先天缺牙相关EDAR基因突变报道及携带双突变位点的HED家系分析

doi:10.3969/j.issn.1674-8115.2024.06.004

上海交通大学学报（医学版） ›› 2024, Vol. 44 ›› Issue (6): 694-701.doi: 10.3969/j.issn.1674-8115.2024.06.004

先天缺牙相关EDAR基因突变报道及携带双突变位点的HED家系分析

兰嵘(), 代庆刚, 喻康, 卞晓玲, 叶丽娟, 吴轶群, 王凤()

上海交通大学医学院附属第九人民医院口腔第二门诊部，上海交通大学口腔医学院，国家口腔医学中心，国家口腔疾病临床医学研究中心，上海市口腔医学重点实验室，上海市口腔医学研究所，上海 201999

收稿日期:2024-02-08 接受日期:2024-03-19 出版日期:2024-06-28 发布日期:2024-06-28
通讯作者: 王凤 E-mail:lanrongcq@163.com;diana_wangfeng@aliyun.com
作者简介:兰　嵘（1998—），女，硕士生；电子信箱：lanrongcq@163.com。
基金资助:
国家自然科学基金(82271004);上海市自然科学基金(21ZR1437700);上海交通大学医学院附属第九人民医院生物样本库项目(YBKB202101);上海交通大学医学院附属第九人民医院研究型医师(2022yxyjxys-wf);上海交通大学医学院附属第九人民医院“交叉”研究基金项目(JYJC202305)

Congenital tooth agenesis-related EDAR variants and pedigree analysis of HED patients with two variants

LAN Rong(), DAI Qinggang, YU Kang, BIAN Xiaoling, YE Lijuan, WU Yiqun, WANG Feng()

Department of 2nd Dental Center, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology, Shanghai 201999, China

Received:2024-02-08 Accepted:2024-03-19 Online:2024-06-28 Published:2024-06-28
Contact: WANG Feng E-mail:lanrongcq@163.com;diana_wangfeng@aliyun.com
Supported by:
National Natural Science Foundation of China(82271004);Natural Science Foundation of Shanghai(21ZR1437700);Project of Biobank of Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine(YBKB202101);Project of Research Physician of Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine(2022yxyjxys-wf);"Cross" Project Cooperation Fund of Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine(JYJC202305)

摘要/Abstract

摘要：

目的·探索先天缺牙相关的外异蛋白A受体（ectodysplasin A receptor，EDAR）基因突变位点，初步分析EDAR基因突变导致综合征型和非综合征型缺牙的原因。方法·研究对象为就诊于上海交通大学医学院附属第九人民医院口腔第二门诊部的先天缺牙患者及其家系成员，提取其外周血中的基因组DNA进行全外显子组测序。通过初步筛选后，用PolyPhen-2、Mutation Taster、Provean对潜在突变位点的有害性进行预测，对分析后的突变位点进行Sanger测序验证。进行突变位点的保守性分析，使用在线工具Swiss-Model进行同源建模，分析EDAR蛋白的三维结构变化。对患者及其家系成员的先天缺牙和全身发育情况进行临床检查。结果·在纳入的先天缺牙患者中共发现5名EDAR基因突变患者，1名患者携带移码突变c.368_369insC（p.L123fs），4名患者携带错义突变。在EDAR错义突变患者中，有2名患有非综合征型缺牙（non-syndromic tooth agenesis，NSTA），分别携带c.77C>A（p.A26E）纯合突变和c.380C>T（p.P127L）杂合突变。另外2名患有少汗型外胚层发育不良（hypohidrotic ectodermal dysplasia，HED），均带有2个基因突变位点：1名为EDAR复合杂合患者，携带来自父亲的EDAR c.77C>T（p.A26V）和来自母亲的EDAR c.1281G>C（p.L427F）；另1名为EDAR、外异蛋白A（ectodysplasin A，EDA）双基因突变患者，EDAR c.1138A>C（p.S380R）和EDA c.1013C>T（p.T338M）均来自母亲，这2个位点在此前的报道中仅与NSTA相关。EDAR c.1281G>C（p.L427F）、c.77C>A（p.A26E）为未被报道过的错义突变新位点。错义突变可能通过改变氨基酸残基极性、电荷或体积等，对蛋白空间构象造成影响；移码突变造成了非3整倍数的碱基增加，可能导致蛋白的截短或降解。结论·发现了2个新的EDAR错义突变位点，报道了由EDAR纯合突变导致的NSTA以及由EDA、EDAR双基因突变导致HED的病例，扩展了对于EDAR突变造成HED和NSTA的致病机制的理解。

