Multigenic etiology of cleft lip and palate
(2012)
Files
Desmyter_thèse.pdf
Closed Access - Adobe PDF
- 5.93 MB
Details
- Authors
- Supervisors
- Vikkula, Miikka
- Abstract
- (en) Orofacial clefts are the most common craniofacial birth defects occurring in 1/700 births. Affected children need caring by a multidisciplinary team from birth until adulthood. Such a team includes many disciplines (nursing, plastic surgery, speech specialist, dentist, ….). Although quality of life can be improved with good care, the disease represents a burden to the patient, the family and society with important financial consequences. Orofacial clefts can be part of a syndrome, but most commonly, they occur as an isolated defect. Non-syndromic clefts have a complex etiology with genetic predisposition as well as environmental factors contributing to the condition. Many candidate genes have been identified based on human and animal studies. They play a role in different cellular processes required for the development of the lip and the palate (migration, proliferation, apoptosis, differentiation and adhesion). Environmental factors suggested to increase the risk of clefts are mainly maternal smoking and alcohol use. Supplementation of folic acid and multivitamins are suggested to be protective. One of the most common cleft syndromes is the van der Woude syndrome accounting for 2% of clefts. It is mainly characterized by the presence of lip pits (85%), cleft lip with or without palate (50%) and hypodontia. In 2002, the Interferon Regulatory-6 factor (IRF6) was identified as the major causal gene of VWS, but also of the Pterygium Popliteal syndrome (PPS). In addition to the features of VWS, PPS patients can have popliteal and/or oral webs, unusual nails, syndactyly, ankyloblepharon and/or genital anomalies. In order to assess the prevalence of IRF6 mutations in the European population, we collected a series of 51 patients with VWS and 17 with PPS. We showed that IRF6 is causal in 66.7% of the VWS patients and in 76.5% of the PPS patients. Moreover, the mutations are not scattered at random with the majority of VWS mutations localized in exons 3, 4, 7 and 9, and the majority of PPS mutations in exon 4, suggesting that these exons should be screened first for clinical diagnosis. Genes responsible for syndromic clefts are strong candidates for non-syndromic cleft lip and palate as sometimes, phenotypes can be indistinguishable. IRF6 is indeed a predisposing factor for isolated clefts. Based on the assumption that non-syndromic patients may have a mutation with a mild effect or polymorphisms acting as modifier, we screened 95 multiplex non-syndromic families for IRF6 mutations. We found three mutations that were already described in VWS patients in three different families. A posteriori careful examination of the families allowed the clinical geneticist to reject the non-syndromic phenotype and change the diagnosis to VWS showing that a genetic result can lead to a more precise diagnosis. Moreover, we could identify a new minor sign that should be looked for when considering VWS. We also suggest that a priori non-syndromic families with autosomal dominant inheritance should be screened for IRF6 (Publication I). Cleft can occur as a result of single nucleotide substitution but also as a result of cytogenetic abnormalities, the characterization of which can lead to the identification of causal genes. To find new candidate genes, we routinely performed 400-band karyotyping. Subsequently, we used molecular karyotyping with Affymetrix SNP arrays to delimit borders of candidate regions or to identify copy number variations with a better resolution. One of the interesting genomic imbalances that we observed was a balanced translocation occurring in a familial case from Lille. In this family, father and child had a cleft of the palate, micro/retrognathia, malar hypoplasia and dental anomalies. The karyotype of both patients was 46,XY,t(1;2)(p34;q33). Characterization of the breakpoints by FISH, chromosome microdissection and reverse array hybridization permitted to localize the relevant breakpoint on chromosome 1 in the first intron of FAF1. Association studies displayed that FAF1 predisposes to cleft palate and Pierre Robin sequence (PRS). In a screening of 228 individuals with isolated clefts, we identified two coding substitutions that might be responsible for the cleft as they are localized in domain important for the function of the gene. These changes were also seen in unaffected individuals. However, these changes could have a mild effect on protein function which without a certain genetic background and/or environmental triggers could not result in a cleft. Therefore, functional studies are required to test the effect of these changes. Knockdown of zFaf1 in the zebrafish allowed us to observe orofacial anomalies due to defects occurring during chondrogenesis via Sox9 expression alteration. We concluded that FAF1 is a key player in jaw development and that disruptions of this gene are associated with orofacial abnormalities (Publication II). We also identified a t(1;17)(p21;q24) translocation in a girl with a priori CP and dislocation of the hip. We mapped the breakpoint 600kb upstream of SOX9, a gene haploinsufficiency of which results in skeletal defects, PRS and genital anomalies referred to as campomelic dysplasia. In the light of the literature data and cytogenetic results, we suggested additional radiographic examination which reveals classical features of acampomelic campomelic dysplasia. In paralleI, we identified a deletion that co-segregated in a PRS family. This deletion was situated 1.2-1.4Mb upstream of SOX9 and overlapped one previously reported craniofacial enhancer. Sequencing of this regulatory element in a cohort of 73 PRS patients showed an enrichment of one SNP in the cohort compared to internal controls. By luciferase reporter assay, we showed that the minor allele weakened the enhancer activity of the regulatory element in which it was localized. Moreover, an association study with an intragenic SNP showed that SOX9 variations play a role in cleft palate in two populations, and in PRS in our cohort (Publication III, submitted and IV, in preparation). Finally, we identified by microarray analysis a deletion of 22q13.33 and a duplication of 12q24.33 in a syndromic patient with cleft palate. Based on clinical and literature data, we hypothesized that the CP arose from the duplication of one or more gene in the 12q24.33 region. In order to assess the role of candidate genes in the region, we conducted an association study using five variants in a set of 189 trios affected with CP or PRS. This is the first study conducted on a PRS cohort. Our results suggest two new associated factors for CP or PRS, SFSWAP and MMP17, respectively. Moreover, we demonstrated that SOX9 and FAF1 are implicated in CP in several populations and PRS in our cohort, giving human evidence for FAF1-SOX9 pathway to play a role in palatogenesis and mandibular chondrogenesis. We also showed cleft type specificity for genetic factors such as IRF6 and 8q24 locus do not associate with CP (Publication IV, in preparation). In conclusion, we show that clefts have a multigenic etiology with several genes, FAF1, SOX9, MMP17 and SFSWAP associated with the condition. We show that syndromic patients and/or chromosomal alterations can lead to the identification of new candidate genes. Moreover, by two examples (IRF6 with VWS and SOX9 wit ACD), we demonstrated that a genetic result can help in differential diagnosis.
- Affiliations
Citations
Desmyter, L. (2012). Multigenic etiology of cleft lip and palate. https://hdl.handle.net/2078.5/46005