The common MTHFR C677T and A1298C variants are not associated with the risk of non-syndromic cleft lip/palate in northern Venezuela

Association of Fetal MTHFR 677C > T Polymorphism with Non-Syndromic Cleft Lip with or without Palate Risk: A Systematic Review and Meta-Analysis

This study was conducted to estimate the precise association of fetal MTHFR 677 C > T polymorphism with risk of nonsyndromic cleft lip with or without cleft palate (NSCL ± P) using a large-scale meta-analysis. Methods: A comprehensive literature search was performed using studies published on PubMed, Science Direct, Scopus and CNKI databases up to November 1, 2019. Results: A total of 38 studies with 6,525 children with NSCL ± P and 8,606 controls were selected. Overall, there was a significant association between MTHFR 677 C > T polymorphism and NSCL ± P risk. Subgroup analysis by ethnicity revealed that MTHFR 677 C > T polymorphism contributed to development of NSCL ± P in Caucasian and Mixed populations, but not in Asians. When stratified by country of origin, we found a significant association in Brazilian, Turkish and Indian populations, but not in Chinese and US-American. Conclusions: This meta-analysis provides strong evidence that fetal MTHFR 677 C > T polymorphism is significantly associated with NSCL ± P risk.

SNPs in folate pathway are associated with the risk of nonsyndromic cleft lip with or without cleft palate, a meta-analysis

Background: Prenatal intake of folic acid is important for prevention of NSCL/P (nonsyndromic cleft lip with or without cleft palate). Associated genes in folate pathway are major enzymes of folic acid metabolism that is crucial for preventing birth defects. The present meta-analysis aims to investigate the association between four SNPs in folate pathway genes and the risk of NSCL/P.

Methods: Comprehensive bioinformatics analysis was used to predict the functional pathogenicity of genetic variation. The PubMed, Embase database and Google Scholar were searched by two researchers. Stata 11.0 software was used to analyze the results. Subgroup analysis was carried out to assess the influence of genetic background. Sensitivity analysis, regression analysis and publication analysis were also conducted to enhance the strength of our results.

Results: It is estimated that the probability of two missense mutation rs1801133 in MTHFR and rs1801394 in MTRR are more likely to be damaging by bioinformatics analysis. A significant association between rs1801133 and risk of NSCL/P in two genetic models: TT genotype vs CC genotype (OR = 1.333 95%CI = 1.062–1.674, P = 0.013), and recessive model (OR = 1.325 95%CI = 1.075–1.634, P = 0.008). A significant protective association between rs1801394 GG genotype and NSCL/P in Asian (GG vs AA, OR = 0.520 95%CI = 0.321–0.841, P = 0.008) was observed. Meta-regression, sensitivity analysis, and publication bias analysis confirmed that the results of the present study were statistically significant.

Conclusions: The present study identified that rs1801133 in MTHFR is associated with the risk of NSCL/P, and rs1801394 GG genotype in MTRR play a protective role in Asian. Further, larger studies should be performed to confirm these findings.

Orofacial clefts embryology, classification, epidemiology, and genetics

Orofacial clefts (OFCs) rank as the second most common congenital birth defect in the United States after Down syndrome and are the most common head and neck congenital malformations. They are classified as cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO). OFCs have significant psychological and socio-economic impact on patients and their families and require a multidisciplinary approach for management and counseling. A complex interaction between genetic and environmental factors contributes to the incidence and clinical presentation of OFCs. In this comprehensive review, the embryology, classification, epidemiology and etiology of clefts are thoroughly discussed and a "state-of-the-art" snapshot of the recent advances in the genetics of OFCs is presented.

Association of MTHFR 1298A > C Polymorphism with Susceptibility to Non-Syndromic Cleft Lip with or without Palate: A Case-Control Study and Meta-Analysis

BACKGROUND

Several studies have evaluated association of the 5,10-methylenetetrahydrofolate reductase (MTHFR) gene 1298A > C polymorphism with non-syndromic cleft lip with or without palate (NSCL ± P) susceptibility, however the results are inconsistent.

