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RESEARCH REPORTS
Clinical
M. Alves-Ferreira1, T. Pinho1,2,
A. Sousa1,3, J. Sequeiros1,3,4, C. Lemos1,3,
Identification of Genetic Risk
and I. Alonso1,3* Factors for Maxillary Lateral
1
UnIGENe, Instituto Biologia Molecular Celular, Universidade
do Porto, Porto, Portugal; 2Centro de Investigação Ciências da
Incisor Agenesis
Saúde, Instituto Superior de Ciências Saúde–Norte / CESPU,
Gandra-PRD, Portugal; 3Instituto Ciências Biomédicas Abel
Salazar, Universidade do Porto, Porto, Portugal; and 4CGPP,
Instituto Biologia Molecular Celular, Universidade do Porto,
Porto, Portugal; *corresponding author, ialonso@ibmc.up.pt
Abstract Introduction
Tooth agenesis affects 20% of the world population,
and maxillary lateral incisors agenesis (MLIA) is one
of the most frequent subtypes, characterized by the M axillary lateral incisors agenesis (MLIA) is characterized by the absence
of formation of deciduous or permanent upper lateral incisors. Tooth
agenesis affects approximately 20% of the world population (Vastardis, 2000),
absence of formation of deciduous or permanent lat-
eral incisors. Odontogenesis is a complex mechanism and MLIA is one of the most frequent forms of hypodontia (agenesis of fewer
regulated by sequential and reciprocal epithelial- than 6 teeth, excluding the third molars) (Arte et al., 2001), with a prevalence
mesenchymal interactions, controlled by activators ranging from 1% to 4%. In Portugal, the prevalence of MLIA was estimated at
and inhibitors involved in several pathways. 1.3% (Pinho et al., 2005). We found evidence of familial aggregation of MLIA
Disturbances in these signaling cascades can lead to in a sample of Portuguese families, suggesting the presence of a strong genetic
abnormalities in odontogenesis, resulting in alterations
component (relative risk =15) for this trait (Pinho et al., 2010a).
in the formation of the normal teeth number. Our aim
Odontogenesis is a complex mechanism regulated by sequential and recip-
was to study a large number of genes encoding either
transcription factors or key components in signaling rocal epithelial-mesenchymal interactions, controlled by genetic factors, and
pathways shown to be involved in tooth odontogene- is responsible for the determination of the position, number, shape, and size
sis. We selected 8 genes—MSX1, PAX9, AXIN2, EDA, of teeth (Thesleff, 2003). Several genes have been identified as being
SPRY2, TGFA, SPRY4, and WNT10A—and performed expressed during odontogenesis, and it is known that mutations in MSX1,
one of the largest case-control studies taking into PAX9, AXIN2, EDA, SPRY2, TGFA, SPRY4, and WNT10A genes are involved
account the number of genes and variants assessed, in several forms of tooth agenesis, including syndromes in which tooth agen-
aiming at the identification of MLIA susceptibility fac- esis is a regular feature (Nieminen, 2009). These genes are related with all
tors. We show the involvement of PAX9, EDA, SPRY2, major signaling pathways and with the transcription factors mediating these
SPRY4, and WNT10A as risk factors for MLIA. signal transduction cascades. New findings on the function of these genes that
Additionally, we uncovered 3 strong synergistic inter-
are mutated in particular human syndromes further strengthen the important
actions between MLIA liability and MSX1-TGFA,
AXIN2-TGFA, and SPRY2-SPRY4 gene pairs. We role of these genes in tooth agenesis (Nieminen, 2009).
report the first evidence of the involvement of sprouty Here, we present a case-control study with the largest number of genes and
genes in MLIA susceptibility. This large study results single-nucleotide polymorphisms (SNPs) assessed in the same population,
in a better understanding of the genetic components aiming at identifying MLIA susceptibility factors focusing on these genes
and mechanisms underlying this trait. involved in tooth odontogenesis.
