Fine-mapping of 5q12.1-13.3 unveils new genetic contributors to caries

Associations of PART1 and DEFB1 polymorphisms with Dental Caries in twelve-year-old children in Southern China: a cross-sectional study

OBJECTIVE

The aim of this study was to assess associations of PART1 rs27565 and DEFB1 rs11362 polymorphisms with the prevalence of dental caries in twelve-year-old children in Nandan County, Guangxi, China.

METHODS

A total of 1,061 children were included in this cross-sectional study and divided into two groups based on the Decayed, Missing and Filled teeth (DMFT) index: caries-free children (DMFT score = 0) and children with caries (DMFT score ≥ 1). Demographic characteristics, oral hygiene behaviour and dietary habits were collected through household records and questionnaires. Genomic DNA was extracted from buccal cells, and PART1 rs27565 and DEFB1 rs11362 polymorphisms were genotyped using a custom-designed 48-Plex single nucleotide polymorphism-scan kit.

RESULTS

Carriers of the PART1 rs27565 C allele (odds ratio [OR] = 1.338, 95% confidence interval (CI) = 1.015-1.764, P value = 0.039) and carriers of the DEFB1 rs11362 T allele (OR = 1.364, 95% CI = 1.056-1.762, P value = 0.017) had a higher risk of caries. Carriers of the PART1 rs27565 TC or CC genotype who ate sugary food more than once a week had a 1.6-fold higher risk of caries than TT carriers who ate sugary food at most once a week (OR = 1.579, 95% CI = 1.032-2.414, P value = 0.035). Carriers of the DEFB1 rs11362 CT or TT genotype who ate sugary food more than once a week had a 2.1-fold higher risk of caries than CC carriers who ate sugary food at most once a week (OR = 2.057, 95% CI = 1.438-2.940, P value < 0.001).

CONCLUSION

PART1 rs27565 and DEFB1 rs11362 polymorphisms were associated with caries in 12-year-old children in Nandan County, Guangxi, China. Carriers of the PART1 rs27565 TC or CC genotype and the DEFB1 rs11362 CT or TT genotype who ate sugary food more than once a week had a high probability of having caries.

Oral microbiome-dental caries associated genotypes analysis of 6- to 19-year-old individuals shows novel associations

The need to determine risk factors for complex diseases continues to drive efforts of identification of etiological factors of common conditions. Molecular tools have created new opportunities to identify risk factors that may act interactively. The goal of this work was exploring potential interactions between oral microbial species and common genetic variants. Ninety-two 6- to 19-year-old individuals recruited through the University of Pittsburgh Dental Registry and DNA Repository project that had oral microbiome and genotyping of 44 single nucleotide polymorphism (SNP) data available were studied. Over-representation of alleles between individuals with or without particular microorganisms was determined using chi-square or Fisher's exact tests. Alpha of 0.001, to account for multiple testing (0.05/44), was considered statistically significant. Associations were found between Candida albicans and enamelin rs3796704 (p = 0.0006), and Staphylococcus epidermidis and tuftelin rs3828054 (p = 0.001). Microbiota and their metabolites might predispose oral disease when interacting with the host genetic variation and future studies should address their causal roles in oral disease.

Genetic Aspects of Dental Erosive Wear and Dental Caries

Objectives

The present review aims to give an overview of the literature focusing on novel genetic aspects of dental erosion and dental caries. Once the tooth erupts into the oral cavity, the regenerative capability of enamel is fundamentally limited due to the loss of dental epithelium during eruption. The susceptibility or resistance to dental erosion and caries is presumably a result of environmental, phenotypic, and/or genetic influence. Even though it is evident that individuals frequently exposing their teeth to acid and sugar are at high risk of developing dental erosion and caries, the findings exclusively based on these factors are elusive. Data resources and study selection. The present review was based on data collected from the National Library of Medicine database with different combinations of the following terms: "tooth," "dental," "dentin," "enamel," "erosion," "erosive wear," "caries," "decay," "gene," and "genetic." A total of forty-six studies met the inclusion criteria. Data were extracted by one reviewer and verified by another.

