Allergic asthma biomarkers using systems approaches

Frontiers in Genetics

Volumn 4, Issue JAN, 2013, Pages

  Sircar, Gaurab ^a   Saha, Bodhisattwa ^a   Bhattacharya, Swati G ^a   Saha, Sudipto ^a  

^a BOSE INSTITUTE   (India)

Author keywords

Allergic asthma; Biomarker; DAAB; TH 2 cytokines and ROS pathway

Indexed keywords

ACYL COENZYME A DESATURASE; ADIPOCYTOKINE; ALPHA1 INTERFERON; APOLIPOPROTEIN B; ARGINASE 1; ARYLDIALKYLPHOSPHATASE 1; BIOLOGICAL MARKER; CALCIUM ACTIVATED CHLORIDE CHANNEL; CALGRANULIN B; CARBOXYPEPTIDASE A; CHITINASE; HYDROLASE; INTERLEUKIN 10; INTERLEUKIN 13; INTERLEUKIN 2; INTERLEUKIN 4; INTERLEUKIN 9; LONG CHAIN FATTY ACID COENZYME A LIGASE; METALLOPROTEINASE; MONOCYTE CHEMOTACTIC PROTEIN 2; MUCIN 5AC; NITRIC OXIDE SYNTHASE; NUCLEAR RECEPTOR NR1D1; RANTES; REACTIVE OXYGEN METABOLITE; RESISTIN; SUPPRESSOR OF CYTOKINE SIGNALING 1; SUPPRESSOR OF CYTOKINE SIGNALING 3; TRANSCRIPTION FACTOR FKHRL1; UNINDEXED DRUG;

ALLERGIC ASTHMA; APOPTOSIS; CD4+ T LYMPHOCYTE; DNA POLYMORPHISM; EPIGENETICS; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE ONTOLOGY; GENETIC ASSOCIATION; GENETIC DATABASE; GENOMICS; HIGH THROUGHPUT SCREENING; HUMAN; MACROPHAGE; MASS SPECTROMETRY; METABOLISM; MICROARRAY ANALYSIS; MOLECULAR INTERACTION; MOLECULAR PATHOLOGY; NONHUMAN; PHENOTYPE; POLYMERASE CHAIN REACTION; PROTEIN EXPRESSION; PROTEOMICS; SHORT SURVEY; SYSTEMS BIOLOGY; TH2 CELL;

EID: 84893644537     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2013.00308     Document Type: Short Survey

References (65)