452
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Candidate Gene and SNP Selection Table 1. Clinical and Demographic Characteristics of the Study
Sample
Details on SNP selection and genotyping are presented as sup-
plementary material. Study Sample No.
Cases 102
Statistical Analysis MLIA only 86
The statistical power of our sample was calculated with the Bilateral (12 and 22) 50
Genetic Power Calculator (http://pngu.mgh.harvard.edu/ Unilateral (12) + microdontia (22) 11
Unilateral (22) + microdontia (12) 1
~purcell/gpc). We performed these estimates assuming a fre-
Unilateral (12) 12
quency of 0.1 for the high-risk allele, a relative risk of 2.5 for
Unilateral (22) 12
the homozygous genotype and 2.2 for the heterozygous geno-
MLIA + other agenesis 16
type, and a prevalence of 1.3% for MLIA in the Portuguese
12; 22; 18; 28; 38; 48 1
population, based on α = 0.05 (Pinho et al., 2005). 12; 22; 18 1
Hardy-Weinberg (H-W) equilibrium was tested with SNPator 12; 22; 45 1
software (Morcillo-Suarez et al., 2008). To compare allele fre- 12; 22; 35 1
quencies between cases and controls, a chi-square test was used, 12; 22; 45; 35 3
and odds ratios (ORs) were estimated with 95% confidence 12; 35; 45 1
intervals (CI), also per SNPator. 22; 35; 45 1
A logistic regression was performed (with the commonest 12; 22; 31; 41 2
allele as the reference category) to evaluate the genotypic asso- 12; 22;41 1
ciations. The significance level was set to α = 0.007 (consider- 12; 22; 15; 25 1
ing 7 logistic regressions), based on the Bonferroni test, to 12; 32; 42 1
correct for multiple comparisons. As EDA gene is located in the 12; 41; 45; and microdontia (22) 1
X chromosome, the analyses were performed taking sex into 22; 31; 41; and microdontia (13) 1
account. These analyses were performed with SPSS 18. Males 29
Haplotype frequencies in cases and controls were compared Females 73
with Haploview 4.1 (Barrett et al., 2005); haplotype sequences Controls 204
were analyzed from 5′ to 3′. To correct for multiple testing, Males 85
Females 119
10,000 permutations were used when allelic and haplotype fre-
quencies were estimated. MLIA, maxillary lateral incisors agenesis
To explore possible gene-gene interactions, we used
Multifactor Dimensionality Reduction software (version 2.0),
which is a nonparametric and genetic model-free approach that
can identify combinations of SNPs involved in disease suscep- PAX9 Genotype as a MLIA Risk Factor
tibility (Ritchie et al., 2001; Moore, 2004). Subsequently, we The A allele of rs8004560 was associated with an increased
used the Permutation Testing Module (version 1.0) of Multifactor MLIA susceptibility (p = .02); however, this result did
Dimensionality Reduction to correct our results for multiple not remain significant after permutation-based correction
testing, based on a 1000-fold permutation test. (Table 2).
Importantly, 2 highly significant genotypic associations were
Results found. The AA genotype of rs7149262 was correlated with
higher trait susceptibility (p < .001). In agreement with the
Here we present a large case-control study composing the analy- allelic results, the AA genotype of rs8004560 was associated
sis of common variation in 8 genes involved in tooth odontogen- with an increased MLIA susceptibility (p = .003). These asso-
esis to identify MLIA susceptibility factors. Our sample had a ciations remained significant after Bonferroni correction
power of 72% to detect a significant association. Genotypic fre- (Table 3). The haplotypic analysis did not reveal any significant
quencies in the control group were in H-W equilibrium (p > .05). association between PAX9 and MLIA susceptibility (data not
In the cases group, H-W equilibrium deviations were found for shown).
