The role of MMP16 in lip development is unclear. This study aimed to identify nonsyndromic cleft lip with or without palate (NSCL ± P) susceptible loci of MMP16 in western Han Chinese.
Design
We performed targeted sequencing around MMP16 combined with a 2-phase association analysis on common variants. Phase 2 association analysis was performed with NSCL ± P specific subphenotypes (NSCL and NSCLP). Then we used rare variants burden analysis and genotyping, accompanied by motif analysis.
Setting
This study was completed in a tertiary medical center.
Patients, Participants
Phase 1 targeted sequencing included 159 patients with NSCL ± P and 542 normal controls; phase 2 included 1626 patients with NSCL ± P (1047 NSCL and 579 NSCLP) and 2255 normal controls.
Interventions
Venous blood samples were collected from patients and used to extract DNA.
Main Outcome Measures
After Bonferroni correction, phase 1 significant threshold of p-value was 4.28 × 10−5 (0.05/1167 single nucleotide polymorphisms [SNPs]), and phase 2 was .00025 (0.05/200 SNPs). Burden analysis significant threshold p-value was .05.
Results
Common variants phase 1 association analysis identified 11 statistically significant SNPs (lowest p = 1.90 × 10−9, odds ratio (OR) = 0.27, 95% CI: 0.17-0.44), phase 2 replication identified 16 SNPs in NSCL ± P (lowest p = 6.26 × 10−6, OR = 0.77, 95% CI: 0.69-0.86) and 9 in NSCL (lowest p = 8.44 × 10−5, OR = 0.76, 95% CI: 0.66-0.87). Rare variants burden analysis showed no significant results, genotyping results showed they were maternally inherited.
Conclusions
Our study identified MMP16 susceptible SNPs in NSCL ± P and NSCL, emphasizing its potential role in lip development. Our study also highlighted the importance to perform association analysis with subphenotypes divided.
FanDWuSLiuL, et al.Prevalence of non-syndromic orofacial clefts: based on 15,094,978 Chinese perinatal infants. Oncotarget. 2018;9(17):13981-13990. doi:10.18632/oncotarget.24238.
2.
MosseyPALittleJMungerRGDixonMJShawWC. Cleft lip and palate. Lancet. 2009;374(9703):1773-1785. doi:10.1016/S0140-6736(09)60695-4.
3.
WyszynskiDF. Cleft lip and palate: from origin to treatment. Oxford University Press; 2002, xviii, 518 p., 4 p. of plates.
4.
DixonMJMarazitaMLBeatyTHMurrayJC. Cleft lip and palate: understanding genetic and environmental influences. Nat Rev Genet. 2011;12(3):167-178. doi:10.1038/nrg2933.
5.
BeatyTHMurrayJCMarazitaML, et al.A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4. Nat Genet. 2010;42(6):525-529. doi:10.1038/ng.580.
6.
BirnbaumSLudwigKUReutterH, et al.Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24. Nat Genet. 2009;41(4):473-477. doi:10.1038/ng.333.
7.
FonsecaRFde CarvalhoFMPolettaFA, et al.Family-based genome-wide association study in Patagonia confirms the association of the DMD locus and cleft lip and palate. Eur J Oral Sci. 2015;123(5):381-384. doi:10.1111/eos.12212.
8.
GrantSFWangKZhangH, et al.A genome-wide association study identifies a locus for nonsyndromic cleft lip with or without cleft palate on 8q24. J Pediatr. 2009;155(6):909-913. doi:10.1016/j.jpeds.2009.06.020.
9.
LeslieEJCarlsonJCShafferJR, et al.Genome-wide meta-analyses of nonsyndromic orofacial clefts identify novel associations between FOXE1 and all orofacial clefts, and TP63 and cleft lip with or without cleft palate. Hum Genet. 2017;136(3):275-286. doi:10.1007/s00439-016-1754-7.
10.
LeslieEJCarlsonJCShafferJR, 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:10.1093/hmg/ddw104.
11.
LudwigKUMangoldEHermsS, et al.Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci. Nat Genet. 2012;44(9):968-971. doi:10.1038/ng.2360.
12.
MangoldELudwigKUBirnbaumS, et al.Genome-wide association study identifies two susceptibility loci for nonsyndromic cleft lip with or without cleft palate. Nat Genet. 2010;42(1):24-26. doi:10.1038/ng.506.
13.
SunYHuangYYinA, et al.Genome-wide association study identifies a new susceptibility locus for cleft lip with or without a cleft palate. Nat Commun. 2015;6(6):6414. doi:10.1038/ncomms7414.