MATERIALS AND METHODS

To address this issue, we performed a case-control study to evaluate the association of MTHFR 1298A > C polymorphism with NSCL ± P risk, followed by a meta-analysis.

RESULTS

Including our study, a total of 22 case-control studies with 2,814 cases and 4,199 controls were selected. The results suggested that there was no significant association between MTHFR 1298A > C polymorphism and NSCL ± P risk overall. The subgroup analysis demonstrated that the polymorphism was significantly associated with NSCL ± P risk in Asians and Iranian populations, but not in Caucasians, mixed and Chinese populations.

CONCLUSION

This meta-analysis indicates that MTHFR 1298A > C polymorphism may not contribute to NSCL ± P risk in overall. However, the MTHFR 1298A > C polymorphism was significantly associated with an increased risk of NSCL ± P in Asians and Iranian populations.

Gestational folate deficiency alters embryonic gene expression and cell function

Folic acid is a nutrient essential for embryonic development. Folate deficiency can cause embryonic lethality or neural tube defects and orofacial anomalies. Folate receptor 1 (Folr1) is a folate binding protein that facilitates the cellular uptake of dietary folate. To better understand the biological processes affected by folate deficiency, gene expression profiles of gestational day 9.5 (gd9.5) Folr1^-/- embryos were compared to those of gd9.5 Folr1^+/+ embryos. The expression of 837 genes/ESTs was found to be differentially altered in Folr1^-/- embryos, relative to those observed in wild-type embryos. The 837 differentially expressed genes were subjected to Ingenuity Pathway Analysis. Among the major biological functions affected in Folr1^-/- mice were those related to 'digestive system development/function', 'cardiovascular system development/function', 'tissue development', 'cellular development', and 'cell growth and differentiation', while the major canonical pathways affected were those associated with blood coagulation, embryonic stem cell transcription and cardiomyocyte differentiation (via BMP receptors). Cellular proliferation, apoptosis and migration were all significantly affected in the Folr1^-/- embryos. Cranial neural crest cells (NCCs) and neural tube explants, grown under folate-deficient conditions, exhibited marked reduction in directed migration that can be attributed, in part, to an altered cytoskeleton caused by perturbations in F-actin formation and/or assembly. The present study revealed that several developmentally relevant biological processes were compromised in Folr1^-/- embryos.

A meta-analysis and meta-regression of association between MTHFR A1298C polymorphism and nonsyndromic cleft lip/palate risk: An evaluation based on five genetic models

OBJECTIVE

The present meta-analysis is intended to assess the association between NSCL/P risk and methylenetetrahydrofolate reductase (MTHFR) A1298C polymorphism in case-control studies.

MATERIALS AND METHODS

The Web of Science, PubMed/Medline, Scopus, and Cochrane Library databases were searched for related articles published by April 2019. Review Manager 5.3 was applied to measure the odds ratios (ORs) with 95% confidence interval (CI) in the analyses assessing the strength of the association between A1298C polymorphism and NSCL/P risk. Results Sixteen studies were involved and analysed in this meta-analysis. Altogether, the reviewed articles included 2677 NSCL/P patients and 3669 controls. The pooled ORs of the allele, homozygote, heterozygote, dominant, and recessive models were 1.11 (95% CI: 0.94, 1.30; P=0.21), 1.14 (95% CI: 0.94, 1.37; P=0.18), 0.98 (95% CI: 0.80, 1.20; P=0.87), 1.03 (95% CI: 0.86, 1.22; P=0.79), and 1.18 (95% CI: 0.99, 1.41; P=0.07), respectively. The analysis did not identify any significant association between the polymorphism and the risk of NSCL/P in any ethnicity or source of controls.

