Abstract In Finland the frequency of isolated cleft palate (CP) is higher than that of isolated cleft lip (CL) or cleft lip with cleft palate (CLP). This trend contrasts to that in other countries but its genetic underpinnings are unknown. We performed a genome-wide association study for orofacial cleft, which includes CL, CLP, and CP in the Finnish population. We identified rs570516915, a single nucleotide polymorphism that is virtually specific to Finns and Estonians, as being strongly associated with orofacial cleft, and predominantly with CP (p = 5.25 x 10 -34 , OR = 8.65, 95% CI 6.11-12.25). The risk allele frequency for rs570516915 parallels the regional variation of CP prevalence in Finland, and the association was replicated in an independent sample of CP cases from Estonia (p < 1.3 x 10 -11 ). The rs570516915 variant lies in an IRF6 (Interferon Regulatory Factor 6) enhancer active in ectodermal and oral epithelial cells. Other variants in the IRF6 locus, including those in the same enhancer, are associated with orofacial cleft, but predominantly with CL or CLP, suggesting shared mechanisms in the distinct processes of lip and palate development. By luciferase and transgenic mouse reporter assays we found that the risk allele of rs570516915 diminishes the activity of the enhancer. CRISPR-Cas9 edited oral epithelial cells demonstrate that rs570516915 disrupts an IRF6 binding site and decreases the expression of IRF6 , suggesting impaired IRF6 autoregulation as the molecular mechanism underlying risk for CP.
Abstract In Finland the frequency of isolated cleft palate (CP) is higher than that of isolated cleft lip with or without cleft palate (CL/P). This trend contrasts to that in other European countries but its genetic underpinnings are unknown. We performed a genome-wide association study for orofacial clefts, which include CL/P and CP, in the Finnish population. We identified rs570516915, a single nucleotide polymorphism that is highly enriched in Finns and Estonians, as being strongly associated with CP ( P = 5.25 × 10 −34 , OR = 8.65, 95% CI 6.11–12.25), but not with CL/P ( P = 7.2 × 10 −5 ), with genome-wide significance. The risk allele frequency of rs570516915 parallels the regional variation of CP prevalence in Finland, and the association was replicated in independent cohorts of CP cases from Finland ( P = 8.82 × 10 −28 ) and Estonia ( P = 1.25 × 10 −5 ). The risk allele of rs570516915 disrupts a conserved binding site for the transcription factor IRF6 within a previously characterized enhancer upstream of the IRF6 gene. Through reporter assay experiments we found that the risk allele of rs570516915 diminishes the enhancer activity. Oral epithelial cells derived from CRISPR-Cas9 edited induced pluripotent stem cells demonstrate that the CP-associated allele of rs570516915 concomitantly decreases the binding of IRF6 and the expression level of IRF6 , suggesting impaired IRF6 autoregulation as a molecular mechanism underlying the risk for CP.
This chapter describes the developmental anatomy and molecular regulation of tooth initiation, morphogenesis, and cell differentiation, as well as of tooth renewal and replacement. Tooth morphogenesis is guided by interactions between epithelial and mesenchymal tissues and progresses through distinct stages defined by morphological features of the dental epithelium. Tooth morphogenesis is regulated by interactions between cells, in particular reciprocal and sequential interactions between the mesenchyme and epithelium. Tooth renewal and replacement require the action of stem cells that are capable of self-renewal and production of new progeny upon inductive signals. The study of tooth replacement using nonmodel animals for continuous lifelong tooth replacement, and the ferret for mammalian replacement, is generating new information on the mechanisms of successional tooth formation and the characteristics of dental stem and progenitor cells. For successful tooth regeneration, more detailed understanding is required of the gene regulatory networks and cellular mechanisms guiding tooth development.
Organ development, function, and regeneration depend on stem cells, which reside within discrete anatomical spaces called stem cell niches. The continuously growing mouse incisor provides an excellent model to study tissue-specific stem cells. The epithelial tissue-specific stem cells of the incisor are located at the proximal end of the tooth in a niche called the cervical loop. They provide a continuous influx of cells to counterbalance the constant abrasion of the self-sharpening tip of the tooth. Presented here is a detailed protocol for the isolation and culture of the proximal end of the mouse incisor that houses stem cells and their niche. This is a modified Trowell-type organ culture protocol that enables in vitro culture of tissue pieces (explants), as well as the thick tissue slices at the liquid/air interface on a filter supported by a metal grid. The organ culture protocol described here enables tissue manipulations not feasible in vivo, and when combined with the use of a fluorescent reporter(s), it provides a platform for the identification and tracking of discrete cell populations in live tissues over time, including stem cells. Various regulatory molecules and pharmacological compounds can be tested in this system for their effect on stem cells and their niches. This ultimately provides a valuable tool to study stem cell regulation and maintenance.
In Finland, the frequency of isolated cleft palate (CP) is higher than that of isolated cleft lip with or without cleft palate (CL/P). This trend contrasts to that in other European countries but its genetic underpinnings are unknown. We conducted a genome-wide association study in the Finnish population and identified rs570516915, a single nucleotide polymorphism highly enriched in Finns, as strongly associated with CP (P = 5.25 × 10−34, OR = 8.65, 95% CI 6.11–12.25), but not with CL/P (P = 7.2 × 10−5), with genome-wide significance. The risk allele frequency of rs570516915 parallels the regional variation of CP prevalence in Finland, and the association was replicated in independent cohorts of CP cases from Finland (P = 8.82 × 10−28) and Estonia (P = 1.25 × 10−5). The risk allele of rs570516915 alters a conserved binding site for the transcription factor IRF6 within an enhancer (MCS-9.7) upstream of the IRF6 gene and diminishes the enhancer activity. Oral epithelial cells derived from CRISPR-Cas9 edited induced pluripotent stem cells demonstrate that the CP-associated allele of rs570516915 concomitantly decreases the binding of IRF6 and the expression level of IRF6, suggesting impaired IRF6 autoregulation as a molecular mechanism underlying the risk for CP. Here, the authors perform a genome-wide study and identify a genetic variant enriched in the Finnish population that is strongly associated with isolated cleft palate. This finding suggests a genetic basis for the high prevalence of cleft palate in Finland.
