Identification of ATPAF1 as a novel candidate gene for asthma in children

Journal of Allergy and Clinical Immunology

Volumn 128, Issue 4, 2011, Pages

  Schauberger, Eric M ^a   Ewart, Susan L ^a   Arshad, Syed H ^b,c   Huebner, Marianne ^a   Karmaus, Wilfried ^d   Holloway, John W ^c   Friderici, Karen H ^a   Ziegler, Julie T ^e   Zhang, Hongmei ^d   Rose Zerilli, Matthew J ^c   Barton, Sheila J ^c   Holgate, Stephen T ^c   Kilpatrick, Jeffrey R ^f   Harley, John B ^f,g   Lajoie Kadoch, Stephane ^h   Harley, Isaac T W ^h   Hamid, Qutayba ⁱ   Kurukulaaratchy, Ramesh J ^b,c   Seibold, Max A ^j   Avila, Pedro C ^k   Rodriguez Cintrón, William ^l   Rodriguez Santana, Jose R ^m   Hu, Donglei ⁿ   Gignoux, Christopher ⁿ   Romieu, Isabelle ^o   London, Stephanie J ^p   Burchard, Esteban G ⁿ   Langefeld, Carl D ^e   Wills Karp, Marsha ^h   more..

^a MICHIGAN STATE UNIVERSITY   (United States)

^b David Hide Asthma and Allergy Research Centre   (United Kingdom)

^c UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^d UNIVERSITY OF SOUTH CAROLINA   (United States)

^e WAKE FOREST SCHOOL OF MEDICINE   (United States)

^f JKA Genomics   (United States)

^g OKLAHOMA MEDICAL RESEARCH FOUNDATION   (United States)

^h Program on Child Abuse Forensic and Treatment Training   (United States)

ⁱ MCGILL UNIVERSITY   (Canada)

^j DEPARTMENT OF MEDICINE   (United States)

^k NORTHWESTERN UNIVERSITY   (United States)

^l VA MEDICAL CENTER   (Puerto Rico)

^m Centro de Neumologia Pediatrica   (Puerto Rico)

ⁿ UNIVERSITY OF CALIFORNIA   (United States)

^o INSTITUTO NACIONAL DE SALUD PÚBLICA   (Mexico)

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

more..

Author keywords

Asthma; ATPAF1; children; gene; genetic; genome wide association; purinergic; respiratory; single nucleotide polymorphism; SNP

Indexed keywords

ATPAF1 PROTEIN; DNA; PEPTIDES AND PROTEINS; UNCLASSIFIED DRUG;

AFRICAN AMERICAN; ARTICLE; ASTHMA; BRONCHUS BIOPSY; CAUCASIAN; CHILD; CONTROLLED STUDY; DISEASE ASSOCIATION; DISEASE SEVERITY; ETHNICITY; FEMALE; GENE EXPRESSION; GENETIC ASSOCIATION; GENOTYPE; HAPLOTYPE; HISPANIC; HUMAN; MAJOR CLINICAL STUDY; MALE; PRIORITY JOURNAL; PROTEIN ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 80053560647     PISSN: 00916749     EISSN: 10976825     Source Type: Journal    
DOI: 10.1016/j.jaci.2011.04.058     Document Type: Article

References (82)

