title: Haplotype association mapping of acute lung injury in mice implicates activin a receptor, type 1.
abstract: BACKGROUND
  Because acute lung injury is a sporadic disease produced by heterogeneous precipitating factors, previous genetic analyses are mainly limited to candidate gene case-control studies.
  
  
  OBJECTIVE
  To develop a genome-wide strategy in which single nucleotide polymorphism associations are assessed for functional consequences to survival during acute lung injury in mice.
  
  
  METHODS
  To identify genes associated with acute lung injury, 40 inbred strains were exposed to acrolein and haplotype association mapping, microarray, and DNA-protein binding were assessed.
  
  
  RESULTS
  The mean survival time varied among mouse strains with polar strains differing approximately 2.5-fold. Associations were identified on chromosomes 1, 2, 4, 11, and 12. Seven genes (Acvr1, Cacnb4, Ccdc148, Galnt13, Rfwd2, Rpap2, and Tgfbr3) had single nucleotide polymorphism (SNP) associations within the gene. Because SNP associations may encompass "blocks" of associated variants, functional assessment was performed in 91 genes within ± 1 Mbp of each SNP association. Using 10% or greater allelic frequency and 10% or greater phenotype explained as threshold criteria, 16 genes were assessed by microarray and reverse real-time polymerase chain reaction. Microarray revealed several enriched pathways including transforming growth factor-β signaling. Transcripts for Acvr1, Arhgap15, Cacybp, Rfwd2, and Tgfbr3 differed between the strains with exposure and contained SNPs that could eliminate putative transcriptional factor recognition sites. Ccdc148, Fancl, and Tnn had sequence differences that could produce an amino acid substitution. Mycn and Mgat4a had a promoter SNP or 3'untranslated region SNPs, respectively. Several genes were related and encoded receptors (ACVR1, TGFBR3), transcription factors (MYCN, possibly CCDC148), and ubiquitin-proteasome (RFWD2, FANCL, CACYBP) proteins that can modulate cell signaling. An Acvr1 SNP eliminated a putative ELK1 binding site and diminished DNA-protein binding.
  
  
  CONCLUSIONS
  Assessment of genetic associations can be strengthened using a genetic/genomic approach. This approach identified several candidate genes, including Acvr1, associated with increased susceptibility to acute lung injury in mice.
authors.affiliation: Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219-3130, USA. gleikauf@pitt.edu
authors.forename: George D
authors.initials: GD
authors.lastname: Leikauf
authors.forename: Vincent J
authors.initials: VJ
authors.lastname: Concel
authors.forename: Pengyuan
authors.initials: P
authors.lastname: Liu
authors.forename: Kiflai
authors.initials: K
authors.lastname: Bein
authors.forename: Annerose
authors.initials: A
authors.lastname: Berndt
authors.forename: Koustav
authors.initials: K
authors.lastname: Ganguly
authors.forename: An Soo
authors.initials: AS
authors.lastname: Jang
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Brant
authors.forename: Maggie
authors.initials: M
authors.lastname: Dietsch
authors.forename: Hannah
authors.initials: H
authors.lastname: Pope-Varsalona
authors.forename: Richard A
authors.initials: RA
authors.lastname: Dopico
authors.forename: Y P Peter
authors.initials: YP
authors.lastname: Di
authors.forename: Qian
authors.initials: Q
authors.lastname: Li
authors.forename: Louis J
authors.initials: LJ
authors.lastname: Vuga
authors.forename: Mario
authors.initials: M
authors.lastname: Medvedovic
authors.forename: Naftali
authors.initials: N
authors.lastname: Kaminski
authors.forename: Ming
authors.initials: M
authors.lastname: You
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Prows
mesh_terms: D000171:Acrolein; D030201:Activin Receptors, Type I / Q000235:genetics*; D055371:Acute Lung Injury / Q000235:genetics*; D000818:Animals; D004195:Disease Models, Animal; D005260:Female; D006239:Haplotypes / Q000235:genetics*; D051379:Mice; D008805:Mice, Inbred A; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040081:Protein Array Analysis
chemical_list: D000171:Acrolein; D030201:Activin Receptors, Type I; C498943:Acvr1 protein, mouse