Genetics of sputum gene expression in chronic obstructive pulmonary disease

PLoS ONE

Volumn 6, Issue 9, 2011, Pages

  Qiu, Weiliang ^a   Cho, Michael H ^a   Riley, John H ^b   Anderson, Wayne H ^c   Singh, Dave ^d   Bakke, Per ^e   Gulsvik, Amund ^e   Litonjua, Augusto A ^a   Lomas, David A ^f   Crapo, James D ^g   Beaty, Terri H ^h   Celli, Bartolome R ^a   Rennard, Stephen ⁱ   Tal Singer, Ruth ^c   Fox, Steven M ^b   Silverman, Edwin K ^a   Hersh, Craig P ^a  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

^b GLAXOSMITHKLINE   (United Kingdom)

^c GLAXOSMITHKLINE   (United States)

^d UNIVERSITY OF MANCHESTER   (United Kingdom)

^e HAUKELAND UNIVERSITY HOSPITAL   (Norway)

^f UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^g DEPARTMENT OF MEDICINE   (United States)

^h JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

ⁱ UNIVERSITY OF NEBRASKA MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHOLINERGIC RECEPTOR; CHOLINERGIC RECEPTOR NICOTINIC ALPHA 5; HLA C ANTIGEN; IRON REGULATORY FACTOR; IRON RESPONSIVE ELEMENT BINDING PROTEIN 2; UNCLASSIFIED DRUG; TRANSCRIPTOME;

ADULT; AGED; AMDHD1 GENE; ARTICLE; CEACAM21 GENE; CHRNA5 GENE; CHROMOSOME 15Q; CHROMOSOME 6; CHRONIC OBSTRUCTIVE LUNG DISEASE; FEMALE; GENE; GENE EXPRESSION PROFILING; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENOTYPE; HUMAN; IREB2 GENE; MAJOR CLINICAL STUDY; MALE; METTL4 GENE; NDC80 GENE; PSORS1C1 GENE; PSORS1C3 GENE; QUANTITATIVE TRAIT LOCUS; QUANTITATIVE TRAIT LOCUS MAPPING; SINGLE NUCLEOTIDE POLYMORPHISM; SPUTUM; GENETIC PREDISPOSITION; GENETICS; GENOMICS; METABOLISM; MIDDLE AGED;

ADULT; AGED; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENOMICS; HUMANS; MALE; MIDDLE AGED; POLYMORPHISM, SINGLE NUCLEOTIDE; PULMONARY DISEASE, CHRONIC OBSTRUCTIVE; QUANTITATIVE TRAIT LOCI; SPUTUM; TRANSCRIPTOME;

EID: 80052832530     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0024395     Document Type: Article

References (61)

1. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, et al. (2003) Genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297-302.
2. Cheung VG, Conlin LK, Weber TM, Arcaro M, Jen KY, et al. (2003) Natural variation in human gene expression assessed in lymphoblastoid cells. Nat Genet 33: 422-425.
3. Cheung VG, Spielman RS, Ewens KG, Weber TM, Morley M, et al. (2005) Mapping determinants of human gene expression by regional and genome-wide association. Nature 437: 1365-1369.
4. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, et al. (2007) Population genomics of human gene expression. Nat Genet 39: 1217-1224.
5. Dixon AL, Liang L, Moffatt MF, Chen W, Heath S, et al. (2007) A genome-wide association study of global gene expression. Nat Genet 39: 1202-1207.
6. Murphy A, Chu JH, Xu M, Carey VJ, Lazarus R, et al. (2010) Mapping of numerous disease-associated expression polymorphisms in primary peripheral blood CD4+ lymphocytes. Hum Mol Genet 19: 4745-4757.
7. Moffatt MF, Kabesch M, Liang L, Dixon AL, Strachan D, et al. (2007) Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature 448: 470-473.
8. Wheeler HE, Metter EJ, Tanaka T, Absher D, Higgins J, et al. (2009) Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging. PLoS Genet 5: e1000685.
9. Hersh CP, DeMeo DL, Silverman EK, (2005) Chronic Obstructive Pulmonary Disease. In: Silverman EK, Shapiro SD, Lomas DA, Weiss ST, editors. Respiratory Genetics New York Hodder Arnold pp. 253-296.
10. Rabe KF, Hurd S, Anzueto A, Barnes PJ, Buist SA, et al. (2007) Global strategy for the diagnosis, management, and prevention of chronic obstructive pulmonary disease: GOLD executive summary. Am J Respir Crit Care Med 176: 532-555.
11. Cho MH, Boutaoui N, Klanderman BJ, Sylvia JS, Ziniti JP, et al. (2010) Variants in FAM13A are associated with chronic obstructive pulmonary disease. Nat Genet 42: 200-202.
12. Pillai SG, Ge D, Zhu G, Kong X, Shianna KV, et al. (2009) A genome-wide association study in chronic obstructive pulmonary disease (COPD): identification of two major susceptibility loci. PLoS Genet 5: e1000421.
13. Wilk JB, Chen TH, Gottlieb DJ, Walter RE, Nagle MW, et al. (2009) A genome-wide association study of pulmonary function measures in the Framingham Heart Study. PLoS Genet 5: e1000429.
14. Vestbo J, Anderson W, Coxson HO, Crim C, Dawber F, et al. (2008) Evaluation of COPD Longitudinally to Identify Predictive Surrogate End-points (ECLIPSE). Eur Respir J 31: 869-873.
15. Lomas DA, Silverman EK, Edwards LD, Miller BE, Coxson HO, et al. (2008) Evaluation of serum CC-16 as a biomarker for COPD in the ECLIPSE cohort. Thorax 63: 1058-1063.
16. Singh D, Edwards L, Tal-Singer R, Rennard S, (2010) Sputum neutrophils as a biomarker in COPD: findings from the ECLIPSE study. Respir Res 11: 77.
17. Singh D, Fox SM, Tal-Singer R, Plumb J, Bates S, et al. (2011) Induced sputum genes associated with spirometric and radiological disease severity in COPD ex-smokers. Thorax 66: 489-495.
18. Zhu G, Warren L, Aponte J, Gulsvik A, Bakke P, et al. (2007) The SERPINE2 gene is associated with chronic obstructive pulmonary disease in two large populations. Am J Respir Crit Care Med 176: 167-173.
19. Brogger J, Steen VM, Eiken HG, Gulsvik A, Bakke P, (2006) Genetic association between COPD and polymorphisms in TNF, ADRB2 and EPHX1. Eur Respir J 27: 682-688.
20. The National Emphysema Treatment Trial Research Group (1999) Rationale and design of The National Emphysema Treatment Trial: a prospective randomized trial of lung volume reduction surgery. Chest 116: 1750-1761.
21. Fishman A, Martinez F, Naunheim K, Piantadosi S, Wise R, et al. (2003) A randomized trial comparing lung-volume-reduction surgery with medical therapy for severe emphysema. N Engl J Med 348: 2059-2073.
22. Bell B, Rose CL, Damon H, (1972) The Normative Aging Study: an interdisciplinary and longitudinal study of health and aging. Aging Hum Dev 3: 5-17.
23. Hersh CP, Pillai SG, Zhu G, Lomas DA, Bakke P, et al. (2010) Multistudy fine mapping of chromosome 2q identifies XRCC5 as a chronic obstructive pulmonary disease susceptibility gene. Am J Respir Crit Care Med 182: 605-613.
24. Patel BD, Coxson HO, Pillai SG, Agusti AG, Calverley PM, et al. (2008) Airway wall thickening and emphysema show independent familial aggregation in chronic obstructive pulmonary disease. Am J Respir Crit Care Med 178: 500-505.
25. Regan EA, Hokanson JE, Murphy JR, Make B, Lynch DA, et al. (2010) Genetic epidemiology of COPD (COPDGene) study design. COPD 7: 32-43.
26. Storm N, Darnhofer-Patel B, van den Boom D, Rodi CP, (2003) MALDI-TOF mass spectrometry-based SNP genotyping. Methods Mol Biol 212: 241-262.
27. Livak KJ, (1999) Allelic discrimination using fluorogenic probes and the 5′ nuclease assay. Genet Anal 14: 143-149.
28. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.
29. Wan ES, Cho MH, Boutaoui N, Klanderman BJ, Sylvia JS, et al. (2010) Genome-Wide Association Analysis of Body Mass in Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol in press.
30. Carey VJ, Davis AR, Lawrence MF, Gentleman R, Raby BA, (2009) Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x. Bioinformatics 25: 1447-1448.
31. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559-575.
