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Novel MSX1 Variants Identified in Families with Nonsyndromic

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Novel MSX1 Variants Identified in Families with Nonsyndromic International Journal of Oral Science www.nature.com/ijos ARTICLE OPEN Novel MSX1 variants identified in families with nonsyndromic oligodontia Jinglei Zheng1, Miao Yu1, Haochen Liu1, Tao Cai2, Hailan Feng1, Yang Liu1 and Dong Han 1 The goal of this study was to identify MSX1 gene variants in multiple Chinese families with nonsyndromic oligodontia and analyse the functional influence of these variants. Whole-exome sequencing (WES) and Sanger sequencing were performed to identify the causal gene variants in five families with nonsyndromic oligodontia, and a series of bioinformatics databases were used for variant confirmation and functional prediction. Phenotypic characterization of the members of these families was described, and an in vitro analysis was performed for functional evaluation. Five novel MSX1 heterozygous variants were identified: three missense variants [c.662A>C (p.Q221P), c.670C>T (p.R224C), and c.809C>T (p.S270L)], one nonsense variant [c.364G>T (p.G122*)], and one frameshift variant [c.277delG (p.A93Rfs*67)]. Preliminary in vitro studies demonstrated that the subcellular localization of MSX1 was abnormal with the p.Q221P, p.R224C, p.G122*, and p.A93Rfs*67 variants compared to the wild type. Three variants (p.Q221P, p.G122*, and p. A93Rfs*67) were classified as pathogenic or likely pathogenic, while p.S270L and p.R224C were of uncertain significance in the current data. Moreover, we summarized and analysed the MSX1-related tooth agenesis positions and found that the type and variant locus were not related to the severity of tooth loss. Our results expand the variant spectrum of nonsyndromic oligodontia and provide valuable information for genetic counselling. International Journal of Oral Science (2021) ;13:2 https://doi.org/10.1038/s41368-020-00106-0 1234567890();,: INTRODUCTION (HD), which is encoded by exon 2 of the gene.10 MSX1 plays crucial Congenital tooth agenesis (TA) is one of the most common dental rolesinregulatingepithelial–mesenchymal interactions that are anomalies and may lead to masticatory dysfunction, speech required for the morphogenesis of a variety of embryonic tissues, alteration, aesthetic problems, and malocclusion.1 Based on the such as the limb bud, embryonic tail, hair follicle, and tooth bud.11 existence of other ectodermal symptoms, TA can be classified as This molecule also has roles in regulating the development of the syndromic or nonsyndromic. Nonsyndromic TA can be further nervous system and tumour growth inhibition.12 Msx1−/− mice are categorized into hypodontia (absence of one to five permanent characterized by a deficiency of both mandibular and maxillary teeth, excluding the third molars), oligodontia (absence of six or alveolar bones, a complete cleft palate, and a failure of tooth more permanent teeth, excluding the third molars), and anodontia development, which is arrested at the bud stage.13,14 In humans, (complete absence of teeth), based on the number of missing MSX1 is associated with nonsyndromic TA (OMIM, #106600—Tooth teeth.2 The overall incidence of TA is reported to be approximately Agenesis, Selective, 1; STHAG1), nonsyndromic cleft lip with or 2–10%, excluding the third molars,3,4 whereas oligodontia is without cleft palate (CL/P, OMIM #608874, Orofacial Cleft 5, OFC5), observed in approximately 0.08–0.16% of the population.5 TA has Witkop syndrome (OMIM, #189500), and Wolf–Hirschhorn syndrome been associated with many factors, including genetics, epige- (WHS, OMIM, #194190).12 To date, according to the Human Gene netics, and environmental factors. Among them, genetic defects Mutation Database (HGMD, http://www.hgmd.cf.ac.uk/)and have been demonstrated to play a major role.6 PubMed database, 36 variants have been identified in the MSX1 A number of genes have been shown to be associated with gene that contribute to nonsyndromic TA, and most of them are nonsyndromic TA, including axin inhibition protein 2 (AXIN2), missense or frameshift variants.1,6,8,10,15–39 ectodysplasin A (EDA), low-density lipoprotein receptor-related This study aimed to continue to expand the variant spectrum of protein 6 (LRP6), muscle segment homeobox 1 (MSX1), paired box MSX1 associated with nonsyndromic oligodontia, explore the 9(PAX9), and wingless-type mouse mammary tumour virus functional impacts of the identified