DNA motifs bind transcription factors (TFs) that control gene expression in normal and diseased skin. AR45192 recently mapped the enhancers and promoters that are sequentially activated during epidermal differentiation, and found them enriched for 15 conserved DNA motif combinations, or DNA motif ?grammars?. This suggested that these grammars, acting through recruitment of motif-binding TFs, may encode the DNA sequence logic that coordinates the temporal and spatial induction of early and late epidermal differentiation genes. AR45192 also found that these grammars were recurrently altered by single nucleotide polymorphisms (eSNPs, for ?expression SNPs?) linked by genome-wide association studies (GWAS) to skin diseases characterized by disrupted epidermal differentiation, including cutaneous squamous cell carcinoma (SCC). This suggests that newly identified DNA motif grammars may control differentiation and that their disruption may contribute to disease pathogenesis.
Aim I will test the hypothesis that specific DNA motif grammars control the physiologic activation of differentiation genes necessary for normal epidermal function. First, it will define the temporal activity of hundreds of examples of each grammar in early and late differentiation within intact epidermis. Second, it will quantitate epidermal differentiation gene expression and barrier function in isogenic epidermal tissues in which a subset of grammars have been altered by gene-editing.
Aim I is designed to characterize the actions of newly identified DNA motif grammars in epidermal differentiation.
Aim II will test the hypothesis that SCC risk eSNPs residing within epidermal differentiation motif grammars alter gene expression in a way that enhances cancer progression. First, it will define SCC eSNP impacts on gene expression in normal epidermis with a goal to understanding the altered target genes, and their biologic functions, that predispose to SCC risk. Second, it will quantitatively assess the impact of these SCC risk eSNPs, singly and in combination, on neoplastic progression of epidermal neoplasia in vivo.
Aim II is designed to define the impact of regulatory DNA variants on epidermal gene expression and disease progression. This AR45192 competing renewal will characterize the role of newly identified regulatory DNA grammars in epidermal homeostasis and neoplastic progression.

Public Health Relevance

Abnormal differentiation is a hallmark of common skin diseases, such as epidermal cancers, psoriasis, atopic dermatitis, and certain ichthyoses. Transcription factors (TFs) bind DNA motifs in enhancers to control differentiation gene expression in skin and other tissues. Characterizing the patterns of normal and disease-linked DNA sequence motifs that control epidermal differentiation may be of broad utility in the future treatment and prevention of skin disorders.

National Institute of Health (NIH)
National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
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Arthritis, Connective Tissue and Skin Study Section (ACTS)
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Tseng, Hung H
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Stanford University
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