Genetic studies of nonsyndromic orofacial clefts (NSOC) focus on identifying susceptibility genes and elucidating underlying pathogenesis. A correlation between orofacial clefts and hypertelorism has been established by previous studies, hinting at shared genetic risk factors.
Materials and Methods
Syndromes characterized by hypertelorism and orofacial clefts were screened, followed by analysis and selection of their causative genes, resulting in 35 candidate genes. After genotyping quality control, 340 single nucleotide polymorphisms (SNPs) were analyzed. Allelic and genotypic associations were evaluated under the additive model with Bonferroni correction. Linkage disequilibrium and haplotype analysis were performed.
Results
Single nucleotide polymorphisms that showed significant allelic associations with NSOC subtypes are notably within TRAPPC9, TBX1, and ZIC2 genes. Single nucleotide polymorphisms within TRAPPC9 were primarily associated with nonsyndromic cleft lip and palate (NSCLP), while SNPs within TBX1 exhibited risk and protective effects across NSCLP, nonsyndromic cleft lip only (NSCLO), and nonsyndromic cleft palate only. ZIC2 SNPs were significantly associated with NSCLP and NSCLO. Although 15 SNPs in CDH1 showed allelic association with NSCLO and were in strong linkage disequilibrium, no statistically significant genotypic or haplotypic associations were identified.
Conclusion
TRAPPC9, TBX1, and ZIC2 are identified as novel susceptibility genes for NSOC in the western Han Chinese population, with TRAPPC9 and TBX1 showing distinct risk and protective effects among subtypes. While further studies are required to confirm their role, these findings deepen our understanding of NSOC genetics, emphasize the importance of subtype analysis, and provide valuable directions for further mechanistic studies.
FanD, WuS, LiuL, Xia Q, Tian G, Wang W, Ye S, Wang L, Rao J, Yang X, et al.Prevalence of non-syndromic orofacial clefts: based on 15,094,978 Chinese perinatal infants. Oncotarget. 2018;9(17):13981-13990. doi:https://doi.org/10.18632/oncotarget.24238
2.
NakatomiM, LudwigKU, KnappM, Kist R, Lisgo S, Ohshima H, Mangold E, Peters H.Msx1 deficiency interacts with hypoxia and induces a morphogenetic regulation during mouse lip development. Development. 2020;147(21):dev189175. doi:https://doi.org/10.1242/dev.189175
3.
YuY, ZuoX, HeM, Gao J, Fu Y, Qin C, Meng L, Wang W, Song Y, Cheng Y, et al.Genome-wide analyses of non-syndromic cleft lip with palate identify 14 novel loci and genetic heterogeneity. Nat Commun. 2017;8:14364. doi:https://doi.org/10.1038/ncomms14364
4.
LeslieEJ, CarlsonJC, ShafferJR, Feingold E, Wehby G, Laurie CA, Jain D, Laurie CC, Doheny KF, McHenry T, et al.A multi-ethnic genome-wide association study identifies novel loci for non-syndromic cleft lip with or without cleft palate on 2p24.2, 17q23 and 19q13. Hum Mol Genet. 2016;25(13):2862-2872. doi:https://doi.org/10.1093/hmg/ddw104
5.
HuangL, JiaZ, ShiY, Du Q, Shi J, Wang Z, Mou Y, Wang Q, Zhang B, Wang Q, et al.Genetic factors define CPO and CLO subtypes of nonsyndromicorofacial cleft. PLoS Genet. 2019;15(10):e1008357. doi:https://doi.org/10.1371/journal.pgen.1008357
6.
SivertsenA, WilcoxAJ, SkjaervenR, Vindenes HA, Abyholm F, Harville E, Lie RT.Familial risk of oral clefts by morphological type and severity: population based cohort study of first degree relatives. Br Med J.2008;336(7641):432-434. doi:https://doi.org/10.1136/bmj.39458.563611.AE
7.
GrosenD, ChevrierC, SkyttheA, Bille C, Mølsted K, Sivertsen A, Murray JC, Christensen K. A cohort study of recurrence patterns among more than 54,000 relatives of oral cleft cases in Denmark: support for the multifactorial threshold model of inheritance. J Med Genet. 2010;47(3):162-168. doi:https://doi.org/10.1136/jmg.2009.069385
8.