Conclusion

The high prevalence of erosion and caries among certain groups, and observations that not all individuals appearing to be at risk develop these lesions, has sparked research on identifying genetic effects to these conditions. A connection of genome-wide and candidate gene studies has increased considerably in the literature. This review reveals largely varying success among studies, demonstrating the difficulties of developing the study with adequate sample sizes and durable phenotype definitions that permit enough statistical power to identify genetic contributors.

A recurrent de novo ZSWIM6 variant in a Japanese patient with severe neurodevelopmental delay and frequent vomiting

A recurrent ZSWIM6 variant, NM_020928.2:c.2737C>T [p.Arg913*], was identified in a Japanese male patient with severe neurodevelopmental delay, epilepsy, distinctive facial features, microcephaly, growth deficiency, abnormal behavior, and frequent vomiting but without frontonasal or limb malformations. In this patient, distinctive facial features gradually became apparent with age, and severe vomiting caused by gastroesophageal reflux continued even after percutaneous endoscopic gastrostomy.

Biomarkers for Lifetime Caries-Free Status

The purpose of this study was to address the hypothesis that extreme outcomes of dental caries, such as edentulism or prematurely losing permanent teeth are associated with genetic variation in enamel-formation genes. After scanning 6206 individuals, samples of 330 were selected for this study. Tested phenotypes included patients who were edentulous by age 30, patients with missing first molars by age 30, patients with missing second molars by age 30, and caries-free patients. Fourteen single nucleotide polymorphisms were genotyped by TaqMan chemistry. The analyses of each phenotype were performed using the software PLINK with an alpha of 0.05. Nominal associations were found between rs12640848 in enamelin (p = 0.05), rs1784418 in matrix metallopeptidase 20 (p = 0.02), and rs5997096 in the tuftelin interacting protein 11 and being caries-free at the age of 60. When combining patients that were missing both first mandibular molars and missing both second mandibular molars, no associations were found. Matrix metallopeptidase 20, and tuftelin interacting protein 11 also showed trends for association with being caries-free. Genetic variation in TFIP11, MMP20, and ENAM may have a protective effect increasing the chances of individuals preserving their teeth caries-free over a lifetime.

Genetic polymorphisms influence shear bond resistance of orthodontic brackets

OBJECTIVES

The purpose of this study was to determine if shear bond resistance of orthodontic brackets bonded to enamel is associated with genes implicated in the enamel mineralization process.

METHODS

Ninety-two permanent, caries-free premolars extracted for orthodontic purposes and their associated saliva samples were obtained. Eighteen single nucleotide polymorphisms (SNPs) were studied for association with shear bond resistance. The genes of interest in this study were those previously associated with dental caries by our group. All tooth samples were bonded on the buccal surface with metallic lower lateral brackets, and then subjected to physical debonding. The force required to debond the bracket was recorded in Newtons (N) and converted to a shear bond resistance value in Megapascals (N/mm²). The data were analyzed for statistical significance as compared with the mean shear bond resistance value via PLINK whole genome analysis software.

RESULTS

Associations were found between the SNPs for tuftelin (rs7526319, P = 0.004) and amelogenin (rs17878486, P = 0.04) and a higher shear bond resistance.

CONCLUSION

The collected data support the proposed hypothesis that genes involved in the mineralization process affect the bonding of orthodontic brackets, and such an association is of value for the field of orthodontics, particularly in evaluating the efficacy of enamel-resin bond strength for patients receiving treatment.

Aquaporins' Influence on Different Dental Erosive Wear Phenotypes in Humans

Dental erosive wear is a multifactorial condition of high prevalence. Nowadays, there is an emphasis on discovering individual genetic predisposition for the development of this condition. Aquaporins (AQPs) are water channel proteins expressed in salivary glands, as well as during tooth development. They are involved in salivary secretion and composition and linked to physiological protection of the oral cavity. The aim of this study was to explore the relationship between different dental erosive wear phenotypes, AQP genes, and selected environmental factors. Data from 705 dental patients were used to investigate the association between dental erosive wear phenotypes and AQPs' single-nucleotide variants. Phenotypes were further analyzed considering diet and oral hygiene data, using logistic regression analysis, as implemented in PLINK, with the assumption that dental erosive wear is a complex gene-environment model. Associations were found between severe erosive tooth wear and rs2878771 (AQP2) for the genotypic (p = 0.02) and dominant (p = 0.03) models, and rs3736309 (AQP5) for the allelic model (p = 0.02). Logistic regression analyses, after implementing the Bonferroni correction, showed that several significant associations were present when covariates were included, suggesting that a strong environmental component is present. Our results show that dental erosive wear establishes under a gene-environmental complex model.

