Comprehensive genetic exploration of selective tooth agenesis of mandibular incisors by exome sequencing

EDA ligand triggers plasma membrane trafficking of its receptor EDAR via PKA activation and SNAP23-containing complexes

BACKGROUND

Ectodysplasin-A (EDA), a skin-specific TNF ligand, interacts with its membrane receptor EDAR to trigger EDA signaling in skin appendage formation. Gene mutations in EDA signaling cause Anhidrotic/Hypohidrotic Ectodermal Dysplasia (A/HED), which affects the formation of skin appendages including hair, teeth, and several exocrine glands.

RESULTS

We report that EDA triggers the translocation of its receptor EDAR from a cytosolic compartment into the plasma membrane. We use protein affinity purification to show that upon EDA stimulation EDAR associates with SNAP23-STX6-VAMP1/2/3 vesicle trafficking complexes. We find that EDA-dependent PKA activation is critical for the association. Notably, either of two HED-linked EDAR mutations, T346M and R420W, prevents EDA-induced EDAR translocation; and both EDA-induced PKA activation and SNAP23 are required for Meibomian gland (MG) growth in a skin appendage model.

CONCLUSIONS

Overall, in a novel regulatory mechanism, EDA increases plasma membrane translocation of its own receptor EDAR, augmenting EDA-EDAR signaling in skin appendage formation. Our findings also provide PKA and SNAP23 as potential targets for the intervention of HED.

The EDA/EDAR/NF-κB pathway in non-syndromic tooth agenesis: A genetic perspective

Non-syndromic tooth agenesis (NSTA) is one of the most common dental developmental malformations affected by genetic factors predominantly. Among all 36 candidate genes reported in NSTA individuals, EDA, EDAR, and EDARADD play essential roles in ectodermal organ development. As members of the EDA/EDAR/NF-κB signaling pathway, mutations in these genes have been implicated in the pathogenesis of NSTA, as well as hypohidrotic ectodermal dysplasia (HED), a rare genetic disorder that affects multiple ectodermal structures, including teeth. This review provides an overview of the current knowledge on the genetic basis of NSTA, with a focus on the pathogenic effects of the EDA/EDAR/NF-κB signaling pathway and the role of EDA, EDAR, and EDARADD mutations in developmental tooth defects. We also discuss the phenotypic overlap and genetic differences between NSTA and HED. Ultimately, this review highlights the importance of genetic analysis in diagnosing and managing NSTA and related ectodermal disorders, and the need for ongoing research to improve our understanding of these conditions.

A Genome-wide association study of premolar agenesis in a chinese population

OBJECTIVE

Premolar agenesis is a common subtype of tooth agenesis. Although a genome-wide study (GWAS) has identified some variants involved in tooth agenesis in Europeans, the genetic mutation related to premolar agenesis in the Chinese population remains unclear.

MATERIALS AND METHODS

We present a GWAS in 218 premolar agenesis cases and 1,222 controls using the Illumina Infinium^® Global Screening Array. 5,585,618 single nucleotide polymorphisms (SNPs) were used for tests of associations with premolar agenesis.

RESULTS

Four independent SNPs on chromosome 2 were identified as susceptibility loci, including rs147680216, rs79743039, rs60540881, and rs6738629. The genome-wide significant SNP rs147680216 (p = 6.09 × 10^-9 ) was predicted to change the structure of the WNT10A protein and interact with hedgehog signaling pathway components. Meta-analysis showed that the rs147680216 A allele significantly increased the risk of tooth agenesis (p = 0.000). The other three SNPs with nominal significance are novel susceptibility loci. Of them, rs6738629 (p = 5.40 × 10^-6 ) acts as a potential transcriptional regulator of GCC2, a gene playing a putative role in dental and craniofacial development.

CONCLUSION

Our GWAS indicates that rs147680216 and additional three novel susceptibility loci on chromosome 2 are associated with the risk of premolar agenesis in the Chinese population.