some SNPs, although in all these cases, an association with MLIA
susceptibility was confirmed. We were able to show the involve-
ment of PAX9, EDA, SPRY2, SPRY4, and WNT10A as risk factors
Nominal Significant Associations of EDA SNPs With
for MLIA. No significant allelic, genotypic, and haplotypic asso- MLIA Susceptibility
ciations were found regarding AXIN2, TGFA, and MSX1 genes The A allele of rs1160315, the C allele of rs2428151, the T allele
(data not shown). All the analyses, were repeated, excluding of rs2520378, and the A allele of rs2853659 were associated
patients with MLIA and other agenesis (always fewer than 6 with an increase in MLIA susceptibility. None of the results
teeth), and the results were similar (data not shown). We assessed remained significant after multiple-testing correction by permu-
gene-gene interactions and uncovered 3 strong synergistic inter- tation tests (Table 2).
actions between MLIA liability and the following gene pairs: Regarding the genotypic analysis, the GA genotype of
MSX1-TGFA, AXIN2-TGFA, and SPRY2-SPRY4. rs12853659 presented a higher risk for MLIA (p = .021), while the
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Table 2. Allelic Association Results for PAX9, EDA, SPRY2, and WNT10A Genes
Alleles (%)
PAX9 SNP
rs8004560 5.59 1.53 (1.07, 2.17) .02*
A 81 (39.7) 123 (30.1)
G 123 (60.3) 285 (69.9)
EDA SNP
rs1160315 4.30 1.48 (1.02, 2.14) .04*
A 101 (57.7) 155 (48.0)
G 74 (42.3) 168 (52.0)
rs2428151 6.49 1.64 (1.12, 2.41) .01*
C 117 (66.9) 178 (55.1)
T 58 (33.1) 145 (44.9)
rs2520378 5.16 1.82 (1.08, 3.07) .02*
T 153 (87.4) 256 (79.3)
C 22 (12.6) 67 (20.7)
rs12853659 6.32 1.61 (1.11, 2.33) .01*
A 103 (58.9) 152 (47.1)
G 72 (41.1) 171 (52.9)
SPRY2 SNP
rs504122
A 89 (43.6) 146 (35.8) 3.54 1.39 (0.99, 1.96) .06
G 115 (56.4) 262 (64.2)
WNT10A SNP
rs11680244 0.05 1.15 (0.35, 3.78) .82
A 4 (2.0) 9 (2.2)
G 200 (98.0) 391 (97.8)
rs2385199 10.25 1.98 (1.30, 3.01) .0014*
G 51 (25.0) 58 (14.4)
A 153 (75.0) 344( 85.6)
rs7349332 3.34 1.54 (0.97, 2.46) .068
T 36 (17.6) 49 (12.2)
C 168 (82.4) 353 (87.8)
CI, confidence interval; EDA, ectodysplasin A; PAX9, paired box gene 9; SNP, single-nucleotide polymorphism; SPRY2, sprouty homolog 2 gene;
WNT10A, wingless-type MMTV integration site family, member 10A.
*p < .05.
GA genotype of rs1160315 (p = .015) and the CT of rs5936523 significant association was found between SPRY2 haplotypes
(p = .038) showed a protective effect. However, the results did not and MLIA.
remain significant after Bonferroni correction (Table 3).
In the haplotypic analysis, a specific EDA haplotype (T-G-T- SPRY4 Gene Haplotypes and MLIA Susceptibility
A-A-C-T-C-A-A-A-G-G-T-G-T) revealed a significant associa-
tion (p = .032) with increased MLIA susceptibility, although it The allelic and genotypic analyses did not reveal any significant
did not retain its significance after permutation correction. association between this gene and MLIA susceptibility (data not
shown).
Importantly, the T-G-G-A-T-C haplotype revealed a nominal
SPRY2 SNP and Increased Risk for MLIA
significant association (p = .016) with an increased MLIA suscep-
No significant differences were found regarding allelic frequen- tibility (OR = 3.46; 95% CI: 1.19, 10.08); however, this did not
cies of SPRY2 SNPs. However, we observed a trend toward an remain significant after permutation-based correction (p = .137).
increased risk for MLIA conferred by the A allele of rs504122
(p = .06) (Table 2). WNT10A Variants Increase the Risk for MLIA
Regarding the genotypic analysis, we found that the GA
genotype of rs504122 presented a higher risk for individuals The G allele of rs2385199 was associated with an increased
with MLIA (p = .005; OR = 2.49; 95% CI: 1.31, 4.73), which MLIA susceptibility (p = .0014), a result that remained signifi-
remained significant after Bonferroni correction (Table 3). No cant after permutation-based correction (Table 2).