CONCLUSIONS

This meta-analysis revealed that A1298C polymorphism is not associated with NSCL/P susceptibility, and the subgroup analyses based on ethnicity and the source of cases further confirmed this result.

Methylenetetrahydrofolate reductase C677T polymorphism is not associated with the risk of nonsyndromic cleft lip/palate: An updated meta-analysis

Both genetic and environmental factors affect the risk of orofacial clefts. The present meta-analysis aimed to evaluate the association between methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism and risk of nonsyndromic cleft lip/palate (NSCL/P) in cases-control studies. The PubMed/Medline, Scopus, Web of Science, and Cochrane Library databases were searched up to April 2019 with no restrictions. The odds ratios (ORs) and 95% confidence intervals (CIs) in all analyses were calculated by Review Manager 5.3 software. The funnel plot analysis was carried out by the Comprehensive Meta-Analysis version 2.0 software. Subgroup analysis, meta-regression, and sensitivity analysis were performed for the pooled analyses. Thirty-one studies reviewed in this meta-analysis included 4710 NSCL/P patients and 7271 controls. There was no significant association between MTHFR C677T polymorphism and NSCL/P susceptibility related to allelic model (OR = 1.04; P = 0.49), homozygote model (OR = 1.11; P = 0.35), heterozygote model (OR = 0.99; P = 0.91), dominant model (OR = 1.00; P = 0.96), or recessive model (OR = 1.08; P = 0.23). There was no significant association between MTHFR C677T polymorphism and NSCL/P susceptibility based on the ethnicity or the source of cases. There was a significant linear relationship between the year of publication and log ORs for the allele model. The results of the present meta-analysis failed to show an association between MTHFR C677T polymorphism and NSCL/P susceptibility. The subgroup analyses based on the ethnicity and the source of cases further confirmed this result.

Assessment of candidate genes and genetic heterogeneity in human non syndromic orofacial clefts specifically non syndromic cleft lip with or without palate

Non syndromic orofacial clefts specifically non-syndromic cleft lip/palate are one of the most common craniofacial malformation among birth defects in human having multifactorial etiology with an incidence of 1:700/1000. On the basis of association with other congenital malformations or their presence as isolated anomaly, OFC can be classified as syndromic (30%) and nonsyndromic (70%) respectively. The major cause of disease demonstrates complex interplay between genetic and environmental factors. The pathogenic mechanism of underlying factors have been provided by different genetic studies on large-scale with significant recent advances in genotyping technologies usually based on linkage or genome wide association studies (GWAS). On the basis of recent studies, new tools to identify causative genes involved in NSCL/P reported approximately more than 30 genetic risk loci that are responsible for pathogenesis of facial deformation. Despite these findings, it is still uncertain that how much of variance in NSCL/P predisposing factors can be explain by identified risk loci, as they all together accounts for only 20%-25% of NSCL/P heritability. So there is need of further findings about the problem of rare low frequency coding variants and other missing responsive factors or genetic modifiers. This review will described those potential genes and loci reported in different studies whose involvement in pathogenesis of nonsyndromic OFC has wide scientific evidence.

Association between methylenetetrahydrofolate reductase polymorphisms and non-syndromic cleft lip with or without palate susceptibility: an updated systematic review and meta-analysis