A Rare Incidence of Nonsyndromic Mandibular Incisor Agenesis in a Three-generation Family: Case Report and Literature Review

Hypodontia is an inherited condition involving the absence of one to six teeth. The permanent dentition is the most frequently affected; however, it may also affect the primary dentition. A congenitally missing tooth (CMT) is the most common dental abnormality, with the missing mandibular second premolar, maxillary lateral incisor, maxillary second premolar, and mandibular central incisor accounting for 90% of CMT in hypodontia studies. The etiology of CMT has been attributed to environmental and genetic contributing factors, with the latter having a strong influence. It may occur in isolation or in association with syndromes. Congenitally missing mandibular incisor is more common in the Asian population and females. Depending on the number and location of missing teeth, hypodontia may be a considerable issue for the clinician since it may impact occlusal balance, mastication, speech, and esthetics and often requires a multidisciplinary approach. Missing mandibular incisors are of particular interest to orthodontists because of the possibility of mandibular retrognathism, the potential for the development of malocclusion, and difficulty in achieving a balanced occlusion. This case report describes the skeletal and dental features of a nonsyndromic familial occurrence of missing mandibular incisors in three generations. A comprehensive literature search was also performed to review the familial cases with missing mandibular incisors.

How to cite this article

Selvaraj M, Sennimalai K, Samrit VD, et al. A Rare Incidence of Nonsyndromic Mandibular Incisor Agenesis in a Three-generation Family: Case Report and Literature Review. Int J Clin Pediatr Dent 2023;16(2):388-395.

A novel EDAR variant identified in non-syndromic tooth agenesis: Insights from molecular dynamics

OBJECTIVE

This study aims to investigate a novel pathogenic variant in a Chinese family of non-syndromic tooth agenesis (NSTA) and study the impact of the variant on related protein and pathway.

DESIGN

One NSTA family was collected. Whole exome sequencing and Sanger sequencing were performed on the proband with NSTA and his 5 family members. The pathogenic influence of the mutant is evaluated by bioinformatics analyses including evolutionary conservation analysis and secondary structure prediction. Molecular dynamics (MD) simulations and binding free energy calculations were then performed to explore changes in the tertiary structure and binding ability of the protein.

RESULTS

We found a novel missense ectodysplasin A receptor (EDAR) variant (c .1292 T > G; p.Ile431Arg) in all affected family members. The results of bioinformatics analyses revealed that the EDAR had harmful changes after mutation. MD simulations and the binding free energy calculations results showed that the mutant EDAR protein and EDAR/ectodysplasin-A receptor-associated adapter (EDARADD) complex displayed tertiary structural change, and EDAR possessed a lower affinity to EDARADD after mutation.

CONCLUSIONS

We found a novel EDAR variant (c.1292 T > G; p.Ile431Arg) in one NSTA family, which affects the binding of EDAR and EDARADD.

Clinical Management of Hypodontia of Two Mandibular Incisors

This article presents the clinical management of a patient with bilateral congenitally missing mandibular incisors. This condition is relatively rare and always needs a careful diagnosis and treatment planning. The chosen treatment strategy for this patient included space closure by protraction of the mandibular posterior teeth and canine substitution of missing incisors. Furthermore, the problems arising from this treatment plan, such as premolar-protected occlusion and tooth size discrepancy, are discussed. From the case presented in this study, we can conclude that space closure may be considered an efficient treatment approach for achieving satisfactory functional and aesthetic results.

Characterisation of a second gain of function EDAR variant, encoding EDAR380R, in East Asia

Ectodysplasin A1 receptor (EDAR) is a TNF receptor family member with roles in the development and growth of hair, teeth and glands. A derived allele of EDAR, single-nucleotide variant rs3827760, encodes EDAR:p.(Val370Ala), a receptor with more potent signalling effects than the ancestral EDAR370Val. This allele of rs3827760 is at very high frequency in modern East Asian and Native American populations as a result of ancient positive selection and has been associated with straighter, thicker hair fibres, alteration of tooth and ear shape, reduced chin protrusion and increased fingertip sweat gland density. Here we report the characterisation of another SNV in EDAR, rs146567337, encoding EDAR:p.(Ser380Arg). The derived allele of this SNV is at its highest global frequency, of up to 5%, in populations of southern China, Vietnam, the Philippines, Malaysia and Indonesia. Using haplotype analyses, we find that the rs3827760 and rs146567337 SNVs arose on distinct haplotypes and that rs146567337 does not show the same signs of positive selection as rs3827760. From functional studies in cultured cells, we find that EDAR:p.(Ser380Arg) displays increased EDAR signalling output, at a similar level to that of EDAR:p.(Val370Ala). The existence of a second SNV with partly overlapping geographic distribution, the same in vitro functional effect and similar evolutionary age as the derived allele of rs3827760, but of independent origin and not exhibiting the same signs of strong selection, suggests a northern focus of positive selection on EDAR function in East Asia.