14.
WolfZTBrandHAShafferJR, et al.Genome-wide association studies in dogs and humans identify ADAMTS20 as a risk variant for cleft lip and palate. PLoS Genet. 2015;11(3):e1005059. doi:10.1371/journal.pgen.1005059.
15.
YuYZuoXHeM, et al.Genome-wide analyses of non-syndromic cleft lip with palate identify 14 novel loci and genetic heterogeneity. Nat Commun. 2017;8(8):14364. doi:10.1038/ncomms14364.
16.
HuangLJiaZShiY, et al.Genetic factors define CPO and CLO subtypes of nonsyndromicorofacial cleft. PLoS Genet. 2019;15(10):e1008357. doi:10.1371/journal.pgen.1008357.
17.
ChungCSBeechertAMLewRE. Test of genetic heterogeneity of cleft lip with or without cleft palate as related to race and severity. Genet Epidemiol. 1989;6(5):625-631. doi:10.1002/gepi.1370060507.
18.
RozarioTDeSimoneDW. The extracellular matrix in development and morphogenesis: a dynamic view. Dev Biol. 2010;341(1):126-140. doi:10.1016/j.ydbio.2009.10.026.
19.
PaivaKBSMaasCSDos SantosPMGranjeiroJMLetraA. Extracellular matrix composition and remodeling: current perspectives on secondary palate formation, cleft lip/palate, and palatal reconstruction. Front Cell Dev Biol. 2019;7(7):340. doi:10.3389/fcell.2019.00340.
20.
SpinaleFG. Myocardial matrix remodeling and the matrix metalloproteinases: influence on cardiac form and function. Physiol Rev. 2007;87(4):1285-1342. doi:10.1152/physrev.00012.2007.
21.
NguyenAHWangYWhiteDEPlattMOMcDevittTC. MMP-mediated mesenchymal morphogenesis of pluripotent stem cell aggregates stimulated by gelatin methacrylate microparticle incorporation. Biomaterials. 2016;76(76):66-75. doi:10.1016/j.biomaterials.2015.10.043.
22.
AcloqueHAdamsMSFishwickKBronner-FraserMNietoMA. Epithelial-mesenchymal transitions: the importance of changing cell state in development and disease. J Clin Invest. 2009;119(6):1438-1449. doi:10.1172/JCI38019.
23.
DuongTDEricksonCA. MMP-2 plays an essential role in producing epithelial-mesenchymal transformations in the avian embryo. Dev Dyn. 2004;229(1):42-53. doi:10.1002/dvdy.10465.
24.
ThieryJPAcloqueHHuangRYNietoMA. Epithelial-mesenchymal transitions in development and disease. Cell. 2009;139(5):871-890. doi:10.1016/j.cell.2009.11.007.
25.
LiYWangYYuL, et al.miR-146b-5p inhibits glioma migration and invasion by targeting MMP16. Cancer Lett. 2013;339(2):260-269. doi:10.1016/j.canlet.2013.06.018.
26.
ChenXZhangRZhangQ, et al.Chondrocyte sheet in vivo cartilage regeneration technique using miR-193b-3p to target MMP16. Aging (Albany NY). 2019;11(17):7070-7082. doi:10.18632/aging.102237.
27.
PlaisierMKapiteijnKKoolwijkP, et al.Involvement of membrane-type matrix metalloproteinases (MT-MMPs) in capillary tube formation by human endometrial microvascular endothelial cells: role of MT3-MMP. J Clin Endocrinol Metab. 2004;89(11):5828-5836. doi:10.1210/jc.2004-0860.
28.
ShiJSonMYYamadaS, et al.Membrane-type MMPs enable extracellular matrix permissiveness and mesenchymal cell proliferation during embryogenesis. Dev Biol. 2008;313(1):196-209. doi:10.1016/j.ydbio.2007.10.017.
29.
GkantidisNBlumerSKatsarosCGrafDChiquetM. Site-specific expression of gelatinolytic activity during morphogenesis of the secondary palate in the mouse embryo. PLoS One. 2012;7(10):e47762. doi:10.1371/journal.pone.0047762.
30.
LiXZhangLYinX, et al.Retinoic acid remodels extracellular matrix (ECM) of cultured human fetal palate mesenchymal cells (hFPMCs) through down-regulation of TGF-beta/Smad signaling. Toxicol Lett. 2014;225(2):208-215. doi:10.1016/j.toxlet.2013.12.013.
