Conservation analysis and pathogenicity prediction of mutant genes of ectodysplasin a

Compound heterozygous WNT10A missense variations exacerbated the tooth agenesis caused by hypohidrotic ectodermal dysplasia

BACKGROUND

The aim of this study was to analyse the differences in the phenotypes of missing teeth between a pair of brothers with hypohidrotic ectodermal dysplasia (HED) and to investigate the underlying mechanism by comparing the mutated gene loci between the brothers with whole-exome sequencing.

METHODS

The clinical data of the patients and their mother were collected, and genomic DNA was extracted from peripheral blood samples. By Whole-exome sequencing filtered for a minor allele frequency (MAF) ≤0.05 non-synonymous single-nucleotide variations and insertions/deletions variations in genes previously associated with tooth agenesis, and variations considered as potentially pathogenic were assessed by SIFT, Polyphen-2, CADD and ACMG. Sanger sequencing was performed to detect gene variations. The secondary and tertiary structures of the mutated proteins were predicted by PsiPred 4.0 and AlphaFold 2.

RESULTS

Both brothers were clinically diagnosed with HED, but the younger brother had more teeth than the elder brother. An EDA variation (c.878 T > G) was identified in both brothers. Additionally, compound heterozygous variations of WNT10A (c.511C > T and c.637G > A) were identified in the elder brother. Digenic variations in EDA (c.878 T > G) and WNT10A (c.511C > T and c.637G > A) in the same patient have not been reported previously. The secondary structure of the variant WNT10A protein showed changes in the number and position of α-helices and β-folds compared to the wild-type protein. The tertiary structure of the WNT10A variant and molecular simulation docking showed that the site and direction where WNT10A binds to FZD5 was changed.

CONCLUSIONS

Compound heterozygous WNT10A missense variations may exacerbate the number of missing teeth in HED caused by EDA variation.

Evidence of selection in the ectodysplasin pathway among endangered aquatic mammals

Synopsis

The ectodysplasin pathway has been a target of evolution repeatedly. Genetic variation in the key genes of this pathway (EDA, EDAR, and EDARADD) results in a rich source of pleiotropic effects across ectodermally-derived structures, including teeth, hair, sweat glands, and mammary glands. In addition, a non-canonical Wnt pathway has a very similar functional role, making variation in the WNT10A gene also of evolutionary significance. The adaptation of mammals to aquatic environments has occurred independently in at least 4 orders, whose species occupy a wide geographic range (from equatorial to polar regions) and exhibit great phenotypic variation in ectodermally-derived structures, including the presence or absence of fur and extreme lactational strategies. The role of the ectodysplasin pathway in the adaptation to aquatic environments has been never explored in mammalian species. In the present study, we analyze the genetic variation in orthologous coding sequences from EDA, EDAR, EDARADD, and WNT10A genes together with ectodermally-derived phenotypic variation from 34 aquatic and non-aquatic mammalian species to assess signals of positive selection, gene-trait coevolution, and genetic convergence. Our study reveals strong evidence of positive selection in a proportion of coding sites in EDA and EDAR genes in 3 endangered aquatic mammals (the Hawaiian monk seal, the Yangtze finless porpoise, and the sea otter). We hypothesize functional implications potentially related to the adaptation to the low-latitude aquatic environment in the Hawaiian monk seal and the freshwater in the Yangtze finless porpoise. The signal in the sea otter is likely the result of an increased genetic drift after an intense bottleneck and reduction of genetic diversity. Besides positive selection, we have not detected robust signals of gene-trait coevolution or convergent amino acid shifts in the ectodysplasin pathway associated with shared phenotypic traits among aquatic mammals. This study provides new evidence of the evolutionary role of the ectodysplasin pathway and encourages further investigation, including functional studies, to fully resolve its relationship with mammalian aquatic adaptation.

