Human biomarker discovery and predictive models for disease progression for idiopathic pneumonia syndrome following allogeneic stem cell transplantation

Molecular and Cellular Proteomics

Volumn 11, Issue 6, 2012, Pages

  Schlatzer, Daniela M ^a   Dazard, Jean Eudes ^a   Ewing, Rob M ^a   Ilchenko, Serguei ^a   Tomcheko, Sara E ^a   Eid, Saada ^a   Ho, Vincent ^b   Yanik, Greg ^c   Chance, Mark R ^a   Cooke, Kenneth R ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^c DANA FARBER CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; CORTICOSTEROID; CYTOKINE; ETANERCEPT; LIPOPOLYSACCHARIDE BINDING PROTEIN; PLASMA PROTEIN; ACUTE PHASE PROTEIN; IMMUNOGLOBULIN G; NONSTEROID ANTIINFLAMMATORY AGENT; TNFR FC FUSION PROTEIN; TNFR-FC FUSION PROTEIN; TUMOR NECROSIS FACTOR RECEPTOR;

ALLOGENEIC STEM CELL TRANSPLANTATION; ARTICLE; CONTROLLED STUDY; DISEASE COURSE; ENZYME LINKED IMMUNOSORBENT ASSAY; HUMAN; IDIOPATHIC DISEASE; IDIOPATHIC PNEUMONIA SYNDROME; MOLECULAR DIAGNOSIS; NONHUMAN; OUTCOME ASSESSMENT; PATHOPHYSIOLOGY; PNEUMONIA; PREDICTION; PREDICTIVE VALIDITY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOMICS; TREATMENT RESPONSE; ALLOTRANSPLANTATION; BIOLOGICAL MODEL; BLOOD; CAPILLARY ELECTROCHROMATOGRAPHY; CASE CONTROL STUDY; HEMATOPOIETIC STEM CELL TRANSPLANTATION; ISOLATION AND PURIFICATION; METABOLISM; PATHOLOGY; PRINCIPAL COMPONENT ANALYSIS; REPRODUCIBILITY;

ACUTE-PHASE PROTEINS; ANTI-INFLAMMATORY AGENTS, NON-STEROIDAL; BIOLOGICAL MARKERS; BLOOD PROTEINS; CAPILLARY ELECTROCHROMATOGRAPHY; CASE-CONTROL STUDIES; DISEASE PROGRESSION; HEMATOPOIETIC STEM CELL TRANSPLANTATION; HUMANS; IMMUNOGLOBULIN G; MODELS, BIOLOGICAL; PNEUMONIA; PRINCIPAL COMPONENT ANALYSIS; PROTEOMICS; RECEPTORS, TUMOR NECROSIS FACTOR; REPRODUCIBILITY OF RESULTS; TRANSPLANTATION, HOMOLOGOUS;

EID: 84860873455     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M111.015479     Document Type: Article

References (74)

1. Clark, J. G., Hansen, J. A., Hertz, M. I., Parkman, R., Jensen, L., and Peavy, H. H. (1993) NHLBI workshop summary. Idiopathic pneumonia syndrome after bone marrow transplantation. Am. Rev. Respir Dis. 147, 1601-1606
2. Panoskaltsis-Mortari, A., Griese, M., Madtes, D. K., Belperio, J. A., Haddad, I. Y., Folz, R. J., and Cooke, K. R. (2011) An official American Thoracic Society research statement: noninfectious lung injury after hematopoietic stem cell transplantation: idiopathic pneumonia syndrome. Am. J. Respir Crit. Care Med. 183, 1262-1279
3. Kantrow, S. P., Hackman, R. C., Boeckh, M., Myerson, D., and Crawford, S. W. (1997) Idiopathic pneumonia syndrome: changing spectrum of lung injury after marrow transplantation. Transplantation 63, 1079-1086
4. Cooke, K. R., Kobzik, L., Martin, T. R., Brewer, J., Delmonte, J., Jr., Crawford, J. M., and Ferrara, J. L. (1996) An experimental model of idiopathic pneumonia syndrome after bone marrow transplantation: I. The roles of minor H antigens and endotoxin. Blood 88, 3230-3239
5. Cooke, K. R., Hill, G. R., Gerbitz, A., Kobzik, L., Martin, T. R., Crawford, J. M., Brewer, J. P., and Ferrara, J. L. (2000) Tumor necrosis factor-alpha neutralization reduces lung injury after experimental allogeneic bone marrow transplantation. Transplantation 70, 272-279
