Association of single-nucleotide polymorphisms in the IRF6 gene with non-syndromic cleft lip with or without cleft palate in the Xinjiang Uyghur population

A comprehensive consolidation of data on the relationship between IRF6 polymorphisms and non-syndromic cleft lip/palate susceptibility: From 79 case-control studies

BACKGROUND

Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a prevalent craniofacial birth defect on a global scale. A number of candidate genes have been identified as having an impact on NSCL/P. However, the association between interferon regulatory factor 6 (IRF6) polymorphisms and NSCL/P has yielded inconsistent results, prompting the need for a meta-analysis to obtain more accurate estimates.

METHODS

We conducted a thorough screening of all relevant articles published up until November 15, 2023, in online bibliographic databases. The statistical analysis of the collected data was performed using the Comprehensive Meta-Analysis (Version 4.0) software.

RESULTS

A total of 79 case-control studies, comprising 14,003 cases and 19,905 controls, were included in our analysis. The combined data indicated that the IRF6 rs642961 and rs2235371 polymorphisms were associated with an increased risk of NSCL/P in the overall population. However, no significant association was found between the rs2013162 and rs2235375 polymorphisms and the risk of NSCL/P in the overall population. Furthermore, subgroup analyses revealed significant correlations between the IRF6 rs642961, rs2235371, and rs2235375 polymorphisms and the risk of NSCL/P based on ethnic background and country of origin. Nevertheless, the rs2013162 polymorphism plays a protective role in Caucasians and mixed populations.

CONCLUSIONS

Our collective data indicates a significant association between the rs642961 and rs2235371 polymorphisms and the risk of NSCL/P in the overall population. The rs2235375 polymorphism could influence the susceptibility to NSCL/P based on ethnic background. Meanwhile, the rs2013162 polymorphism provides protective effects in Caucasian, mixed populations, and the Brazilian population.

Association of single nucleotide polymorphisms in the IRF6 gene with nonsyndromic cleft lip with or without cleft palate in Kinh Vietnamese patients

BACKGROUND

The interferon regulatory factor 6 (IRF6) gene, which causes Van der Woude syndrome, is associated with nonsyndromic cleft lip with or without cleft palate (NSCL/P). Single nucleotide polymorphisms (SNPs) in the IRF6 gene were identified as susceptibility indicators of this defect in several populations. To further evaluate its role in this birth defect, we conducted this study with the aim of identifying allele frequencies, genotype frequencies, and associations of 5 SNPs (rs2235373, rs2235371, rs2235375, rs2013162, and rs2236907) in the IRF6 gene with NSCL/P in Kinh Vietnamese patients.

METHODS

A total of 132 patients with NSCL/P and 132 healthy individuals were included in our study group. Direct sequencing was performed to genotype the tag SNPs. Genetic models were used to compare genotype and allele frequencies between the case and control groups.

RESULTS

In the recessive model, the genotypes C/C of rs2236907, C/C of rs2013162, G/G of rs2235375, and A/A of rs2235373 were associated with an increased risk of NSCL/P, whereas there was no clear association between rs2235371 and the malformation in any genetic model. When subgroup analysis was performed, we observed a similar risk trend in the cleft lip and palate, cleft palate only and cleft lip only phenotypes. In haplotype analysis, haplotype models of 5 tag SNPs were associated with increased risks of this defect in all phenotypic models (OR_GCGCC/CCAA = 23.64, 95% CI 12.28-45.49, p < 0.0001).

CONCLUSIONS

These findings point to a considerable contribution of rs2236907, rs2013162, rs2235373, and rs2235375 to the NSCL/P defect in Kinh Vietnamese individuals.

Histological and Immunohistochemical Studies to Determine the Mechanism of Cleft Palate Induction after Palatal Fusion in Mice Exposed to TCDD

Rupture of the basement membrane in fused palate tissue can cause the palate to separate after fusion in mice, leading to the development of cleft palate. Here, we further elucidate the mechanism of palatal separation after palatal fusion in 8–10-week-old ICR female mice. On day 12 of gestation, 40 μg/kg of 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), sufficient to cause cleft palate in 100% of mice, was dissolved in 0.4 mL of olive oil containing toluene and administered as a single dose via a gastric tube. Fetal palatine frontal sections were observed by H&E staining, and epithelial cell adhesion factors, apoptosis, and cell proliferation were observed from the anterior to posterior palate. TUNEL-positive cells and Ki67-positive cells were observed around the posterior palatal dissection area of the TCDD-treated group. Moreover, in fetal mice exposed to TCDD, some fetuses exhibited cleft palate dehiscence during fusion. The results suggest that palatal dehiscence may be caused by abnormal cell proliferation in epithelial tissues, decreased intercellular adhesion, and inhibition of mesenchymal cell proliferation. By elucidating the mechanism of cleavage after palatal fusion, this research can contribute to establishing methods for the prevention of cleft palate development.

