Functional genomic assessment of phosgene-induced acute lung injury in mice

George D. Leikauf, Vincent J. Concel, Kiflai Bein, Pengyuan Liu, Annerose Berndt, Timothy M. Martin, Koustav Ganguly, An Soo Jang, Kelly A. Brant, Richard A. Dopico, Swapna Upadhyay, Clinton Cario, Y. P. Peter Di, Louis J. Vuga, Emrah Kostem, Eleazar Eskin, Ming You, Naftali Kaminski, Daniel R. Prows, Daren L. KnoellJames P. Fabisiak

Research output: Contribution to journalArticle

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Abstract

In this study, a genetically diverse panel of 43 mouse strains was exposed to phosgene and genome-wide association mapping performed using a high-density single nucleotide polymorphism (SNP) assembly. Transcriptomic analysis was also used to improve the genetic resolution in the identification of genetic determinants of phosgene-induced acute lung injury (ALI). We prioritized the identified genes based on whether the encoded protein was previously associatedwith lung injury or contained a nonsynonymous SNPwithin a functional domain. Candidates were selected that contained a promoter SNP that could alter a putative transcription factor binding site and had variable expression by transcriptomic analyses. The latter two criteria also required that ≥10% of mice carried the minor allele and that this allele could account for ≥10% of the phenotypic difference noted between the strains at the phenotypic extremes. This integrative, functional approach revealed 14 candidate genes that included Atp1a1, Alox5, Galnt11, Hrh1, Mbd4, Phactr2, Plxnd1, Ptprt, Reln, and Zfand4, which hadsignificant SNPassociations, and Itga9, Man1a2, Mapk14, and Vwf,which had suggestive SNP associations. Of thegeneswith significant SNP associations, Atp1a1, Alox5, Plxnd1, Ptprt, and Zfand4 could be associatedwith ALI in several ways. Using a competitive electrophoretic mobility shift analysis, Atp1a1 promoter (rs215053185) oligonucleotide containing the minor G allele formed a major distinct faster-migrating complex. In addition, a genewith a suggestive SNP association, Itga9, is linked to transforming growth factor β1 signaling, which previously has been associated with the susceptibility to ALI in mice.

Original languageEnglish (US)
Pages (from-to)368-383
Number of pages16
JournalAmerican journal of respiratory cell and molecular biology
Volume49
Issue number3
DOIs
StatePublished - Sep 1 2013

Fingerprint

Phosgene
Acute Lung Injury
Polymorphism
Single Nucleotide Polymorphism
Nucleotides
Genes
Alleles
Association reactions
Electrophoretic mobility
Lung Injury
Transforming Growth Factors
Oligonucleotides
Transcription Factors
Binding Sites
Genome
Proteins

Keywords

  • ARDS
  • Countermeasures
  • Genetics
  • Lipoxygenase
  • Sodium absorption

ASJC Scopus subject areas

  • Molecular Biology
  • Pulmonary and Respiratory Medicine
  • Clinical Biochemistry
  • Cell Biology

Cite this

Leikauf, G. D., Concel, V. J., Bein, K., Liu, P., Berndt, A., Martin, T. M., ... Fabisiak, J. P. (2013). Functional genomic assessment of phosgene-induced acute lung injury in mice. American journal of respiratory cell and molecular biology, 49(3), 368-383. https://doi.org/10.1165/rcmb.2012-0337OC

Functional genomic assessment of phosgene-induced acute lung injury in mice. / Leikauf, George D.; Concel, Vincent J.; Bein, Kiflai; Liu, Pengyuan; Berndt, Annerose; Martin, Timothy M.; Ganguly, Koustav; Jang, An Soo; Brant, Kelly A.; Dopico, Richard A.; Upadhyay, Swapna; Cario, Clinton; Peter Di, Y. P.; Vuga, Louis J.; Kostem, Emrah; Eskin, Eleazar; You, Ming; Kaminski, Naftali; Prows, Daniel R.; Knoell, Daren L.; Fabisiak, James P.

In: American journal of respiratory cell and molecular biology, Vol. 49, No. 3, 01.09.2013, p. 368-383.

Research output: Contribution to journalArticle

Leikauf, GD, Concel, VJ, Bein, K, Liu, P, Berndt, A, Martin, TM, Ganguly, K, Jang, AS, Brant, KA, Dopico, RA, Upadhyay, S, Cario, C, Peter Di, YP, Vuga, LJ, Kostem, E, Eskin, E, You, M, Kaminski, N, Prows, DR, Knoell, DL & Fabisiak, JP 2013, 'Functional genomic assessment of phosgene-induced acute lung injury in mice', American journal of respiratory cell and molecular biology, vol. 49, no. 3, pp. 368-383. https://doi.org/10.1165/rcmb.2012-0337OC
Leikauf, George D. ; Concel, Vincent J. ; Bein, Kiflai ; Liu, Pengyuan ; Berndt, Annerose ; Martin, Timothy M. ; Ganguly, Koustav ; Jang, An Soo ; Brant, Kelly A. ; Dopico, Richard A. ; Upadhyay, Swapna ; Cario, Clinton ; Peter Di, Y. P. ; Vuga, Louis J. ; Kostem, Emrah ; Eskin, Eleazar ; You, Ming ; Kaminski, Naftali ; Prows, Daniel R. ; Knoell, Daren L. ; Fabisiak, James P. / Functional genomic assessment of phosgene-induced acute lung injury in mice. In: American journal of respiratory cell and molecular biology. 2013 ; Vol. 49, No. 3. pp. 368-383.
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