关键词: 外胚层发育不良, 家族性缺牙, 外异蛋白A受体, 外异蛋白A, 全外显子组测序

Abstract:

Objective ·To explore EDAR (ectodysplasin A receptor) gene variants that lead to congenital tooth agenesis, and preliminarily analyze the reasons why variants in EDAR can cause both syndromic and non-syndromic tooth agenesis. Methods ·Patients with congenital tooth agenesis admitted to the Department of 2nd Dental Center, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine and their family members were included, and genomic DNA from their peripheral blood was extracted for whole exome sequencing (WES). After preliminary screening, PolyPhen-2, Mutation Taster, and Provean were used to predict the harmfulness of potential variants. The screened variants in patients and their families were verified by Sanger sequencing. Conservation analysis of variants was performed, and Swiss-Model was used to analyze the changes in the three-dimensional structure of EDAR. The teeth and syndromic phenotype of the patients and their family members were investigated. Results ·Among the included congenital tooth agenesis patients, five patients with EDAR mutations were found, one with EDAR frameshift mutation c.368_369insC(p.L123fs) and the other four with EDAR missense mutations. Two of these four patients were diagnosed as non-syndromic tooth agenesis (NSTA), resulted from c.77C>A(p.A26E) homozygous mutation and c.380C>T(p.P127L) heterozygous mutation, respectively. The other two patients with two variants were diagnosed as hypohidrotic ectodermal dysplasia (HED). One compound heterozygous missense mutation patient carried EDAR c.77C>T(p.A26V) from her father and EDAR c.1281G>C (p.L427F) from her mother; the other patient with both EDAR and EDA mutations carried EDAR c.1138A>C(p.S380R) heterozygous mutation and EDA c.1013C>T(p.T338M) hemizygous mutation. Both variants were from his mother and were reported to be related with NSTA. Two of these missense mutations, EDAR c.1281G>C(p.L427F) and EDAR c.77C>A (p.A26E), had not been reported before. The missense mutations affected the protein's spatial conformation by altering the polarity, charge, or volume of the amino acid residues. The frameshift mutation caused a non-triplet base addition, which probably led to protein truncation or degradation. Conclusion ·Two new EDAR missense mutations are discovered. An NSTA patients with EDAR homozygous mutations and an HED patient with both EDA and EDAR mutations are reported. It expands the understanding of pathogenic mechanisms of EDAR mutations causing HED and NSTA.

Key words: ectodermal dysplasia, familial tooth agenesis, ectodysplasin A receptor, ectodysplasin A, whole exome sequencing

中图分类号:

R783.4

兰嵘, 代庆刚, 喻康, 卞晓玲, 叶丽娟, 吴轶群, 王凤. 先天缺牙相关EDAR基因突变报道及携带双突变位点的HED家系分析[J]. 上海交通大学学报（医学版）, 2024, 44(6): 694-701.

LAN Rong, DAI Qinggang, YU Kang, BIAN Xiaoling, YE Lijuan, WU Yiqun, WANG Feng. Congenital tooth agenesis-related EDAR variants and pedigree analysis of HED patients with two variants[J]. Journal of Shanghai Jiao Tong University (Medical Science), 2024, 44(6): 694-701.

图/表 4

表1 5名先天缺牙患者 EDAR 及 EDA 突变位点致病性预测

Tab 1 Pathogenicity prediction of EDAR and EDA mutations in five patients

ID	Gene	Gender	Age/year	Pheno-type	Nucleotide change (amino acid change)	Zygosity	Mutation type	ACMG criteria	Polyphen⁃2 (score)	Mutation taster	Provean (score)	Novel or reported
1	EDAR	Female	31	HED	c.368_369insC (p.L123fs)	Hom	Frameshift	LP(PVS1, PM2, PP1)	NA	Disease causing	NA	YU, et al.^[8]
2	EDAR	Female	9	HED	c.77C>T (p.A26V)	cHet	Missense	LP(PS1, PM2, PP3)	PD (0.99)	Polymor-phism	Neutral (-1.399)	PLAISANCIÉ, et al.^[9]
2	EDAR	Female	9	HED	c.1281G>C (p.L427F)	cHet	Missense	LP(PM1, PM2, PP3, PM3)	PD (1.00)	Disease causing	Neutral (-1.061)	Novel
3	EDAR	Male	9	HED	c.1138A>C (p.S380R)	Het	Missense	VUS(PM3, BP3, BP5)	PD (1.00)	Polymor-phism	Neutral (-0.948)	ZHANG, et al.^[10]
3	EDA	Male	9	HED	c.1013C>T (p.T338M)	Hemi	Missense	P(PS3, PM1, PM2, PP1, PP3)	PD (1.00)	Disease causing	Neutral (-2.145)	LI, et al.^[11]
4	EDAR	Male	16	NSTA	c.380C>T (p.P127L)	Het	Missense	VUS(PM2, PP1, PP3)	PD (0.99)	Disease causing	Neutral (-0.335)	YU, et al.^[8]
5	EDAR	Male	19	NSTA	c.77C>A (p.A26E)	Hom	Missense	VUS(PM2, PM3, PM5)	PD (0.99)	Polymor-phism	Neutral (-1.271)	Novel

