Variation in Enamel Formation Genes Influences Enamel Demineralization In Vitro in a Streptococcus mutans Biofilm Model

In silico screening of non-synonymous SNPs in human TUFT1 gene

BACKGROUND

Tuftelin 1 (TUFT1) gene is important in the development and mineralization of dental enamel. The study aimed to identify potential functionally deleterious non-synonymous SNPs (nsSNPs) in the TUFT1 gene by using different in silico tools. The deleterious missense SNPs were identified from SIFT, PolyPhen-2, PROVEAN, SNPs & GO, PANTHER, and SNAP2. The stabilization, conservation, and three-dimensional modeling of mutant proteins were analyzed by I-Mutant 3.0, Consurf, and Project HOPE, respectively. The protein-protein interaction using STRING, GeneMANIA for gene-gene interaction, and DynaMut for evaluating the impact of the mutation on protein stability, conformation, and flexibility.

RESULTS

Eight deleterious nsSNPs (E242A, R303W, K182N, K123N, R117W, H289Q, R203W, and Q107R) out of 304 were found to have high-risk damaging effects using six in silico tools. Among them, K182N and K123N alone had increased stability, whereas E242A, R303W, R117W, H289Q, Q107R, and R203W exhibited a decrease in protein stability, based on DDG values. Meanwhile, all the eight deleterious nsSNPs altered the size, charge, hydrophobicity, and spatial organization of the amino acids and predominantly had alpha helix domains. These deleterious variants were located in highly conserved regions except R203W. Protein-protein interaction predicted that TUFT1 interacted with ten proteins that are involved in enamel mineralization and odontogenesis. Gene-gene interaction network showed that TUFT1 is involved in physical interactions, gene co-localization, and pathway interactions. DynaMut ΔΔG values predicted that five nsSNPs were destabilizing the protein, ΔΔG ENCoM values showed a destabilizing effect for all mutants, and seven nsSNPs increased the molecular flexibility of TUFT1.

CONCLUSION

Our study predicted eight functional SNPs that had detrimental effects on the structure and function of the TUFT1 gene. This will aid in the development of candidate deleterious markers as a potential target for disease diagnosis and therapeutic interventions.

Association of genetic variants in enamel-formation genes with dental caries: A meta- and gene-cluster analysis

Previous studies have reported the association between multiple genetic variants in the enamel-formation genes and the risk of dental caries with inconsistent results. We performed a systematic literature search of the PubMed, Cochrane Library, HuGE and Google Scholar databases for studies published before March 21, 2020 and conducted meta-, gene-based and gene-cluster analysis on the association between genetic variants in the enamel-formation genes and the risk of dental caries. We identified 21 relevant publications including a total of 24 studies for analysis. The genetic variant rs17878486 in AMELX was significantly associated with dental caries risk (OR = 1.40, 95% CI: 1.02–1.93, P = 0.037). We found no significant association between the risk of dental caries with rs12640848 in ENAM (OR = 1.15, 95% CI: 0.88–1.52, P = 0.310), rs1784418 in MMP20 (OR = 1.07, 95% CI: 0.76–1.49, P = 0.702) and rs3796704 in ENAM (OR = 1.06, 95% CI: 0.96–1.17, P = 0.228). Gene-based analysis indicated that multiple genetic variants in AMELX showed joint association with the risk of dental caries (6 variants; P < 10⁻⁵), so did genetic variants in MMP13 (3 variants; P = 0.004), MMP2 (3 variants; P < 10⁻⁵), MMP20 (2 variants; P < 10⁻⁵) and MMP3 (2 variants; P < 10⁻⁵). The gene-cluster analysis indicated a significant association between the genetic variants in this enamel-formation gene cluster and the risk of dental caries (P < 10⁻⁵). The present meta-analysis revealed that genetic variant rs17878486 in AMELX was associated with dental caries, and multiple genetic variants in the enamel-formation genes jointly contributed to the risk of dental caries, supporting the role of genetic variants in the enamel-formation genes in the etiology of dental caries.

A New Model for Caries Risk Prediction in Teenagers Using a Machine Learning Algorithm Based on Environmental and Genetic Factors

Dental caries is a multifactorial disease that can be caused by interactions between genetic and environmental risk factors. Despite the availability of caries risk assessment tools, caries risk prediction models incorporating new factors, such as human genetic markers, have not yet been reported. The aim of this study was to construct a new model for caries risk prediction in teenagers, based on environmental and genetic factors, using a machine learning algorithm. We performed a prospective longitudinal study of 1,055 teenagers (710 teenagers for cohort 1 and 345 teenagers for cohort 2) aged 13 years, of whom 953 (633 teenagers for cohort 1 and 320 teenagers for cohort 2) were followed for 21 months. All participants completed an oral health questionnaire, an oral examination, biological (salivary and cariostate) tests, and single nucleotide polymorphism sequencing analysis. We constructed a caries risk prediction model based on these data using a random forest with an AUC of 0.78 in cohort 1 (training cohort). We further verified the discrimination and calibration abilities of this caries risk prediction model using cohort 2. The AUC of the caries risk prediction model in cohort 2 (testing cohort) was 0.73, indicating high discrimination ability. Risk stratification revealed that our caries risk prediction model could accurately identify individuals at high and very high caries risk but underestimated risks for individuals at low and very low caries risk. Thus, our caries risk prediction model has the potential for use as a powerful community-level tool to identify individuals at high caries risk.

