866 A single nucleotide activity map of skin disease variants and transcription factors that modulate them

Noncoding single nucleotide variants (SNVs) in promoter and enhancer DNA comprise the majority of disease risk loci for polygenic disorders of skin and visceral tissues, but functional disease-linked ncSNVs and their target genes have not been mapped. Interrogation of genetic risk loci for 15 common skin diseases with massively parallel reporter assays across an epidermal differentiation timecourse produced a map of 355 differentially active SNVs (daSNVs). Integrating this with DNA looping, eQTL and epigenomic data nominated 782 pathogenic target eGenes. These eGenes concentrated in specific biological processes dysregulated in skin disease. For example, eGenes controlling epidermal barrier formation and inflammation were prominently enriched in psoriasis and atopic dermatitis, suggesting dysregulation of these processes contributes to lifetime disease risk. Gene editing was performed to validate daSNV targets by, for example, demonstrating that non-coding alleles linked to risk for atopic dermatitis downregulate FLG expression. daSNVs frequently disrupted TF binding motifs. To identify the TFs responsible for daSNV function, all 1,782 human TFs were knocked out in CRISPR-flow screens, with a subset of 502 also assessed by single-cell perturb sequencing. This identified and classified 183 TFs essential for normal epidermal gene expression, from which 6 novel factors were validated in targeted experiments. Knockout-MPRAs and direct binding data of epidermis-essential TFs mapped TF-daSNV relationships, revealing new principles of gene dysregulation in polygenic disease risk. Together, these results support a model in which differentiation eGenes are targets of skin disease dsSNVs and their differential activity is modulated by pro-differentiation TFs, indicating that a dysregulated pro-differentiation network underlies pathogenic risk for diverse human polygenic skin diseases.