Genetic and genomic approaches to asthma: New insights for the origins

Current Opinion in Pulmonary Medicine

Volumn 18, Issue 1, 2012, Pages 6-13

  Zhang, Youming ^a   Moffatt, Miriam F ^a   Cookson, William O C ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

asthma; genetics; genome wide association studies; genomics; IgE

Indexed keywords

GASDERMIN A; GASDERMIN B; HLA DQ ANTIGEN; IMMUNOGLOBULIN E; INTERLEUKIN 1 RECEPTOR LIKE 1 PROTEIN; INTERLEUKIN 18 RECEPTOR ALPHA; INTERLEUKIN 2 RECEPTOR BETA; INTERLEUKIN 33; PHOSPHODIESTERASE; PROTEIN; PROTEIN ADAM33; PROTEIN DENNDB1; PROTEIN DPP10; PROTEIN FCER1A; PROTEIN GPRA; PROTEIN ORMDL3; PROTEIN PHF11; SMAD3 PROTEIN; UNCLASSIFIED DRUG;

ALLERGIC ASTHMA; ASTHMA; ATOPY; GENE FUNCTION; GENE LOCUS; GENE OVEREXPRESSION; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENOTYPE; HUMAN; IMMUNOGLOBULIN BLOOD LEVEL; IMMUNOGLOBULIN PRODUCTION; MOLECULAR CLONING; NONHUMAN; PATHOGENESIS; RESPIRATORY EPITHELIUM; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

ASTHMA; GENE KNOCKDOWN TECHNIQUES; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HLA-DQ ANTIGENS; HUMANS; HYPERSENSITIVITY, IMMEDIATE; IMMUNOGLOBULIN E; INTERLEUKIN-18 RECEPTOR ALPHA SUBUNIT; INTERLEUKIN-2 RECEPTOR BETA SUBUNIT; INTERLEUKINS; MEMBRANE PROTEINS; SMAD3 PROTEIN;

EID: 83155173902     PISSN: 10705287     EISSN: 15316971     Source Type: Journal    
DOI: 10.1097/MCP.0b013e32834dc532     Document Type: Review

References (79)