Methylenetetrahydrofolate reductase (MTHFR) polymorphisms are thought to be involved in the development of cleft lip with or without cleft palate (NSCL/P), but published results are contradictory. We therefore designed an updated meta-analysis to pool eligible studies and to evaluate further the possible relations between MTHFR polymorphisms (c.677C>T and c.1298A>C) and susceptibility to NSCL/P. A comprehensive search based on PubMed, Medline, Web of Science, and Embase databases was made up to February 2018. Twenty-three case-control and 10 case-parent trio studies (including 1149 cases and 1161 controls) were retrieved. Odds ratio (OR) with 95% CI were used to estimate the pooled strength of association under different genetic models. The Q test and I² test were used to estimate heterogeneity among studies, the quality of which was assessed using the Newcastle-Ottawa scale. In the MTHFR c.677C>T polymorphism group, there were significant overall results for the recessive (OR 1.231, 95%CI 1.092 to 1.387) and homozygote (OR 1.252, 95%CI 1.078 to 1.456) models. Subgroup analysis by subjects and ethnicity identified only associations in European mothers for the recessive model and the homozygote model. For the c.1298A>C group, there were no significant results for either European or Asian patients for all genetic models. The MTHFR c.677C>T polymorphism might increase susceptibility to NSCL/P in European mothers, but was negatively associated in Asian patients, and the MTHFR c.1298A>C polymorphism is not involved in the development of NSCL/P in either European or Asian patients.

Strong Association of C677T Polymorphism of Methylenetetrahydrofolate Reductase Gene With Nosyndromic Cleft Lip/Palate (nsCL/P)

Methylenetetrahydrofolate reductase (MTHFR) is essential for DNA biosynthesis and the epigentic process of DNA methylation. It has been reported that abnormal DNA methylation contributes to the pathogenesis of congenital anomalies. There were many published case control studies assessing the associations of MTHFR C677T polymorphism with risks of nosyndromic cleft lip with and without palate (nsCL/P), but with inconsistent results. To derive a more precise estimation of the relationship, a meta-analysis was performed. Eligible articles were identified by search of databases including PubMed, Science Direct, Google Scholar and Springer Link up to December, 2015. Finally, a total of 22 studies with 3724 nsCL/P cases and 5275 controls were included in the present meta-analysis. Odds ratios (ORs) with corresponding 95% confidence intervals (95% CIs) were pooled to assess the association. Subgroup analysis based on ethnicity was also performed. All statistical analyses were done by MIX program. Meta-analysis results suggested that MTHFR C677T polymorphism contributed to the increased nsCL/P risk in overall population using four genetic models except homozygote model (for T vs. C: OR = 1.24, 95% CI = 1.1-1.4; for TT + CT vs. CC: OR = 1.29, 95% CI = 1.04-1.59; for CT vs. CC: OR = 1.26, 95% CI = 0.98-1.63; for TT vs. CC: OR = 1.02, 95% CI = 0.74-1.4; for TT vs. CT + CC: OR = 1.36, 95% CI = 1.05-1.74). In conclusion, results of present meta-analysis suggested that MTHFR C677T polymorphism is significantly associated with nonsyndromic orofacial cleft.

Association Studies and Direct DNA Sequencing Implicate Genetic Susceptibility Loci in the Etiology of Nonsyndromic Orofacial Clefts in Sub-Saharan African Populations

Orofacial clefts (OFCs) are congenital dysmorphologies of the human face and oral cavity, with a global incidence of 1 per 700 live births. These anomalies exhibit a multifactorial pattern of inheritance, with genetic and environmental factors both playing crucial roles. Many loci have been implicated in the etiology of nonsyndromic cleft lip with or without cleft palate (NSCL/P) in populations of Asian and European ancestries, through genome-wide association studies and candidate gene studies. However, few populations of African descent have been studied to date. Here, the authors show evidence of an association of some loci with NSCL/P and nonsyndromic cleft palate only (NSCPO) in cohorts from Africa (Ghana, Ethiopia, and Nigeria). The authors genotyped 48 single-nucleotide polymorphisms that were selected from previous genome-wide association studies and candidate gene studies. These markers were successfully genotyped on 701 NSCL/P and 163 NSCPO cases, 1,070 unaffected relatives, and 1,078 unrelated controls. The authors also directly sequenced 7 genes in 184 nonsyndromic OFC (NSOFC) cases and 96 controls from Ghana. Population-specific associations were observed in the case-control analyses of the subpopulations, with West African subpopulations (Ghana and Nigeria) showing a similar pattern of associations. In meta-analyses of the case-control cohort, PAX7 (rs742071, P = 5.10 × 10(-3)), 8q24 (rs987525, P = 1.22 × 10(-3)), and VAX1 (rs7078160, P = 0.04) were nominally associated with NSCL/P, and MSX1 (rs115200552, P = 0.01), TULP4 (rs651333, P = 0.04), CRISPLD2 (rs4783099, P = 0.02), and NOG1 (rs17760296, P = 0.04) were nominally associated with NSCPO. Moreover, 7 loci exhibited evidence of threshold overtransmission in NSOFC cases through the transmission disequilibrium test and through analyses of the family-based association for disease traits. Through DNA sequencing, the authors also identified 2 novel, rare, potentially pathogenic variants (p.Asn323Asp and p.Lys426IlefsTer6) in ARHGAP29 In conclusion, the authors have shown evidence for the association of many loci with NSCL/P and NSCPO. To the best of this knowledge, this study is the first to demonstrate any of these association signals in any African population.

