title: Irf6 directly regulates Klf17 in zebrafish periderm and Klf4 in murine oral epithelium, and dominant-negative KLF4 variants are present in patients with cleft lip and palate.
abstract: Non-syndromic (NS) cleft lip with or without cleft palate (CL/P) is a common disorder with a strong genetic underpinning. Genome-wide association studies have detected common variants associated with this disorder, but a large portion of the genetic risk for NSCL/P is conferred by unidentified rare sequence variants. Mutations in IRF6 (Interferon Regulatory Factor 6) and GRHL3 (Grainyhead-like 3) cause Van der Woude syndrome, which includes CL/P. Both genes encode members of a regulatory network governing periderm differentiation in model organisms. Here, we report that Krüppel-like factor 17 (Klf17), like Grhl3, acts downstream of Irf6 in this network in zebrafish periderm. Although Klf17 expression is absent from mammalian oral epithelium, a close homologue, Klf4, is expressed in this tissue and is required for the differentiation of epidermis. Chromosome configuration capture and reporter assays indicated that IRF6 directly regulates an oral-epithelium enhancer of KLF4. To test whether rare missense variants of KLF4 contribute risk for NSCL/P, we sequenced KLF4 in approximately 1000 NSCL/P cases and 300 controls. By one statistical test, missense variants of KLF4 as a group were enriched in cases versus controls. Moreover, two patient-derived KLF4 variants disrupted periderm differentiation upon forced expression in zebrafish embryos, suggesting that they have dominant-negative effect. These results indicate that rare NSCL/P risk variants can be found in members of the gene regulatory network governing periderm differentiation.
authors.affiliation: Department of Anatomy and Cell Biology, College of Medicine, State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan 430079, China.
authors.forename: Huan
authors.initials: H
authors.lastname: Liu
authors.affiliation: Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
authors.forename: Elizabeth J
authors.initials: EJ
authors.lastname: Leslie
authors.affiliation: Department of Pediatrics, College of Medicine and, State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China and.
authors.forename: Zhonglin
authors.initials: Z
authors.lastname: Jia
authors.affiliation: Department of Anatomy and Cell Biology, College of Medicine.
authors.forename: Tiffany
authors.initials: T
authors.lastname: Smith
authors.affiliation: Department of Burns and Plastic Surgery, Addis Ababa University, Addis Ababa, Ethiopia.
authors.forename: Mekonen
authors.initials: M
authors.lastname: Eshete
authors.affiliation: Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, USA.
authors.forename: Azeez
authors.initials: A
authors.lastname: Butali
authors.affiliation: Department of Pediatrics, College of Medicine and.
authors.forename: Martine
authors.initials: M
authors.lastname: Dunnwald
authors.affiliation: Department of Pediatrics, College of Medicine and.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Murray
authors.affiliation: Department of Anatomy and Cell Biology, College of Medicine, robert-cornell@uiowa.edu.
authors.forename: Robert A
authors.initials: RA
authors.lastname: Cornell
mesh_terms: D000818:Animals; D016022:Case-Control Studies; D002971:Cleft Lip / Q000235:genetics* / Q000378:metabolism; D002972:Cleft Palate / Q000235:genetics* / Q000378:metabolism; D005260:Female; D018507:Gene Expression Regulation, Developmental; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D006801:Humans; D050835:Interferon Regulatory Factors / Q000235:genetics / Q000378:metabolism*; D000090062:Kruppel-Like Factor 4; D051741:Kruppel-Like Transcription Factors / Q000235:genetics* / Q000378:metabolism*; D008297:Male; D051379:Mice; D009154:Mutation; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D015027:Zebrafish; D029961:Zebrafish Proteins / Q000235:genetics / Q000378:metabolism*
chemical_list: C504917:IRF6 protein, zebrafish; D050835:Interferon Regulatory Factors; C000715467:KLF4 protein, human; C000715468:Klf4 protein, mouse; D000090062:Kruppel-Like Factor 4; D051741:Kruppel-Like Transcription Factors; D014157:Transcription Factors; D029961:Zebrafish Proteins; C418487:klf4 protein, zebrafish