Novel EDAR mutation in tooth agenesis and variable associated features

Tooth agenesis (TA) is the developmental absence of one or more permanent teeth. We report on 10 members of a Pakistani family afflicted with TA with variable associated features inherited in autosomal dominant fashion with full penetrance. The malformation is bilateral in the majority of cases, and hallmark feature is the absence of lateral and central incisors and canines whereas first and second premolars are involved less often. Affected individuals also have pronounced variable features associated with TA such as diastema between central incisors, overgrown labial frenum, peg-shaped lower incisors, delayed exfoliation, over-erupted upper incisors and malocclusion but have no other signs of ectodermal dysplasia. Through linkage analysis coupled with exome sequencing, we identified novel nonsense variant EDAR c.1302G>A, p.(Trp434*). The variant is deduced to create a premature termination codon that leads to the deletion of the 15 C-terminal residues. Heterozygous EDAR variants most commonly cause hypohydrotic ectodermal dysplasia, but recently one nonsense and 10 missense variants have been reported in nonsyndromic TA, some with few mild features of hypohydrotic ectodermal dysplasia. The phenotype in the family we present, the largest with EDAR-related TA reported to date, is highly variable and without any signs of ectodermal dysplasia.

KDF1 is a novel candidate gene of non-syndromic tooth agenesis

OBJECTIVE

Tooth agenesis (TA) is featured by congenital loss of teeth, and can be divided into two subtypes, non-syndromic TA (NSTA) and syndromic TA (STA). Although 12 candidate genes of NSTA have been revealed, the genetic basis of NSTA needs to be further studied. We noticed an overlap of candidate genes between NSTA and STA, and hypothesized that some candidate genes of STA may be new candidate genes of NSTA.

METHODS

Sanger sequencing, whole exome sequencing, bioinformatics analyses and immunohistochemical staining were performed to reveal the genetic basis of the patients in a family with NSTA.

RESULTS

No pathogenic mutation was found in the 12 candidate genes of NSTA. We screened the variants of 76 STA candidate genes and identified a novel pathogenic mutation c.G908C (p.R303 P) in Keratinocyte Differentiation Factor 1 (KDF1). This mutation was cosegregated with the disease in the family. Bioinformatics analyses predicted the mutation to be pathogenic. Immunohistochemical staining of kdf1 in developing tooth germs indicated that kdf1 expression is important for the development of teeth.

CONCLUSIONS

This study identified KDF1 as a novel candidate gene for NSTA. STA candidate genes may be a promising source of new NSTA genes.

Hypodontia of mandibular incisors: considerations on the orthodontic treatment

Hypodontia is the most prevalent craniofacial malformation in mankind. It may present a wide variety of manifestations and, depending on the number and location of missing teeth, it may affect the esthetics, mastication, speech and occlusal balance. This paper discusses the therapeutic approaches to solve this condition, describing a case report with hypodontia of one mandibular lateral incisor, which treatment option included space closure at the region of hypodontia associated with composite resin restorations in the mandibular central incisors. The three-year follow-up after treatment revealed occlusal stability, adequate intercuspation in Class I relationship and excellent micro and macroesthetics.

The Changing Landscape in the Genetic Etiology of Human Tooth Agenesis

Despite much progress in understanding the genetics of syndromic tooth agenesis (TA), the causes of the most common, isolated TA remain elusive. Recent studies have identified novel genes and variants contributing to the etiology of TA, and revealed new pathways in which tooth development genes belong. Further, the use of new research approaches including next-generation sequencing has provided increased evidence supporting an oligogenic inheritance model for TA, and may explain the phenotypic variability of the condition. In this review, we present current knowledge about the genetic mechanisms underlying syndromic and isolated TA in humans, and highlight the value of incorporating next-generation sequencing approaches to identify causative and/or modifier genes that contribute to the etiology of TA.