1. W. Eder, M.J. Ege, and E. von Mutius The asthma epidemic N Engl J Med 355 2006 2226 2235 (Pubitemid 44791164)
2. N. Pearce, N. Ait-Khaled, R. Beasley, J. Mallol, U. Keil, and E. Mitchell Worldwide trends in the prevalence of asthma symptoms: phase III of the International Study of Asthma and Allergies in Childhood (ISAAC) Thorax 62 2007 757 765 (Pubitemid 47435029)
3. O.D. Carter-Pokras, and P.J. Gergen Reported asthma among Puerto Rican, Mexican-American, and Cuban children, 1982 through 1984 Am J Public Health 83 1993 580 582 (Pubitemid 23109842)
4. D.M. Homa, D.M. Mannino, and M. Lara Asthma mortality in U.S. Hispanics of Mexican, Puerto Rican, and Cuban heritage, 1990-1995 Am J Respir Crit Care Med 161 2000 504 509 (Pubitemid 30129460)
5. M.F. Moffatt, M. Kabesch, L.M. Liang, A.L. Dixon, D. Strachan, and S. Heath Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma Nature 448 2007 470 473 (Pubitemid 47123521)
6. D. Vercelli Discovering susceptibility genes for asthma and allergy Nat Rev Immunol 8 2008 169 182 (Pubitemid 351323288)
7. J.W. Holloway, and G.H. Koppelman Identifying novel genes contributing to asthma pathogenesis Curr Opin Allergy Clin Immunol 7 2007 69 74 (Pubitemid 46095889)
8. R.J. Kurukulaaratchy, M.H. Fenn, L.M. Waterhouse, S.M. Matthews, S.T. Holgate, and S.H. Arshad Characterization of wheezing phenotypes in the first 10 years of life Clin Exp Allergy 33 2003 573 578 (Pubitemid 36629680)
9. Long-term effects of budesonide or nedocromil in children with asthma. The Childhood Asthma Management Program Research Group N Engl J Med 343 2000 1054 1063
10. E.G. Burchard, P.C. Avila, S. Nazario, J. Casal, A. Torres, and J.R. Rodriguez-Santana Lower bronchodilator responsiveness in Puerto Rican than in Mexican subjects with asthma Am J Respir Crit Care Med 169 2004 386 392 (Pubitemid 38134819)
11. G.L. David, I. Romieu, J.J. Sienra-Monge, W.J. Collins, M. Ramirez-Aguilar, and B.E. del Rio-Navarro Nicotinamide adenine dinucleotide (phosphate) reduced:quinone oxidoreductase and glutathione S-transferase M1 polymorphisms and childhood asthma Am J Respir Crit Care Med 168 2003 1199 1204 (Pubitemid 37421836)
12. D.B. Hancock, I. Romieu, M. Shi, J.J. Sienra-Monge, H. Wu, and G.Y. Chiu Genome-wide association study implicates chromosome 9q21.31 as a susceptibility locus for asthma in Mexican children PLoS Genet 5 2009 e1000623
13. B.E. Himes, G.M. Hunninghake, J.W. Baurley, N.M. Rafaels, P. Sleiman, and D.P. Strachan Genome-wide association analysis identifies PDE4D as an asthma-susceptibility gene Am J Hum Genet 84 2009 581 593
14. P. Van Eerdewegh, R.D. Little, J. Dupuis, R.G. Del Mastro, K. Falls, and J. Simon Association of the ADAM33 gene with asthma and bronchial hyperresponsiveness Nature 418 2002 426 430 (Pubitemid 34826843)
15. T.W. Guilbert, W.J. Morgan, M. Krawiec, R.F. Lemanske Jr., C. Sorkness, and S.J. Szefler The Prevention of Early Asthma in Kids study: design, rationale and methods for the Childhood Asthma Research and Education network Control Clin Trials 25 2004 286 310 (Pubitemid 38626165)
16. M.D. Mailman, M. Feolo, Y. Jin, M. Kimura, K. Tryka, and R. Bagoutdinov The NCBI dbGaP database of genotypes and phenotypes Nat Genet 39 2007 1181 1186 (Pubitemid 47482671)
17. Wellcome Trust Case Control Consortium Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls Nature 447 2007 661 678
18. J.B. Harley, M.E. Alarcon-Riquelme, L.A. Criswell, C.O. Jacob, R.P. Kimberly, and K.L. Moser Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci Nat Genet 40 2008 204 210 (Pubitemid 351171405)
19. S.C. Foley, A.K. Mogas, R. Olivenstein, P.O. Fiset, J. Chakir, and J. Bourbeau Increased expression of ADAM33 and ADAM8 with disease progression in asthma J Allergy Clin Immunol 119 2007 863 871 (Pubitemid 46527832)
20. J. Shannon, P. Ernst, Y. Yamauchi, R. Olivenstein, C. Lemiere, and S. Foley Differences in airway cytokine profile in severe asthma compared to moderate asthma Chest 133 2 2008 420 426 (Pubitemid 351272400)