novel variant loci, and analyse integration site family member 10A (WNT10A)and10B(WNT10B). the genotype–phenotype correlations. Variants in the above seven genes account for approximately 90% of the variants responsible for nonsyndromic TA.7 As the first gene identified in a family with TA,8 the MSX1 gene is a hotspot candidate. RESULTS The MSX1 gene is located on 4p16.2, belongs to the homeobox Clinical findings and variant detection gene family, and encodes a transcription factor, MSX1.9 MSX1 has a The TA patterns (excluding the third molars) and pedigrees of five highly conserved and important domain called the homeodomain Chinese families are shown in Figs. 1 and 2. Using whole-exome 1Department of Prosthodontics, Peking University School and Hospital of Stomatology & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing, China and 2National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA Correspondence: Yang Liu ([email protected]) or Dong Han ([email protected]) These authors contributed equally: Jinglei Zheng, Miao Yu. Received: 27 May 2020 Revised: 24 November 2020 Accepted: 26 November 2020 Novel MSX1 variants identified in families with nonsyndromic oligodontia Zheng et al. 2 Family 1 a d Right quadrants Left quadrants e h Right quadrants Left quadrants MAX 7 6 5 4 3 2 1 1 2 3 4 5 6 7 MAX 7 6 5 4 3 2 1 1 2 3 4 5 6 7 MAND 7 6 5 4 3 2 1 1 2 3 4 5 6 7 MAND 7 6 5 4 3 2 1 1 2 3 4 5 6 7 b f c g Family 2 Family 3 i l Right quadrants Left quadrants m p Right quadrants Left quadrants MAX 7 6 5 4 3 2 1 1 2 3 4 5 6 7 MAX 7 6 5 4 3 2 1 1 2 3 4 5 6 7 MAND 7 6 5 4 3 2 1 1 2 3 4 5 6 7 MAND 7 6 5 4 3 2 1 1 2 3 4 5 6 7 j n o k Family 4 q t Right quadrants Left quadrants u x Right quadrants Left quadrants MAX 7 6 5 4 3 2 1 1 2 3 4 5 6 7 MAX 7 6 5 4 3 2 1 1 2 3 4 5 6 7 MAND 7 6 5 4 3 2 1 1 2 3 4 5 6 7 MAND 7 6 5 4 3 2 1 1 2 3 4 5 6 7 r v s w Family 5 yy’zz’Right quadrants Left quadrants Right quadrants Left quadrants MAX 7 6 5 4 3 2 1 1 2 3 4 5 6 7 MAX 7 6 5 4 3 2 1 1 2 3 4 5 6 7 MAND 7 6 5 4 3 2 1 1 2 3 4 5 6 7 MAND 7 6 5 4 3 2 1 1 2 3 4 5 6 7 Fig. 1 Dental characteristics of five families with nonsyndromic oligodontia with MSX1 variants. a–h Digital photographs, panoramic radiographs, and schematics of oligodontia in family 1, including proband #1 and her mother. i–l Digital photographs, a panoramic radiograph, and a schematic of oligodontia in family 2, including proband #2. m–p Digital photographs, a panoramic radiograph, and a schematic of oligodontia in family 3, including proband #3. q–x Digital photographs, panoramic radiographs, and schematics of oligodontia in family 4, including proband #4 and his mother. The red arrow indicates taurodontism of the left mandibular first primary molar. y–z’ Digital photographs, panoramic radiographs, and schematics of oligodontia in family 5, including proband #5 and his mother. Asterisks and solid squares indicate congenitally missing teeth. Crosses and squares with crosses indicate the extracted teeth International Journal of Oral Science (2021) 13:2 Novel MSX1 variants identified in families with nonsyndromic oligodontia Zheng et al. 3 abFamily 1 Family 2cd Family 3 Family 4 e Family 5 c.364G>T (p.G122*) c.277delG (p.A93Rfs*67) c.809C>T (p.S270L) c.662A>C (p.Q221P) c.670C>T (p.R224C) I I I I-1 I-2 I-1 I-2 I I-1 I-2 I I-1 I-2 I-3 I-4 I-1 I-2 II II II II II-1 II-2 II-1 II-2 II-3 II-4 II-5 II II-1 II-2 II-3 II-1 II-2 II-3 II-1 III III III III-1 III-1 III ? III-1 III-1 III-2 Wild-type Wild-type Wild-type Wild-type Wild-type —V— —G— —G— —L— —G— —S— —A— —Q— —P— —G— —A— —S— —L— —Y— —W— —F— —Q— —N— —R— —N— —R— —R— —A— I-1 Normal I-3 Heterogeneous mutant II-1 Normal II-2 Heterogeneous mutant —W— —F— —Q— —N— —R— —N— —R— --R/C-- —A— —V— —G— —G— —L— (Direct sequencing) II-1 Heterogeneous mutant —G— —S— —G— —A— --S/L-- —L— —Y— I-2 Normal I-4 Normal II-2 Heterogeneous mutant —W— —F— —Q— —N— —R— —N— —R— —R— —A— —V— —G— --G/X-- II-2 Heterogeneous mutant (Cloning sequencing) —G— —S— —R— —S— II-2 Heterogeneous mutant II-2 Normal III-1 Heterogeneous mutant —W— —F— --Q/P-- —N— —R— —N— —R— —R— —A— —V— —G— --G/X-- III-1 Heterogeneous mutant II-3 Heterogeneous mutant —W— —F— -Q/P- —N— —R— —N— —R— --R/C-- —A— III-1 Heterogeneous mutant —N— —R— --R/C-- —A— f p.G122* p.A93Rfs*67 p.Q221P p.S270L p.R224C Homeodomain 172 231 156 303 g 1 Exon 1 Exon 2 h p.A93Rfs*67 p.G122* p.Q221P p.R224C p.S270L Homo sapiens Pan troglodytes Macaca mulatta Canis lupus familiaris Bos taurus Mus musculus Rattus norvegicus Gallus gallus Fig.
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