Measuring the Microscopic Structures of Human Dental Enamel Can Predict Caries Experience

OBJECTIVES

The hierarchical structure of enamel gives insight on the properties of enamel and can influence its strength and ultimately caries experience. Currently, past caries experience is quantified using the decayed, missing, filled teeth/decayed, missing, filled surface (DMFT/DMFS for permanent teeth; dmft/dmfs for primary teeth), or international caries detection and assessment system (ICDAS) scores. By analyzing the structure of enamel, a new measurement can be utilized clinically to predict susceptibility to future caries experience based on a patient's individual's biomarkers. The purpose of this study was to test the hypothesis that number of prisms by square millimeter in enamel and average gap distance between prisms and interprismatic areas, influence caries experience through genetic variation of the genes involved in enamel formation.

MATERIALS AND METHODS

Scanning electron microscopy (SEM) images of enamel from primary teeth were used to measure (i) number of prisms by square millimeter and interprismatic spaces, (ii) prism density, and (iii) gap distances between prisms in the enamel samples. The measurements were tested to explore a genetic association with variants of selected genes and correlations with caries experience based on the individual's DMFT+ dmft score and enamel microhardness at baseline, after an artificial lesion was created and after the artificial lesion was treated with fluoride.

RESULTS

Associations were found between variants of genes including ameloblastin, amelogenin, enamelin, tuftelin, tuftelin interactive protein 11, beta defensin 1, matrix metallopeptidase 20 and enamel structure variables measured (number of prisms by square millimeter in enamel and average gap distance between prisms and interprismatic areas). Significant correlations were found between caries experience and microhardness and enamel structure. Negative correlations were found between number of prisms by square millimeter and high caries experience (r value= -0.71), gap distance between prisms and the enamel microhardness after an artificial lesion was created (r value= -0.70), and gap distance between prisms and the enamel microhardness after an artificial lesion was created and then treated with fluoride (r value= -0.81). There was a positive correlation between number of prisms by square millimeter and prism density of the enamel (r value = 0.82).

CONCLUSIONS

Our data support that genetic variation may impact enamel formation, and therefore influence susceptibility to dental caries and future caries experience.

CLINICAL RELEVANCE

The evaluation of enamel structure that may impact caries experience allows for hypothesizing that the identification of individuals at higher risk for dental caries and implementation of personalized preventative treatments may one day become a reality.

Are mTOR and Endoplasmic Reticulum Stress Pathway Genes Associated with Oral and Bone Diseases?

The purpose of this cohort study was to identify associations between combined oral and bone disease phenotypes and genes present in cell regulatory pathways. The studied pathways play important roles in cellular growth, proliferation, differentiation, and homeostasis. DNA samples extracted from whole saliva of 3,912 individuals were genotyped and these data analyzed according to dental caries experience, periapical lesions, periodontitis, osteoporosis, or temporomandibular joint discomfort. Samples were obtained from the Dental Registry and DNA Repository project at the University of Pittsburgh. Twenty-seven polymorphisms in eight genes related to mTOR or endoplasmic reticulum stress pathways were selected for genotyping. Allele frequencies and Hardy-Weinberg equilibrium were calculated. Analyses were performed comparing genotypes between affected and unaffected individuals for each phenotype, as well as for the associated phenotypes combined. For all analyses, we used the software PLINK with an alpha of 0.002. Borderline associations with multiple variants of several genes were found, suggesting that both pathways may be involved in the susceptibility to multiple conditions affecting the oral cavity and bones. When combining patients that had concomitant dental caries, periodontitis, and periapical pathology, several markers in RHEB showed statistically significant association. Multiple conditions affecting bone and teeth (i.e., dental caries, periodontitis, periapical lesion formation, and osteoporosis) appear to share similar underlying genetic etiological factors, which allow us to hypothesize that instead of individually, they should be studied in conjunction in human populations.