21. The database of genotypes and phenotypes (dbGaP). [Cited 2010.] Available from: http://www.ncbi.nlm.nih.gov/gap. Accessed June 4, 2011.
22. H.C. Yang, C.C. Pan, R.C.Y. Lu, and C.S.J. Fann New adjustment factors and sample size calculation in a DNA-pooling experiment with preferential amplification Genetics 169 2005 399 410 (Pubitemid 40239180)
23. S. Purcell, B. Neale, K. Todd-Brown, L. Thomas, M.A.R. Ferreira, and D. Bender PLINK: a tool set for whole-genome association and population-based linkage analyses Am J Hum Genet 81 2007 559 575 (Pubitemid 47330214)
24. J.R. Gonzalez, L. Armengol, X. Sole, E. Guino, J.M. Mercader, and X. Estivill SNPassoc: an R package to perform whole genome association studies Bioinformatics 23 2007 644 645 (Pubitemid 46522604)
25. Team, R. D. C. (2008). R: A language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing 1, ISBN 3-900051-07-0. Available at: http://www.r-project.org. Accessed June 4, 2011.
26. S.L. Lake, H. Lyon, K. Tantisira, E.K. Silverman, S.T. Weiss, and N.M. Laird Estimation and tests of haplotype-environment interaction when linkage phase is ambiguous Hum Hered 55 2003 56 65 (Pubitemid 36928747)
27. H. Wu, I. Romieu, M. Shi, D.B. Hancock, H.L. Li, and J.J. Sienra-Monge Evaluation of candidate genes in a genome-wide association study of childhood asthma in Mexicans J Allergy Clin Immunol 125 2010 321 327
28. J.C. Barrett, B. Fry, J. Maller, and M.J. Daly Haploview: analysis and visualization of LD and haplotype maps Bioinformatics 21 2005 263 265 (Pubitemid 40202029)
29. W.J. Kent, C.W. Sugnet, T.S. Furey, K.M. Roskin, T.H. Pringle, and A.M. Zahler The human genome browser at UCSC Genome Res 12 2002 996 1006 (Pubitemid 34662293)
30. R.A. Gibbs, J.W. Belmont, P. Hardenbol, T.D. Willis, F.L. Yu, and H.M. Yang The International HapMap Project Nature 426 2003 789 796
31. M.N. Blumenthal, C.D. Langefeld, T.H. Beaty, E.R. Bleecker, C. Ober, and L. Lester A genome-wide search for allergic response (atopy) genes in three ethnic groups: Collaborative Study on the Genetics of Asthma Hum Genet 114 2004 157 164 (Pubitemid 38195342)
32. E. Bouzigon, M.H. Dizier, C. Krahenbuhl, A. Lemainque, I. Annesi-Maesano, and C. Betard Clustering patterns of LOD scores for asthma-related phenotypes revealed by a genome-wide screen in 295 French EGEA families Hum Mol Genet 13 2004 3103 3113 (Pubitemid 40050857)
33. E. Bouzigon, V. Siroux, M.H. Dizier, A. Lemainque, C. Pison, and M. Lathrop Scores of asthma and asthma severity reveal new regions of linkage in EGEA study families Eur Respir J 30 2007 253 259 (Pubitemid 47194178)
34. S. Colilla, D. Nicolae, A. Pluzhnikov, M.N. Blumenthal, T.H. Beaty, and E.R. Bleecker Evidence for gene-environment interactions in a linkage study of asthma and smoking exposure J Allergy Clin Immunol 111 2003 840 846 (Pubitemid 36470258)
35. M.H. Dizier, C. Besse-Schmittler, M. Guilloud-Bataille, I. Annesi-Maesano, M. Boussaha, and J. Bousquet Genome screen for asthma and related phenotypes in the French EGEA study Am J Respir Crit Care Med 162 2000 1812 1818
36. A. Haagerup, T. Bjerke, P.O. Schiotz, H.G. Binderup, R. Dahl, and T.A. Kruse Asthma and atopy - a total genome scan for susceptibility genes Allergy 57 2002 680 686 (Pubitemid 34836834)
37. R.A. Mathias, L.R. Freidhoff, M.N. Blumenthal, D.A. Meyers, L. Lester, and R. King Genome-wide linkage analyses of total serum IgE using variance components analysis in asthmatic families Gen Epidemiol 20 2001 340 355 (Pubitemid 32245113)
38. J.F. Xu, D.A. Meyers, C. Ober, M.N. Blumenthal, B. Mellen, and K.C. Barnes Genomewide screen and identification of gene-gene interactions for asthma-susceptibility loci in three US populations: collaborative study on the genetics of asthma Am J Hum Genet 68 2001 1437 1446 (Pubitemid 32510619)
39. A genome-wide search for asthma susceptibility loci in ethnically diverse populations. The Collaborative Study on the Genetics of Asthma (CSGA) Nat Genet 15 1997 389 392
40. M. Rebhan, V. Chalifa-Caspi, J. Prilusky, and D. Lancet GeneCards: integrating information about genes, proteins and diseases Trends Genet 13 1997 163 (Pubitemid 127739947)