Spanish

La vía de la ectodisplasina ha sido objeto de la evolución repetidamente. La variación genética en los principales genes de esta vía (EDA, EDAR y EDARADD) da como resultado una gran diversidad de efectos pleiotrópicos en las estructuras derivadas del ectodermo, incluidos los dientes, el cabello, las glándulas sudoríparas y las glándulas mamarias. Además, una vía wnt no canónica tiene un papel funcional muy similar, por lo que la variación en el gen WNT10A también tiene importancia evolutiva. La adaptación de los mamíferos a los entornes acuáticos se ha producido de forma independiente en al menos cuatro órdenes, cuyas especies ocupan un amplio rango geográfico (desde regiones ecuatoriales a polares) y presentan una gran variación fenotípica en las estructuras derivadas del ectodermo, incluyendo la presencia o ausencia de pelaje y estrategias de lactancia muy diferentes. El papel de la vía de la ectodisplasina en la adaptación a entornos acuáticos no se ha explorado nunca en especies de mamíferos. En este estudio, analizamos la variación genética en las secuencias codificantes ortólogas de los genes EDA, EDAR, EDARADD y WNT10A junto con la variación fenotípica derivada del ectodermo de 34 especies de mamíferos acuáticos y no acuáticos para evaluar señales de selección positiva, coevolución gen-rasgo y convergencia genética. Nuestro estudio revela señales de selección positiva en regiones de las secuencias codificantes de los genes EDA y EDAR en tres mamíferos acuáticos en peligro de extinción (la foca monje de Hawái, la marsopa lisa y la nutria marina). Estas señales podrían tener implicaciones funcionales potencialmente relacionadas con la adaptación al entorno acuático de baja latitud en la foca monje de Hawái y el agua dulce en la marsopa lisa. La señal en la nutria marina es probablemente el resultado de una mayor deriva genética tras un intenso un cuello de botella y una reducción de la diversidad genética. A parte de selección positiva, no hemos detectado señales sólidas de coevolución gen-rasgo o cambios convergentes de aminoácidos en la vía de la ectodisplasina asociados a rasgos fenotípicos compartidos entre mamíferos acuáticos. Este estudio proporciona nuevas evidencias del papel evolutivo de la vía de la ectodisplasina y quiere promover futuras investigaciones con estudios funcionales para acabar de resolver la relación de esta vía con la adaptación acuática de los mamíferos.

Pathogenic EDA Mutations in Chinese Han Families With Hypohidrotic Ectodermal Dysplasia and Genotype-Phenotype: A Correlation Analysis

Background

This study aimed to investigate the genetic causes of hypohidrotic ectodermal dysplasia (HED) in two families and elucidate the molecular pathogenesis of HED in Chinese Han patients.

Methods

Whole-exome sequencing (WES) was used to screen HED-related genes in two family members, followed by confirmatory Sanger sequencing. Bioinformatics analysis was performed for the mutations. We reviewed HED-related articles in PubMed. χ²- and Fisher's tests were used to analyze the genotype–phenotype correlations.

Results

(1) WES identified EDA missense mutations [c.1127 C > T (p.T376M; NM_001005609)] in family 1 and an EDA nonframeshift deletion mutation [c.648_683delACCTGGTCCTCCAGGTCCTCCTGGTCCTCAAGGACC (p.216_228delPPGPPGPPGPQGP; NM_001005609)] in family 2. Sanger sequencing validated the results. ANNOVAR (ANNOtate VARiation) annotation indicated that c.1127 c > T was a deleterious mutation. (2) The review of published papers revealed 68 novel mutations related to HED: 57 (83.8%) were EDA mutations, 8 (11.8%) were EDAR mutations, 2 (2.9%) were EDARADD mutations, 1 (1.5%) was a WNT10A mutation, 31 (45.6%) were missense mutations, 23 (33.8%) were deletion mutations, and 1 (1.5%) was an indel. Genotype–phenotype correlation analysis revealed that patients with EDA missense mutations had a higher frequency of hypohidrosis (P = 0.021).

Conclusions

This study identified two EDA gene mutations in two Chinese Han HED families and provides a foundation for genetic diagnosis and counseling.

A novel EDA1 missense mutation in X-linked hypohidrotic ectodermal dysplasia

A mutation in the epithelial morphogen gene ectodysplasin-A1 (EDA1) is responsible for the disorder X-linked hypohidrotic ectodermal dysplasia (XLHED), the most common form of ectodermal dysplasia. XLHED is characterized by impaired development of hair, eccrine sweat glands, and teeth. This study aimed to identify potentially pathogenic mutations in four Chinese XLHED families.Genomic DNA was extracted from the peripheral blood and sequenced. Sanger sequencing was used to carry out mutational analysis of the EDA1 gene, and the three-dimensional structure of the novel mutant residues in the EDA trimer was determined. Transcriptional activity of NF-κB was tested by Dual luciferin assay.We identified a novel EDA1 mutation (c.1046C>T) and detected 3 other previously-reported mutations (c.146T>A; c.457C>T; c.467G>A). Our findings demonstrated that novel mutation c.1046C>T (p.A349 V) resulted in XLHED. The novel mutation could cause volume repulsion in the protein due to enlargement of the amino acid side chain. Dual luciferase assay revealed that transcriptional NF-κB activation induced by XLHED EDA1 protein was significantly reduced compared with wild-type EDA1.These results extend the spectrum of EDA1 mutations in XLHED patients and suggest a functional role of the novel mutation in XLHED.