Host genetics role in the pathogenesis of periodontal disease and caries

BACKGROUND

This study aimed to produce the latest summary of the evidence for association of host genetic variants contributing to both periodontal diseases and caries.

MATERIALS AND METHODS

Two systematic searches of the literature were conducted in Ovid Medline, Embase, LILACS and Cochrane Library for large candidate gene studies (CGS), systematic reviews and genome-wide association studies reporting data on host genetic variants and presence of periodontal disease and caries.

RESULTS

A total of 124 studies were included in the review (59 for the periodontitis outcome and 65 for the caries outcome), from an initial search of 15,487 titles. Gene variants associated with periodontitis were categorized based on strength of evidence and then compared with gene variants associated with caries. Several gene variants showed moderate to strong evidence of association with periodontitis, although none of them had also been associated with the caries trait.

CONCLUSIONS

Despite some potential aetiopathogenic similarities between periodontitis and caries, no genetic variants to date have clearly been associated with both diseases. Further studies or comparisons across studies with large sample size and clear phenotype definition could shed light into possible shared genetic risk factors for caries and periodontitis.

Genome-Wide Association Study of Erosive Tooth Wear in a Finnish Cohort

Erosive tooth wear is defined as irreversible loss of dental tissues due to intrinsic or extrinsic acids, exacerbated by mechanical forces. Recent studies have suggested a higher prevalence of erosive tooth wear in males, as well as a genetic contribution to susceptibility to erosive tooth wear. Our aim was to examine erosive tooth wear by performing a genome-wide association study (GWAS) in a sample of the Northern Finland Birth Cohort 1966 (n = 1,962). Erosive tooth wear was assessed clinically using the basic erosive wear examination. A GWAS was performed for the whole sample as well as separately for males and females. We identified one genome-wide significant signal (rs11681214) in the GWAS of the whole sample near the genes PXDN and MYT1L. When the sample was stratified by sex, the strongest genome-wide significant signals were observed in or near the genes FGFR1, C8orf86, CDH4, SCD5, F2R, and ING1. Additionally, multiple suggestive association signals were detected in all GWASs performed. Many of the signals were in or near the genes putatively related to oral environment or tooth development, and some were near the regions considered to be associated with dental caries, such as 2p24, 4q21, and 13q33. Replications of these associations in other samples, as well as experimental studies to determine the biological functions of associated genetic variants, are needed.

Redefining the Phenotype of Dental Caries

Dental caries is a multifactorial infectious disease and a major public health problem estimated to affect 60-90% of school children as well as a vast number of adults. The aim of this work was to define patterns of progression of the disease based on longitudinal data in contrast to using a cross-sectional assessment. dmft/DMFT scores were collected at ages 5, 12, 14, 16, 17, and 18 from 876 individuals. We tested our newly defined phenotypes for association with genetic variants in genes shown to be associated with caries. We generated genotyping data using Taqman chemistry in markers of genes involved in processes such as enamel formation and salivary contributions. Kallikrein 4 (KLK4) was found to show a significant association with the created phenotypes (p = 0.0008 in a recessive model for low caries experience in the primary dentition vs. high caries experience in the primary dentition, and p = 0.0004 in a recessive model for caries free primary dentition vs. high caries experience in the primary dentition).

Single Nucleotide Polymorphism in the Aetiology of Caries: Systematic Literature Review

Recent progress in the field of molecular biology and techniques of DNA sequence analysis allowed determining the meaning of hereditary factors of many common human diseases. Studies of genetic mechanisms in the aetiology of caries encompass, primarily, 4 main groups of genes responsible for (1) the development of enamel, (2) formation and composition of saliva, (3) immunological responses, and (4) carbohydrate metabolism. The aim of this study was to present current knowledge about the influence of single nucleotide polymorphism (SNP) genetic variants on the occurrence of dental caries. PubMed/Medline, Embase, and Cochrane Library databases were searched for papers on the influence of genetic factors connected with SNP on the occurrence of dental caries in children, teenagers, and adults. Thirty original papers written in English were included in this review. Study groups ranged from 30 to 13,000 subjects. SNPs were observed in 30 genes. Results of the majority of studies confirm the participation of hereditary factors in the aetiology of caries. Three genes, AMELX, AQP5, and ESRRB, have the most promising evidence based on multiple replications and data, supporting a role of these genes in caries. The review of the literature proves that SNP is linked with the aetiology of dental caries.