1. Willis-Owen SA, Cookson WO, Moffatt MF. Genome-wide association studies in the genetics of asthma. Curr Allergy Asthma Rep 2009; 9:3-9.
2. Dudbridge F, Gusnanto A. Estimation of significance thresholds for genomewide association scans. Genet Epidemiol 2008; 32:227-234. (Pubitemid 351550369)
3. The Wellcome Trust Case Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3000 shared controls. Nature 2007; 447:661-678.
4. Moffatt MF, Kabesch M, Liang L, et al. Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature 2007; 448:470-473. (Pubitemid 47123521)
5. Li X, Howard TD, Zheng SL, et al. Genome-wide association study of asthma identifies RAD50-IL13 and HLA-DR/DQ regions. J Allergy Clin Immunol 2010; 125:328 e11-335 e11.
6. Hancock DB, Romieu I, Shi M, et al. Genome-wide association study implicates chromosome 9q21.31 as a susceptibility locus for asthma in Mexican children. PLoS Genet 2009; 5:e1000623.
7. Weidinger S, Gieger C, Rodriguez E, et al. Genome-wide scan on total serum IgE levels identifies FCER1A as novel susceptibility locus. PLoS Genet 2008; 4:e1000166.
8. Barnes KC. Genetic studies of the etiology of asthma. Proc Am Thorac Soc 2011; 8:143-148.
9. Michel S, Liang L, Depner M, et al. Unifying candidate gene and GWAS approaches in asthma. PLoS One 2010; 5:e13894.
10. Moffatt MF, Gut IG, Demenais F, et al. A large-scale, consortium-based genomewide association study of asthma. N Engl J Med 2010; 363: 1211-1221.
11. Weidinger S, Baurecht H, Naumann A, Novak N. Genome-wide association studies on IgE regulation: are genetics of IgE also genetics of atopic disease? Curr Opin Allergy Clin Immunol 2010; 10:408-417.
12. Sleiman PM, Flory J, Imielinski M, et al. Variants of DENND1B associated with asthma in children. N Engl J Med 2010; 362:36-44.
13. Ober C, Tan Z, Sun Y, et al. Effect of variation in CHI3L1 on serum YKL-40 level, risk of asthma, and lung function. N Engl J Med 2008; 358:1682-1691. (Pubitemid 351549915)
14. Gudbjartsson DF, Bjornsdottir US, Halapi E, et al. Sequence variants affecting eosinophil numbers associate with asthma and myocardial infarction. Nat Genet 2009; 41:342-347.
15. Himes BE, Hunninghake GM, Baurley JW, et al. Genome-wide association analysis identifies PDE4D as an asthma-susceptibility gene. Am J Hum Genet 2009; 84:581-593.
16. Dunne A, O'Neill LA. The interleukin-1 receptor/Toll-like receptor superfamily: signal transduction during inflammation and host defense. Sci STKE 2003; 2003:re3.
17. Schmitz J, Owyang A, Oldham E, et al. IL-33, an interleukin-1-like cytokine that signals via the IL-1 receptor-related protein ST2 and induces T helper type 2-associated cytokines. Immunity 2005; 23:479-490. (Pubitemid 41587888)
18. Fukao T, Matsuda S, Koyasu S. Synergistic effects of IL-4 and IL-18 on IL-12-dependent IFN-gamma production by dendritic cells. J Immunol 2000; 164:64-71. (Pubitemid 30012973)
19. Baekkevold ES, Roussigne M, Yamanaka T, et al. Molecular characterization of NF-HEV, a nuclear factor preferentially expressed in human high endothelial venules. Am J Pathol 2003; 163:69-79. (Pubitemid 36759592)
20. Carriere V, Roussel L, Ortega N, et al. IL-33, the IL-1-like cytokine ligand for ST2 receptor, is a chromatin-associated nuclear factor in vivo. Proc Natl Acad Sci USA 2007; 104:282-287. (Pubitemid 46068023)
21. Kurowska-Stolarska M, Hueber A, Stolarski B, McInnes IB. Interleukin-33: a novel mediator with a role in distinct disease pathologies. J Intern Med 2011; 269:29-35.
22. Moussion C, Ortega N, Girard JP. The IL-1-like cytokine IL-33 is constitutively expressed in the nucleus of endothelial cells and epithelial cells in vivo: a novel 'alarmin'? PLoS One 2008; 3:e3331.
23. Oboki K, Ohno T, Kajiwara N, et al. IL-33 is a crucial amplifier of innate rather than acquired immunity. Proc Natl Acad Sci USA 2010; 107:18581-18586.
24. Lloyd CM. IL-33 family members and asthma-bridging innate and adaptive immune responses. Curr Opin Immunol 2010; 22:800-806.
25. Yang YA, Zhang GM, Feigenbaum L, Zhang YE. Smad3 reduces susceptibility to hepatocarcinoma by sensitizing hepatocytes to apoptosis through downregulation of Bcl-2. Cancer Cell 2006; 9:445-457. (Pubitemid 43832193)
26. Tian F, DaCosta Byfield S, Parks WT, et al. Reduction in Smad2/3 signaling enhances tumorigenesis but suppresses metastasis of breast cancer cell lines. Cancer Res 2003; 63:8284-8292. (Pubitemid 37549480)
27. Daly AC, Vizan P, Hill CS. Smad3 protein levels are modulated by Ras activity and during the cell cycle to dictate transforming growth factor-beta responses. J Biol Chem 2010; 285:6489-6497.