1. Balzar, S., Fajt, M. L., Comhair, S. A., Erzurum, S. C., Bleecker, E., Busse, W. W., et al. (2011). Mast cell phenotype, location, and activation in severe asthma: data from the severe asthma research program. Am. J. Respir. Crit. Care Med. 183, 299-309. doi: 10.1164/rccm.201002-0295OC
2. Barnes, F. A., Bingle, L., and Bingle, C. D. (2008). Pulmonary genomics, proteomics, and PLUNCs. Am. J. Respir. Cell Mol. Biol. 38, 377-379. doi: 10.1165/rcmb.2007-0388TR
3. Bierbaum, S., Nickel, R., Koch, A., Lau, S., Deichmann, K. A., Wahn, U., et al. (2005). Polymorphisms and haplotypes of acid mammalian chitinase are associated with bronchial asthma. Am. J. Respir. Crit. Care Med. 172, 1505. doi: 10.1164/rccm.200506-890OC
4. Breton, C. V., Byun, H.-M., Wang, X., Salam, M. T., Siegmund, K., and Gilliland, F. D. (2011). DNA methylation in the arginase-nitric oxide synthase pathway is associated with exhaled nitric oxide in children with asthma. Am. J. Respir. Crit. Care Med. 184, 191. doi: 10.1164/rccm.201012-2029OC
5. Chu, H. W., Thaikoottathil, J., Rino, J. G., Zhang, G., Wu, Q., Moss, T., et al. (2007). Function and regulation of SPLUNC1 protein in Mycoplasma infection and allergic inflammation. J. Immunol. 179, 3995-4002.
6. Cloots, R. H., Sankaranarayanan, S., De Theije, C. C., Poynter, M. E., Terwindt, E., Van Dijk, P., et al. (2013). Ablation of Arg1 in hematopoietic cells improves respiratory function of lung parenchyma, but not that of larger airways or inflammation in asthmatic mice. Am. J. Physiol. Lung Cell. Mol. Physiol. 305, L364-L376. doi: 10.1152/ajplung.00341
7. Cookson, W. (2002). Genetics and genomics of asthma and allergic diseases. Immunol. Rev. 1, 195-206. doi: 10.1034/j.1600-065X.2002.19015.x
8. Diego, D., Goto, S., Fahy, J. V., Erle, D. J., Woodruff, P. G., Wheelock, Å. M., et al. (2012). Network analysis identifies a putative role for the PPAR and type 1 interferon pathways in glucocorticoid actions in asthmatics. BMC Med. Genomics 5:27. doi: 10.1186/1755-8794-5-27
9. Doherty, T. A., Khorram, N., Sugimoto, K., Sheppard, D., Rosenthal, P., Cho, J. Y., et al. (2012). Alternaria induces STAT6-dependent acute airway eosinophilia and epithelial FIZZ1 expression that promotes airway fibrosis and epithelial thickness. J. Immunol. 188, 2622-2629. doi: 10.4049/jimmunol.1101632
10. Dougherty, R. H., Sidhu, S. S., Raman, K., Solon, M., Solberg, O. D., Caughey, G. H., et al. (2010). Accumulation of intraepithelial mast cells with a unique protease phenotype in Th-2 high asthma. J. Allergy Clin. Immunol. 5, 1046-1053. doi: 10.1016/j.jaci.2010.03.003
11. Durham, A. L., Wiegman, C., and Adcock, I. M. (2011). Epigenetics of asthma. Biochim. Biophys. Acta 11, 1103-1109. doi: 10.1016/j.bbagen.2011.03.006
12. Fu, J. J., Baines, K. J., Wood, L. G., and Gibson, P. G. (2013). Systemic inflammation is associated with differential gene expression and airway neutrophilia in asthma. OMICS 17, 187-199. doi: 10.1089/omi.2012.0104
13. Gabazza, E. C., Taguchi, O., Tamaki, S., Murashima, S., Kobayashi, H., Yasui, H., et al. (2003). Role of nitric oxide in airway remodelling. Clin. Sci. 98, 291-294. doi: 10.1042/CS19990176
14. Gergen, P. J., and Weiss, K. B. (1995). "Epidemiology of asthma" in Asthma and Rhinitis, Chap. 3, eds W. W. Busse and S. T. Holgate (Boston, MA: Blackwell Scientific Publications), 17-32.
15. Ghafouri, B., Kristina, I., John, L., Christer, T., and Mats, L. (2006). Comparative proteomics of nasal fluid in seasonal allergic rhinitis. J. Proteome Res. 5, 330-338. doi: 10.1021/pr050341h
16. Ghosh, S., and Erzurum, S. C. (2011). Nitric oxide metabolism in asthma pathophysiology. Biochim. Biophys. Acta 11, 1008-1016. doi: 10.1016/j.bbagen.2011.06.009