In Vitro Acid-Mediated Initial Dental Enamel Loss Is Associated with Genetic Variants Previously Linked to Caries Experience

We have previously shown that AQP5 and BTF3 genetic variation and expression in whole saliva are associated with caries experience suggesting that these genes may have a functional role in protecting against caries. To further explore these results, we tested ex vivo if variants in these genes are associated with subclinical dental enamel mineral loss. DNA and enamel samples were obtained from 53 individuals. Enamel samples were analyzed for Knoop hardness of sound enamel, integrated mineral loss after subclinical carious lesion creation, and change in integrated mineral loss after remineralization. DNA samples were genotyped for single nucleotide polymorphisms using TaqMan chemistry. Chi-square and Fisher's exact tests were used to compare individuals above and below the mean sound enamel microhardness of the cohort with alpha of 0.05. The A allele of BTF3 rs6862039 appears to be associated with harder enamel at baseline (p = 0.09), enamel more resistant to demineralization (p = 0.01), and enamel that more efficiently regain mineral and remineralize (p = 0.04). Similarly, the G allele of AQP5 marker rs3759129 and A allele of AQP5 marker rs296763 are associated with enamel more resistant to demineralization (p = 0.03 and 0.05, respectively). AQP5 and BTF3 genetic variations influence the initial subclinical stages of caries lesion formation in the subsurface of enamel.

Aquaporin 5 Interacts with Fluoride and Possibly Protects against Caries

Aquaporins (AQP) are water channel proteins and the genes coding for AQP2, AQP5, and AQP6 are clustered in 12q13. Since AQP5 is expressed in serous acinar cells of salivary glands, we investigated its involvement in caries. DNA samples from 1,383 individuals from six groups were studied. Genotypes of eight single nucleotide polymorphisms covering the aquaporin locus were tested for association with caries experience. Interaction with genes involved in enamel formation was tested. The association between enamel microhardness at baseline, after creation of artificial caries lesion, and after exposure to fluoride and the genetic markers in AQP5 was tested. Finally, AQP5 expression in human whole saliva, after exposure to fluoride in a mammary gland cell line, which is known to express AQP5, and in Wistar rats was also verified. Nominal associations were found between caries experience and markers in the AQP5 locus. Since these associations suggested that AQP5 may be inhibited by levels of fluoride in the drinking water that cause fluorosis, we showed that fluoride levels above optimal levels change AQP5 expression in humans, cell lines, and rats. We have shown that AQP5 is involved in the pathogenesis of caries and likely interacts with fluoride.

Lactotransferrin Gene Polymorphism Associated with Caries Experience

Dental caries is a common multifactorial disease, resulting from the interaction of biofilm, cariogenic diet and host response over time. Lactotransferrin (LTF) is a main salivary glycoprotein, which modulates the host immune-inflammatory and antibacterial response. Although a genetic component for caries outcome has been identified, little is known over the genetic aspects underlying its susceptibility. Thus, the aim of this study was to investigate the association between LTF polymorphisms and caries susceptibility. Six hundred seventy seven 12-year-old students were selected: 346 with (DMFT ≥ 1) and 331 without caries experience (DMFT = 0). Also, individuals concentrating higher levels of disease (polarization group, DMFT ≥ 2, n = 253) were tested against those with DMFT ≤ 1 (n = 424). Along with clinical parameters, three representative LTF tag SNPs (rs6441989, rs2073495, rs11716497) were genotyped and the results were evaluated using univariate and multivariate analyses. Allele A for tag SNP rs6441989 was found to be significantly less frequent in the polarization group, conferring a protective effect against caries experience [AA + AG × GG (OR: 0.710, 95% CI: 0.514-0.980, p = 0.045)], and remained significantly associated with caries protection in the presence of gingivitis (p = 0.020) and plaque (p = 0.035). These results might contribute to the understanding of the genetic control of caries susceptibility in humans.

