Genetics and genomics of longitudinal lung function patterns in individuals with asthma

American Journal of Respiratory and Critical Care Medicine

Volumn 194, Issue 12, 2016, Pages 1465-1474

  McGeachie, Michael J ^a,b   Yates, Katherine P ^c   Zhou, Xiaobo ^a,b   Guo, Feng ^a,b   Sternberg, Alice L ^c   Van Natta, Mark L ^c   Wise, Robert A ^d   Szefler, Stanley J ^e,f   Sharma, Sunita ^g   Kho, Alvin T ^a,b,h   Cho, Michael H ^a,b   Croteau Chonka, Damien C ^a,b   Castaldi, Peter J ^a,b   Jain, Gaurav ⁱ   Sanyal, Amartya ^i,j   Zhan, Ye ⁱ   Lajoie, Bryan R ⁱ   Dekker, Job ^k   Stamatoyannopoulos, John ^l   Covar, Ronina A ^e,f,m   Zeiger, Robert S ^n,o   Adkinson, N Franklin ^d   Williams, Paul V ^p   Kelly, H William ^q   Grasemann, Hartmut ^r   Vonk, Judith M ^s   Koppelman, Gerard H ^s   Postma, Dirkje S ^t   Raby, Benjamin A ^a,b   Houston, Isaac ^a,b   Lu, Quan ^u   Fuhlbrigge, Anne L ^a,b,v   Tantisira, Kelan G ^a,b   Silverman, Edwin K ^a,b   Tonascia, James ^c   Strunk, Robert C ^b   Weiss, Scott T ^a,b   more..

^a CHANNING LABORATORY   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

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

^d JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e DEPARTMENT OF MEDICINE   (United States)

^f Children's Hospital Colorado   (United States)

^g UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^h BOSTON CHILDREN S HOSPITAL   (United States)

ⁱ Program in Systems Biology   (United States)

^j NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^k UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^l UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^m UNIVERSITY OF COLORADO   (United States)

ⁿ UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^o KAISER PERMANENTE   (United States)

^p Northwest Asthma & Allergy Center   (United States)

^q UNIVERSITY OF NEW MEXICO HEALTH SCIENCES CENTER   (United States)

^r HOSPITAL FOR SICK CHILDREN   (Canada)

^s UNIVERSITY OF GRONINGEN   (Netherlands)

^t UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

^u HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^v WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

more..

Author keywords

Asthma; Chronic obstructive pulmonary disease; CSMD3; Genome wide association studies; Longitudinal lung function patterns

Indexed keywords

ADULT; ARTICLE; ASTHMA; CAUCASIAN; CHILD; CHROMATIN; CHROMOSOME 8; CHRONIC OBSTRUCTIVE LUNG DISEASE; COHORT ANALYSIS; FEMALE; FORCED EXPIRATORY VOLUME; GENETICS; GENOME-WIDE ASSOCIATION STUDY; HUMAN; LUNG FUNCTION; MAJOR CLINICAL STUDY; MALE; PRIORITY JOURNAL; PROMOTER REGION; SINGLE NUCLEOTIDE POLYMORPHISM; GENETIC PREDISPOSITION; GENOMICS; LONGITUDINAL STUDY; LUNG; NETHERLANDS; PATHOPHYSIOLOGY; PHYSIOLOGY; PRESCHOOL CHILD; PROCEDURES;

ASTHMA; CHILD; CHILD, PRESCHOOL; FEMALE; FORCED EXPIRATORY VOLUME; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HUMANS; LONGITUDINAL STUDIES; LUNG; MALE; NETHERLANDS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 85007418295     PISSN: 1073449X     EISSN: 15354970     Source Type: Journal    
DOI: 10.1164/rccm.201602-0250OC     Document Type: Article

References (55)