Exploring GRHL3 polymorphisms and SNP-SNP interactions in the risk of non-syndromic oral clefts in the Brazilian population

OBJECTIVE

To investigate the association of single-nucleotide polymorphisms (SNP) in grainyhead-like 3 (GRHL3) and to verify its possible interactions with others genes responsible for craniofacial development in the risk of non-syndromic oral cleft (NSOC).

METHODS

Applying TaqMan allelic discrimination assays, we evaluated GRHL3 SNPs (rs10903078, rs41268753, and rs4648975) in an ancestry-structured case-control sample composed of 1,127 Brazilian participants [272 non-syndromic cleft palate only (NSCPO), 242 non-syndromic cleft lip only (NSCLO), 319 non-syndromic cleft lip and palate (NSCLP), and 294 healthy controls]. Additionally, SNP-SNP interactions of GRHL3 and previously reported variants in FAM49A, FOXE1, NTN1, and VAX1 were verified in non-syndromic cleft lip with or without cleft palate (NSCL ± P). To eliminate false-positive associations, Bonferroni correction or 1,000 permutation method was applied.

RESULTS

The multiple logistic regression analysis showed that the CC genotype of rs10903078 (p = .03) and the haplotype C-C formed by the SNPs rs10903078 and rs41268753 (p = .04) were associated with NSCLO, but the p-values did not withstand Bonferroni correction. However, SNP-SNP test revealed significant interactions between GRHL3 SNPs and FAM49A (rs7552), FOXE1 (rs3758249), VAX1 (rs7078160 and rs751231), and NTN1 (rs9891446).

CONCLUSIONS

Our results confirm the importance of GRHL3 and its interactions with previously NSOC-associated genes, including FAM49A, FOXE1, NTN1, and VAX1, in the pathogenesis of NSOC in the Brazilian population.

Association Between an Interferon Regulatory Factor 6 Gene Polymorphism and Nonsyndromic Cleft Palate Risk

Background: Involvement of interferon regulatory factor 6 (IRF6) gene polymorphisms in nonsyndromic cleft palate (NSCP) risk remains controversial. This investigation was performed to evaluate the relationship between IRF6 gene polymorphisms and NSCP risk. Materials and Methods: Two hundred forty-one patients with NSCP (including 103 complete trio families) were recruited, and 242 unaffected individuals were included as controls. Polymorphisms for the IRF6 rs2235371, rs801619, rs642961, rs44844880, and rs8049367 loci were characterized in both groups. Furthermore, eligible studies were identified from the databases through June 1, 2017, and were included in a meta-analysis to enhance the robustness of our conclusions. Results: The IRF6 rs2235371 A allele and AA genotype in the case group were found at higher frequencies than in the control group (A allele: p < 0.0016; AA genotype: p < 0.0049). The IRF6 rs801619 AA genotype and G allele were associated with NSCP risk (G allele: p < 0.0061; AA genotype: p < 0.0195). At the IRF6 rs642961, rs44844880, and rs8049367 loci genotype and allele frequencies were not statistically different between the NSCP group and normal controls. In the meta-analysis, the IRF6 A/G gene polymorphism (rs2235371) and IRF6 A/G gene polymorphism (rs642961) were associated with NSCP risk in the general population, whereas the IRF6 A/C gene polymorphism (rs2013162) was not. Conclusion: The IRF6 A/G gene polymorphisms at rs2235371 and rs642961, but not the IRF6 A/C gene polymorphism rs2013162, were associated with NSCP risk.

TGFα/HinfI Polymorphisms Contribute to Nonsyndromic Cleft Lip and Palate in Turkish Patients

BACKGROUND

Nonsyndromic cleft lip with/without cleft palate (nsCL ± P) is one of the most common birth defects of complex etiology, occurring in ∼1/700 live births worldwide. A series of epidemiological studies were conducted to investigate the association between a transforming growth factor alpha (TGFα) polymorphism and nsCL ± P risk. The aim of this study was to investigate the association between the TGFα/HinfI polymorphisms and nsCL ± P in Turkish patients.

METHODS

One hundred fifty-five Turkish subjects were enrolled: 70 nsCL ± P patients and 85 unrelated control individuals. Genomic DNA was isolated from peripheral blood leukocytes, and molecular analysis of gene polymorphisms was carried out using polymerase chain reaction and restriction enzyme digestions.

RESULTS

We found significant difference between the TGFα gene HinfI allele frequencies of the controls and: 1) the occurrence of nonsyndromic cleft lip (p = 0.029,); 2) the occurrence of nonsyndromic cleft lip and palate (nsCL + P) cases (p = 0.024; and 3) the occurrence of both nsCL ± nsCLP cases (p = 0.0365). The association between age of parents, gender, maternal exposures, socioeconomic status and clefts was assessed in each group separately.