图1 EDAR 突变的保守性分析及突变蛋白质结构预测Note： A. Schematic diagram of wild-type EDAR protein and the localization of identified EDAR variants (red squares indicate variants found in NSTA patients, and yellow ones represent those in HED patients). B. Conservation analysis of affected amino acids among seven vertebrate species. C. Three-dimensional structure of wild-type EDAR and five missense variants (p.A26E, p.A26V, p.P127L, p.S380R, and p.L427F). E—exon; TM—transmembrane domain; Wt—wild-type.

Fig 1 Conservation analysis of EDAR variants and the structure prediction of mutant proteins

图2 EDAR 突变的先天缺牙患者恒牙和/或恒牙牙胚缺失情况Note：A. #1 HED patient with all the teeth and/or germs missing. B. #2 HED patient with all the teeth and/or germs missing. C. #3 HED patient with 21 teeth and/or germs missing, and 6 deciduous teeth retained. D. #4 NSTA patient with 7 teeth and/or germs missing, and 5 deciduous teeth retained. E. #5 NSTA patient with 14 teeth missing.

Fig 2 Permanent teeth and/or permanent teeth germs missing in congenital tooth agenesis patients with EDAR variants

图3 2位携带双突变位点的HED患者家系分析及Sanger测序结果Note： A. #2 proband carried compound heterozygous missense mutation, EDAR c.77C>T(p.A26V) from her father and EDAR c.1281G>C(p.L427F) from her mother; B. #3 proband carried EDAR c.1138A>C(p.S380R) heterozygous mutation and EDA c.1013C>T(p.T338M) hemizygous mutation, both from his mother. Squares indicate males, and circles indicate females. Filled squares/circles represent individuals with tooth agenesis, and empty ones represent unaffected subjects. Red knots mean that variants were verified by Sanger sequencing.

Fig 3 Pedigree analysis and Sanger sequencing of two HED patients with two variants