CarlsonJC, AnandD, ButaliA, Buxo CJ, Christensen K, Deleyiannis F, Hecht JT, Moreno LM, Orioli IM, Padilla C, et al.A systematic genetic analysis and visualization of phenotypic heterogeneity among orofacial cleft GWAS signals. Genet Epidemiol. 2019;43(6):704-716. doi:https://doi.org/10.1002/gepi.22214
9.
VilhjálmssonBJNordborgM. The nature of confounding in genome-wide association studies. Nat Rev Genet. 2013;14(1):1-2. doi:https://doi.org/10.1038/nrg3382
10.
SpeedDBaldingDJ. Relatedness in the post-genomic era: is it still useful?Nat Rev Genet. 2015;16(1):33-44. doi:https://doi.org/10.1038/nrg3821
11.
PriceALZaitlenNAReichDPattersonN. New approaches to population stratification in genome-wide association studies. Nat Rev Genet. 2010;11(7):459-463. doi:https://doi.org/10.1038/nrg2813
12.
EsheteMA, LiuH, LiM, et al.Loss-of-function GRHL3 variants detected in African patients with isolated cleft palate. J Dent Res. 2018;97(1):41-48. doi:https://doi.org/10.1177/0022034517729819
13.
MangoldE, BöhmerAC, IshorstN, et al.Sequencing the GRHL3 coding region reveals rare truncating mutations and a common susceptibility variant for nonsyndromic cleft palate. Am J Hum Genet.2016;98(4):755-762. doi:https://doi.org/10.1016/j.ajhg.2016.02.013
14.
VieiraARModestoAMeiraRBarbosaARSLidralACMurrayJC. Interferon regulatory factor 6 (IRF6) and fibroblast growth factor receptor 1 (FGFR1) contribute to human tooth agenesis. Am J Med Genet A. 2007;143A(6):538-545. doi:https://doi.org/10.1002/ajmg.a.31620
HirschfeldWJAdussH. Interorbital distance in cleft lip and palate: significant differences found by sign test. J Dent Res. 1974;53(4):947. doi:https://doi.org/10.1177/00220345740530044001
19.
FigalovaPHajnisKSmahelZ. The interocular distance in children with cleft before the operation. Acta Chir Plast. 1974;16(2):65-77.
20.
SunY, HuangY, YinA, Pan Y, Wang Y, Wang C, Du Y, Wang M, Lan F, Hu Z, et al.Genome-wide association study identifies a new susceptibility locus for cleft lip with or without a cleft palate. Nat Commun. 2015;6:6414. doi:https://doi.org/10.1038/ncomms7414
21.
AguiarDPSghariSCreuzetS. The facial neural crest controls fore- and midbrain patterning by regulating Foxg1 expression through Smad1 activity. Development. 2014;141(12):2494-2505. doi:https://doi.org/10.1242/dev.101790
22.
AthanasiouAEHackBEnemarkHSindet-PedersenS. Transverse dentofacial structure of young men who have undergone surgical correction of unilateral cleft lip and palate: a posteroanterior cephalometric study. Int J Adult Orthodon Orthognath Surg. 1996;11(1):19-28.
23.
Raposo-do-AmaralCMKriegerHCabelloPHBeiguelmanB. Heritability of quantitative orbital traits. Hum Biol. 1989;61(4):551-557.
24.
ImSW, KimHJ, LeeMK, Yi JH, Jargal G, Sung J, Cho SI, Kim JI.Genome-wide linkage analysis for ocular and nasal anthropometric traits in a Mongolian population. Exp Mol Med. 2010;42(12):799-804. doi:https://doi.org/10.3858/emm.2010.42.12.080
25.
FarkasLG, KaticMJ, ForrestCR, Alt KW, Bagic I, Baltadjiev G, Cunha E, Cvicelová M, Davies S, Erasmus I, et al.International anthropometric study of facial morphology in various ethnic groups/races. J Craniofac Surg. 2005;16(4):615-646. doi:https://doi.org/10.1097/01.scs.0000171847.58031.9e
PryorHB. Objective measurement of interpupillary distance. Pediatrics. 1969;44(6):973-977.
28.
