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Molecular mechanisms underlying variations in lung function: a systems genetics analysis

(2015) LANCET RESPIRATORY MEDICINE. 3(10). p.782-795
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Abstract
Background: Lung function measures reflect the physiological state of the lung, and are essential to the diagnosis of chronic obstructive pulmonary disease (COPD). The SpiroMeta-CHARGE consortium undertook the largest genome-wide association study (GWAS) so far (n=48 201) for forced expiratory volume in 1 s (FEV1) and the ratio of FEV1 to forced vital capacity (FEV1/FVC) in the general population. The lung expression quantitative trait loci (eQTLs) study mapped the genetic architecture of gene expression in lung tissue from 1111 individuals. We used a systems genetics approach to identify single nucleotide polymorphisms (SNPs) associated with lung function that act as eQTLs and change the level of expression of their target genes in lung tissue; termed eSNPs. Methods: The SpiroMeta-CHARGE GWAS results were integrated with lung eQTLs to map eSNPs and the genes and pathways underlying the associations in lung tissue. For comparison, a similar analysis was done in peripheral blood. The lung mRNA expression levels of the eSNP-regulated genes were tested for associations with lung function measures in 727 individuals. Additional analyses identified the pleiotropic effects of eSNPs from the published GWAS catalogue, and mapped enrichment in regulatory regions from the ENCODE project. Finally, the Connectivity Map database was used to identify potential therapeutics in silico that could reverse the COPD lung tissue gene signature. Findings: SNPs associated with lung function measures were more likely to be eQTLs and vice versa. The integration mapped the specific genes underlying the GWAS signals in lung tissue. The eSNP-regulated genes were enriched for developmental and inflammatory pathways; by comparison, SNPs associated with lung function that were eQTLs in blood, but not in lung, were only involved in inflammatory pathways. Lung function eSNPs were enriched for regulatory elements and were over-represented among genes showing differential expression during fetal lung development. An mRNA gene expression signature for COPD was identified in lung tissue and compared with the Connectivity Map. This in-silico drug repurposing approach suggested several compounds that reverse the COPD gene expression signature, including a nicotine receptor antagonist. These findings represent novel therapeutic pathways for COPD. Interpretation: The system genetics approach identified lung tissue genes driving the variation in lung function and susceptibility to COPD. The identification of these genes and the pathways in which they are enriched is essential to understand the pathophysiology of airway obstruction and to identify novel therapeutic targets and biomarkers for COPD, including drugs that reverse the COPD gene signature in silico.
Keywords
VITAMIN-A, BRANCHING MORPHOGENESIS, EXPRESSION, COPD, CANCER, GENES, IDENTIFICATION, RECEPTORS, GENOME-WIDE ASSOCIATION, OBSTRUCTIVE PULMONARY-DISEASE