Association between Maternal MTHFR Polymorphisms and Nonsyndromic Cleft Lip with or without Cleft Palate in Offspring, A Meta-Analysis Based on 15 Case-Control Studies

Background

The methylenetetrahydrofolate reductase (MTHFR) is thought to be involved in the development of nonsyndromic cleft lip with or without cleft palate (NSCL/P). However, conflicting results have been obtained when evaluating the association between maternal MTHFR C677T and A1298C polymorphisms and the risk of NSCL/P. In light of this gap, a meta-analysis of all eligible case-control studies was conducted in the present study.

Materials and Methods

A total of 15 case-control studies were ultimately identified after a comprehensive literature search and Hardy-Weinberg equilibrium (HWE) examination. Cochrane’s Q test and index of heterogeneity (I²) indicated no obvious heterogeneity among studies.

Results

Fixed or random-effects models were used to calculate the pooled odds ratios (ORs). The results showed that the TT genotype in mothers increased the likelihood of having NSCL/P offspring 1.25 times (95% CI: 1.047-1.494) more than the CC homozygotes. Meanwhile, maternal TT genotype increased the risk of producing NSCL/P offspring in recessive model (OR=1.325, 95% CI: 1.124-1.562). However, the CT heterozygote and the CT+TT dominant models had no association with NSCL/P offspring compared with the CC wild-type homozygote model. Subgroup analyses based on ethnicity indicated that maternal TT genotype increased the likelihood of having NSCL/P offspring in Whites (OR=1.308, 95% CI: 1.059-1.617) and Asians (OR=1.726, 95% CI: 1.090-2.733) in recessive model. Also, subgroup analyses based on source of control showed that mothers with the 677TT genotype had a significantly increased susceptibility of having NSCL/P children in hospital based population (HB) when compared with CC homozygotes (OR=1.248, 95% CI: 1.024-1.520) and un- der the recessive model (OR=1.324, 95% CI: 1.104-1.588). Furthermore, maternal A1298C polymorphism had no significant association with producing NSCL/P offspring (dominant model OR=0.952, 95% CI: 0.816-1.111, recessive model OR=0.766, 95% CI: 0.567-1.036).

Conclusion

MTHFR C677T polymorphism is associated with the risk of generating NSCL/P offspring, and being a 677TT homozygote is a risk factor. MTHFR A1298C polymorphism was not associated with generating NSCL/P offspring. However, further work should be performed to confirm these findings.