41. M. Idzko, H. Hammad, M. van Nimwegen, M. Kool, M.A.M. Willart, and F. Muskens Extracellular ATP triggers and maintains asthmatic airway inflammation by activating dendritic cells Nat Med 13 2007 913 919 (Pubitemid 47222044)
42. M. Schnurr, F. Then, P. Galambos, C. Scholz, B. Siegmund, and S. Endres Extracellular ATP and TNF-alpha synergize in the activation and maturation of human dendritic cells J Immunol 165 2000 4704 4709
43. C.A. Hudson, G.P. Christophi, R.C. Gruber, J.R. Wilmore, D.A. Lawrence, and P.T. Massa Induction of IL-33 expression and activity in central nervous system glia J Leukoc Biol 84 2008 631 643
44. Z.G. Wang, and S.H. Ackerman The assembly factor Atp11p binds to the beta-subunit of the mitochondrial F-1-ATPase J Biol Chem 275 2000 5767 5772 (Pubitemid 30115220)
45. D. Sheluho, and S.H. Ackerman An accessible hydrophobic surface is a key element of the molecular chaperone action of Atp11p J Biol Chem 276 2001 39945 39949
46. Z.G. Wang, P.S. White, and S.H. Ackerman Atp11p and Atp12p are assembly factors for the F-1-ATPase in human mitochondria J Biol Chem 276 2001 30773 30778 (Pubitemid 37384935)
47. A. Pickova, M. Potocky, and J. Houstek Assembly factors of F1F0-ATP synthase across genomes Proteins 59 2005 393 402 (Pubitemid 40594286)
48. A.I. Su, T. Wiltshire, S. Batalov, H. Lapp, K.A. Ching, and D. Block A gene atlas of the mouse and human protein-encoding transcriptomes Proc Natl Acad Sci U SA 101 2004 6062 6067 (Pubitemid 38520528)
49. D.C. King, J. Taylor, L. Elnitski, F. Chiaromonte, W. Miller, and R.C. Hardison Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences Genome Res 15 2005 1051 1060 (Pubitemid 41126860)
50. R. Chen, A.A. Morgan, J. Dudley, T. Deshpande, L. Li, and K. Kodama FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease Genome Biol 9 2008 R170
51. J.W. Holloway, I.A. Yang, and S.T. Holgate Genetics of allergic disease J Allergy Clin Immunol 125 2010 S81 S94
52. A.J. Rogers, B.A. Raby, J.A. Lasky-Su, A. Murphy, R. Lazarus, and B.J. Klanderman Assessing the reproducibility of asthma candidate gene associations, using genome-wide data Am J Respir Crit Care Med 179 2009 1084 1090
53. R.J. Kurukulaaratchy, M.H. Fenn, L.M. Waterhouse, S.M. Matthews, S.T. Holgate, and S.H. Arshad Characterization of wheezing phenotypes in the first 10 years of life Clin Exp Allergy 33 2003 573 578 (Pubitemid 36629680)
54. The International Study of Asthma and Allergies in Childhood (ISAAC) Steering Committee Worldwide variation in prevalence of symptoms of asthma, allergic rhinoconjunctivitis, and atopic eczema: ISAAC Lancet 351 1998 1225 1232
55. P. Van Eerdewegh, R.D. Little, J. Dupuis, R.G. Del Mastro, K. Falls, and J. Simon Association of the ADAM33 gene with asthma and bronchial hyperresponsiveness Nature 418 2002 426 430 (Pubitemid 34826843)
56. B. Beghe, S. Barton, S. Rorke, Q. Peng, I. Sayers, and T. Gaunt Polymorphisms in the interleukin-4 and interleukin-4 receptor alpha chain genes confer susceptibility to asthma and atopy in a Caucasian population Clin Exper Allergy 33 2003 1111 1117 (Pubitemid 36976238)
57. The database of Genotypes and Phenotypes (dbGaP), National Center for Biotechnology Information, U.S. National Library of Medicine. Available from: http://www.ncbi.nlm.nih.gov/gap.
58. T.W. Guilbert, W.J. Morgan, M. Krawiec, R.F. Lemanske Jr., C. Sorkness, and S.J. Szefler The Prevention of Early Asthma in Kids study: design, rationale and methods for the Childhood Asthma Research and Education network Control Clin Trials 25 2004 286 310 (Pubitemid 38626165)
59. The Childhood Asthma Management Program Research Group Long-term effects of budesonide or nedocromil in children with asthma N Engl J Med 343 2000 1054 1063
60. B.E. Himes, G.M. Hunninghake, J.W. Baurley, N.M. Rafaels, P. Sleiman, and D.P. Strachan Genome-wide association analysis identifies PDE4D as an asthma-susceptibility gene Am J Hum Genet 84 2009 581 593