6. Hildebrandt, G. C., Olkiewicz, K. M., Corrion, L. A., Chang, Y., Clouthier, S. G., Liu, C., and Cooke, K. R. (2004) Donor-derived TNF-alpha regulates pulmonary chemokine expression and the development of idiopathic pneumonia syndrome after allogeneic bone marrow transplantation. Blood 104, 586-593
7. Hildebrandt, G. C., Olkiewicz, K. M., Corrion, L. A., Clouthier, S. G., Pierce, E., Liu, C., and Cooke, K. R. (2008) A role for TNF receptor type II in leukocyte infiltration into the lung during experimental idiopathic pneumonia syndrome. Biol. Blood Marrow Transplant. 14, 385-396
8. Gerbitz, A., Nickoloff, B. J., Olkiewicz, K., Willmarth, N. E., Hildebrandt, G., Liu, C., Kobzik, L., Eissner, G., Holler, E., Ferrara, J. L., and Cooke, K. R. (2004) A role for tumor necrosis factor-alpha-mediated endothelial apoptosis in the development of experimental idiopathic pneumonia syndrome. Transplantation 78, 494-502
9. Yanik, G. A., Ho, V. T., Levine, J. E., White, E. S., Braun, T., Antin, J. H., Whitfield, J., Custer, J., Jones, D., Ferrara, J. L., and Cooke, K. R.(2008) The impact of soluble tumor necrosis factor receptor etanercept on the treatment of idiopathic pneumonia syndrome after allogeneic hematopoietic stem cell transplantation. Blood 112, 3073-3081
10. Clark, J. G., Madtes, D. K., Martin, T. R., Hackman, R. C., Farrand, A. L., and Crawford, S. W. (1999) Idiopathic pneumonia after bone marrow transplantation: cytokine activation and lipopolysaccharide amplification in the bronchoalveolar compartment. Crit. Care Med. 27, 1800-1806
11. Rifai, N., Gillette, M. A., and Carr, S. A. (2006) Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol. 24, 971-983
12. Veenstra, T. D., Conrads, T. P., Hood, B. L., Avellino, A. M., Ellenbogen, R. G., and Morrison, R. S. (2005) Biomarkers: mining the biofluid proteome. Mol. Cell Proteomics 4, 409-418
13. Zhao, Y., Lee, W. N., and Xiao, G. G. (2009) Quantitative proteomics and biomarker discovery in human cancer. Expert Rev. Proteomics 6, 115-118
14. Paczesny, S., Krijanovski, O. I., Braun, T. M., Choi, S. W., Clouthier, S. G., Kuick, R., Misek, D. E., Cooke, K. R., Kitko, C. L., Weyand, A., Bickley, D., Jones, D., Whitfield, J., Reddy, P., Levine, J. E., Hanash, S. M., and Ferrara, J. L.(2009) A biomarker panel for acute graft-versus-host disease. Blood 113, 273-278
15. Wang, W., Zhou, H., Lin, H., Roy, S., Shaler, T. A., Hill, L. R., Norton, S., Kumar, P., Anderle, M., and Becker, C. H. (2003) Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal. Chem. 75, 4818-4826
16. Chelius, D., and Bondarenko, P. V. (2002) Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J. Proteome Res. 1, 317-323
17. Schlatzer, D. M., Dazard, J. E., Dharsee, M., Ewing, R. M., Ilchenko, S., Stewart, I., Christ, G., and Chance, M. R. (2009) Urinary protein profiles in a rat model for diabetic complications. Mol. Cell Proteomics 8, 2145-2158
18. Elias, J. E., Haas, W., Faherty, B. K., and Gygi, S. P. (2005) Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat. Methods 2, 667-675