32. Lange C, DeMeo D, Silverman EK, Weiss ST, Laird NM, (2004) PBAT: tools for family-based association studies. Am J Hum Genet 74: 367-369.
33. Kwan T, Grundberg E, Koka V, Ge B, Lam KC, et al. (2009) Tissue effect on genetic control of transcript isoform variation. PLoS Genet 5: e1000608.
34. Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, et al. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464: 773-777.
35. Gibbs JR, van der Brug MP, Hernandez DG, Traynor BJ, Nalls MA, et al. (2010) Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet 6: e1000952.
36. DeMeo DL, Mariani T, Bhattacharya S, Srisuma S, Lange C, et al. (2009) Integration of genomic and genetic approaches implicates IREB2 as a COPD susceptibility gene. Am J Hum Genet 85: 493-502.
37. Saccone NL, Culverhouse RC, Schwantes-An TH, Cannon DS, Chen X, et al. (2010) Multiple independent loci at chromosome 15q25.1 affect smoking quantity: a meta-analysis and comparison with lung cancer and COPD. PLoS Genet 6: e1001053.
38. Wang JC, Cruchaga C, Saccone NL, Bertelsen S, Liu P, et al. (2009) Risk for nicotine dependence and lung cancer is conferred by mRNA expression levels and amino acid change in CHRNA5. Hum Mol Genet 18: 3125-3135.
39. Falvella FS, Galvan A, Frullanti E, Spinola M, Calabro E, et al. (2009) Transcription deregulation at the 15q25 locus in association with lung adenocarcinoma risk. Clin Cancer Res 15: 1837-1842.
40. Amos CI, Wu X, Broderick P, Gorlov IP, Gu J, et al. (2008) Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1. Nat Genet 40: 616-622.
41. Hung RJ, McKay JD, Gaborieau V, Boffetta P, Hashibe M, et al. (2008) A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. Nature 452: 633-637.
42. Thorgeirsson TE, Geller F, Sulem P, Rafnar T, Wiste A, et al. (2008) A variant associated with nicotine dependence, lung cancer and peripheral arterial disease. Nature 452: 638-642.
43. Caporaso N, Gu F, Chatterjee N, Sheng-Chih J, Yu K, et al. (2009) Genome-wide and candidate gene association study of cigarette smoking behaviors. PLoS One 4: e4653.
44. Lambrechts D, Buysschaert I, Zanen P, Coolen J, Lays N, et al. (2010) The 15q24/25 susceptibility variant for lung cancer and chronic obstructive pulmonary disease is associated with emphysema. Am J Respir Crit Care Med 181: 486-493.
45. Wang J, Spitz MR, Amos CI, Wilkinson AV, Wu X, et al. (2010) Mediating effects of smoking and chronic obstructive pulmonary disease on the relation between the CHRNA5-A3 genetic locus and lung cancer risk. Cancer 116: 3458-3462.
46. Dubois PC, Trynka G, Franke L, Hunt KA, Romanos J, et al. (2010) Multiple common variants for celiac disease influencing immune gene expression. Nat Genet 42: 295-302.
47. Fransen K, Visschedijk MC, van Sommeren S, Fu JY, Franke L, et al. (2010) Analysis of SNPs with an effect on gene expression identifies UBE2L3 and BCL3 as potential new risk genes for Crohn's disease. Hum Mol Genet 19: 3482-3488.
48. Chang YT, Chou CT, Shiao YM, Lin MW, Yu CW, et al. (2006) Psoriasis vulgaris in Chinese individuals is associated with PSORS1C3 and CDSN genes. Br J Dermatol 155: 663-669.
49. Holm SJ, Sanchez F, Carlen LM, Mallbris L, Stahle M, et al. (2005) HLA-Cw*0602 associates more strongly to psoriasis in the Swedish population than variants of the novel 6p21.3 gene PSORS1C3. Acta Derm Venereol 85: 2-8.
50. Nair RP, Stuart PE, Nistor I, Hiremagalore R, Chia NV, et al. (2006) Sequence and haplotype analysis supports HLA-C as the psoriasis susceptibility 1 gene. Am J Hum Genet 78: 827-851.
51. Dreiher J, Weitzman D, Shapiro J, Davidovici B, Cohen AD, (2008) Psoriasis and chronic obstructive pulmonary disease: a case-control study. Br J Dermatol 159: 956-960.
52. Setty AR, Curhan G, Choi HK, (2007) Smoking and the risk of psoriasis in women: Nurses' Health Study II. Am J Med 120: 953-959.
53. Kauffmann F, Kleisbauer JP, Cambon-De-Mouzon A, Mercier P, Constans J, et al. (1983) Genetic markers in chronic air-flow limitation. A genetic epidemiologic study. Am Rev Respir Dis 127: 263-269.
54. Anagnostopoulou U, Toumbis M, Konstantopoulos K, Kotsovoulou-Fouskaki V, Zervas J, (1993) HLA-A and-B antigens in chronic bronchitis. J Clin Epidemiol 46: 1413-1416.
55. Naukkarinen J, Surakka I, Pietilainen KH, Rissanen A, Salomaa V, et al. (2010) Use of genome-wide expression data to mine the "Gray Zone" of GWA studies leads to novel candidate obesity genes. PLoS Genet 6: e1000976.
56. Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, et al. (2010) Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet 6: e1000888.
57. Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, et al. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464: 768-772.
58. Franke L, Jansen RC, (2009) eQTL analysis in humans. Methods Mol Biol 573: 311-328.
59. Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, et al. (2008) Genetics of gene expression and its effect on disease. Nature 452: 423-428.
60. Heinzen EL, Ge D, Cronin KD, Maia JM, Shianna KV, et al. (2008) Tissue-Specific Genetic Control of Splicing: Implications for the Study of Complex Traits. PLoS Biology 6: e1.
61. Dimas AS, Deutsch S, Stranger BE, Montgomery SB, Borel C, et al. (2009) Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 325: 1246-1250.