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Table 3. Results from the PAX9, EDA, SPRY2, and WNT10A Multivariable Logistic Regression Analysis
Genotype (%)
PAX9 SNP
rs8004560 .011
GG (ref) 45 (44.1) 104 (51.0) 1.00 (—)
GA 33 (32.4) 77 (37.7) 1.27 (0.72, 2.24) .412
AA 24 (23.5) 23 (11.3) 3.03 (1.47, 6.28) .003*
rs7149262 .001
CC (ref) 66 (64.7) 132 (64.7) 1.00 (—)
AC 23 (22.6) 68 (33.3) 0.88 (0.49, 1.58) .662
AA 13 (12.7) 4 (2.0) 9.39 (2.79, 30.97) <.001*
EDA SNP
rs1160315 .019
GG(ref) 15 (44.1) 30 (51.0) 1.00 (—)
GA 33 (32.4) 62 (37.7) 0.05 (0.01, 0.57) .015
AA 25 (23.5) 27 (11.3) 0.33 (0.02, 5.72) .446
rs5936523 .003
CC(ref) 14 (64.7) 11 (64.7) 1.00 (—)
CT 23 (22.6) 67 (33.3) 0.46 (0.22, 0.96) .038
TT 36 (12.7) 41 (2.0) 2.59 (0.82, 8.21) .105
rs12853659 .038
GG(ref) 12 (44.1) 31 (51.0) 1.00 (—)
GA 38 (32.4) 61 (37.7) 14.43 (1.51, 138.12) .021
AA 23(23.5) 27 (11.3) 3.24 (0.21, 49.00) .397
SPRY2 SNP
rs504122 .02
GG (ref) 25 (24.5) 81 (39.7) 1.00 (—)
AA 12 (11.8) 23 (11.3) 1.97 (0.73, 5.28) .18
GA 65 (63.7) 100 (49.0) 2.49 (1.31, 4.73) .005*
WNT10A SNP
rs2385199 .006*
GG (ref) 56 (54.9) 147 (73.1) 1.00 (—)
GA 41(40.2) 50 (24.9) 2.14 (1.28, 3.58) .004*
AA 5 (4.9) 4 (2.0) 3.26 (0.84, 12.58) .09
Importantly, a highly significant genotypic association was rs11911 (which is in LD with rs504122) may affect miRNA
found for this SNP. Its GA genotype was correlated with higher binding sites.
MLIA susceptibility (p = .004) that withstood Bonferroni cor- We found a strong synergistic interaction, as shown in the den-
rection (Table 3). The haplotypic analysis showed a significant dogram (Figure 1a) for the best model, between the AC and CC
association between MLIA susceptibility and the G-G-T haplo- genotypes of rs3775261 in the MSX1 gene and the CT genotype of
type that remained significant after permutation-based correc- rs3771494 of TGFA, with a testing balanced accuracy (TBA) of
tion (p = .0176). 0.62, a cross-validation consistency (CVC) of 10/10, and a signifi-
cant p value (p = .015) after a 1000-fold permutation test. The CVC
is the number of times that a model is selected as the best model
Functional Impact and Gene-Gene Interactions
among the validation sets indicating the importance of the model
We performed an in silico analysis using FuncPred. Particular (Heidema et al., 2007). A best model was selected to maximize the
attention was paid to rs504122, a nonsynonymous polymor- testing accuracy; this is the model most likely to generalize to inde-
phism that results in a missense mutation (p.Pro106Ser), pre- pendent data sets (Beretta et al., 2008).
dicted as benign. We also analyzed SNPs that are in linkage In addition, we have found a significant interaction between
disequilibrium (LD) with those found to be associated with the TT genotype (rs426081) of TGFA and the AC and AA geno-
MLIA. This analysis showed that SNPs in LD with rs504122 types of rs3923086 in the AXIN2 gene, with a TBA of 0.63 and
(rs497857 and rs541731) may alter transcription factor binding a CVC of 10/10 (Figure 1b). After permutation testing, this
sites in this gene. Additionally, this analysis predicts that model remained significant (p = .026).