19. Brosch, M., Yu, L., Hubbard, T., and Choudhary, J. (2009) Accurate and sensitive peptide identification with Mascot Percolator. J. Proteome Res. 8, 3176-3181
20. Chan, E. Y., Sutton, J. N., Jacobs, J. M., Bondarenko, A., Smith, R. D., and Katze, M. G. (2009) Dynamic host energetics and cytoskeletal proteomes in human immunodeficiency virus type 1-infected human primary CD4 cells: analysis by multiplexed label-free mass spectrometry. J. Virol. 83, 9283-9295
21. Neubert, H., Bonnert, T. P., Rumpel, K., Hunt, B. T., Henle, E. S., and James, I. T. (2008) Label-free detection of differential protein expression by LC/MALDI mass spectrometry. J. Proteome Res. 7, 2270-2279
22. Wang, P., Tang, H., Zhang, H., Whiteaker, J., Paulovich, A. G., and McIntosh, M. (2006) Normalization regarding non-random missing values in high-throughput mass spectrometry data. In Pac Symp Biocomput. Lihue, Hawaii: World Scientific Press. 315-326
23. Weng, L., Dai, H., Zhan, Y., He, Y., Stepaniants, S. B., and Bassett, D. E. (2006) Rosetta error model for gene expression analysis. Bioinformatics 22, 1111-1121
24. Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646-4658
25. Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392
26. Dazard, J.-E., and Rao, J. S. (2012) Joint Adaptive Mean-Variance Regularization and Variance Stabilization of High Dimensional Data. Comput. Statist. Data Anal. (in press)
27. Dazard, J.-E., Xu, H., and Rao, J. S. (2011) R package MVR for Joint Adaptive Mean-Variance Regularization and Variance Stabilization. In JSM Proceedings. Section for Statistical Programmers and Analysts. Miami Beach, FL. U.S.A.: American Statistical Association. (in press)
28. Dazard, J.-E., Xu, H., Santana, A., and Rao, J. S. (2011) R package MVR. In Comprehensive R Archive Network
29. Storey, J. D. (2002) A direct approach to false discovery rates. J. R. Statist. Soc. 64, 479-498
30. Storey, J. D. (2003) The positive false discovery rate: A Bayesian interpretation and the q-value. Ann. Statistics 31, 2013-2035
31. Liu, P., and Hwang, J. T. (2007) Quick calculation for sample size while controlling false discovery rate with application to microarray analysis. Bioinformatics 23, 739-746
32. Hotelling, H. (1933) Analysis of a complex of statistical variables into principal components. J. Ed. Psychol. 24, 417-441
33. Tibshirani, R. (2001) Estimating the number of clusters in a data set via the gap statistic. J. R. Statist. Soc. 63, 411-423
34. Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. 57, 289-300
35. Smyth, G. K. (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl. Genet Mol. Biol. 3, Article3
36. Smyth, G. K., Thorne, N., and Wettenhall, J. (2004) Limma R package: linear models for microarray. Comprehensive R Archive Network
37. Dabney, A., and Storey, J. D. (2003) Qvalue R package: Q-value estimation for false discovery rate control. Comprehensive R Archive Network
38. Ishwaran, H., and Rao, J. S. (2011) Generalized ridge regression: geometry and computational solutions when p is larger than n. Miami, University of Miami. Pg. 1-39
39. Ishwaran, H., and Rao, J. S. (2005) Spike and slab variable selection: frequentist and Bayesian strategies. Ann. Statistics 33, 730-773