KnolMJ, PawlakMA, LamballaisS, Terzikhan N, Hofer E, Xiong Z, Klaver CCW, Pirpamer L, Vernooij MW, Ikram MA, et al.Genetic architecture of orbital telorism. Hum Mol Genet. 2022;31(9):1531-1543. doi:https://doi.org/10.1093/hmg/ddab334
29.
JainRBKrogmanWM. Craniofacial growth in clefting from one month to ten years as studied by P-A headfilms. Cleft Palate J. 1983;20(4):314-326.
30.
IshiguroK, KrogmanWM, MazaheriM, HardingRL. A longitudinal study of morphological craniofacial patterns via P-A x-ray headfilms in cleft patients from birth to six years of age. Cleft Palate J. 1976;13(1):104-126.
31.
Penon-PortmannMHodoglugilUArunPWYipTSlavotinekATenneyJL. TRAPPC9-related neurodevelopmental disorder: report of a homozygous deletion in TRAPPC9 due to paternal uniparental isodisomy. Am J Med Genet A. 2023;191(4):1077-1082. doi:https://doi.org/10.1002/ajmg.a.63100
32.
HuWH, PendergastJS, MoXM, Brambilla R, Bracchi-Ricard V, Li F, Walters WM, Blits B, He L, Schaal SM, et al.NIBP, a novel NIK and IKK(beta)-binding protein that enhances NF-(kappa)B activation. J Biol Chem. 2005;280(32):29233-29241. doi:https://doi.org/10.1074/jbc.M501670200
33.
LeinES, HawrylyczMJ, AoN, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ, et al.Genome-wide atlas of gene expression in the adult mouse brain. Nature. 2007;445(7124):168-176. doi:https://doi.org/10.1038/nature05453
34.
MochidaGH, MahajnahM, HillAD, Basel-Vanagaite L, Gleason D, Hill RS, Bodell A, Crosier M, Straussberg R, Walsh CA.A truncating mutation of TRAPPC9 is associated with autosomal-recessive intellectual disability and postnatal microcephaly. Am J Hum Genet. 2009;85(6):897-902. doi:https://doi.org/10.1016/j.ajhg.2009.10.027
LiJ, RodriguezG, HanX, Janečková E, Kahng S, Song B, Chai Y.Regulatory mechanisms of soft palate development and malformations. J Dent Res. 2019;98(9):959-967. doi:https://doi.org/10.1177/0022034519851786
37.
YanY, SuM, SongY, Tang Y, Tian XC, Rood D, Lai L.Tbx1 modulates endodermal and mesodermal differentiation from mouse induced pluripotent stem cells. Stem Cells Dev. 2014;23(13):1491-1500. doi:https://doi.org/10.1089/scd.2013.0488
38.
WeaverKNRutledgeKDGrantJHRobinNH. Imperforate anus is a rare associated finding in blepharocheilodontic syndrome. Am J Med Genet A. 2010;152A(2):438-440. doi:https://doi.org/10.1002/ajmg.a.33207
39.
AlviziLNaniDBritoLAKobayashiGSPassos-BuenoMRMayorR. Neural crest E-cadherin loss drives cleft lip/palate by epigenetic modulation via pro-inflammatory gene-environment interaction. Nat Commun. 2023;14(1):2868. doi:https://doi.org/10.1038/s41467-023-38526-1
40.
CoxLL, CoxTC, UribeM, ML, Zhu Y, Richter CT, Nidey N, Standley JM, Deng M, Blue E, Chong JX, et al.Mutations in the epithelial cadherin-p120-catenin complex cause Mendelian non-syndromic cleft lip with or without cleft palate. Am J Hum Genet. 2018;102(6):1143-1157. doi:https://doi.org/10.1016/j.ajhg.2018.04.009
41.
LiM, WangH. Pathway analysis identified a significant association between cell-cell adherens junctions-related genes and non-syndromic cleft lip/palate in 895 Asian case-parent trios. Arch Oral Biol. 2022;136(5):105384. doi:https://doi.org/10.1016/j.archoralbio.2022.105384
42.
GreenBL, FasayeGA, SamaranayakeSG, DuemlerA, GambleLA, DavisJL. Frequent cleft lip and palate in families with pathogenic germline CDH1 variants. Front Genet. 2022;13(4)(4):1012025. doi:https://doi.org/10.3389/fgene.2022.1012025
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