Whole exome sequencing in an Italian family with isolated maxillary canine agenesis and canine eruption anomalies

OBJECTIVE

The aim of this study was the clinical and molecular characterization of a family segregating a trait consisting of a phenotype specifically involving the maxillary canines, including agenesis, impaction and ectopic eruption, characterized by incomplete penetrance and variable expressivity.

DESIGN

Clinical standardized assessment of 14 family members and a whole-exome sequencing (WES) of three affected subjects were performed. WES data analyses (sequence alignment, variant calling, annotation and prioritization) were carried out using an in-house implemented pipeline. Variant filtering retained coding and splice-site high quality private and rare variants. Variant prioritization was performed taking into account both the disruptive impact and the biological relevance of individual variants and genes. Sanger sequencing was performed to validate the variants of interest and to carry out segregation analysis.

RESULTS

Prioritization of variants "by function" allowed the identification of multiple variants contributing to the trait, including two concomitant heterozygous variants in EDARADD (c.308C>T, p.Ser103Phe) and COL5A1 (c.1588G>A, p.Gly530Ser), specifically associated with a more severe phenotype (i.e. canine agenesis). Differently, heterozygous variants in genes encoding proteins with a role in the WNT pathway were shared by subjects showing a phenotype of impacted/ectopic erupted canines.

CONCLUSIONS

This study characterized the genetic contribution underlying a complex trait consisting of isolated canine anomalies in a medium-sized family, highlighting the role of WNT and EDA cell signaling pathways in tooth development.

A biallelic ANTXR1 variant expands the anthrax toxin receptor associated phenotype to tooth agenesis

Tooth development is regulated by multiple genetic pathways, which ultimately drive the complex interactions between the oral epithelium and mesenchyme. Disruptions at any time point during this process may lead to failure of tooth development, also known as tooth agenesis (TA). TA is a common craniofacial abnormality in humans and represents the failure to develop one or more permanent teeth. Many genes and potentially subtle variants in these genes contribute to the TA phenotype. We report the clinical and genetic impact of a rare homozygous ANTXR1 variant (c.1312C>T), identified by whole exome sequencing (WES), in a consanguineous Turkish family with TA. Mutations in ANTXR1 have been associated with GAPO (growth retardation, alopecia, pseudoanodontia, and optic atrophy) syndrome and infantile hemangioma, however no clinical characteristics associated with these conditions were observed in our study family. We detected the expression of Antxr1 in oral and dental tissues of developing mouse embryos, further supporting a role for this gene in tooth development. Our findings implicate ANTXR1 as a candidate gene for isolated TA, suggest the involvement of specific hypomorphic alleles, and expand the previously known ANTXR1-associated phenotypes.

Novel EDA or EDAR Mutations Identified in Patients with X-Linked Hypohidrotic Ectodermal Dysplasia or Non-Syndromic Tooth Agenesis

Both X-linked hypohidrotic ectodermal dysplasia (XLHED) and non-syndromic tooth agenesis (NSTA) result in symptoms of congenital tooth loss. This study investigated genetic causes in two families with XLHED and four families with NSTA. We screened for mutations of WNT10A, EDA, EDAR, EDARADD, PAX9, MSX1, AXIN2, LRP6, and WNT10B through Sanger sequencing. Whole exome sequencing was performed for the proband of NSTA Family 4. Novel mutation c.1051G>T (p.Val351Phe) and the known mutation c.467G>A (p.Arg156His) of Ectodysplasin A (EDA) were identified in families with XLHED. Novel EDA receptor (EDAR) mutation c.73C>T (p.Arg25*), known EDA mutation c.491A>C (p.Glu164Ala), and known Wnt family member 10A (WNT10A) mutations c.511C>T (p.Arg171Cys) and c.742C>T (p.Arg248*) were identified in families with NSTA. The novel EDA and EDAR mutations were predicted as being pathogenic through bioinformatics analyses and structural modeling. Two variants of WNT10A, c.374G>A (p.Arg125Lys) and c.125A>G (p.Asn42Ser), were found in patients with NSTA. The two WNT10A variants were predicted to affect the splicing of message RNA, but minigene experiments showed normal splicing of mutated minigenes. This study uncovered the genetic foundations with respect to six families with XLHED or NSTA. We identified six mutations, of which two were novel mutations of EDA and EDAR. This is the first report of a nonsense EDAR mutation leading to NSTA.