Lack of Association Between MTHFR, MTR, MTRR, and TCN2 Genes and Nonsyndromic CL±P in a Chinese Population: Case-Control Study and Meta-Analysis

Nonsyndromic cleft lip with or without cleft palate (NSCLP) is a common congenital deformity, often associated with folate deficiency. The genes MTHFR, MTR, MTRR, and TCN2 play key roles in folate metabolism. The risk of NSCLP associated with particular variants in the folic acid pathway differs among ethnic groups. The goal of this study was to explore whether genetic variations in these four genes, as well as gene-gene interactions, are associated with NSCLP. We investigated 7 tagSNPs for MTHFR, 18 tagSNPs for MTR, 15 tagSNPs for MTRR, and 7 tagSNPs for TCN2 selected from HapMap data in a Chinese population. These single nucleotide polymorphisms (SNPs) were examined for associations with NSCLP in 204 patients and 226 controls. We then performed a meta-analysis of association between rs1801133 and NSCLP. There was a significant difference in the allele frequency and haplotype analysis of rs4077829 and rs10802565 in MTR between the NSCLP and control groups but not a significant difference after correction with 10,000 times permutations. The allele frequency, haplotype analysis, and gene-gene interactions of other SNPs did not show a significant difference. The meta-analysis results showed that no significant differences were found for allele comparison, heterozygote comparison, homozygote comparison, dominant model comparison, or recessive model comparison. The alterations of folate metabolism related to these polymorphisms are not involved in NSCLP in the Chinese population.

MTHFR C677T and A1298C polymorphisms and risk of nonsyndromic orofacial clefts in a south Indian population

OBJECTIVES

Several lines of evidence suggest that the decrease in folate in periconceptional period or maternal use of folate antagonists has been associated with a higher risk of orofacial clefts (OFCs). MTHFR is a critical enzyme in folate metabolism that catalyzes the irreversible conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate, thus playing a vital role in DNA synthesis and DNA methylation. The aim of our study was to determine whether there is any association between the susceptibility to Nonsyndromic cleft lip with or without cleft palate (NSCL/P) amongst the variations of MTHFR genotypes in South Indian population.

METHODS

Our sample comprised 123 cases with NSCL/P and 141 controls without clefts or family history of clefting. The most common polymorphisms C677T (rs1801133) and A1298C (rs1801131) on the MTHFR gene were screened for the genotypes using PCR-RFLP.

RESULTS

Both C677T and A1298C are polymorphic with minor allele frequencies of 0.131 and 0.429, respectively, for controls. Genotype data in control and cleft groups are following the Hardy Weinberg Equilibrium. There were no significant differences in genotypes of both polymorphisms between controls and NSCL/P. The pairwise LD values (D' and r(2)) between C677T and A1298C are 1.0 and 0.096 respectively indicating no significant LD between these two SNPs. Haplotype phenotype analysis did not show the evidence for association. Gene-gene interaction showed the distribution of the observed combinations of the two MTHFR polymorphisms was not different between NSCL/P and controls (p=0.887).

CONCLUSIONS

Our results do not support the hypothesis, that variants in the MTHFR gene confer a risk for NSCL/P in the South Indian population.

Determination of Methylenetetrahydrofolate Reductase (MTHFR) gene polymorphism in Turkish patients with nonsyndromic cleft lip and palate

OBJECTIVE

To investigate the association between MTHFR C677T polymorphism and Turkish patients with nonsyndromic cleft lip and/or palate (nsCL/P) and to determine the prevalence of the Turkish population.

PATIENTS AND METHODS

Molecular analysis of gene polymorphisms were carried out using polymerase chain reactions and restriction enzyme digestions. In our study, 80 patients with nsCL/P and 125 unrelated individuals from Turkey were studied.

RESULTS

We found that MTHFR C677T polymorphism is a significant risk factor for nsCL/P in Turkey (p=0.0004). These results support the impact of MTHFR C677T polymorphism and importance of folic acid intake in the etiology of nsCL/P.

CONCLUSIONS

MTHFR gene which is localized in the relevant region of chromosome 1p36.3 not been studied Turkish patients with nsCL/P and the prevalence of our country not to be determined. We revealed statistically association between the MTHFR C677T gene polymorphism and nonsyndromic cleft lip and/or palate in the Turkish population.