参考文献 26

1	AL-ANI A H, ANTOUN J S, THOMSON W M, et al. Hypodontia: an update on its etiology, classification, and clinical management[J]. Biomed Res Int, 2017, 2017: 9378325.
2	LAN R, WU Y Q, DAI Q G, et al. Gene mutations and chromosomal abnormalities in syndromes with tooth agenesis[J]. Oral Dis, 2023, 29(6): 2401-2408.
3	TRZECIAK W H, KOCZOROWSKI R. Molecular basis of hypohidrotic ectodermal dysplasia: an update[J]. J Appl Genet, 2016, 57(1): 51-61.
4	CHASSAING N, BOURTHOUMIEU S, COSSEE M, et al. Mutations in EDAR account for one-quarter of non-ED1-related hypohidrotic ectodermal dysplasia[J]. Hum Mutat, 2006, 27(3): 255-259.
5	GAO Y Z, JIANG X H, WEI Z, et al. The EDA/EDAR/NF-κB pathway in non-syndromic tooth agenesis: a genetic perspective[J]. Front Genet, 2023, 14: 1168538.
6	ZHOU M Q, ZHANG H, CAMHI H, et al. Analyses of oligodontia phenotypes and genetic etiologies[J]. Int J Oral Sci, 2021, 13(1): 32.
7	PARVEEN A, KHAN S A, MIRZA M U, et al. Deleterious variants in WNT10A, EDAR, and EDA causing isolated and syndromic tooth agenesis: a structural perspective from molecular dynamics simulations[J]. Int J Mol Sci, 2019, 20(21): 5282.
8	YU K, DOU J Q, HUANG W, et al. Expanding the genetic spectrum of tooth agenesis using whole-exome sequencing[J]. Clin Genet, 2022, 102(6): 503-516.
9	PLAISANCIÉ J, BAILLEUL-FORESTIER I, GASTON V, et al. Mutations in WNT10A are frequently involved in oligodontia associated with minor signs of ectodermal dysplasia[J]. Am J Med Genet A, 2013, 161A(4): 671-678.
10	ZHANG L T, YU M, WONG S W, et al. Comparative analysis of rare EDAR mutations and tooth agenesis pattern in EDAR- and EDA-associated nonsyndromic oligodontia[J]. Hum Mutat, 2020, 41(11): 1957-1966.
11	LI S F, LI J H, CHENG J, et al. Non-syndromic tooth agenesis in two Chinese families associated with novel missense mutations in the TNF domain of EDA (ectodysplasin A)[J]. PLoS One, 2008, 3(6): e2396.
12	张刘陶. EDAR基因突变导致的非综合征型先天缺牙的易感牙位和功能研究[D]. 北京: 北京大学, 2021.
	ZHANG L T. Functional study and susceptible tooth position of non-syndromic tooth agenesis caused by EDAR mutations[D]. Beijing: Peking University, 2021.
13	WOHLFART S, SCHNEIDER H. Variants of the ectodysplasin A1 receptor gene underlying homozygous cases of autosomal recessive hypohidrotic ectodermal dysplasia[J]. Clin Genet, 2019, 95(3): 427-432.
14	ZENG B H, ZHAO Q, LI S J, et al. Novel EDA or EDAR mutations identified in patients with X-linked hypohidrotic ectodermal dysplasia or non-syndromic tooth agenesis[J]. Genes, 2017, 8(10): 259.
15	FOURNIER B P, BRUNEAU M H, TOUPENAY S, et al. Patterns of dental agenesis highlight the nature of the causative mutated genes[J]. J Dent Res, 2018, 97(12): 1306-1316.
16	CHEN Y T, LIU H C, HAN D, et al. Association between EDAR polymorphisms and non-syndromic tooth agenesis in the Chinese Han population[J]. Chin J Dent Res, 2017, 20(3): 153-159.
17	张红玉, 杨丽媛, 孟令强, 等. 全外显子测序检测非综合征型多数牙先天缺失家系中EDAR基因新突变的研究[J]. 实用口腔医学杂志, 2021, 7(6): 783-789.
	ZHANG H Y, YANG L Y, MENG L Q, et al. A novel EDAR mutation identified in nonsyndromic oligodontia patients by whole exome sequencing[J]. Journal of Practical Stomatology, 2021, 7(6): 783-789.
18	柳星宇, 朱俊霞, 赵玉鸣. 少汗性外胚层发育不良患者全外显子组测序分析[J]. 中华口腔医学杂志, 2022, 57(2): 154-160.
	LIU X Y, ZHU J X, ZHAO Y M. Whole exome sequencing and analysis of hypohidrotic ectodermal dysplasia patients[J]. Chinese Journal of Stomatology, 2022, 57(2): 154-160.
19	CASAL M L, LEWIS J R, MAULDIN E A, et al. Significant correction of disease after postnatal administration of recombinant ectodysplasin A in canine X-linked ectodermal dysplasia[J]. Am J Hum Genet, 2007, 81(5): 1050-1056.
20	YU K, HUANG C H, WAN F T, et al. Structural insights into pathogenic mechanism of hypohidrotic ectodermal dysplasia caused by ectodysplasin A variants[J]. Nat Commun, 2023, 14(1): 767.
21	VAN DER HOUT A H, OUDESLUIJS G G, VENEMA A, et al. Mutation screening of the ectodysplasin-A receptor gene EDAR in hypohidrotic ectodermal dysplasia[J]. Eur J Hum Genet, 2008, 16(6): 673-679.
22	PÉREZ-PÉREZ J M, CANDELA H, MICOL J L. Understanding synergy in genetic interactions[J]. Trends Genet, 2009, 25(8): 368-376.
23	DELTAS C. Digenic inheritance and genetic modifiers[J]. Clin Genet, 2018, 93(3): 429-438.
24	CHU K Y, WANG Y L, CHOU Y R, et al. Synergistic mutations of LRP6 and WNT10A in familial tooth agenesis[J]. J Pers Med, 2021, 11(11): 1217.
25	HAN Y, WANG X L, ZHENG L Y, et al. Pathogenic EDA mutations in Chinese Han families with hypohidrotic ectodermal dysplasia and genotype-phenotype: a correlation analysis[J]. Front Genet, 2020, 11: 21.
26	LIN Y, ZHENG L W, FAN L, et al. The epigenetic regulation in tooth development and regeneration[J]. Curr Stem Cell Res Ther, 2018, 13(1): 4-15.

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先天缺牙相关EDAR基因突变报道及携带双突变位点的HED家系分析

Congenital tooth agenesis-related EDAR variants and pedigree analysis of HED patients with two variants

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