28. Lloyd CM, Hawrylowicz CM. Regulatory T cells in asthma. Immunity 2009; 31:438-449.
29. Kariyawasam HH, Pegorier S, Barkans J, et al. Activin and transforming growth factor-beta signaling pathways are activated after allergen challenge in mild asthma. J Allergy Clin Immunol 2009; 124:454-462.
30. Anthoni M, Wang G, Leino MS, et al. Smad3-signalling and Th2 cytokines in normal mouse airways and in a mouse model of asthma. Int J Biol Sci 2007; 3:477-485. (Pubitemid 350277604)
31. Ashcroft GS, Yang X, Glick AB, et al. Mice lacking Smad3 show accelerated wound healing and an impaired local inflammatory response. Nat Cell Biol 1999; 1:260-266. (Pubitemid 129495775)
32. Ge X, McFarlane C, Vajjala A, et al. Smad3 signaling is required for satellite cell function and myogenic differentiation of myoblasts. Cell Res 2011; 21:1591-1604.
33. Zhang K, Kaufman RJ. From endoplasmic-reticulum stress to the inflammatory response. Nature 2008; 454:455-462.
34. Sriburi R, Bommiasamy H, Buldak GL, et al. Coordinate regulation of phospholipid biosynthesis and secretory pathway gene expression in XBP-1(S)-induced endoplasmic reticulum biogenesis. J Biol Chem 2007; 282:7024-7034. (Pubitemid 47093662)
35. Breslow DK, Collins SR, Bodenmiller B, et al. Orm family proteins mediate sphingolipid homeostasis. Nature 2010; 463:1048-1053.
36. Uhlig S, Gulbins E. Sphingolipids in the lungs. Am J Respir Crit Care Med 2008; 178:1100-1114.
37. Ammit AJ, Hastie AT, Edsall LC, et al. Sphingosine 1-phosphate modulates human airway smooth muscle cell functions that promote inflammation and airway remodeling in asthma. FASEB J 2001; 15:1212-1214.
38. Cantero-Recasens G, Fandos C, Rubio-Moscardo F, et al. The asthmaassociated ORMDL3 gene product regulates endoplasmic reticulummediated calcium signaling and cellular stress. Hum Mol Genet 2010; 19:111-121.
39. Lluis A, Schedel M, Liu J, et al. Asthma-associated polymorphisms in 17q21 influence cord blood ORMDL3 and GSDMA gene expression and IL-17 secretion. J Allergy Clin Immunol 2010; 127:1587e6-1594e6.
40. Saeki N, Kuwahara Y, Sasaki H, et al. Gasdermin (Gsdm) localizing to mouse Chromosome 11 is predominantly expressed in upper gastrointestinal tract but significantly suppressed in human gastric cancer cells. Mamm Genome 2000; 11:718-724.
41. Tamura M, Tanaka S, Fujii T, et al. Members of a novel gene family, Gsdm, are expressed exclusively in the epithelium of the skin and gastrointestinal tract in a highly tissue-specific manner. Genomics 2007; 89:618-629. (Pubitemid 46604751)
42. Saeki N, Usui T, Aoyagi K, et al. Distinctive expression and function of four GSDM family genes (GSDMA-D) in normal and malignant upper gastrointestinal epithelium. Genes Chromosomes Cancer 2009; 48:261-271.
43. Letourneau S, Krieg C, Pantaleo G, Boyman O. IL-2-and CD25-dependent immunoregulatory mechanisms in the homeostasis of T-cell subsets. J Allergy Clin Immunol 2009; 123:758-762.
44. Gaffen SL. Signaling domains of the interleukin 2 receptor. Cytokine 2001; 14:63-77. (Pubitemid 32579259)
45. Montes de Oca P, Malarde V, Proust R, et al. Ectodomain shedding of interleukin-2 receptor beta and generation of an intracellular functional fragment. J Biol Chem 2010; 285:22050-22058.
46. Doganci A, Karwot R, Maxeiner JH, et al. IL-2 receptor beta-chain signaling controls immunosuppressive CD4\+ T cells in the draining lymph nodes and lung during allergic airway inflammation in vivo. J Immunol 2008; 181:1917-1926.
47. Marat AL, McPherson PS. The connecdenn family, Rab35 guanine nucleotide exchange factors interfacing with the clathrin machinery. J Biol Chem 2010; 285:10627-10637.
48. Houslay MD, Baillie GS, Maurice DH. cAMP-specific phosphodiesterase-4 enzymes in the cardiovascular system: a molecular toolbox for generating compartmentalized cAMP signaling. Circ Res 2007; 100:950-966. (Pubitemid 46598920)
49. Blackman BE, Horner K, Heidmann J, et al. PDE4D and PDE4B function in distinct subcellular compartments in mouse embryonic fibroblasts. J Biol Chem 2011; 286:12590-12601.
50. Chupp GL, Lee CG, Jarjour N, et al. A chitinase-like protein in the lung and circulation of patients with severe asthma. N Engl J Med 2007; 357:2016-2027. (Pubitemid 350106709)
51. Marsh DG, Meyers DA, Bias WB. The epidemiology and genetics of atopic allergy. N Engl J Med 1981; 305:1551-1559. (Pubitemid 12249150)
52. Cookson WO, Moffatt MF. Genetics of complex airway disease. Proc Am Thorac Soc 2011; 8:149-153.
