Transcription factors (TFs) bind regulatory DNA to control differentiation genes in normal and diseased tissue, including cutaneous epidermis. We mapped regulatory DNA active in human epidermis and found it enriched for single nucleotide polymorphisms (eSNPs, for ?expression SNPs?) linked by genome-wide association studies (GWAS) to inflammatory skin diseases in which altered epidermal differentiation contributes to pathogenesis, including atopic dermatitis (AD) and psoriasis vulgaris (PV). AD and PV-linked eSNPs alter DNA motifs and transcription-directing activity in human keratinocytes, suggesting they serve as binding quantitative trait loci (bQTLs) for TFs whose modified activity at these sites pathogenically dysregulates target genes (eGenes). Such eSNP regulatory variants, the TFs whose binding they alter, and the eGenes whose expression they dysregulate, form a regulatory risk framework for polygenic disease. This proposal will elucidate features of such regulatory risk frameworks in the context of human tissue, using AD and PV as polygenic disease prototypes. First, we will define phenotypic impacts of disease-linked eSNPs in human skin tissue, focusing on the epidermis-intrinsic component of AD and PV. We will assess disease eSNP impacts on the gene expression, architecture and function of intact human epidermal tissue. To do this, we will generate otherwise identical, isogenic human skin xenografts that differ only by the single regulatory DNA nucleotides studied using a hybrid gene editing approach. eSNPs will be studied singly and in combination.
Aim I will define the impacts of AD and PV-linked regulatory variants in human tissue. Second, we will identify the TFs whose DNA binding and function is changed at specific eSNPs to extend understanding of disease-linked regulatory DNA variants to the level of biochemical mechanism. To do this, we will use new proteomic and genetic methods. The first method, DNA Protein Identification Detection (DAPID) uses DNA-tethered proximity proteomics to detect and quantify TF binding to any DNA sequence of interest in living cells. The second, Perturb-MPRA, couples CRISPR screening to the massively parallel reporter assay (MPRA) to identify the TFs essential for the transcriptional activity directed by any DNA sequence.
Aim II will identify the TFs whose DNA binding and activity is affected by disease-linked eSNPs in AD and PV. This project will use new methods and a human tissue context to define the eSNP, TF, and eGene regulatory risk frameworks in common human polygenic skin diseases.
Genetic variants outside protein-coding genes can control the expression of genes important for the development of many human diseases, with specific variants linked to increased risk of specific diseases. This proposal will define the regulatory variants in selected human skin diseases and characterize how they dysregulate gene expression. This effort is designed to help understand the principles whereby inherited variants predispose to disease. 1
