanctis GT, Merchant M, Beier DR, Dredge RD, Grobholz JK, Martin TR, Lander ES, Drazen JM. Quantitative locus analysis of airway hyperresponsiveness in A/J and C57BL/6J mice. Nat Genet 1995;11:150-154.
26. 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.
27. Quackenbush J. Computational analysis of microarray data. Nat Rev Genet 2001;2:418-427.
28. Munger JS, Huang X, Kawakatsu H, Griffiths MJ, Dalton SL, Wu J, Pittet JF, Kaminski N, Garat C, Matthay MA, et al. The integrin alpha v beta 6 binds and activates latent TGF beta 1: a mechanism for regulating pulmonary inflammation and fibrosis. Cell 1999;96:319-328.
29. 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.
30. Crystal RG, Fulmer JD, Roberts WC, Moss ML, Line BR, Reynolds HY. Idiopathic pulmonary fibrosis: clinical, histologic, radiographic, physiologic, scintigraphic, cytologic, and biochemical aspects. Ann Intern Med 1976;85:769-788.
31. Bitterman PB, Adelberg S, Crystal RG. Mechanisms of pulmonary fibrosis: spontaneous release of the alveolar macrophage-derived growth factor in the interstitial lung disorders. J Clin Invest 1983;72:1801-1813.
32. Sadlier DM, Connolly SB, Kieran NE, Roxburgh S, Brazil DP, Kairaitis L, Wang Y, Harris DC, Doran P, Brady HR. Sequential extracellular matrix-focused and baited-global cluster analysis of serial transcriptomic profiles identifies candidate modulators of renal tubulointerstitial fibrosis in murine adriamycin-induced nephropathy. J Biol Chem 2004;279:29670-29680.
33. Elkon R, Linhart C, Sharan R, Shamir R, Shiloh Y. Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res 2003;13:773-780.
34. Burch LH, Yang IV, Whitehead GS, Chao FG, Berman KG, Schwartz DA. Transcriptional response to endotoxin reveals role for interferon γ in lung neutrophil recruitment. Am J Physiol Lung Cell Mol Physiol 2006;9:9.
35. Whitmarsh AJ, Davis RJ. Transcription factor AP-1 regulation by mitogen-activated protein kinase signal transduction pathways. J Mol Med 1996;74:589-607.
36. 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.
37. 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.
38. 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.
39. 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.
40. Krein PM, Winston BW. Roles for insulin-like growth factor I and transforming growth factor-beta in fibrotic lung disease. Chest 2002;122:289S-293S.
41. Wallace WA, Howie SE, Lamb D, Salter DM. Tenascin immunoreactivity in cryptogenic fibrosing alveolitis. J Pathol 1995;175:415-420.
42. Zhao Y, Young SL, McIntosh JC. Induction of tenascin in rat lungs undergoing bleomycin-induced pulmonary fibrosis. Am J Physiol 1998;274:L1049-L1057.
43. Takahashi F, Takahashi K, Okazaki T, Maeda K, Ienaga H, Maeda M, Kon S, Uede T, Fukuchi Y. Role of osteopontin in the pathogenesis of bleomycin-induced pulmonary fibrosis. Am J Respir Cell Mol Biol 2001;24:264-271.
44. Selman M, Ruiz V, Cabrera S, Segura L, Ramirez R, Barrios R, Pardo A. TIMP-1, -2, -3, and -4 in idiopathic pulmonary fibrosis: a prevailing nondegradative lung microenvironment? Am J Physiol Lung Cell Mol Physiol 2000;279:L562-L574.
45. Madtes DK, Elston AL, Kaback LA, Clark JG. Selective induction of tissue inhibitor of metalloproteinase-1 in bleomycin-induced pulmonary fibrosis. Am J Respir Cell Mol Biol 2001;24:599-607.
46. Olman MA, Mackman N, Gladson CL, Moser KM, Loskutoff DJ. Changes in procoagulant and fibrinolytic gene expression during bleomycin-induced lung injury in the mouse. J Clin Invest 1995;96:1621-1630.
47. Thomas AQ, Lane K, Phillips J III, Prince M, Markin C, Speer M, Schwartz DA, Gaddipati R, Marney A, Johnson J, et al. Heterozygosity for a surfactant protein C gene mutation associated with usual interstitial pneumonitis and cellular nonspecific interstitial pneumonitis in one kindred. Am J Respir Crit Care Med 2002;165:1322-1328.