53. Kraft S, Kinet JP. New developments in FcepsilonRI regulation, function and inhibition. Nat Rev Immunol 2007; 7:365-378. (Pubitemid 46674486)
54. Lee GR, Fields PE, Griffin TJ, Flavell RA. Regulation of the Th2 cytokine locus by a locus control region. Immunity 2003; 19:145-153. (Pubitemid 36859908)
55. Rogers AJ, Raby BA, Lasky-Su JA, et al. Assessing the reproducibility of asthma candidate gene associations, using genome-wide data. Am J Respir Crit Care Med 2009; 179:1084-1090.
56. Van Eerdewegh P, Little RD, Dupuis J, et al. Association of the ADAM33 gene with asthma and bronchial hyperresponsiveness. Nature 2002; 418:426-430. (Pubitemid 34826843)
57. Zhang Y, Leaves NI, Anderson GG, et al. Positional cloning of a quantitative trait locus on chromosome 13q14 that influences immunoglobulin E levels and asthma. Nat Genet 2003; 34:181-186. (Pubitemid 36666929)
58. Adcock IM, Kirkham PA. PHF11 and DPP10: a tale of two genes in asthma. Respiration 2010; 79:14-16.
59. Clarke E, Rahman N, Page N, et al. Functional characterization of the atopyassociated gene PHF11. J Allergy Clin Immunol 2008; 121:1148 e3-1154 e3.
60. Jang N, Stewart G, Jones G. Polymorphisms within the PHF11 gene at chromosome 13q14 are associated with childhood atopic dermatitis. Genes Immun 2005; 6:262-264. (Pubitemid 40645571)
61. Rahman N, Stewart G, Jones G. A role for the atopy-associated gene PHF11 in T-cell activation and viability. Immunol Cell Biol 2010; 88:817-824.
62. Holt RJ, Zhang Y, Binia A, et al. Allele-specific transcription of the asthmaassociated PHD finger protein 11 gene (PHF11) modulated by octamerbinding transcription factor 1 (Oct-1). J Allergy Clin Immunol 2011; 127:1054 e2-1062 e2.
63. Allen M, Heinzmann A, Noguchi E, et al. Positional cloning of a novel gene influencing asthma from chromosome 2q14. Nat Genet 2003; 35:258-263. (Pubitemid 37363180)
64. Schade J, Stephan M, Schmiedl A, et al. Regulation of expression and function of dipeptidyl peptidase 4 (DP4), DP8/9, and DP10 in allergic responses of the lung in rats. J Histochem Cytochem 2008; 56:147-155. (Pubitemid 351170967)
65. Maffie J, Rudy B. Weighing the evidence for a ternary protein complex mediating A-type K\+ currents in neurons. J Physiol 2008; 586 (Pt 23): 5609-5623.
66. Laitinen T, Polvi A, Rydman P, et al. Characterization of a common susceptibility locus for asthma-related traits. Science 2004; 304:300-304. (Pubitemid 38452184)
67. Vergara C, Jimenez S, Acevedo N, et al. Association of G-protein-coupled receptor 154 with asthma and total IgE in a population of the Caribbean coast of Colombia. Clin Exp Allergy 2009; 39:1558-1568.
68. Allen IC, Pace AJ, Jania LA, et al. Expression and function of NPSR1/GPRA in the lung before and after induction of asthma-like disease. Am J Physiol Lung Cell Mol Physiol 2006; 291:L1005-L1017. (Pubitemid 44772063)
69. Barnes KC. Genomewide association studies in allergy and the influence of ethnicity. Curr Opin Allergy Clin Immunol 2010; 10:427-433.
70. Akhabir L, Sandford AJ. Genome-wide association studies for discovery of genes involved in asthma. Respirology 2011; 16:396-406.
71. Franke A, McGovern DP, Barrett JC, et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat Genet 2010; 42:1118-1125.
72. McGovern DP, Gardet A, Torkvist L, et al. Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat Genet 2010; 42:332-337.
73. Eckhardt F, Lewin J, Cortese R, et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 2006; 38:1378-1385. (Pubitemid 44837559)
74. Boks MP, Derks EM, Weisenberger DJ, et al. The relationship of DNA methylation with age, gender and genotype in twins and healthy controls. PLoS One 2009; 4:e6767.
75. Hilty M, Burke C, Pedro H, et al. Disordered microbial communities in asthmatic airways. PLoS One 2010; 5:e8578.
76. Yates L, McMurray F, Zhang Y, et al. ENU mutagenesis as a tool for understanding lung development and disease. Biochem Soc Trans 2009; 37 (Pt 4): 838-842.
77. Finotto S, Neurath MF, Glickman JN, et al. Development of spontaneous airway changes consistent with human asthma in mice lacking T-bet. Science 2002; 295:336-338. (Pubitemid 34074365)
78. Pai SY, Truitt ML, Ho IC. GATA-3 deficiency abrogates the development and maintenance of T helper type 2 cells. Proc Natl Acad Sci USA 2004; 101:1993-1998. (Pubitemid 38229003)
79. Liu P, Jenkins NA, Copeland NG. A highly efficient recombineering-based method for generating conditional knockout mutations. Genome Res 2003; 13:476-484. (Pubitemid 36395405)