Early childhood caries is associated with genetic variants in enamel formation and immune response genes

Early childhood caries (ECC) is a chronic, infectious disease that affects the primary dentition of young children. It is the result of an imbalance of risk factors and protective factors that influence the disease. The aim of this study was to assess genetic and environmental factors that may contribute to ECC. Two hundred and fifty-nine unrelated children were evaluated using a cross-sectional design. Data on oral habits were obtained through a questionnaire, and caries experience data were collected by clinical examination. Twenty-three markers in 10 genes were studied. Genotyping of the selected polymorphisms was carried out by real-time PCR. Regression analyses were performed comparing individuals with and without caries experience. Of 259 subjects, 123 were caries free. The genotype TT in ALOX15 (rs7217186) was a risk factor for ECC, whereas the genotypes GG in ENAM (rs1264848), AG and GG in KLK4 (rs198968), CT in LTF (rs4547741), and GG in TUFT1 (rs3790506) were protective for EEC. In conclusion, environmental factors and gene interactions can act as protective or risk factors for ECC. These factors together contribute to the presence and severity of the disease.

Role of estrogen related receptor beta (ESRRB) in DFN35B hearing impairment and dental decay

BACKGROUND

Congenital forms of hearing impairment can be caused by mutations in the estrogen related receptor beta (ESRRB) gene. Our initial linkage studies suggested the ESRRB locus is linked to high caries experience in humans.

METHODS

We tested for association between the ESRRB locus and dental caries in 1,731 subjects, if ESRRB was expressed in whole saliva, if ESRRB was associated with the microhardness of the dental enamel, and if ESRRB was expressed during enamel development of mice.

RESULTS

Two families with recessive ESRRB mutations and DFNB35 hearing impairment showed more extensive dental destruction by caries. Expression levels of ESRRB in whole saliva samples showed differences depending on sex and dental caries experience.

CONCLUSIONS

The common etiology of dental caries and hearing impairment provides a venue to assist in the identification of individuals at risk to either condition and provides options for the development of new caries prevention strategies, if the associated ESRRB genetic variants are correlated with efficacy.

Caries: review of human genetics research

The NIH Consensus Development Program released a statement in 2001 (http://consensus.nih.gov/2001/2001DentalCaries115html.htm) and listed six major clinical caries research directions. One of these directions was the need for genetic studies to identify genes and genetic markers of diagnostic, prognostic and therapeutic value. This last decade has seen a steep increase in studies investigating the presence of genetic factors influencing individual susceptibility to caries. This review revisits recent caries human genetic studies and provides a perspective for future studies in order to fulfil their promise of revolutionizing our understanding of and the standard of care for the most prevalent bacteria-mediated non-contagious disease in the world.

Genetic variation in the promoter region of beta-defensin 1 (DEFB 1) is associated with high caries experience in children born with cleft lip and palate

OBJECTIVE

Caries is a common disease in humans and has a multifactorial etiology. It has been suggested that children born with cleft lip and/or palate (CL/P) have a higher susceptibility to caries, but data from several independent cohorts does not support this assumption. Previous work from our group suggested DEFB 1 is associated with higher caries experience. Since it is suspected that children born with CL/P have the same risk factors predisposing them to caries as other children of the same ages, the aim was to test if DEFB 1 was associated with caries experience in children born with CL/P.

MATERIALS AND METHODS

Sixty-nine children born with CL/P (aged 2-12 years) were included. Twenty-seven males and seven females had cleft lip and palate (CLP), six males and seven females had cleft lip (CL) and 13 males and nine females had cleft palate (CP). Caries was evaluated with the DMFT/dmft index by a calibrated evaluator. Two single nucleotide polymorphisms in DEFB 1 were selected (rs11362 and rs1800972) based on being associated with higher caries experience in previous work. Genotyping were carried out by real-time PCR using the Taqman assay method. The statistical analysis was performed between 'low-to-moderate caries experience group' and the 'high caries experience group'. Odds ratio calculations between caries experience and variant alleles and chi-square of Fisher exact tests at a level of significance of 0.05 were used.

