Rare Variants in LRP4 Are Associated with Mesiodens, Root Maldevelopment, and Oral Exostoses in Humans

Abstract

Background: Low density lipoprotein receptor-related protein 4 (LRP4; MIM 604270) modulates WNT/β-catenin signaling, through its binding of WNT ligands, and to co-receptors LRP5/6, and WNT inhibitors DKK1, SOSTDC1, and SOST. LRP4 binds to SOSTDC1 and WNT proteins establishing a negative feedback loop between Wnt/β-catenin, Bmp, and Shh signaling during the bud and cap stages of tooth development. Consistent with a critical role for this complex in developing teeth, mice lacking Lrp4 or Sostdc1 have multiple dental anomalies including supernumerary incisors and molars. However, there is limited evidence supporting variants in LRP4 in human dental pathologies.

Methods: We clinically, radiographically, and molecularly investigated 94 Thai patients with mesiodens. Lrp4 mutant mice were generated in order to study the effects of aberrant Lrp4 expression in mice.

Results: Whole exome and Sanger sequencing identified three extremely rare variants (c.4154A>G, p.Asn1385Ser; c.3940G>A, p.Gly1314Ser; and c.448G>A, p.Asp150Asn) in LRP4 in seven patients with mesiodens. Two patients had oral exostoses and two patients had root maldevelopments. Supernumerary incisors were observed in Lrp4 mutant mice.

Conclusions: Our study implicates heterozygous genetic variants in LRP4 as contributing factors in the presentation of mesiodens, root maldevelopments, and oral exostoses, possibly as a result of altered WNT/β-catenin-BMP-SHH signaling.

Keywords: buccal exostoses; root anomalies; root malformations; torus mandibularis; torus palatinus.

Figure 1

Pedigrees of (A) family 1 and (B) family 4. Patient II-3 of family1 had mesiodens but not available for genetic study. Patient II-2 of family 4 is not available for study.

Figure 2

Mesiodens phenotypes. Extracted mesiodens of (A) patient 1, (B) patient 2. (C) patient 3. (D,E) Periapical radiographs show (D) Patient 5—Inverted mesiodens (arrow). (E) Patient 6—Unerupted mesiodens (arrow). (F) Patient 1—Buccal exostoses (arrows). (G) Panoramic radiograph showing inverted mesiodens (arrow) and unseparated roots of the maxillary first permanent molars (asterisks).

Figure 3

Patient 4. (A) Torus palatinus (arrow). (B) Torus mandibularis (arrows). (C) Panoramic radiograph showing long roots of mandibular permanent canines, short roots of second premolars, and unseparated roots of second and third permanent molars (arrows).

Figure 4

Sequence chromatograms of LRP4 variants. (A) The c.4154A > G, p.Asn1385Ser (rs768733310) variant in patients 1–3. Patient 3 is homozygous for the variant; (B) The c.3940G>A; p.Gly1314Ser (rs371961330) variant in patients 4–6; and (C) the c.448G>A; p.Asp150Asn (rs200746048) variant in patient 7.

Figure 5

Structural context of LRP4 mutations. (A) Map of structural domains and mutations within the LRP4 protein sequence. Structural domains are coded by color as indicated. The residue numbering is based on accession number NCBI: NP_002325.2. The starting position of each structural domain is marked on the bottom and the ending position on the top. (B) Three-dimensional model of the LRP4 structure predicted by AlphaFold2 with structural domains in the same colors as in part A. Magnified views of the wild type and mutated amino acids and surrounding amino acids in stick representation are shown to the side to indicate the molecular environment. Possible polar interactions are shown as dashed lines. Oxygen atoms are shown in red, nitrogen in blue and sulfur atoms in yellow, while carbon atoms are colored according to the domain color. The intracellular domain has no predicted structure and is shown schematically as a box.

Figure 6

Lrp4 mutant mice. Arrowheads indicating endogenous incisors, while arrows indicating supernumerary incisors.

Figure 7

Hypothetical flowchart of pathogenetic pathways for mesiodens formation as a result of LRP4 variants. When the mutant Lrp4 does not properly interact with Sostdc1 as a result of mutation, it upregulates Wnt/β-catenin signaling by forming the Wnt-Fzd-Lrp4 complex. The resulting increase in WNT/β-catenin signaling and/or broadening of the placodal regions is responsible for the subsequent formation of the supernumerary teeth. Overactivation of WNT/β-catenin signaling leading to ectopic expression of SHH signaling is the key to mesiodens formation [3,4,6,12].