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MLIA has a high impact in individuals with this trait; therefore, Previous studies provided evidence for the involvement of FGF
it is important to understand the underlying causes of tooth signaling in odontogenesis (Jernvall and Thesleff, 2000; Klein
agenesis susceptibility. et al., 2006; Klein et al., 2008). Therefore, we selected SPRY2
This study aimed to identify polymorphisms in a group of and SPRY4 as candidate genes owing to their role as inhibitors
genes underlying multiple pathways related with MLIA through of this pathway.
a large-scale candidate gene approach, thus allowing a better In mice, SPRY2 gene expression possibly prevents SHH
understanding of the mechanisms involved in MLIA. Our expression in the diastema bud by inhibiting FGF signaling
results show that PAX9, EDA, SPRY2, SPRY4 and WNT10A from the mesenchyme. Another member of the sprouty family is
genes play a role in MLIA susceptibility as protective factors or the SPRY4 gene, which antagonizes the response to FGF signal-
as risk factors, with important interactions between them. ing from the enamel knot (Klein et al., 2006). Importantly, stud-
ies in mice show that double knockout of Spry2 and Spry4
results in enlarged incisors, with enamel present on both the
Role of Transcription Factors in Hypodontia
lingual and labial sides (Klein et al., 2008). Additionally, in both
PAX9 is a transcription factor involved in craniofacial and tooth Spry2- and Spry4- null mice embryos, a toothless gap known as
development. Some mutations in the coding region of PAX9 diastema develops supernumerary teeth, reinforcing their role in
gene were already identified in individuals with nonsyndromic normal tooth formation.
oligodontia (Stockton et al., 2000; Lammi et al., 2003; We found that the GA genotype of rs504122 in the SPRY2
Jumlongras et al., 2004; Klein et al., 2005; Suda et al., 2011; gene leads to an increased risk in individuals with MLIA, point-
Zhu et al., 2012). In a previous study, a polymorphism ing to an effect of this gene in our sample. Additionally, we
(rs4904210) in PAX9 gene was identified by sequencing 12 found a SPRY4 haplotype associated with an increased MLIA
Portuguese families with MLIA; however, no statistically sig- risk. Although this result does not stand after permutation test-
nificant association was found (Pinho et al., 2010b). Wang et al. ing, we cannot exclude a possible involvement of this haplotype
(2011) also performed a sequencing analysis of this gene in a in MLIA etiology.
Chinese family with oligodontia, and the same SNP was found
in the proband and in the maternal family members; therefore, it
WNT Signaling and MLIA
is likely that this polymorphism is involved in oligodontia. By
applying a case-control approach, we found that rs7149262 and A number of studies aimed to find causal mutations implicated
rs8004560 are associated with a high risk of MLIA. The A allele in teeth agenesis. More recently, WNT10A gene mutations have
of both SNPs were found at a significantly higher frequency in been linked to syndromic and isolated severe tooth agenesis.
cases when compared with controls; this fact is reinforced by the Additionally, some studies found that this gene could play a role
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in nonsyndromic tooth agenesis; however, the frequency of Ciência, POPH–QREN–Tipologia 4.2–Promoção do Emprego
WNT10A mutations is much higher when more than 4 teeth are Científico, cofunded by ESF and national funds by the Ministério
missing, showing that this gene must be involved in severe da Ciência e Ensino Superior. The authors declare no potential
forms of this trait (van den Boogaard et al., 2012). conflicts of interest with respect to the authorship and/or publi-
Our results confirm the involvement of WNT10A and the cation of this article.
WNT signaling pathway in this trait susceptibility with the con-
tribution of a common variant.
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