Functional Effects of WNT10A Rare Variants Associated with Tooth Agenesis

Abstract

Mutations in WNT10A have frequently been reported as etiologic for tooth agenesis (TA). However, the effects of WNT10A variation on gene/protein function and contribution to TA phenotypes remain poorly understood. Here, we performed bioinformatic and functional characterization analysis of WNT10A variants. In silico prediction of variant function was performed with VIPUR for all WNT10A missense variants reported in the Exome Aggregation Consortium database. Functional characterization experiments were then performed for selected WNT10A variants previously associated with TA. Expression vectors for wild-type and mutant WNT10A were made and transfected into stem cells from human exfoliated deciduous teeth (SHED) for evaluation of gene/protein function, WNT signaling activity, and effects on expression of relevant genes. While 75% of WNT10A variants were predicted neutral, most of the TA-associated variants received deleterious scores by potentially destabilizing or preventing the disulfide bond formation required for proper protein function. WNT signaling was significantly decreased with 8 of 13 variants tested, whereas wild-type–like activity was retained with 4 of 13 variants. WNT10A-mutant cells (T357I, R360C, and R379C mutants) showed reduced or impaired binding affinity to FZD5, suggesting a potential mechanism for the decreased WNT signaling. Mutant cells also had decreased WNT10A protein expression in comparison to wild-type cells. mRNA expression of PAX9, MSX1, AXIN2, and RUNX2 (known tooth development genes) was perturbed in mutant cells and quite significantly for PAX9 and RUNX2. Transcriptome analysis of wild-type and T357I-mutant cells identified 36 differentially expressed genes (26 downregulated, 10 upregulated) involved in skeletal system development and morphogenesis and pattern specification. WNT10A variants deemed pathogenic for TA likely affect protein folding and/or stabilization, leading to decreased WNT signaling and concomitant dysregulated expression of relevant genes. These findings may allow for improved interpretation of TA phenotypes upon clinical diagnosis while providing important insights toward the development of future tooth replacement therapies.

Mutation analysis in patients with nonsyndromic tooth agenesis using exome sequencing

“…WNT10A mutants were found to inhibit Wnt signalling and dysregulate the expression levels of genes involved in protein folding and stability (Y. Zeng et al, 2021). The nonsense WNT10A mutation c.742C > T (p.R248*) detected in family 1 has been reported in two nonconsanguineous patients, one with nonsyndromic TA (B.…”

“…Mutations in WNT10A were further identified as common causative factors contributing to the aetiology of TA (van den Boogaard et al, 2012). WNT10A mutants were found to inhibit Wnt signalling and dysregulate the expression levels of genes involved in protein folding and stability (Y. Zeng et al, 2021). The nonsense WNT10A mutation c.742C > T (p.R248*) detected in family 1 has been reported in two nonconsanguineous patients, one with nonsyndromic TA (B. Zeng et al, 2017) and the other with OODD (Yu, Liu, et al, 2019).…”

Prediction of the invasiveness of PTMC by a combination of ultrasound and the WNT10A gene

“…WNT10A is a member of the WNT gene family, which is clustered in the 2q35 region on human chromosomes ( 8 ). It has been confirmed that WNT10A mutation plays an important role in tooth dysplasia and ectoderm dysplasia ( 9 – 11 ), and WNT10A is highly expressed in a variety of malignant tumors, such as thyroid cancer, ovarian cancer, esophageal squamous cell carcinoma, renal cell carcinoma, and colorectal cancer ( 12 – 16 ). Dong et al ( 12 ) indicated that WNT10A may plays a crucial role in carcinogenesis and aggressiveness in papillary thyroid cancer by activating β-catenin-dependent pathway.…”

The Genes Involved in Dentinogenesis

“… 56 , 57 mediation of dentinogenesis. 58 , 59 VPS4B Regulate tooth development. 60 Shh Signaling Pathway Shh Shh regulates growth and determines the shape of the tooth.…”