Effect of poly (γ-glutamic acid)/tricalcium phosphate (γ-PGA/TCP) composite for dentin remineralization in vitro

The poly (γ-glutamic acid)/tricalcium phosphate (γ-PGA/TCP) composite was fabricated as a novel biomineralization material function in preventing caries. Demineralized bovine dentin specimens were prepared and randomly divided into 5 groups (i. α-TCP, ⅱ. γ-PGA, ⅲ. γ-PGA/TCP, ⅳ. CPP-ACP, and ⅴ. deionized water) and subjected to 14 days of pH cycling. Remineralization ability was evaluated by lesion depth, mineral loss and microhardness. The morphology of dentin depositions was observed with scanning electron microscope (SEM), the crystal structure was determined by X-ray diffraction (XRD), and the wettability was tested by contact angle measurements. ANOVA revealed specimens treated by γ-PGA/TCP presented the statistically least lesion depth (p<0.01) and mineral loss (p<0.001), and the highest hardness (p<0.001). SEM revealed prominent intra- and inter-tubular precipitates in both γ-PGA and γ-PGA/TCP groups. The XRD patterns of the deposition structures in all groups were similar to those of sound dentin, and the contact angle of water decreased after γ-PGA/TCP treatment.

Interactions with the aquaporin 5 gene increase the susceptibility to molar-incisor hypomineralization

OBJECTIVE

The aim of this study was to evaluate whether individual genetic factors involved in amelogenesis, the immune response and water channel proteins may increase the susceptibility to Molar-Incisor Hypomineralization (MIH) in Chinese children.

DESIGN

DNA samples were collected from 86 cases with MIH cases and 344 controls. Sixteen single-nucleotide polymorphisms (SNPs) were investigated. Logistic regression analysis was performed to assess association between SNPs and the risk of MIH.

RESULTS

Our results showed that the risk of MIH in the rs13115627-AA genotype carriers and the rs1784418-TT genotype carriers were significantly higher than that among those with the rs13115627-GG genotype (OR (95 % CI)) = 4.942 (0.658-37.131) and the rs1784418-CT genotype (OR (95 % CI)) = 2.023 (1.63-3.521). The population with the rs1800972-CC genotype and the rs1800972-C allele had a higher risk to develop MIH, OR (95 % CI) = 2.284 (1.267-4.115), OR (95 % CI) = 2.427 (1.493-3.953) respectively. In the Aquaporin 5(AQP5) gene, we individually analyzed two SNPs, rs1996315 and rs923911. We found no significant associations between them and MIH. However, in the analysis of the gene-gene interactions, we discovered a significant two-locus model (P = 0.023) involving rs1996315 and rs923911. Participants with the rs1996315-AG and rs923911-AC genotypes had the highest MIH risk, compared to participants with the rs1996315-GG and rs923911-CC genotypes, OR (95 % CI) = 3.603 (1.147-11.318).

CONCLUSION

This study showed that genetic variants in the AMBN, MMP20 and DEFB1 genes may contribute to MIH in the permanent dentition of children. Moreover, interactions among AQP5 gene may also increase the MIH susceptibility.

MMP13 Contributes to Dental Caries Associated with Developmental Defects of Enamel

The aim of this study was to investigate the association between genetic polymorphisms in MMP8, MMP13, and MMP20 with caries experience and developmental defects of enamel (DDE) in children from the Amazon region of Brazil. Den tal caries and DDE data were collected through clinical examination from 216 children. Genomic DNA was extracted from saliva, and genotyping of selected polymorphisms in MMP8 (rs17099443 and rs3765620), MMP13 (rs478927 and rs2252070), and MMP20 (rs1784418) was performed using TaqMan chemistry and endpoint analysis. χ2 or Fisher's exact tests were used to compare allele and genotype distributions between children with caries experience and caries-free children and between DDE-affected and -unaffected children with an established alpha of 5%. The polymorphism rs478927 in MMP13 was associated with caries experience and DDE (p < 0.05). The analysis performed comparing children with both conditions (caries experience plus DDE) and children with neither of the conditions (caries-free chil dren without DDE) demonstrated that children carrying the MMP13 rs478927 TT genotype were more likely to have concomitant occurrence of these two conditions (OR = 5.8, 95% CI 2.1-15.8; p = 0.0003). In conclusion, the genetic polymorphism rs478927 in MMP13 was associated with caries experience and DDE.