Objective:To preliminarily investigate the role of methylation in the epigenetic regulation of the pathogenesis of non-syndromic orofacial clefts (NSOC), and to address the gaps in previous explorations of susceptibility genes associated with NSOC.Methods:We conducted an association analysis of single nucleotide polymorphisms (SNPs) and genes related to methylation using data from a large-scale genome-wide association study involving Han Chinese patients with non-syndromic orofacial clefts and healthy controls.Results:A significant association was found between NSOC and the DNA methylation gene TET1, as well as the histone methylation gene NSD1. Specifically, the minor allele G of rs3733875 significantly increased the risk of non-syndromic cleft lip with or without palate (NSCLP) ( P=1.18×10 -4, OR=1.292), while the minor allele C of rs10998379 elevated the risk of non-syndromic cleft palate only (NSCPO) ( P=7.29×10 -5, OR=1.268); conversely, the minor allele T of rs4558056 was identified as a protective factor for NSCL/P ( P=1.17×10 -4, OR=0.792). Conclusions:This study revealed that the DNA methylation gene TET1 and the histone methylation gene NSD1 are associated with NSOC. The pathogenesis of NSOC involves interactions among multiple factors, including genetic, environmental, and epigenetic determinants, among which methylation modifications represent a crucial component.

OBJECTIVES: This study aims to explore the association between single nucleotide polymorphisms (SNPs) loci near the haplotype region hg19 chr9:100560865-100660865 of the forkhead box E1 (FOXE1) gene and the occurrence of non-syndromic cleft lip with or without cleft palate (NSCL/P) in western Han Chinese population. METHODS: In the first stage, our study recruited 159 NSCL/P patients and performed targeted region sequencing to screen SNPs loci near the haplotype region of the FOXE1 gene associated with NSCL/P. In the second stage, we selected 21 common SNPs and re-enrolled 1 000 non-syndromic cleft lip only (NSCLO) patients, 1 000 non-syndromic cleft palate only (NSCPO) patients, and 1 000 normal controls to verify the association. PLINK software was used to perform Hardy-Weinberg equilibrium (HWE) test. Association analysis for common variants, gene burden analysis for rare mutations, and function prediction of SNPs with non-synonymous mutations were performed using Mutation Taster and other software programs. RESULTS: In the first stage, 126 variants, including 76 single nucleotide variants and 50 insertion-deletions were identified. All the included SNPs confirmed to HWE, and the results of gene burden analysis and prediction of functional harmfulness for rare variants were not statistically significant. Association analysis showed that rs13292899 of the FOXE1 gene was significantly associated with NSCL/P (P=1.85E-27) and was also correlated with NSCLO (P=6.41E-23) and non-syndromic cleft lip with cleft palate (NSCLP) (P=2.36E-15) subtypes. In the validation phase, rs79268293 (P=0.013, P=0.022), rs10983951 (P=0.009 2, P=0.007 6), rs117227387 (P=0.009 2, P=0.007 6), rs3758250 (P=0.009 2, P=0.007 6), and rs116899397 (P=0.009 2, P=0.007 6) were significantly associated with NSCLO and NSCPO; rs13292899 (P=0.008 5), rs74606599 (P=0.008 3), rs143226042 (P=0.008 3), and rs117236550 (P=0.01) were associated with the occurrence of NSCLO; and rs12343182 (P=0.008 7), rs10119760 (P=0.012), rs10113907 (P=0.012), and rs13299924 (P=0.012) were associated with the occurrence of NSCPO. CONCLUSIONS This study found a new susceptible SNP rs13292899 of the FOXE1 gene that is closely associated with NSCL/P and NSCLO subtype and 13 other SNPs associated with NSCLO or NSCPO.
Female ; Humans ; Male ; China ; Cleft Lip/genetics* ; Cleft Palate/genetics* ; Forkhead Transcription Factors/genetics* ; Haplotypes ; Polymorphism, Single Nucleotide ; East Asian People/genetics*

Objective:To preliminarily investigate the role of methylation in the epigenetic regulation of the pathogenesis of non-syndromic orofacial clefts (NSOC), and to address the gaps in previous explorations of susceptibility genes associated with NSOC.Methods:We conducted an association analysis of single nucleotide polymorphisms (SNPs) and genes related to methylation using data from a large-scale genome-wide association study involving Han Chinese patients with non-syndromic orofacial clefts and healthy controls.Results:A significant association was found between NSOC and the DNA methylation gene TET1, as well as the histone methylation gene NSD1. Specifically, the minor allele G of rs3733875 significantly increased the risk of non-syndromic cleft lip with or without palate (NSCLP) ( P=1.18×10 -4, OR=1.292), while the minor allele C of rs10998379 elevated the risk of non-syndromic cleft palate only (NSCPO) ( P=7.29×10 -5, OR=1.268); conversely, the minor allele T of rs4558056 was identified as a protective factor for NSCL/P ( P=1.17×10 -4, OR=0.792). Conclusions:This study revealed that the DNA methylation gene TET1 and the histone methylation gene NSD1 are associated with NSOC. The pathogenesis of NSOC involves interactions among multiple factors, including genetic, environmental, and epigenetic determinants, among which methylation modifications represent a crucial component.