17. Greenlee, K. J., Corry, D. B., Engler, D. A., Matsunami, R. K., Tessier, P., Cook, R. G., et al. (2006). Proteomic identification of in vivo substrates for matrix metalloproteinases 2 and 9 reveals a mechanism for resolution of inflammation. J. Immunol. 10, 7312-7321.
18. Guzik, T. J., Mangalat, D., and Korbut, R. (2006). Adipocytokines novel link between inflammation. J. Physiol. Pharmacol. 4, 505-528.
19. Hansel, N. N., Cheadle, C., Diette, G. B., Wright, J., Thompson, K. M., Barnes, K. C., et al. (2008). Analysis of CD4+ T-cell gene expression in allergic subjects using two different microarray platforms. Allergy 3, 366-369. doi: 10.1111/j.1398-9995.2007.01540.x
20. Huiling, L., Romieu, I., Sienra-Monge, J.-J., Ramirez-Aguilar, M., Estela del Rio-Navarro, B., Kistner, E. O., et al. (2006). Genetic polymorphisms in Arginase I and II and childhood asthma and atopy. J. Allergy Clin. Immunol. 117, 119-126. doi: 10.1016/j.jaci.2005.09.026
21. Islam, T., Breton, C., Salam, M. T., McConnell, R., Wenten, M., Gauderman, W. J., et al. (2010). Role of inducible nitric oxide synthase in asthma risk and lung function growth during adolescence. Thorax 65, 139-145. doi: 10.1136/thx.2009.114355
22. Ito, K., Caramori, G., Lim, S., Oates, T., Chung, K. F., Barnes, P. J., et al. (2002). Expression and activity of histone deacetylases in human asthmatic airways. Am. J. Respir. Crit. Care Med. 3, 392-396. doi: 10.1164/rccm.2110060
23. Jeong, H. C., Lee, S. Y., Lee, E. J., Jung, K. H., Kang, E. H., Lee, S. Y., et al. (2007). Proteomic analysis of peripheral T-lymphocytes in patients with asthma. Chest 132, 489-496. doi: 10.1378/chest.06-2980
24. Jiménez-Morales, S., Gamboa-Becerra, R., Baca, V., Río-Navarro, D., López-Ley, D. Y., Velázquez-Cruz, R., et al. (2012). MiR-146a polymorphism is associated with asthma but not with systemic lupus erythematosus and juvenile rheumatoid arthritis in Mexican patients. Tissue Antigens 4, 317-321. doi: 10.1111/j.1399-0039.2012.01929.x
25. Kanoh, S., Tanabe, T., and Rubin, B. K. (2011). IL-13-induced MUC5AC production and goblet cell differentiation is steroid resistant in human airway cells. Clin. Exp. Allergy 41, 1747-1756. doi: 10.1111/j.1365-2222.2011.03852.x
26. Karaaslan, C., Birben, E., Keskin, O., Sahiner, U., Sackesen, C., and Kalayci, O. (2012). The role of SCCA1 in asthma related physiological events in the airway epithelium and the effect of promoter variants on asthma and gene function. Respir. Med. 107, 368-379. doi: 10.1016/j.rmed.2012.11.003
27. Kumar, M., Ahmad, T., Sharma, A., Mabalirajan, U., Kulshreshtha, A., Agrawal, A., et al. (2011). Let-7 microRNA-mediated regulation of IL-13 and allergic airway inflammation. J. Allergy Clin. Immunol. 5, 1077-1085. doi: 10.1016/j.jaci.2011.04.034
28. Laitinen, L. A., Heino, M., Laitinen, A., Kava, T., and Haahtela, T. (1985). Damage of the airway epithelium and bronchial reactivity in patients with asthma. Am. Rev. Respir. Dis. 4, 599-606.
29. Laprise, C., Sladek, R., Ponton, A., Bernier, M.-C., Hudson, T. J., and Laviolette, M. (2004). Functional classes of bronchial mucosa genes that are differentially expressed in asthma. BMC Genomics 1:21. doi: 10.1186/1471-2164-5-21
30. Lee, T. H., Jang, A. S., Park, J. S., Kim, T. H., Choi, Y. S., Shin, H. R., et al. (2013). Elevation of S100 calcium binding protein A9 in sputum of neutrophilic inflammation in severe uncontrolled asthma. Ann. Allergy Asthma Immunol. 111, 268-275. doi: 10.1016/j.anai.2013.06.028
31. López, E., Zafra, M. P., Sastre, B., Gámez, C., Lahoz, C., and del Pozo, V. (2011). Gene expression profiling in lungs of chronic asthmatic mice treated with galectin-3: downregulation of inflammatory and regulatory genes. Mediat. Inflamm. 2011, 823279. doi: 10.1155/2011/823279