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Chicago
Obeidat, Ma’en, Ke Hao, Yohan Bossé, David C Nickle, Yunlong Nie, Dirkje S Postma, Michel Laviolette, et al. 2015. “Molecular Mechanisms Underlying Variations in Lung Function: a Systems Genetics Analysis.” Lancet Respiratory Medicine 3 (10): 782–795.
APA
Obeidat, M., Hao, K., Bossé, Y., Nickle, D. C., Nie, Y., Postma, D. S., Laviolette, M., et al. (2015). Molecular mechanisms underlying variations in lung function: a systems genetics analysis. LANCET RESPIRATORY MEDICINE, 3(10), 782–795.
Vancouver
1.
Obeidat M, Hao K, Bossé Y, Nickle DC, Nie Y, Postma DS, et al. Molecular mechanisms underlying variations in lung function: a systems genetics analysis. LANCET RESPIRATORY MEDICINE. 2015;3(10):782–95.
MLA
Obeidat, Ma’en, Ke Hao, Yohan Bossé, et al. “Molecular Mechanisms Underlying Variations in Lung Function: a Systems Genetics Analysis.” LANCET RESPIRATORY MEDICINE 3.10 (2015): 782–795. Print.
@article{6978223,
  abstract     = {Background: Lung function measures reflect the physiological state of the lung, and are essential to the diagnosis of chronic obstructive pulmonary disease (COPD). The SpiroMeta-CHARGE consortium undertook the largest genome-wide association study (GWAS) so far (n=48 201) for forced expiratory volume in 1 s (FEV1) and the ratio of FEV1 to forced vital capacity (FEV1/FVC) in the general population. The lung expression quantitative trait loci (eQTLs) study mapped the genetic architecture of gene expression in lung tissue from 1111 individuals. We used a systems genetics approach to identify single nucleotide polymorphisms (SNPs) associated with lung function that act as eQTLs and change the level of expression of their target genes in lung tissue; termed eSNPs. 
Methods: The SpiroMeta-CHARGE GWAS results were integrated with lung eQTLs to map eSNPs and the genes and pathways underlying the associations in lung tissue. For comparison, a similar analysis was done in peripheral blood. The lung mRNA expression levels of the eSNP-regulated genes were tested for associations with lung function measures in 727 individuals. Additional analyses identified the pleiotropic effects of eSNPs from the published GWAS catalogue, and mapped enrichment in regulatory regions from the ENCODE project. Finally, the Connectivity Map database was used to identify potential therapeutics in silico that could reverse the COPD lung tissue gene signature. 
Findings: SNPs associated with lung function measures were more likely to be eQTLs and vice versa. The integration mapped the specific genes underlying the GWAS signals in lung tissue. The eSNP-regulated genes were enriched for developmental and inflammatory pathways; by comparison, SNPs associated with lung function that were eQTLs in blood, but not in lung, were only involved in inflammatory pathways. Lung function eSNPs were enriched for regulatory elements and were over-represented among genes showing differential expression during fetal lung development. An mRNA gene expression signature for COPD was identified in lung tissue and compared with the Connectivity Map. This in-silico drug repurposing approach suggested several compounds that reverse the COPD gene expression signature, including a nicotine receptor antagonist. These findings represent novel therapeutic pathways for COPD. 
Interpretation: The system genetics approach identified lung tissue genes driving the variation in lung function and susceptibility to COPD. The identification of these genes and the pathways in which they are enriched is essential to understand the pathophysiology of airway obstruction and to identify novel therapeutic targets and biomarkers for COPD, including drugs that reverse the COPD gene signature in silico.},
  author       = {Obeidat, Ma'en and Hao, Ke and Boss{\'e}, Yohan and Nickle, David C and Nie, Yunlong and Postma, Dirkje S and Laviolette, Michel and Sandford, Andrew J and Daley, Denise D and Hogg, James C and Elliott, W Mark and Fishbane, Nick and Timens, Wim and Hysi, Pirro G and Kaprio, Jaakko and Wilson, James F and Hui, Jennie and Rawal, Rajesh and Schulz, Holger and Stubbe, Beate and Hayward, Caroline and Polasek, Ozren and J{\"a}rvelin, Marjo-Riitta and Zhao, Jing Hua and Jarvis, Deborah and K{\"a}h{\"o}nen, Mika and Franceschini, Nora and North, Kari E and Loth, Daan W and Brusselle, Guy and Smith, Albert Vernon and Gudnason, Vilmundur and Bartz, Traci M and Wilk, Jemma B and O'Connor, George T and Cassano, Patricia A and Tang, Wenbo and Wain, Louise V and Artigas, Maria Soler and Gharib, Sina A and Strachan, David P and Sin, Don D and Tobin, Martin D and London, Stephanie J and Hall, Ian P and Par{\'e}, Peter D},
  issn         = {2213-2600},
  journal      = {LANCET RESPIRATORY MEDICINE},
  language     = {eng},
  number       = {10},
  pages        = {782--795},
  title        = {Molecular mechanisms underlying variations in lung function: a systems genetics analysis},
  url          = {http://dx.doi.org/10.1016/S2213-2600(15)00380-X},
  volume       = {3},
  year         = {2015},
}

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