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Cited by 94Dermatology and Skin DiseasesContact Dermatitis and AllergiesAsthma and respiratory diseases

Multiple Transcriptome Data Analysis Reveals Biologically Relevant Atopic Dermatitis Signature Genes and Pathways

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Ghosh, Debajyoti, Ding, Lili, Sivaprasad, Umasundari, Geh, Esmond, Biagini Myers, Jocelyn, Bernstein, Jonathan A., Khurana Hershey, Gurjit K, Mersha, Tesfaye B.·2015·PLOS ONE
DOI 10.1371/journal.pone.0144316PMC PMC4696650
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Abstract

Several studies have identified genes that are differentially expressed in atopic dermatitis (AD) compared to normal skin. However, there is also considerable variation in the list of differentially expressed genes (DEGs) reported by different groups and the exact cause of AD is still not fully understood. Using a rank-based approach, we analyzed gene expression data from five different microarray studies, comprising a total of 127 samples and more than 250,000 transcripts. A total of 89 AD gene expression signatures '89ADGES', including FLG gene, were identified to show dysregulation consistently across these studies. Using a Support Vector Machine, we showed that the '89ADGES' discriminates AD from normal skin with 98% predictive accuracy. Functional annotation of these genes implicated their roles in immune responses (e.g., betadefensin, microseminoprotein), keratinocyte differentiation/epidermal development (e.g., FLG, CORIN, AQP, LOR, KRT16), inflammation (e.g., IL37, IL27RA, CCL18) and lipid metabolism (e.g., AKR1B10, FAD7, FAR2). Subsequently, we validated a subset of signature genes using quantitative PCR in a mouse model. Using a bioinformatic approach, we identified keratinocyte pathway over-represented (P = <0.0006) among the 89 signature genes. Keratinocytes are known to play a major role in barrier function due to their location in the epidermis. Our result suggests that besides immune- mediated pathway, skin barrier pathways such as the keratinocyte differentiation pathway play a key role in AD pathogenesis. A better understanding of the role of keratinocytes in AD will be important for developing novel "barrier therapy" for this disease.

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  • AD classification models with microarrays identify genes related to epidermal development, keratinocyte function, immune responses, and pyroptosis.

    “AD classification models with microarrays identify genes related to epidermal development, keratinocyte function, immune responses, and pyroptosis (Ghosh et al, 2015; Wu et al, 2023).”

    From Artificial intelligence–enabled precision medicine for inflammatory skin diseases (2026) · cites this paper as Ghosh et al, 2015

    The Abstract reports a microarray-derived AD gene signature that classified AD versus normal skin and includes genes involved in immune responses and keratinocyte differentiation or epidermal development. The Results section on functional annotation likewise identifies these categories. Our copy does not identify pyroptosis as a function or pathway of the signature genes; a search for pyroptosis found no matching passage. (LLM, conf=0.88)

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References 79 · Cited by 94

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Authors
Ghosh, D., Ding, L., Sivaprasad, U., Geh, E., Biagini Myers, J., Bernstein, J. A., Khurana Hershey, G. K., & Mersha, T. B.
Affiliations
  • University of Cincinnati (US)
  • Cincinnati Children's Hospital Medical Center (US)
ORCID
Venue
PLOS ONE
Publisher
Public Library of Science (PLoS)
Published
2015-12-30
Volume
10
Issue
12
Pages
e0144316
ISSN
1932-6203 (ISSN-L)
DOI
10.1371/journal.pone.0144316
PMC
PMC4696650
OpenAlex
W2206293491
Cited by
94
References
79
Citations by year
2026: 9 · 2025: 7 · 2024: 7 · 2023: 14 · 2022: 11 · 2021: 12 · 2020: 13 · 2019: 6 · 2018: 5 · 2017: 5 · 2016: 5
FWCI
5.60
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Figshare (submittedVersion, cc-by)
Funders
  • Cincinnati Children's Hospital Medical Center
  • National Institutes of Health (UL1TR001425)
  • National Heart, Lung, and Blood Institute (K01HL103165)
  • National Center for Advancing Translational Sciences
  • National Institute on Minority Health and Health Disparities
Topics
  • Health Sciences › Medicine › Dermatology › Dermatology and Skin Diseases
  • Health Sciences › Medicine › Dermatology › Contact Dermatitis and Allergies
  • Health Sciences › Medicine › Physiology › Asthma and respiratory diseases
Keywords
atopic dermatitis, gene expression signatures, signature genes, keratinocyte differentiation, skin barrier function, epidermal development, lipid metabolism, immune response, FLG, disease classification
MeSH terms
Filaggrin Proteins, Animals, Cell Differentiation, Dermatitis, Atopic, Gene Expression Regulation, Humans, Reproducibility of Results, Signal Transduction, Keratinocytes, Cluster Analysis, Discriminant Analysis, Case-Control Studies, Computational Biology, Gene Expression Profiling, Databases, Genetic, Mice, Gene Regulatory Networks, Molecular Sequence Annotation, Transcriptome, Support Vector Machine

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