FOXE1 polymorphisms and non-syndromic orofacial cleft susceptibility in a Chinese Han population

Advances in research regarding the roles of non-coding RNAs in non-syndromic cleft lip with or without cleft palate: A systematic review

OBJECTIVE

To investigate by means of a literature review, what non-coding RNAs engage in non-syndromic cleft lip with or without cleft palate (NSCL/P) and how they lead to the occurrence of this malformation.

DESIGN

A literature search of online databases (Medline via PubMed, Web of Science, Scopus, and Embase) was performed using appropriate keywords (e.g. non-coding RNA, miRNA, lncRNA, NSCL/P, non-syndromic cleft lip only, and non-syndromic orofacial cleft). The risk of bias in the included studies was then assessed, and a comprehensive review of reported non-coding RNAs associated with NSCL/P was performed.

RESULTS

The initial search retrieved 133 studies reporting non-coding RNAs associated with NSCL/P; after excluding 18 replicates and 77 ineligible studies, 35 remained. Of these, 16 studies fulfilled all the criteria and were included in the systematic review. These studies established the roles of non-coding RNAs in the development of craniofacial structures. The differential expression of these non-coding RNAs could lead to orofacial clefts, indicating their significance in NSCL/P and their profound research value.

CONCLUSION

There is evidence that non-coding RNAs are involved in the formation of NSCL/P. Specifically, they play significant roles in the regulation of genes and signalling pathways related to NSCL/P.

Role of epigenetics and miRNAs in orofacial clefts

Orofacial clefts (OFCs) have multiple etiologies and likely result from an interplay between genetic and environmental factors. Within the last decade, studies have implicated specific epigenetic modifications and noncoding RNAs as additional facets of OFC etiology. Altered gene expression through DNA methylation and histone modification offer novel insights into how specific genes contribute to distinct OFC subtypes. Epigenetics research has also provided further evidence that cleft lip only (CLO) is a cleft subtype with distinct etiology. Polymorphisms or misexpression of genes encoding microRNAs, as well as their targets, contribute to OFC risk. The ability to experimentally manipulate epigenetic changes and noncoding RNAs in animal models, such as zebrafish, Xenopus, mice, and rats, has offered novel insights into the mechanisms of various OFC subtypes. Although much remains to be understood, recent advancements in our understanding of OFC etiology may advise future strategies of research and preventive care.

Association between forkhead box E1 polymorphisms and risk of non-syndromic cleft lip with or without cleft palate: A meta-analysis

OBJECTIVE

The purpose of the present work was to investigate the association between forkhead box E1 (FOXE1) and the risk of non-syndromic cleft lip with or without cleft palate (NSCL/P).

MATERIALS AND METHODS

Relevant studies were searched in several professional databases up to 31 July 2019. The pooled odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated using a fixed-effect model or a random-effect model to analyse the relationship between FOXE1 polymorphisms and NSCL/P.

RESULTS

A total of four single nucleotide polymorphisms (SNPs), including rs3758249, rs4460498, rs1443434 and rs10217225, were analysed. The overall findings showed that FOXE1 rs4460498 was statistically associated with NSCL/P (including cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO)). Genotypes CC and CT of rs4460498 were significantly more closely correlated with NSCL/P (including CL/P and CPO) than genotype TT (NSCL/P: TT vs CC, OR = 0.630, P = .000; TT vs TC + CC, OR = 0.775, P = .020; CL/P: TT vs CC, OR = 0.664, P = .000; TT vs TC + CC, OR = 0.738, P = .006. CPO: TT vs CC, OR = 0.761, P = .027; TT vs TC + CC, OR = 0.792, P = .045). For rs10217225, only the TT genotype might have contributed to the elevated risk of CL/P (TT vs CC OR = 2.236, P = .000). The other FOXE1 polymorphisms were not associated with NSCLP, CL/P or CPO.

CONCLUSION

The meta-analysis provided confirmation that the polymorphism of FOXE1 rs10217225 was correlated with an increased risk of CL/P, and the polymorphism of FOXE1 rs4460498 was a protective factor for NSCL/P, including CLP and CPO.

A systematic review and meta-analysis on protective role of forkhead box E1 (FOXE1) polymorphisms in susceptibility to non-syndromic cleft lip/palate

INTRODUCTION

Several environmental and genetic factors have a role in the aetiology of non-syndromic cleft lip/palate (NSCL/P). This meta-analysis evaluated the association of rs3758249 and rs4460498 forkhead box E1 (FOXE1) polymorphisms with the NSCL/P risk.

