title: Genes associated with polymorphic variants predicting lung function are differentially expressed during human lung development.
abstract: Recent meta-analyses of genome-wide association studies have identified single nucleotide polymorphisms (SNPs) within/near 54 genes associated with lung function measures. Current understanding of the contribution of these genes to human lung development is limited. We set out to further define i) the expression profile of these genes during human lung development using a unique set of resources to examine both mRNA and protein expression and ii) the link between key polymorphisms and genes using expression quantitative trait loci (eQTL) approaches.
  
  
  
  The mRNA expression profile of lung function associated genes across pseudoglandular and canalicular stages of lung development were determined using expression array data of 38 human fetal lungs. eQTLs were investigated for selected genes using blood cell and lung tissue data. Immunohistochemistry of the top 5 candidates was performed in a panel of 24 fetal lung samples.
  
  
  
  Twenty-nine lung function associated genes were differentially expressed during lung development at the mRNA level. The greatest magnitude of effect was observed for 5 genes; TMEM163, FAM13A and HHIP which had increasing expression and CDC123 and PTCH1 with decreased expression across developmental stages. Focussed eQTL analyses investigating SNPs in these five loci identified several cis-eQTL's. Protein expression of TMEM163 increased and CDC123 decreased with fetal lung age in agreement with mRNA data. Protein expression in FAM13A, HHIP and PTCH1 remained relatively constant throughout lung development.
  
  
  
  We have identified that > 50 % of lung function associated genes show evidence of differential expression during lung development and we show that in particular TMEM163 and CDC123 are differentially expressed at both the mRNA and protein levels. Our data provides a systematic evaluation of lung function associated genes in this context and offers some insight into the potential role of several of these genes in contributing to human lung development.
authors.affiliation: Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK. suzanne.miller@nottingham.ac.uk.
authors.forename: S
authors.identifier: 0000-0001-8508-1871
authors.initials: S
authors.lastname: Miller
authors.affiliation: Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.|Sachs' Children's Hospital, Stockholm, Sweden.
authors.forename: E
authors.initials: E
authors.lastname: Melén
authors.affiliation: Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
authors.forename: S K
authors.initials: SK
authors.lastname: Merid
authors.affiliation: Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK.
authors.forename: I P
authors.initials: IP
authors.lastname: Hall
authors.affiliation: Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK.
authors.forename: I
authors.initials: I
authors.lastname: Sayers
mesh_terms: D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism; D016208:Databases, Factual; D020690:GTPase-Activating Proteins / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods; D018507:Gene Expression Regulation, Developmental; D005838:Genotype; D005865:Gestational Age; D006801:Humans; D007150:Immunohistochemistry; D008168:Lung / Q000196:embryology / Q000378:metabolism / Q000502:physiology*; D008562:Membrane Glycoproteins / Q000235:genetics / Q000378:metabolism; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D000072081:Patched-1 Receptor / Q000235:genetics / Q000378:metabolism; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D002352:Carrier Proteins; D018797:Cell Cycle Proteins; C570078:FAM13A protein, human; D020690:GTPase-Activating Proteins; C117596:HHIP protein, human; D008562:Membrane Glycoproteins; D008565:Membrane Proteins; C000606236:PTCH1 protein, human; D000072081:Patched-1 Receptor; D012333:RNA, Messenger; C579751:TMEM163 protein, human; C098828:CDC123 protein, human
keywords: CDC123; Development; Expression; Genetics; Lung function; TMEM163