1. Speizer FE, Tager IB. Epidemiology of chronic mucus hypersecretion and obstructive airways disease. Epidemiol Rev 1979;1:124-142.
2. McGeachie MJ, Yates KP, Zhou X, Guo F, Sternberg AL, Van Natta ML, Wise RA, Szefler SJ, Sharma S, Kho AT, et al.; CAMP Research Group. Patterns of growth and decline in lung function in persistent childhood asthma. N Engl J Med 2016;374:1842-1852.
3. Tager IB, Segal MR, Speizer FE, Weiss ST. The natural history of forced expiratory volumes. Effect of cigarette smoking and respiratory symptoms. Am Rev Respir Dis 1988;138:837-849.
4. Wang X, Mensinga TT, Schouten JP, Rijcken B, Weiss ST. Determinants of maximally attained level of pulmonary function. Am J Respir Crit Care Med 2004;169:941-949.
5. Lange P, Celli B, Agustí A, Boje Jensen G, Divo M, Faner R, Guerra S, Marott JL, Martinez FD, Martinez-Camblor P, et al. Lung-function trajectories leading to chronic obstructive pulmonary disease. N Engl J Med 2015;373:111-122.
6. Weiss S, Speizer F. Epidemiology and natural history. In: Weiss EB, Stein M, editors. Bronchial asthma mechanisms and therapeutics, 3rd ed. Boston: Little, Brown; 1993. p. 15.
7. Fletcher C. The natural history of chronic bronchitis and emphysema: an eight-year study of early chronic obstructive lung disease in working men in London. New York: Oxford University Press; 1976.
8. Vonk JM, Jongepier H, Panhuysen CI, Schouten JP, Bleecker ER, Postma DS. Risk factors associated with the presence of irreversible airflow limitation and reduced transfer coefficient in patients with asthma after 26 years of follow up. Thorax 2003;58:322-327.
9. Young RP, Hopkins R, Eaton TE. Forced expiratory volume in one second: not just a lung function test but a marker of premature death from all causes. Eur Respir J 2007;30:616-622.
10. Sears MR, Greene JM, Willan AR, Wiecek EM, Taylor DR, Flannery EM, Cowan JO, Herbison GP, Silva PA, Poulton R. A longitudinal, population-based, cohort study of childhood asthma followed to adulthood. N Engl J Med 2003;349:1414-1422.
11. Ulrik CS. Outcome of asthma: longitudinal changes in lung function. Eur Respir J 1999;13:904-918.
12. Jamrozik E, Knuiman MW, James A, Divitini M, Musk AW. Risk factors for adult-onset asthma: a 14-year longitudinal study. Respirology 2009;14:814-821.
13. Svanes C, Sunyer J, Plana E, Dharmage S, Heinrich J, Jarvis D, De Marco R, Norbäck D, Raherison C, Villani S, et al. Early life origins of chronic obstructive pulmonary disease. Thorax 2010;65:14-20.
14. Dijkstra A, Vonk JM, Jongepier H, Koppelman GH, Schouten JP, Ten Hacken NH, Timens W, Postma DS. Lung function decline in asthma: association with inhaled corticosteroids, smoking and sex. Thorax 2006;61:105-110.
15. Grol MH, Gerritsen J, Vonk JM, Schouten JP, Koëter GH, Rijcken B, Postma DS. Risk factors for growth and decline of lung function in asthmatic individuals up to age 42 years. A 30-year follow-up study. Am J Respir Crit Care Med 1999;160:1830-1837.
16. Stern DA, Morgan WJ, Wcenter AL, Guerra S, Martinez FD. Poor airway function in early infancy and lung function by age 22 years: a nonselective longitudinal cohort study. Lancet 2007;370:758-764.
17. Poon AH, Houseman EA, Ryan L, Sparrow D, Vokonas PS, Litonjua AA. Variants of asthma and chronic obstructive pulmonary disease genes and lung function decline in aging. J Gerontol A Biol Sci Med Sci 2014;69:907-913.
18. Imboden M, Bouzigon E, Curjuric I, Ramasamy A, Kumar A, Hancock DB, Wilk JB, Vonk JM, Thun GA, Siroux V, et al. Genome-wide association study of lung function decline in adults with and without asthma. J Allergy Clin Immunol 2012;129:1218-1228.