32. Louten, J., Mattson, J. D., Malinao, M. C., Li, Y., Emson, C., Vega, F., et al. (2012). Biomarkers of disease and treatment in murine and cynomolgus models of chronic asthma. Biomark. Insights 7, 87. doi: 10.4137/BMI.S9776
33. Lovinsky-Desir, S., and Miller, R. L. (2012). Epigenetics, asthma, and allergic diseases: a review of the latest advancements. Curr. Allergy Asthma Rep. 12, 211-220. doi: 10.1007/s11882-012-0257-4
34. Lu, T. X., Munitz, A., and Rothenberg, M. E. (2009). MicroRNA-21 is up-regulated in allergic airway inflammation and regulates IL-12p35 expression. J. Immunol. 8, 4994-5002. doi: 10.4049/jimmunol.0803560
35. Lukacs, N. W. (2001). Role of chemokines in the pathogenesis of asthma. Nat. Rev. Immunol. 2, 108-116. doi: 10.1038/35100503
36. Lyon, H., Lange, C., Lake, S., Silverman, E. K., Randolph, A. G., Kwiatkowski, D., et al. (2004). IL10 gene polymorphisms are associated with asthma phenotypes in children. Genet. Epidemiol. 26, 155-165. doi: 10.1002/gepi.10298
37. Martinez-Nunez, R. T., Louafi, F., and Sanchez-Elsner, T. (2011). The interleukin 13 (IL-13) pathway in human macrophages is modulated by microRNA-155 via direct targeting of interleukin 13 receptor a1 (IL13Ra1). J. Biol. Chem. 3, 1786-1794. doi: 10.1074/jbc. M110.169367
38. Michel, O., Doyen, V., Leroy, B., Bopp, B., Dinh, D. H., Corazza, F., et al. (2013). Expression of calgranulin A/B heterodimer after acute inhalation of endotoxin: proteomic approach and validation. BMC Pulm. Med. 13:65. doi: 10.1186/1471-2466-13-65
39. Miller, R. L., and Ho, S.-M. (2008). Environmental epigenetics and asthma: current concepts and call for studies. Am. J. Respir. Crit. Care Med. 177, 567. doi: 10.1164/rccm.200710-1511PP
40. Murugan, A., Prys-Picard, C., and Calhoun, W. J. (2009). Biomarkers in asthma. Curr. Opin. Pulm. Med. 1, 12-18. doi: 10.1097/MCP.0b013e32831de235
41. North, M. L., Khanna, N., Marsden, P. A., Grasemann, H., and Scott, J. A. (2009). Functionally important role for arginase 1 in the airway hyperresponsiveness of asthma. Am. J. Physiol. Lung Cell. Mol. Physiol. 296, L911-L920. doi: 10.1152/ajplung.00025.2009
42. Ordonez, C. L., Khashayar, R., Wong, H. H., Ferrando, R., Wu, R., Hyde, D. M., et al. (2001). Mild and moderate asthma is associated with airway goblet cell hyperplasia and abnormalities in mucin gene expression. Am. J. Respir. Crit. Care Med. 163, 517-523. doi: 10.1164/ajrccm.163.2.2004039
43. Park, S. G., Choi, J.-W., Kim, H. J., Roh, G. S., Jeong, B., Min, J. G., et al. (2008). Genome-wide profiling of antigen-induced time course expression using murine models for acute and chronic asthma. Int. Arch. Allergy Immunol. 146, 44-56. doi: 10.1159/000112502
44. Pascual, M., Sanz, C., Isidoro-Garcia, M., Davila, I., Moreno, E., Laffond, E., et al. (2008). (CCTTT) n polymorphism of NOS2A in nasal polyposis and asthma: a case-control study. J. Investig. Allergol. Clin. Immunol. 18, 239.
45. Pesce, J. T., Ramalingam, T. R., Wilson, M. S., Mentink-Kane, M. M., Thompson, R. W., Cheever, A. W., et al. (2009). Retnla (relma/fizz1) suppresses helminth-induced Th2-type immunity. PLoS Pathog. 5:e1000393. doi: 10.1371/journal.ppat.1000393
46. Ricciardolo, F. L., Sterk, P. J., Gaston, B., and Folkerts, G. (2004). Nitric oxide in health and disease of the respiratory system. Physiol. Rev. 84, 731-765. doi: 10.1152/physrev.00034.2003
47. Shi, O., Morris, S. M., Zoghbi, H., Porter, C. W., and O'Brien, W. E. (2001). Generation of a mouse model for arginase II deficiency by targeted disruption of the arginase II gene. Mol. Cell. Biol. 21, 811-813. doi: 10.1128/MCB.21.3.811-813.2001
48. Siddiqui, S., Eric, R. S. Jr., and Lawrence, K. S. (2013). Broncho-alveolar macrophages express chemokines associated with leukocyte migration in a mouse model of asthma. Cell. Immunol. 2, 159-169. doi: 10.1016/j.cellimm.2013.03.001
