The TPM1 And VANGL Polymorphisms And Nonsyndromic Orofacial Clefts Susceptibility In A Chinese Han Population

Orofacial clefts are common congenital birth malformations in humans characterized by defective fusions of different facial processes.According to whether or not accompanied by any other structural and/or congenitally abnormalities,orofacial clefts can be categorized as syndromic or nonsyndromic orofacial clefts(NSOC).With a prevalence of approximately 1/800 live births worldwide,almost 70% of orofacial clefts cases belong to the NSOC category.The prevalence of CL/P shows notable influence of ethnicity and socioeconomic status,varies from the highest rate in Asian and American Indians(1/500)to the lowest in African(1 /2,500).Although rehabilitation is possible by good systemic treatments,orofacial clefts inevitably pose enormous burdens to the individual,the family and society.The high birth prevalence of NSOC and substantial burdens on the patients’ families and society make it urgent to reveal the etiology of NSOC.Animal models,linkage studies,candidate gene association studies,chromosomal rearrangements,direct sequencing and genome-wide association studies(GWAS)have been applied to uncover the related genes and pathways for NSOC.Located at 15q22,a new susceptibility regions of NSOC elucidated by the first meta-analysis combining two largest GWAS,TPM1 encodes a group of highly conserved,widely distributed multiple isoforms of tropomyosins.Through different isoforms of tropomyosins,TPM1 plays an important role in muscle contraction,cytoskeleton organization,cell migration and embryonic development.Located at 1p13.1 and 1q22-q23 respectively,VANGL1 and VANGL2 are core protein coding genes in PCP pathway,which belongs to non-canonical WNT signaling.VANGL1 and VANGL2 are important in neural crest migration and has been reported to be related with NTD(neural tube defects,NTD).Thus,we hypothesize that TPM1 and VANGL1/VANGL2 polymorphisms might be related to the risk of NSOC or its subgroups.We selected four tag SNPs of TPM1,five functional SNPs of VANGL1 as well as two functional SNPs of VANGL2 and genotyped these variants in a casecontrol study of 1272 NSOC cases and 1295 controls(stage1: 599 NSOC cases and 590 controls;stage2: 673 NSOC cases and 705 controls)in a Chinese Han population to verify this assumption.The case–control study revealed that SNP rs1972041 GA heterozygous of TPM1 showed a decreased risk of NSOC(P = 0.038,OR = 0.77,95% CI = [0.61,0.99]).Further stratified analysis manifested a protective effect of rs1972041 G allele on cleft lip with cleft palate(CLP)and cleft lip with or without cleft palate(CL/P)groups by heterozygous comparison and dominant comparison.No association was observed between the remaining three polymorphisms(rs11071720,rs3803499,and rs12148828)and NSOC or its subgroups.T allele of VANGL1 SNPs rs17034226 and rs3811006 showed an increased risk of NSOC and its subgroups,especially in CPO.No association was observed between the remaining five polymorphisms(rs6700610,rs3811007,rs4839469 in VANGL1 and rs11582932,rs12086448 in VANGL1)and NSOC or its subgroups.Further function study revealed that T allele mutation of rs17034226 increased the binding capacity with miR-371 a mimics and so the expression of VANGL1.However,T allele mutation of rs3811006 showed different binding capacity with miR-1267 mimics in HEPM and HEK293 A cells.We also detected the different expressions of VANGL1 during palate formation in mice by IHC.Our study suggested that TPM1 and VANGL1 polymorphisms might contribute to the etiology of NSOC.More emphasis should be placed on TPM1 and VANGL1 during craniofacial development.