19. Postma DS, Meyers DA, Jongepier H, Howard TD, Koppelman GH, Bleecker ER. Genomewide screen for pulmonary function in 200 families ascertained for asthma. Am J Respir Crit Care Med 2005;172:446-452.
20. McGeachie MJ, Yates KP, Cho MH, Croteau-Chonka DC, Castaldi PJ, Silverman EK, Zhou X, Wise RA, Tonascia J, Sternberg AL, et al. Phenotypic and genetic risk factors for reduced growth and early decline in FEV1 into early adulthood in childhood asthmatics [abstract]. Am J Respir Crit Care Med 2014;189:A1004.
21. Childhood Asthma Management Program Research Group. The Childhood Asthma Management Program (CAMP): design, rationale, and methods. Control Clin Trials 1999;20:91-120.
22. The Childhood Asthma Management Program Research Group. Long-term effects of budesonide or nedocromil in children with asthma. N Engl J Med 2000;343:1054-1063.
23. Hankinson JL, Odencrantz JR, Fedan KB. Spirometric reference values from a sample of the general U. S. population. Am J Respir Crit Care Med 1999;159:179-187.
24. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 2010;34:816-834.
25. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, De Bakker PI, Daly MJ, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007;81:559-575.
26. Portelli MA, Siedlinski M, Stewart CE, Postma DS, Nieuwenhuis MA, Vonk JM, Nurnberg P, Altmuller J, Moffatt MF, Wardlaw AJ, et al. Genome-wide protein QTL mapping identifies human plasma kallikrein as a post-translational regulator of serum uPAR levels. FASEB J 2014;28:923-934.
27. Cho MH, McDonald ML, Zhou X, Mattheisen M, Castaldi PJ, Hersh CP, Demeo DL, Sylvia JS, Ziniti J, Laird NM, et al.; NETT Genetics, ICGN, ECLIPSE and COPDGene Investigators. Risk loci for chronic obstructive pulmonary disease: a genome-wide association study and meta-analysis. Lancet Respir Med 2014;2:214-225.
28. Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet 2012;44:955-959.
29. Willer CJ, Li Y, Abecasis GR. METAL: fast and efficient meta-analysis of genome-wide association scans. Bioinformatics 2010;26:2190-2191.
30. Sharma S, Tantisira K, Carey V, Murphy AJ, Lasky-Su J, Celedón JC, Lazarus R, Klanderman B, Rogers A, Soto-Quirós M, et al. A role for Wnt signaling genes in the pathogenesis of impaired lung function in asthma. Am J Respir Crit Care Med 2010;181:328-336.
31. Lieberman-Aiden E, Van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009;326:289-293.
32. Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. Hi-C: a comprehensive technique to capture the conformation of genomes. Methods 2012;58:268-276.
33. Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, Dekker J, Mirny LA. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods 2012;9:999-1003.
34. Crane E, Bian Q, McCord RP, Lajoie BR, Wheeler BS, Ralston EJ, Uzawa S, Dekker J, Meyer BJ. Condensin-driven remodelling of X chromosome topology during dosage compensation. Nature 2015;523:240-244.
35. Smith EM, Lajoie BR, Jain G, Dekker J. Invariant TAD boundaries constrain cell-type-specific looping interactions between promoters and distal elements around the CFTR locus. Am J Hum Genet 2016;98:185-201.
36. Van De Werken HJ, Landan G, Holwerda SJ, Hoichman M, Klous P, Chachik R, Splinter E, Valdes-Quezada C, Oz Y, Bouwman BA, et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat Methods 2012;9:969-972.
37. Simonis M, Kooren J, De Laat W. An evaluation of 3C-based methods to capture DNA interactions. Nat Methods 2007;4:895-901.