CONCLUSION

Our study indicates that the TGFα HinfI gene polymorphism might be associated with nsCL ± P susceptibility, thus contributing to the occurrence of nsCL ± P in Turkish patients. The relatively small sample size of our study is one limitation of our study, and future research with larger specimen sets from different ethnicities will be required to validate our findings.

Association of single nucleotide polymorphisms in AXIN2, BMP4, and IRF6 with Non-Syndromic Cleft Lip with or without Cleft Palate in a sample of the southeast Iranian population

Non-syndromic cleft lip with or without palate (NSCL/P) is a common congenital malformation worldwide, with complex etiology. It has been proposed that interaction of genes and environmental factors play a role in the predisposition to this disease.

Association between genotype and phenotype of virulence gene in Van der Woude syndrome families

Members from two Van der Woude syndrome (VWS) families were screened to determine the prevalence of interferon regulatory factor 6 (IRF6) as a disease‑causing gene and to analyze the interrelationships between patient genotype and phenotype. The peripheral blood of 24 members from two VWS families and 200 control samples were collected. The family members were interviewed for medical histories and other clinical abnormalities using questionnaires. Polymerase chain reaction was directly performed on the peripheral blood to screen for the coding region of the IRF6 gene. Of the 24 family members, a total of 6 patients had mutations of IRF6 gene. c.1234C>T (p.R412X) heterozygous mutation was detected in 3 members of family 1. In families 2 and 3, members carried the c.1210G>A (p.E404K) heterozygous mutations. The other members of the families, were wild type (wt/wt) for IRF6. Genetic testing demonstrated that the disease mutations c.1234C>T and c.1210G>A co‑segregated with the two families' pathogenic mutations. The existence of genetic heterogeneity and the complexity of the clinical phenotype was demonstrated in Chinese VWS patients.

Association between IRF6 and 8q24 polymorphisms and nonsyndromic cleft lip with or without cleft palate: Systematic review and meta-analysis

BACKGROUND

We conducted a systematic review and meta-analysis of interferon regulatory factor 6 and 8q24 polymorphisms with nonsyndromic cleft lip with/without cleft palate (NSCL/P).

METHODS

Data extraction was independently performed by two reviewers. Genotypic effects of four polymorphisms from 31 studies were pooled separately by ethnicity using a mixed-effect logit model with accounting for heterogeneity.

RESULTS

For rs2235371, AA and GA carried, respectively, 51% (95% confidence interval [CI], 37%-61%) and 42% (95% CI, 32%-50%) lower risks of NSCL/P than GG genotypes in Asians, but these genotypes were not significant in Caucasians. For rs2013162, only AA was significant, that is, carried 0.65 (95% CI, 0.52-0.82) times lower odds than CC in Caucasians but not for Asians. For rs642961, AA and GA genotypes, respectively, carried 2.47 (95% CI, 1.41-4.35) and 1.40 (95% CI, 1.12-1.75) times higher odds in Asian, and 2.03 (95% CI, 1.52-2.71) and 1.58 (95% CI, 1.37-1.82) times higher odds in Caucasians compare with GG genotypes. For rs987525, AA and CA genotypes carried 2.27 (95% CI, 1.43-3.60) and 1.34 (95% CI, 1.02-1.77) times higher odds in Asian, and 5.25 (95% CI, 3.98-6.91) and 2.13 (95% CI-1.82, 2.49) times higher odds in Caucasians, and 1.42 (95% CI, 1.10-1.82) and 1.28 (95% CI, 1.09-1.50) times higher odds in mixed ethnicities compared with CC genotypes. These variant effects remained significant based on applying Bonferroni corrected-thresholds, except in the mixed ethnicity.

CONCLUSION

We show robust variant effects in NSCL/P. Considering them with other genes and risk factors might be useful to improve prediction of NSCL/P occurrence. Birth Defects Research (Part A) 106:773-788, 2016. © 2016 The Authors Birth Defects Research Part A: Clinical and Molecular Teratology Published by Wiley Periodicals, Inc.

Genomic expression in non syndromic cleft lip and palate patients: A review

Cleft lip and palate are common congenital anomalies with significant medical, psychological, social, and economic ramifications, affecting one in seven hundred live births. Genetic causes of non syndromic cleft lip and/or palate (NSCLP) include chromosomal rearrangements, genetic susceptibility to teratogenic exposures, and complex genetic contributions of multiple genes. Development of the orofacial clefts in an individual will depend on the interaction of several moderately effecting genes with environmental factors. Several candidate genes have been genotyped in different population types, using case parent trio or case control design; also genes have been sequenced and SNPs have been reported. Quantitative and molecular analysis have shown linkage and association studies to be more relevant. Recent literature search shows genome wide association studies using microarray. The aim of this paper was to review the approaches to identify genes associated with NSCLP and to analyze their differential expressions. Although no major gene has been confirmed, a lot of research is ongoing to provide an understanding of the pathophysiology of the orofacial clefts.