title: Identification of microRNAs associated with allergic airway disease using a genetically diverse mouse population.
abstract: BACKGROUND
  Allergic airway diseases (AADs) such as asthma are characterized in part by granulocytic airway inflammation. The gene regulatory networks that govern granulocyte recruitment are poorly understood, but evidence is accruing that microRNAs (miRNAs) play an important role. To identify miRNAs that may underlie AADs, we used two complementary approaches that leveraged the genotypic and phenotypic diversity of the Collaborative Cross (CC) mouse population. In the first approach, we sought to identify miRNA expression quantitative trait loci (eQTL) that overlap QTL for AAD-related phenotypes. Specifically, CC founder strains and incipient lines of the CC were sensitized and challenged with house dust mite allergen followed by measurement of granulocyte recruitment to the lung. Total lung RNA was isolated and miRNA was measured using arrays for CC founders and qRT-PCR for incipient CC lines.
  
  
  RESULTS
  Among CC founders, 92 miRNAs were differentially expressed. We measured the expression of 40 of the most highly expressed of these 92 miRNAs in the incipient lines of the CC and identified 18 eQTL corresponding to 14 different miRNAs. Surprisingly, half of these eQTL were distal to the corresponding miRNAs, and even on different chromosomes. One of the largest-effect local miRNA eQTL was for miR-342-3p, for which we identified putative causal variants by bioinformatic analysis of the effects of single nucleotide polymorphisms on RNA structure. None of the miRNA eQTL co-localized with QTL for eosinophil or neutrophil recruitment. In the second approach, we constructed putative miRNA/mRNA regulatory networks and identified three miRNAs (miR-497, miR-351 and miR-31) as candidate master regulators of genes associated with neutrophil recruitment. Analysis of a dataset from human keratinocytes transfected with a miR-31 inhibitor revealed two target genes in common with miR-31 targets correlated with neutrophils, namely Oxsr1 and Nsf.
  
  
  CONCLUSIONS
  miRNA expression in the allergically inflamed murine lung is regulated by genetic loci that are smaller in effect size compared to mRNA eQTL and often act in trans. Thus our results indicate that the genetic architecture of miRNA expression is different from mRNA expression. We identified three miRNAs, miR-497, miR-351 and miR-31, that are candidate master regulators of genes associated with neutrophil recruitment. Because miR-31 is expressed in airway epithelia and is predicted to target genes with known links to neutrophilic inflammation, we suggest that miR-31 is a potentially novel regulator of airway inflammation.
authors: Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA. hrutledg@email.unc.edu.
authors: Holly
authors: H
authors: Rutledge
authors: Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA. jtbaran@email.unc.edu.|Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA. jtbaran@email.unc.edu.
authors: Jeanette
authors: J
authors: Baran-Gale
authors: Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA. fernando@med.unc.edu.|Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA. fernando@med.unc.edu.|Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA. fernando@med.unc.edu.|Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA. fernando@med.unc.edu.
authors: Fernando Pardo-Manuel
authors: FP
authors: de Villena
authors: The Jackson Laboratory, Bar Harbor, ME, USA. Elissa.Chesler@jax.org.
authors: Elissa J
authors: EJ
authors: Chesler
authors: The Jackson Laboratory, Bar Harbor, ME, USA. Gary.Churchill@jax.org.
authors: Gary A
authors: GA
authors: Churchill
authors: Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA. praveen_sethupathy@med.unc.edu.|Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA. praveen_sethupathy@med.unc.edu.|Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA. praveen_sethupathy@med.unc.edu.|Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA. praveen_sethupathy@med.unc.edu.
authors: Praveen
authors: P
authors: Sethupathy
authors: Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA. samir_kelada@med.unc.edu.|Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, USA. samir_kelada@med.unc.edu.|Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA. samir_kelada@med.unc.edu.|Marsico Lung Institute, University of North Carolina, Chapel Hill, NC, USA. samir_kelada@med.unc.edu.
authors: Samir N P
authors: SN
authors: Kelada
mesh_terms: D000818:Animals; D001249:Asthma / Q000235:genetics / Q000473:pathology / Q000662:veterinary*; D018703:Founder Effect; D005786:Gene Expression Regulation; D006098:Granulocytes / Q000378:metabolism; D008168:Lung / Q000276:immunology / Q000473:pathology; D008297:Male; D051379:Mice; D035683:MicroRNAs / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D039981:Pyroglyphidae / Q000502:physiology; D040641:Quantitative Trait Loci; D012376:Rodent Diseases / Q000235:genetics* / Q000473:pathology
chemical_list: C580764:MIRN351 microRNA, 351; D035683:MicroRNAs; C539917:Mirn31 microRNA, mouse; C550139:mirn497 microRNA, mouse