38. Wellcome Trust Case Control Consortium. Genome-wide association study of 14, 000 cases of seven common diseases and 3, 000 shared controls. Nature 2007;447:661-678.
39. Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 2012;485:376-380.
40. The Genotype-Tissue Expression (GTEx) project. Nat Genet 2013;45:580-585.
41. Croteau-Chonka DC, Qiu W, Martinez FD, Strunk RC, Lemanske RF Jr, Liu AH, Gilliland FD, Millstein J, Gauderman WJ, Ober C, et al.; Asthma BioRepository for Integrative Genomic Exploration (Asthma BRIDGE) Consortium. Gene expression profiling in blood provides reproducible molecular insights into asthma control. Am J Respir Crit Care Med [online ahead of print] 5 Aug. 2016; DOI: 10.1164/rccm.201601-0107OC.
42. Lin PI, Vance JM, Pericak-Vance MA, Martin ER. No gene is an island: the flip-flop phenomenon. Am J Hum Genet 2007;80:531-538.
43. Lee SH, Yang J, Goddard ME, Visscher PM, Wray NR. Estimation of pleiotropy between complex diseases using single-nucleotide polymorphism-derived genomic relationships and restricted maximum likelihood. Bioinformatics 2012;28:2540-2542.
44. Pontius JU, Wagner L, Schuler G. UniGene: a unified view of the transcriptome. The NCBI Handbook. Bethesda, MD: National Center for Biotechnology Information; 2003.
45. Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, et al. Expression Atlas update-a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Nucleic Acids Res 2014;42:D926-D932.
46. Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M, Zwahlen M, Kampf C, Wester K, Hober S, et al. Towards a knowledge-based Human Protein Atlas. Nat Biotechnol 2010;28:1248-1250.
47. Pandey AK, Lu L, Wang X, Homayouni R, Williams RW. Functionally enigmatic genes: a case study of the brain ignorome. PLoS One 2014;9:e88889.
48. Hardin M, Cho M, McDonald ML, Beaty T, Ramsdell J, Bhatt S, Van Beek EJ, Make BJ, Crapo JD, Silverman EK, et al. The clinical and genetic features of COPD-asthma overlap syndrome. Eur Respir J 2014;44:341-350.
49. Liu P, Morrison C, Wang L, Xiong D, Vedell P, Cui P, Hua X, Ding F, Lu Y, James M, et al. Identification of somatic mutations in non-small cell lung carcinomas using whole-exome sequencing. Carcinogenesis 2012;33:1270-1276.
50. Watanabe M, Maemura K, Kanbara K, Tamayama T, Hayasaki H. GABA and GABA receptors in the central nervous system and other organs. Int Rev Cytol 2002;213:1-47.
51. Gallos G, Townsend E, Yim P, Virag L, Zhang Y, Xu D, Bacchetta M, Emala CW. Airway epithelium is a predominant source of endogenous airway GABA and contributes to relaxation of airway smooth muscle tone. Am J Physiol Lung Cell Mol Physiol 2013;304:L191-L197.
52. Mizuta K, Xu D, Pan Y, Comas G, Sonett JR, Zhang Y, Panettieri RA Jr, Yang J, Emala CW Sr. GABAA receptors are expressed and facilitate relaxation in airway smooth muscle. Am J Physiol Lung Cell Mol Physiol 2008;294:L1206-L1216.
53. Price D, Fromer L, Kaplan A, Van Der Molen T, Román-Rodríguez M. Is there a rationale and role for long-acting anticholinergic bronchodilators in asthma? NPJ Prim Care Respir Med 2014;24:14023.
54. Canning BJ, Woo A, Mazzone SB. Neuronal modulation of airway and vascular tone and their influence on nonspecific airways responsiveness in asthma. J Allergy (Cairo) 2012;2012:108149.
55. Kelly VJ, Brown NJ, Sands SA, Borg BM, King GG, Thompson BR. Effect of airway smooth muscle tone on airway distensibility measured by the forced oscillation technique in adults with asthma. J Appl Physiol (1985) 2012;112:1494-1503.