48. Lawson WE, Polosukhin VV, Stathopoulos GT, Zoia O, Han W, Lane KB, Li B, Donnelly EF, Holburn GE, Lewis KG, et al. Increased and prolonged pulmonary fibrosis in surfactant protein C-deficient mice following intratracheal bleomycin. Am J Pathol 2005;167:1267-1277.
49. Phillips RJ, Burdick MD, Hong K, Lutz MA, Murray LA, Xue YY, Belperio JA, Keane MP, Strieter RM. Circulating fibrocytes traffic to the lungs in response to CXCL12 and mediate fibrosis. J Clin Invest 2004;114:438-446.
50. Azuma A, Li YJ, Abe S, Usuki J, Matsuda K, Henmi S, Miyauchi Y, Ueda K, Izawa A, Sone S, et al. Interferon-β inhibits bleomycin-induced lung fibrosis by decreasing transforming growth factor-β and thrombospondin. Am J Respir Cell Mol Biol 2005;32:93-98.
51. Pascual RM, Peters SP. Airway remodeling contributes to the progressive loss of lung function in asthma: an overview. J Allergy Clin Immunol 2005;116:477-486. [Quiz: 487.]
52. Jeffery PK. Remodeling and inflammation of bronchi in asthma and chronic obstructive pulmonary disease. Proc Am Thorac Soc 2004;1:176-183.
53. George CL, Jin H, Wohlford-Lenane CL, O'Neill ME, Phipps JC, O'Shaughnessy P, Kline JN, Thorne PS, Schwartz DA. Endotoxin responsiveness and subchronic grain dust-induced airway disease. Am J Physiol Lung Cell Mol Physiol 2001;280:L203-L213.
54. Savov JD, Gavett SH, Brass DM, Costa DL, Schwartz DA. Neutrophils play a critical role in development of LPS-induced airway disease. Am J Physiol Lung Cell Mol Physiol 2002;283:L952-L962.
55. Brass DM, Savov JD, Gavett SH, Haykal-Coates N, Schwartz DA. Subchronic endotoxin inhalation causes persistent airway disease. Am J Physiol Lung Cell Mol Physiol 2003;285:L755-761. Epub 2003 Jun 6.
56. Brass DM, Savov JD, Whitehead GS, Maxwell AB, Schwartz DA. LPS binding protein is important in the airway response to inhaled endotoxin. J Allergy Clin Immunol 2004;114:586-592.
57. Savov JD, Brass DM, Berman KG, McElvania E, Schwartz DA. Fibrinolysis in LPS-induced chronic airway disease. Am J Physiol Lung Cell Mol Physiol 2003;285:L940-L948.
58. Bonner JC, Rice AB, Moomaw CR, Morgan DL. Airway fibrosis in rats induced by vanadium pentoxide. Am J Physiol Lung Cell Mol Physiol 2000;278:L209-L216.
59. Bonner JC, Rice AB, Ingram JL, Moomaw CR, Nyska A, Bradbury A, Sessoms AR, Chulada PC, Morgan DL, Zeldin DC, et al. Susceptibility of cyclooxygenase-2-deficient mice to pulmonary fibrogenesis. Am J Pathol 2002;161:459-470.
60. Walters D, Gladwell W, Bonner J, Kleeburger S. 2006. Genetic susceptibility to vanadium pentoxide induced interstitial pulmonary fibrosis. Presented at the ATS International Conference 2006 San Diego, California. Abstract 504.
61. Cook DN, Wang S, Wang Y, Howles GP, Whitehead GS, Berman KG, Church TD, Frank BC, Gaspard RM, Yu Y, et al. Genetic regulation of endotoxin-induced airway disease. Genomics 2004;83:961-969.
62. 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.
63. Lemay AM, Haston CK. Bleomycin-induced pulmonary fibrosis susceptibility genes in AcB/BcA recombinant congenic mice. Physiol Genomics 2005;23:54-61.
64. Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, Wiltshire T, Su AI, Vellenga E, Wang J, Manly KF, et al. Uncovering regulatory pathways that affect hematopoietic stem cell function using "genetical genomics." Nat Genet 2005;37:225-232.
65. Chesler EJ, Lu L, Shou S, Qu Y, Gu J, Wang J, Hsu HC, Mountz JD, Baldwin NE, Langston MA, et al. Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat Genet 2005;37:233-242.
66. Hubner N, Wallace CA, Zimdahl H, Petretto E, Schulz H, Maciver F, Mueller M, Hummel O, Monti J, Zidek V, et al. Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease. Nat Genet 2005;37:243-253.
67. Broman KW. Mapping expression in randomized rodent genomes. Nat Genet 2005;37:209-210.