61. E.G. Burchard, P.C. Avila, S. Nazario, J. Casal, A. Torres, and J.R. Rodriguez-Santana Lower bronchodilator responsiveness in Puerto Rican than in Mexican subjects with asthma Am J Respir Crit Care Med 169 2004 386 392 (Pubitemid 38134819)
62. G.L. David, I. Romieu, J.J. Sienra-Monge, W.J. Collins, M. Ramirez-Aguilar, and B.E. del Rio-Navarro Nicotinamide adenine dinucleotide (phosphate) reduced:quinine oxidoreductoase and glutathione S-transferase M1 polymorphisms and childhood asthma Am J Respir Crit Care Med 168 2003 1199 1204 (Pubitemid 37421836)
63. D.B. Hancock, I. Romieu, M. Shi, J.J. Sienra-Monge, H. Wu, and G.Y. Chiu Genome-wide association study implicates chromosome 9q21.31 as a susceptibility locus for asthma in Mexican children PLoS Genet 5 2009 e1000623
64. H. Wu, I. Romieu, M. Shi, D.B. Hancock, H. Li, and J.J. Sienra-Monge Evaluation of candidate genes in a genome-wide association study of childhood asthma in Mexicans J Allergy Clin Immunol 125 2010 321 327
65. National Heart, Lung, and Blood Institute (NHLBI) Global Initiative for Asthma (GINA) 1998 National Institutes of Health Bethesda
66. The Wellcome Trust Case Control Consortium Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls Nature 447 2007 661 678
67. J.B. Harley, M.E. Alarcon-Riquelme, L.A. Criswell, C.O. Jacob, R.P. Kimberly, and K.L. Moser Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci Nat Genet 40 2008 204 210 (Pubitemid 351171405)
68. S.C. Foley, A.K. Mogas, R. Olivenstein, P.O. Fiset, J. Chakir, and J. Bourbeau Increased expression of ADAM33 and ADAM8 with disease progression in asthma J Allergy Clin Immunol 119 2007 863 871 (Pubitemid 46527832)
69. J. Shannon, P. Ernst, Y. Yamauchi, R. Olivenstein, C. Lemiere, and S. Foley Differences in airway cytokine profile in severe asthma compared to moderate asthma Chest 133 2 2008 420 426 (Pubitemid 351272400)
70. Affymetrix. Genechip® genotyping analysis software (gtype). 2007. Available from: http://www.affymetrix.com/products/software/specific/gtype.affx. Accessed June 4, 2011.
71. R.A. Gibbs, J.W. Belmont, P. Hardenbol, T.D. Willis, F.L. Yu, and H.M. Yang The International HapMap project Nature 426 2003 789 796
72. P.I.W. de Bakker, R. Yelensky, I. Pe'er, S.B. Gabriel, M.J. Daly, and D. Altshuler Efficiency and power in genetic association studies Nature Genet 37 2005 1217 1223 (Pubitemid 41568704)
73. F.M. De La Vega, H.I. Isaac, and C.R. Scafe A tool for selecting SNPs for association studies based on observed linkage disequilibrium patterns Pac Symp Biocomput 2006 487 498
74. J.C. Barrett, B. Fry, J. Maller, and M.J. Daly Haploview: analysis and visualization of LD and haplotype maps Bioinformatics 21 2005 263 265 (Pubitemid 40202029)
75. KBiosciences. December 2008. Available from: http://www.kbioscience.co. uk.
76. Y. Li, C.J. Willer, J. Ding, P. Scheet, and G.R. Abecasis MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes Genet Epidemiol 34 2006 816 834
77. C. Lange, D. DeMeo, E.K. Silverman, S.T. Weiss, and N.M. Laird PBAT: tools for family-based association studies Am J Hum Genet 74 2004 367 369 (Pubitemid 38168624)
78. S. Purcell, B. Neale, K. Todd-Brown, L. Thomas, M.A.R. Ferreira, and D. Bender PLINK: a tool set for whole-genome association and population-based linkage analyses Am J Hum Genet 81 2007 559 575 (Pubitemid 47330214)
79. G. Thomas, K.B. Jacobs, M. Yeager, P. Kraft, S. Wacholder, and N. Orr Multiple loci identified in a genome-wide association study of prostate cancer Nat Genet 40 2008 310 315 (Pubitemid 351311773)
80. H.C. Yang, C.C. Pan, R.C.Y. Lu, and C.S.J. Fann New adjustment factors and sample size calculation in a DNA-pooling experiment with preferential amplification Genetics 169 2005 399 410 (Pubitemid 40239180)
81. S.L. Lake, H. Lyon, K. Tantisira, E.K. Silverman, S.T. Weiss, and N.M. Laird Estimation and tests of haplotype-environment interaction when linkage phase is ambiguous Hum Hered 55 2003 56 65 (Pubitemid 36928747)
82. P. Scheet, and M. Stephens A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase Am J Hum Genet 78 2006 629 644