49. Strimbu, K., and Tavel, J. A. (2010). What are biomarkers? Curr. Opin. HIV AIDS 6, 463-466. doi: 10.1097/COH.0b013e32833ed177
50. Subbarao, P., Mandhane, P. J., and Sears, M. R. (2009). Asthma: epidemiology, etiology and risk factors. Can. Med. Assoc. J. 181, E181-E190. doi: 10.1503/cmaj.080612
51. Theoharides, T. C., Makris, M., and Kalogeromitros, D. (2008). Allergic inflammation and adipocytokines. Int. J. Immunopathol. Pharmacol. 1, 1-4.
52. Tilg, H., and Moschen, A. R. (2006). Adipocytokines: mediators linking adipose tissue, inflammation and immunity. Nat. Rev. Immunol. 6, 772-783. doi: 10.1038/nri1937
53. Toda, M., and Ono, S. J. (2002). Genomics and proteomics of allergic disease. Immunology 106, 1-10. doi: 10.1046/j.1365-2567.2002.01407.x
54. Torrone, D. Z., Kuriakose, J. S., Moors, K., Jiang, H., Niedzwiecki, M. M., Perera, F. F., et al. (2012). Reproducibility and intraindividual variation over days in buccal cell DNA methylation of two asthma genes, interferon g (IFNg) and inducible nitric oxide synthase (iNOS). Clin. Epigenet. 4:3. doi: 10.1186/1868-7083-4-3
55. Tumes, D. J., Connolly, A., and Dent, L. A. (2009). Expression of survivin in lung eosinophils is associated with pathology in a mouse model of allergic asthma. Int. Immunol. 6, 633-644. doi: 10.1093/intimm/dxp032
56. Webb, D. C., McKenzie, A. N., and Foster, P. S. (2001). Expression of the ym2 lectin-binding protein is dependent on interleukin (IL)-4 AND IL-13 signal transduction identification of a novel allergy-associated protein. J. Biol. Chem. 276, 41969-41976. doi: 10.1074/jbc. M106223200
57. Woodruff, P. G., Boushey, H. A., Dolganov, G. M., Barker, C. S., Yang, Y. H., Donnelly, S., et al. (2007). Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids. Proc. Natl. Acad. Sci. U.S.A. 40, 15858-15863. doi: 10.1073/pnas.0707413104
58. Wu, J., Kobayashi, M., Sousa, E. A., Liu, W., Cai, J., Goldman, S. J., et al. (2005). Differential proteomic analysis of bronchoalveolar lavage fluid in asthmatics following segmental antigen challenge. Mol. Cell. Proteomics 4, 1251-1264. doi: 10.1074/mcp. M500041-MCP200
59. Zhao, J., Zhu, H., Wong, C. H., Leung, K. Y., and Wong, W. S. (2005). Increased lungkine and chitinase levels in allergic airway inflammation: a proteomics approach. Proteomics 11, 2799-2807. doi: 10.1002/pmic.200401169
60. Zhou, Y., Dong, Q., Louahed, J., Dragwa, C., Savio, D., Huang, M., et al. (2001). Characterization of a calcium-activated chloride channel as a shared target of Th2 cytokine pathways and its potential involvement in asthma. Am. J. Respir. Cell Mol. Biol. 25, 486-491. doi: 10.1165/ajrcmb.25.4.4578
61. Zhu, Z., Zheng, T., Homer, R. J., Kim, Y. K., Chen, N. Y., Cohn, L., et al. (2004). Acidic mammalian chitinase in asthmatic Th2 inflammation and IL-13 pathway activation. Science 5677, 1678-1682. doi: 10.1126/science.1095336
62. Zimmermann, N., King, N. E., Laporte, J., Yang, M., Mishra, A., Pope, S. M., et al. (2003). Dissection of experimental asthma with DNA microarray analysis identifies arginase in asthma pathogenesis. J. Clin. Investig. 12, 1863-1874. doi: 10.1172/JCI200317912
63. Zou, J., Young, S., Zhu, F., Gheyas, F., Skeans, S., Wan, Y., et al. (2002). Microarray profile of differentially expressed genes in a monkey model of allergic asthma. Genome Biol. 5, 20. doi: 10.1186/gb-2002-3-5-research0020
64. Zuo, L., and Clanton, T. L. (2005). Reactive oxygen species formation in the transition to hypoxia in skeletal muscle. Am. J. Physiol. Cell Physiol. 1, C207-C216. doi: 10.1152/ajpcell.00449.2004
65. Zuo, L., Otenbaker, N. P., Rose, B. A., and Salisbury, K. S. (2013). Molecular mechanisms of reactive oxygen species-related pulmonary inflammation and asthma. Mol. Immunol. 1, 57-63. doi: 10.1016/j.molimm.2013.04.002