Identification of functional non-coding variants associated with orofacial cleft
Oral facial cleft (OFC) comprises cleft lip with or without cleft palate (CL/P) or cleft palate only. Genome wide association studies (GWAS) of isolated OFC have identified common single nucleotide polymorphisms (SNPs) in many genomic loci where the presumed effector gene (for example, IRF6 in the 1q32 locus) is expressed in embryonic oral epithelium. To identify candidates for functional SNPs at eight such loci we conduct a massively parallel reporter assay in a fetal oral epithelial cell line, revealing SNPs with allele-specific effects on enhancer activity. We filter these SNPs against chromatin-mark evidence of enhancers and test a subset in traditional reporter assays, which support the candidacy of SNPs at loci containing FOXE1, IRF6, MAFB, TFAP2A, and TP63. For two SNPs near IRF6 and one near FOXE1, we engineer the genome of induced pluripotent stem cells, differentiate the cells into embryonic oral epithelium, and discover allele-specific effects on the levels of effector gene expression, and, in two cases, the binding affinity of transcription factors FOXE1 or ETS2. Conditional analyses of GWAS data suggest the two functional SNPs near IRF6 account for the majority of risk for CL/P at this locus. This study connects genetic variation associated with OFC to mechanisms of pathogenesis.
Authors
- Axel Visel (ORCID: https://orcid.org/0000-0002-4130-7784)
- Martine Dunnwald (ORCID: https://orcid.org/0000-0002-5182-8874)
- Julie Mathieu (ORCID: https://orcid.org/0000-0002-3826-3549)
- Hannele Ruohola‐Baker (ORCID: https://orcid.org/0000-0002-5588-4531)
- Robert A. Cornell (ORCID: https://orcid.org/0000-0003-4207-9100)
- Kitt Paraiso (ORCID: https://orcid.org/0000-0002-6489-810X)
- Anjali P. Patni (ORCID: https://orcid.org/0000-0002-1745-6552)
- Ryan Z. Friedman (ORCID: https://orcid.org/0000-0001-9013-8676)
- Barak A. Cohen (ORCID: https://orcid.org/0000-0002-3350-2715)
- Karol Bomsztyk (ORCID: https://orcid.org/0000-0002-9169-7573)
- Sarah W. Curtis (ORCID: https://orcid.org/0000-0002-9131-9601)
- Daniel Mar
- Priyanka Kumari (ORCID: https://orcid.org/0000-0002-7210-172X)
- Michael A. White (ORCID: https://orcid.org/0000-0001-8511-6026)
- Lindsey Rhea
- Elizabeth J. Leslie (ORCID: https://orcid.org/0000-0002-5735-1712)
- Lira Pi
Institutions
- University of Iowa (US)
- Lawrence Berkeley National Laboratory (US)
- Emory University (US)
- University of California, Merced (US)
- California Institute for Regenerative Medicine (US)
- Joint Genome Institute (US)
- University of Washington (US)
- Washington University in St. Louis (US)
- Cornell University (US)
- World Institute on Disability (US)
- Macula Vision Research Foundation (US)
- Brotman Baty Institute (US)
- Systima Technologies (United States) (US)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-07-16
- DOI
- https://doi.org/10.1038/s41467-025-61734-w
- Citations
- 3
- Primary Topic
- Cleft Lip and Palate Research
- Type
- article
- Field-Weighted Citation Impact
- 5.45
Funders
- U.S. Department of Energy
- University of Washington
- Universidad Autónoma de Madrid
- National Institutes of Health
- National Human Genome Research Institute
- National Institute of Dental and Craniofacial Research
- Lawrence Berkeley National Laboratory