40. Ishwaran, H., and Rao, J. S. (2005) Spike and slab gene selection for multigroup microarray data. J. Amer. Stat Assoc. 100, 764-780
41. Breiman, L. (2001) Random forests. Mach. Learn. 45, 5-32
42. Efron, B., Hastie, T., Johnstone, I., and Tibshirani, R. (2004) Least angle regression. Ann. Statistics 32, 407-499
43. Zou, H., and Hastie, T. (2005) Regularization and variable selection via the elastic net. J. R Statist Soc. 67, 301-320
44. Friedman, J., Hastie, T., and Tibshirani, R. (2010) Regularization Paths for Generalized Linear Models via Coordinate Descent. Journal of Statistical Software 33, 1-22
45. Ishwaran, H., and Rao, J. S. (2003) Detecting differentially expressed genes in microarrays using Bayesian model selection. J. Amer. Stat. Assoc. 98, 438-455
46. Panoskaltsis-Mortari, A., Griese, M., Madtes, D. K., Belperio, J. A., Haddad, I. Y., Folz, R. J., and Cooke, K. R. (2011) An official American Thoracic Society research statement: noninfectious lung injury after hematopoietic stem cell transplantation: idiopathic pneumonia syndrome. Am. J. Respir Crit. Care Med. 183, 1262-1279
47. Ihnatko, R., and Kubes, M. (2007) TNF signaling: early events and phosphorylation. Gen. Physiol. Biophys. 26, 159-167
48. Heinrich, P. C., Castell, J. V., and Andus, T. (1990) Interleukin-6 and the acute phase response. Biochem. J. 265, 621-636
49. Schuett, H., Luchtefeld, M., Grothusen, C., Grote, K., and Schieffer, B. (2009) How much is too much? Interleukin-6 and its signalling in atherosclerosis. Thromb. Haemost. 102, 215-222
50. Chen, Y., Lim, B. K., Peh, S. C., Abdul-Rahman, P. S., and Hashim, O. H. (2008) Profiling of serum and tissue high abundance acute-phase proteins of patients with epithelial and germ line ovarian carcinoma. Proteome Sci. 6, 20
51. Medzhitov, R., and Janeway, C., Jr. (2000) Innate immune recognition: mechanisms and pathways. Immunol. Rev. 173, 89-97
52. Heumann, D., Lauener, R., and Ryffel, B. (2003) The dual role of LBP and CD14 in response to Gram-negative bacteria or Gram-negative compounds. J. Endotoxin Res. 9, 381-384
53. Mogensen, T. H. (2009) Pathogen recognition and inflammatory signaling in innate immune defenses. Clin. Microbiol. Rev. 22, 240-273, Table of Contents
54. Akira, S., Uematsu, S., and Takeuchi, O. (2006) Pathogen recognition and innate immunity. Cell 124, 783-801
55. Trent, M. S., Stead, C. M., Tran, A. X., and Hankins, J. V. (2006) Diversity of endotoxin and its impact on pathogenesis. J. Endotoxin Res. 12, 205-223
56. Cooke, K. R., Gerbitz, A., Crawford, J. M., Teshima, T., Hill, G. R., Tesolin, A., Rossignol, D. P., and Ferrara, J. L. (2001) LPS antagonism reduces graft-versus-host disease and preserves graft-versus-leukemia activity after experimental bone marrow transplantation. J. Clin. Invest. 107, 1581-1589
57. Cooke, K. R., Hill, G. R., Crawford, J. M., Bungard, D., Brinson, Y. S., Delmonte, J., Jr., and Ferrara, J. L. (1998) Tumor necrosis factor- alpha production to lipopolysaccharide stimulation by donor cells predicts the severity of experimental acute graft-versus-host disease. J. Clin. Invest. 102, 1882-1891