MATERIALS AND METHODS

The Scopus, Cochrane Library, Web of Science, and PubMed databases were searched for articles published until March 2019. The analyses were performed by Review Manager 5.3 using the crude odds ratio (OR) and 95% confidence interval (CI) for a strong association between FOXE1 polymorphisms and the risk of NSCL/P.

RESULTS

Out of 161 articles retrieved from the databases, four case-control articles were involved in the meta-analysis. The pooled ORs of rs4460498 polymorphism based on allelic, homozygous, heterozygous, dominant, and recessive models were 0.74 (95% CI: 0.69, 0.80; P<0.00001), 0.43 (95% CI: 0.30, 0.61; P<0.00001), 0.66 (95% CI: 0.55, 0.80; P<0.0001), 0.66 (95% CI: 0.59, 0.73; P<0.00001), and 0.70 (95% CI: 0.60, 0.82; P<0.0001), respectively; whereas, the pooled OR of rs3758249 polymorphism were 0.86 (95% CI: 0.71, 1.04; P=0.12), 0.68 (95% CI: 0.57, 0.82; P<0.0001), 0.79 (95% CI: 0.57, 1.09; P=0.15), 0.79 (95% CI: 0.58, 1.08; P=0.14), and 0.80 (95% CI: 0.68, 0.95; P=0.010) for the afore-mentioned models, respectively.

CONCLUSIONS

The results showed that the T allele, TT, and CT genotypes of rs4460498 polymorphism were significantly associated with a decreased risk of NSCL/P; whereas, for rs3758249 polymorphism, only the AA genotype had a significant protective role in NSCL/P. Thus, FOXE1 is strongly associated with NSCL/P in the populations.

Association of SNP rs1867277 in FOXE1 Gene and Cleft Lip with or without Cleft Palate in a Han Chinese Population

BACKGROUND

The genetic factors causing cleft lip with or without cleft palate (CL ± P) are still unclear. The SNPs in FOXE1 gene were associated with CL ± P. However, the results have been inconsistent.

OBJECTIVE

We explored the associations of four SNPs in FOXE1 gene and CL ± P by a family based study.

MATERIALS AND METHODS

128 children with CL ± P and their parents were recruited. rs3758249 and rs1867277 were genotyped by high-resolution melting curve (HRM) method, whereas rs1443434 and rs907577 were genotyped by Sequenom MassARRAY® method. The software PLINK, FBAT and FAMHAP were used for analyzing data.

RESULTS

rs1867277 was associated with CL ± P (P_m = 0.0395). The patients were divided into two subgroups, individuals with cleft lip only and persons with cleft lip and palate. There were no associations in subgroup analyses.

CONCLUSION

We confirmed the association of FOXE1 gene and CL ± P by a family based study. For the first time, rs1867277 was significantly associated with CL ± P.

Determinants of orofacial clefting I: Effects of 5-Aza-2'-deoxycytidine on cellular processes and gene expression during development of the first branchial arch

In this study, we identify gene targets and cellular events mediating the teratogenic action(s) of 5-Aza-2'-deoxycytidine (AzaD), an inhibitor of DNA methylation, on secondary palate development. Exposure of pregnant mice (on gestation day (GD) 9.5) to AzaD for 12h resulted in the complete penetrance of cleft palate (CP) in fetuses. Analysis of cells of the embryonic first branchial arch (1-BA), in fetuses exposed to AzaD, revealed: 1) significant alteration in expression of genes encoding several morphogenetic factors, cell cycle inhibitors and regulators of apoptosis; 2) a decrease in cell proliferation; and, 3) an increase in apoptosis. Pyrosequencing of selected genes, displaying pronounced differential expression in AzaD-exposed 1-BAs, failed to reveal significant alterations in CpG methylation levels in their putative promoters or gene bodies. CpG methylation analysis suggested that the effects of AzaD on gene expression were likely indirect.

Genetic variation of FOXE1 and risk for orofacial clefts in a California population

We investigated whether orofacial clefts are associated with polymorphic variation within and around FOXE1. This California population-based case control study focused on white Hispanic and white nonHispanic infants among which there were 262 infants with cleft lip with or without cleft palate (CL/P), 103 with cleft palate only (CPO), and 382 unaffected controls. These cases and controls were genotyped for 13 SNPs across 220 Kb at the FOXE1 Locus. We observed associations with multiple FOXE1 SNPs for CL/P and for CPO, especially for the Hispanic study population. Increased risks were associated with the more common allele for all SNPs tested. Our results implicate FOXE1 as an important locus whose polymorphic variation increases risks for all types of isolated clefts, and opens a new biological pathway to investigate in efforts to understand genetic factors underlying human clefting. © 2016 Wiley Periodicals, Inc.