Douglas F Porter, Robin M Meyers, Weili Miao, David L Reynolds, Audrey W Hong et al.
Identifying noncoding single nucleotide variants (SNVs) in regulatory DNA linked to polygenic disease risk, the transcription factors (TFs) they bind, and the genes they dysregulate is a goal in polygenic disease research. Here, we use massively parallel reporter analysis of 3451 SNVs linked to risk for polygenic skin diseases with disrupted epidermal homeostasis to identify 355 differentially active SNVs (daSNVs). daSNV target gene analysis, combined with daSNV editing, underscored dysregulated epidermal differentiation as a shared pathomechanism. CRISPR knockout screens of 1772 human TFs revealed 123 TFs essential for epidermal homeostasis, highlighting ZNF217 and CXXC1. Population sampling CUT&RUN of 27 homeostatic TFs identified allele-specific DNA binding (ASB) differences at daSNVs enriched near epidermal homeostasis and monogenic skin disease genes, with notable representation of SP/KLF and AP-1/2 TFs. High TF-occupancy promoters were “buffered” against ASB. This resource implicates dysregulated binding of specific homeostatic TF families in risk for diverse polygenic skin diseases.
Douglas F Porter, Robin M Meyers, Weili Miao, David L Reynolds, Audrey W Hong, Xue Yang, Suhas Srinivasan, Smarajit Mondal, Zurab Siprashvili, Tania Fabo, Ronghao Zhou, Tri Nguyen, Luca Ducoli, Jordan M Meyers, Duy T Nguyen, Lisa A Ko, Laura N Kellman, Ibtihal Elfaki, Margaret Guo, Mårten Cg Winge, Leandra V Jackrazi, Vanessa Lopez-Pajares, Betty B Liu, Yuanhao Qu, Imani E Porter, Samuel H Kim, Gyuhyeon Kim, Shiying Tao, Jesse M Engreitz, Paul A Khavari. Disease-linked regulatory DNA variants and homeostatic transcription factors in epidermis. 2025-09-25. https://doi.org/10.1038/s41467-025-63070-5
A follow-up trans-factor perturbation MPRA tested the same disease-linked variant library in primary human neonatal foreskin keratinocytes with CRISPR/Cas9 guides targeting IRF6, NRF1, or SNAI2 and an ST26 safe-target control at D0, D3, and D6. The clean table contains variant-level allelic effects, knockout-guide element effects, and guide-by-allele interactions for 3,450 QC-passing groups.
An integrated lentiviral MPRA tested reference and alternative alleles from the skin-disease regulatory library in primary human neonatal foreskin keratinocytes at D0, D3, and D6. The clean table contains one row per variant group after the reported plasmid-barcode QC, with sequence, regulatory annotation, raw count summaries, and official MPRAnalyze allele-effect statistics.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 10 files (ZIP)41467_2025_63070_MOESM2_ESM.xlsx41467_2025_63070_MOESM3_ESM.xlsxGSE302353_family.soft.gzGSE302353_mpra_count_table.directional.csv.gzGSE302353_skin_disease_barcode_ref.csv.gzGSE302353_skin_disease_variant_ref.csv.gzGSE302354_family.soft.gzGSE302354_mpra_activity_table.directional.csv.gzGSE302354_skin_disease_barcode_ref.csv.gzGSE302354_skin_disease_variant_ref.csv.gz