58. Gioannini, T. L., Teghanemt, A., Zhang, D., Levis, E. N., and Weiss, J. P. (2005) Monomeric endotoxin:protein complexes are essential for TLR4-dependent cell activation. J. Endotoxin Res. 11, 117-123
59. Jerala, R. (2007) Structural biology of the LPS recognition. Int. J. Med. Microbiol. 297, 353-363
60. Beutler, B., and Rietschel, E. T. (2003) Innate immune sensing and its roots: the story of endotoxin. Nat. Rev. Immunol. 3, 169-176
61. Ulevitch, R. J., and Tobias, P. S. (1999) Recognition of gram-negative bacteria and endotoxin by the innate immune system. Curr. Opin. Immunol. 11, 19-22
62. Kang, D., Liu, G., Lundström, A., Gelius, E., and Steiner, H. (1998) A peptidoglycan recognition protein in innate immunity conserved from insects to humans. Proc. Natl. Acad. Sci. U.S.A. 95, 10078-10082
63. Dziarski, R., and Gupta, D. (2006) The peptidoglycan recognition proteins (PGRPs). Genome Biol. 7, 232
64. Werner, T., Liu, G., Kang, D., Ekengren, S., Steiner, H., and Hultmark, D. (2000) A family of peptidoglycan recognition proteins in the fruit fly Drosophila melanogaster. Proc. Natl. Acad. Sci. U.S.A. 97, 13772-13777
65. Gelius, E., Persson, C., Karlsson, J., and Steiner, H. (2003) A mammalian peptidoglycan recognition protein with N-acetylmuramoyl-L-alanine amidase activity. Biochem. Biophys. Res. Commun. 306, 988-994
66. Saha, S., Qi, J., Wang, S., Wang, M., Li, X., Kim, Y. G., Nuñez, G., Gupta, D., and Dziarski, R. (2009) PGLYRP-2 and Nod2 are both required for peptidoglycan-induced arthritis and local inflammation. Cell Host Microbe. 5, 137-150
67. Chakravarti, S. (2002) Functions of lumican and fibromodulin: lessons from knockout mice. Glycoconj J. 19, 287-293
68. Iozzo, R. V. (1999) The biology of the small leucine-rich proteoglycans. Functional network of interactive proteins. J. Biol. Chem. 274, 18843-18846
69. Vij, N., Roberts, L., Joyce, S., and Chakravarti, S. (2005) Lumican regulates corneal inflammatory responses by modulating Fas-Fas ligand signaling. Invest Ophthalmol Vis. Sci. 46, 88-95
70. Wu, F., Vij, N., Roberts, L., Lopez-Briones, S., Joyce, S., and Chakravarti, S. (2007) A novel role of the lumican core protein in bacterial lipopolysaccharide-induced innate immune response. J. Biol. Chem. 282, 26409-26417
71. Duke-Cohan, J. S., Tang, W., and Schlossman, S. F. (2000) Attractin: a cub-family protease involved in T cell-monocyte/macrophage interactions. Adv. Exp. Med. Biol. 477, 173-185
72. Wrenger, S., Faust, J., Friedrich, D., Hoffmann, T., Hartig, R., Lendeckel, U., Kähne, T., Thielitz, A., Neubert, K., and Reinhold, D. (2006) Attractin, a dipeptidyl peptidase IV/CD26-like enzyme, is expressed on human peripheral blood monocytes and potentially influences monocyte function. J. Leukoc Biol. 80, 621-629
73. Ohnuma, K., Dang, N. H., and Morimoto, C. (2008) Revisiting an old acquaintance: CD26 and its molecular mechanisms in T cell function. Trends Immunol. 29, 295-301
74. Duke-Cohan, J. S., Gu, J., McLaughlin, D. F., Xu, Y., Freeman, G. J., and Schlossman, S. F. (1998) Attractin (DPPT-L), a member of the CUB family of cell adhesion and guidance proteins, is secreted by activated human T lymphocytes and modulates immune cell interactions. Proc. Natl. Acad. Sci. U.S.A. 95, 11336-11341