Filaggrin-stratified transcriptomic analysis of pediatric skin identifies mechanistic pathways in patients with atopic dermatitis

Christian Cole, Karin Kroboth, Nicholas J. Schurch, Aileen Sandilands, Alexander Sherstnev, Grainne M. O'Regan, Rosemarie M. Watson, W. H. Irwin McLean, Geoffrey J. Barton (Lead / Corresponding author), Alan D. Irvine (Lead / Corresponding author), Sara J. Brown (Lead / Corresponding author)

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    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. Conclusion: 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.

    Original languageEnglish
    Pages (from-to)82-91
    Number of pages10
    JournalJournal of Allergy and Clinical Immunology
    Volume134
    Issue number1
    Early online date28 May 2014
    DOIs
    Publication statusPublished - Jul 2014

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    Atopic Dermatitis
    Pediatrics
    Skin
    Genotype
    Extracellular Space
    Lipid Metabolism
    Down-Regulation
    RNA Sequence Analysis
    Haploinsufficiency
    Interferon Type I
    Mutation
    Gene Ontology
    Eczema
    Genetic Association Studies
    Gene Expression Profiling
    Dermatitis
    filaggrin
    Genes
    Genome
    Pathology

    Cite this

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    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. Conclusion: 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.",
    author = "Christian Cole and Karin Kroboth and Schurch, {Nicholas J.} and Aileen Sandilands and Alexander Sherstnev and O'Regan, {Grainne M.} and Watson, {Rosemarie M.} and McLean, {W. H. Irwin} and Barton, {Geoffrey J.} and Irvine, {Alan D.} and Brown, {Sara J.}",
    year = "2014",
    month = "7",
    doi = "10.1016/j.jaci.2014.04.021",
    language = "English",
    volume = "134",
    pages = "82--91",
    journal = "Journal of Allergy and Clinical Immunology",
    issn = "0091-6749",
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    }

    TY - JOUR

    T1 - Filaggrin-stratified transcriptomic analysis of pediatric skin identifies mechanistic pathways in patients with atopic dermatitis

    AU - Cole, Christian

    AU - Kroboth, Karin

    AU - Schurch, Nicholas J.

    AU - Sandilands, Aileen

    AU - Sherstnev, Alexander

    AU - O'Regan, Grainne M.

    AU - Watson, Rosemarie M.

    AU - McLean, W. H. Irwin

    AU - Barton, Geoffrey J.

    AU - Irvine, Alan D.

    AU - Brown, Sara J.

    PY - 2014/7

    Y1 - 2014/7

    N2 - 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. Conclusion: 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.

    AB - 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. Conclusion: 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.

    UR - http://www.scopus.com/inward/record.url?scp=84901112853&partnerID=8YFLogxK

    U2 - 10.1016/j.jaci.2014.04.021

    DO - 10.1016/j.jaci.2014.04.021

    M3 - Article

    VL - 134

    SP - 82

    EP - 91

    JO - Journal of Allergy and Clinical Immunology

    JF - Journal of Allergy and Clinical Immunology

    SN - 0091-6749

    IS - 1

    ER -