RESULTS

There was no significant difference for caries experience between cleft types (p = 0.551). An association was found for the marker rs11362 and genotype distribution (p = 0.047). When analyzed in a recessive model, the genotype GG in this polymorphism increased the risk for caries susceptibility by more than 3-times (p = 0.031; OR = 3.16; 95% CI = 0.97-10.62).

CONCLUSION

The genetic variant rs11362 in DEFB 1 influences caries susceptibility in CL/P children. The results support the hypothesis that expression of DEFB 1 in saliva may serve as a biomarker for future caries risk.

Genetic mapping of high caries experience on human chromosome 13

Background

Our previous genome-wide linkage scan mapped five loci for caries experience. The purpose of this study was to fine map one of these loci, the locus 13q31.1, in order to identify genetic contributors to caries.

Methods

Seventy-two pedigrees from the Philippines were studied. Caries experience was recorded and DNA was extracted from blood samples obtained from all subjects. Sixty-one single nucleotide polymorphisms (SNPs) in 13q31.1 were genotyped. Association between caries experience and alleles was tested. We also studied 1,481 DNA samples obtained from saliva of subjects from the USA, 918 children from Brazil, and 275 children from Turkey, in order to follow up the results found in the Filipino families. We used the AliBaba2.1 software to determine if the nucleotide changes of the associated SNPs changed the prediction of the presence of transcription-binding site sequences and we also analyzed the gene expression of the genes selected based on binding predictions. Mutation analysis was also performed in 33 Filipino individuals of a segment of 13q31.1 that is highly conserved in mammals.

Results

Statistically significant association with high caries experience was found for 11 markers in 13q31.1 in the Filipino families. Haplotype analysis also confirmed these results. In the populations used for follow-up purposes, associations were found between high caries experience and a subset of these markers. Regarding the prediction of the transcription-binding site, the base change of the SNP rs17074565 was found to change the predicted-binding of genes that could be involved in the pathogenesis of caries. When the sequence has the allele C of rs17074565, the potential transcription factors binding the sequence are GR and GATA1. When the subject carries the G allele of rs17074565, the potential transcription factor predicted to bind to the sequence is GATA3. The expression of GR in whole saliva was higher in individuals with low caries experience when compared to individuals with high caries experience (p = 0.046). No mutations were found in the highly conserved sequence.

Conclusions

Genetic factors contributing to caries experience may exist in 13q31.1. The rs17074565 is located in an intergenic region and is predicted to disrupt the binding sites of two different transcription factors that might be involved with caries experience. GR expression in saliva may be a biomarker for caries risk and should be further explored.

Role of TRAV locus in low caries experience

Caries is the most common chronic, multifactorial disease in the world today; and little is still known about the genetic factors influencing susceptibility. Our previous genome-wide linkage scan has identified five loci related to caries susceptibility: 5q13.3, 13q31.1, 14q11.2, 14q 24.3, and Xq27. In the present study, we fine mapped the 14q11.2 locus to identify genetic contributors to caries susceptibility. Four hundred seventy-seven subjects from 72 pedigrees with similar cultural and behavioral habits and limited access to dental care living in the Philippines were studied. An additional 387 DNA samples from unrelated individuals were used to determine allele frequencies. For replication purposes, a total of 1,446 independent subjects from four different populations were analyzed based on their caries experience (low versus high). Forty-eight markers in 14q11.2 were genotyped using TaqMan chemistry. Transmission disequilibrium test was used to detect over transmission of alleles in the Filipino families, and Chi-square, Fisher's exact and logistic regression were used to test for association between low caries experience and variant alleles in the replication data sets. We finally assessed the mRNA expression of TRAV4 in the saliva of 143 study subjects. In the Filipino families, statistically significant associations were found between low caries experience and markers in TRAV4. We were able to replicate these results in the populations studied that were characteristically from underserved areas. Direct sequencing of 22 subjects carrying the associated alleles detects one missense mutation (Y30R) that is predicted to be probably damaging. Finally, we observed higher expression in children and teenagers with low caries experience, correlating with specific alleles in TRAV4. Our results suggest that TRAV4 may have a role in protecting against caries.