31.
de Oliveira DemarchiACZambuzziWFPaivaKB, et al.Development of secondary palate requires strict regulation of ECM remodeling: sequential distribution of RECK, MMP-2, MMP-3, and MMP-9. Cell Tissue Res. 2010;340(1):61-69. doi:10.1007/s00441-010-0931-6.
32.
Moreno UribeLMFominaTMungerRG, et al.A population-based study of effects of genetic loci on orofacial clefts. J Dent Res. 2017;96(11):1322-1329. doi:10.1177/0022034517716914.
33.
ZhangBHHuangNShiJYShiBJiaZL. Homozygote C/C at rs12543318 was risk factor for non-syndromic cleft lip only from western Han Chinese population. J Oral Pathol Med. 2018;47(6):620-626. doi:10.1111/jop.12719.
34.
MillerCTSwartzMEKhuuPAWalkerMBEberhartJKKimmelCB. Mef2ca is required in cranial neural crest to effect Endothelin1 signaling in zebrafish. Dev Biol. 2007;308(1):144-157. doi:10.1016/j.ydbio.2007.05.018.
35.
VerziMPAgarwalPBrownCMcCulleyDJSchwarzJJBlackBL. The transcription factor MEF2C is required for craniofacial development. Dev Cell. 2007;12(4):645-652. doi:10.1016/j.devcel.2007.03.007.
36.
SolomonBDLacbawanFMercierS, et al.Mutations in ZIC2 in human holoprosencephaly: description of a novel ZIC2 specific phenotype and comprehensive analysis of 157 individuals. J Med Genet. 2010;47(8):513-524. doi:10.1136/jmg.2009.073049.
37.
JiangZZhuLHuL, et al.Zic3 is required in the extra-cardiac perinodal region of the lateral plate mesoderm for left-right patterning and heart development. Hum Mol Genet. 2013;22(5):879-889. doi:10.1093/hmg/dds494.
38.
GergicsPSmithCBandoH, et al.High-throughput splicing assays identify missense and silent splice-disruptive POU1F1 variants underlying pituitary hormone deficiency. Am J Hum Genet. 2021;108(8):1526-1539. doi:10.1016/j.ajhg.2021.06.013.
39.
YuWLiXEliasonS, et al.Irx1 regulates dental outer enamel epithelial and lung alveolar type II epithelial differentiation. Dev Biol. 2017;429(1):44-55. doi:10.1016/j.ydbio.2017.07.011.
40.
NewbernJZhongJWickramasingheRS, et al.Mouse and human phenotypes indicate a critical conserved role for ERK2 signaling in neural crest development. Proc Natl Acad Sci U S A. 2008;105(44):17115-17120. doi:10.1073/pnas.0805239105.
41.
DeardorffMAKaurMYaegerD, et al.Mutations in cohesin complex members SMC3 and SMC1A cause a mild variant of Cornelia de Lange syndrome with predominant mental retardation. Am J Hum Genet. 2007;80(3):485-494. doi:10.1086/511888.
42.
OhtsukaNBadurekSBusslingerMBenesFMMinichielloLRudolphU. GABAergic neurons regulate lateral ventricular development via transcription factor Pax5. Genesis. 2013;51(4):234-245. doi:10.1002/dvg.22370.
43.
BohmerACMangoldETessmannP, et al.Analysis of susceptibility loci for nonsyndromic orofacial clefting in a European trio sample. Am J Med Genet A. 2013;161A(10):2545-2549. doi:10.1002/ajmg.a.36141.
44.
JiaZLeslieEJCooperME, et al.Replication of 13q31.1 association in nonsyndromic cleft lip with cleft palate in Europeans. Am J Med Genet A. 2015;167A(5):1054-1060. doi:10.1002/ajmg.a.36912.
45.
de AquinoSNMessettiACHoshiR, et al.Analysis of susceptibility polymorphisms for nonsyndromic cleft lip with or without cleft palate in the Brazilian population. Birth Defects Res A Clin Mol Teratol. 2014;100(1):36-42. doi:10.1002/bdra.23204.
46.
LudwigKUWahlePReutterH, et al.Evaluating eight newly identified susceptibility loci for nonsyndromic cleft lip with or without cleft palate in a Mesoamerican population. Birth Defects Res A Clin Mol Teratol. 2014;100(1):43-47. doi:10.1002/bdra.23209.
47.
BrownSAWarburtonDBrownLY, et al.Holoprosencephaly due to mutations in ZIC2, a homologue of drosophila odd-paired. Nat Genet. 1998;20(2):180-183. doi:10.1038/2484.
Supplementary Material
Please find the following supplemental material available below.
For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.
For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.
