title: Filaggrin-stratified transcriptomic analysis of pediatric skin identifies mechanistic pathways in patients with atopic dermatitis.
abstract: BACKGROUND
  Atopic dermatitis (AD; eczema) is characterized by a widespread abnormality in cutaneous barrier function and propensity to inflammation. Filaggrin is a multifunctional protein and plays a key role in skin barrier formation. Loss-of-function mutations in the gene encoding filaggrin (FLG) are a highly significant risk factor for atopic disease, but the molecular mechanisms leading to dermatitis remain unclear.
  
  
  OBJECTIVE
  We sought to interrogate tissue-specific variations in the expressed genome in the skin of children with AD and to investigate underlying pathomechanisms in atopic skin.
  
  
  METHODS
  We applied single-molecule direct RNA sequencing to analyze the whole transcriptome using minimal tissue samples. Uninvolved skin biopsy specimens from 26 pediatric patients with AD were compared with site-matched samples from 10 nonatopic teenage control subjects. Cases and control subjects were screened for FLG genotype to stratify the data set.
  
  
  RESULTS
  Two thousand four hundred thirty differentially expressed genes (false discovery rate, P < .05) were identified, of which 211 were significantly upregulated and 490 downregulated by greater than 2-fold. Gene ontology terms for "extracellular space" and "defense response" were enriched, whereas "lipid metabolic processes" were downregulated. The subset of FLG wild-type cases showed dysregulation of genes involved with lipid metabolism, whereas filaggrin haploinsufficiency affected global gene expression and was characterized by a type 1 interferon-mediated stress response.
  
  
  CONCLUSIONS
  These analyses demonstrate the importance of extracellular space and lipid metabolism in atopic skin pathology independent of FLG genotype, whereas an aberrant defense response is seen in subjects with FLG mutations. Genotype stratification of the large data set has facilitated functional interpretation and might guide future therapy development.
authors.affiliation: Division of Computational Biology, College of Life Sciences, University of Dundee, Dundee, United Kingdom.
authors.forename: Christian
authors.initials: C
authors.lastname: Cole
authors.affiliation: Centre for Dermatology and Genetic Medicine, Division of Molecular Medicine, Colleges of Life Sciences and Medicine, Dentistry & Nursing, University of Dundee, Dundee, United Kingdom.
authors.forename: Karin
authors.initials: K
authors.lastname: Kroboth
authors.affiliation: Division of Computational Biology, College of Life Sciences, University of Dundee, Dundee, United Kingdom.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Schurch
authors.affiliation: Centre for Dermatology and Genetic Medicine, Division of Molecular Medicine, Colleges of Life Sciences and Medicine, Dentistry & Nursing, University of Dundee, Dundee, United Kingdom.
authors.forename: Aileen
authors.initials: A
authors.lastname: Sandilands
authors.affiliation: Division of Computational Biology, College of Life Sciences, University of Dundee, Dundee, United Kingdom.
authors.forename: Alexander
authors.initials: A
authors.lastname: Sherstnev
authors.affiliation: Department of Dermatology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland.
authors.forename: Grainne M
authors.initials: GM
authors.lastname: O'Regan
authors.affiliation: Department of Dermatology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland.
authors.forename: Rosemarie M
authors.initials: RM
authors.lastname: Watson
authors.affiliation: Centre for Dermatology and Genetic Medicine, Division of Molecular Medicine, Colleges of Life Sciences and Medicine, Dentistry & Nursing, University of Dundee, Dundee, United Kingdom.
authors.forename: W H Irwin
authors.initials: WH
authors.lastname: McLean
authors.affiliation: Division of Computational Biology, College of Life Sciences, University of Dundee, Dundee, United Kingdom. Electronic address: g.j.barton@dundee.ac.uk.
authors.forename: Geoffrey J
authors.initials: GJ
authors.lastname: Barton
authors.affiliation: Department of Dermatology, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland; National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland; Clinical Medicine, Trinity College Dublin, Dublin, Ireland. Electronic address: irvinea@tcd.ie.
authors.forename: Alan D
authors.initials: AD
authors.lastname: Irvine
authors.affiliation: Centre for Dermatology and Genetic Medicine, Division of Molecular Medicine, Colleges of Life Sciences and Medicine, Dentistry & Nursing, University of Dundee, Dundee, United Kingdom; National Children's Research Centre, Our Lady's Children's Hospital, Crumlin, Dublin, Ireland. Electronic address: s.j.brown@dundee.ac.uk.
authors.forename: Sara J
authors.initials: SJ
authors.lastname: Brown
mesh_terms: D000293:Adolescent; D016022:Case-Control Studies; D002648:Child; D003876:Dermatitis, Atopic / Q000235:genetics* / Q000276:immunology / Q000378:metabolism / Q000473:pathology; D005110:Extracellular Space / Q000276:immunology; D005260:Female; D000091344:Filaggrin Proteins; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007381:Intermediate Filament Proteins / Q000235:genetics* / Q000276:immunology; D050356:Lipid Metabolism / Q000276:immunology; D008297:Male; D012867:Skin / Q000276:immunology / Q000378:metabolism* / Q000473:pathology; D014158:Transcription, Genetic / Q000276:immunology*; D055815:Young Adult
chemical_list: C000717249:FLG protein, human; D000091344:Filaggrin Proteins; D007381:Intermediate Filament Proteins
keywords: Atopic dermatitis; direct RNA sequencing; eczema; filaggrin; gene expression; single molecule; skin; tissue; transcriptome