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

Role of MTHFR, IRF6, PAX7 and TP63 SNPs in susceptibility to non-syndromic orofacial cleft, a candidate gene study in a Portuguese population

BACKGROUND

Non-syndromic orofacial cleft (NSOC) is a complex phenotype, involving multiple genetic and environmental factors. Association studies exploring the genetic susceptibility to this prevalent oral malformation show variability of results in different populations. Using a candidate gene approach, we aimed to verify the role of four single-nucleotide polymorphisms (SNPs) in the susceptibility to NSOC in Portuguese patients.

METHODS

A total of 254 non-consanguineous individuals of Portuguese were recruited, including 120 patients with NSOC and 134 controls. About 92% of these patients had non-syndromic cleft lip with or without cleft palate (NSCL/P) and 8% had only non-syndromic cleft palate (NSCP). SNPs in the MTHFR (rs1801133), IRF6 (rs642961), PAX7 (rs742071) and TP63 (rs9332461) genes were studied, using a real-time approach with TaqMan probes. Allelic, genotypic, dominant, recessive and over-dominant models were explored using a chi-squared test. Adjusted p-value was calculated for multiple comparisons using the Benjamini-Hochberg false discovery rate (FDR).

RESULTS

All SNPs were in Hardy-Weinberg equilibrium. For MTHFR, IRF6, and PAX7 SNPs, no statistically significant difference was highlighted for any of the evaluated models. For TP63 SNP, data fitted an over-dominant model, with a protective effect for heterozygotes (OR 1.897; CI 95% [1.144-3.147]; p < .016, when comparing controls vs. cases), but significance was lost when applying adjusted p-value for multiple comparisons (4 × 5 tests).

CONCLUSION

In this Portuguese population, there was no evidence of an association between the evaluated SNPs and NSOC. For TP63 SNP, the possibility of a protective effect of heterozygotes should be further investigated.

Evidence Mapping and Quality Analysis of Systematic Reviews on Various Aspects Related to Cleft Lip and Palate

BACKGROUND

Management of cleft lip and palate is interdisciplinary. An evidence-mapping approach was envisaged to highlight the existing gaps in this field, using only the highest level of evidence.

OBJECTIVES

To conduct evidence mapping and quality analysis of systematic reviews and meta-analyses related to any aspect of cleft lip and palate.

SEARCH METHODS

The cleft lip and palate field was divided into 9 domains and 50 subdomains and a method of categorization of systematic reviews was established. A comprehensive search strategy was carried out in seven databases along with the search of gray literature and references of included articles.

SELECTION CRITERIA

Systematic reviews related to any aspect of cleft lip and palate, conducted by a minimum of two reviewers, with a comprehensive search strategy and adequate quality analysis were included.

DATA COLLECTION AND ANALYSIS

A self-designed, pre-piloted data-extraction sheet was used to collect information that was analyzed through an expert group discussion. Quality analysis was performed using ROBIS-I, AMSTAR 2, and the PRISMA checklist.

RESULTS

A total of 144 systematic reviews published between 2008 and 2022 were included. The largest number of these could be categorized in the therapeutic domain (n = 58). A total of 27% of the studies were categorized as inconclusive, 40% as partially conclusive, and 33% as conclusive. As per ROBIS-I, 77% of reviews had high risk of bias while 58% were graded as critically low in quality as per AMSTAR 2. The majority of systematic reviews showed low reporting errors.

CONCLUSIONS

The majority of systematic reviews related to cleft lip and palate relate to therapeutic and prognostic domains and show high risk of bias and critically low quality regardless of the source journal. The results of this paper might serve as a starting point encouraging authors to carry out high-quality research where evidence is lacking.

REGISTRATION

A multidisciplinary expert-group formulated an a priori protocol, registered in Open Science Framework (DOI 10.17605/OSF.IO/NQDV2).

Maternal genotypes of folate/one-carbon metabolism gene variants and nonsyndromic cleft lip with or without cleft palate risk in Chile

The aim of this study was to evaluate, in a case-control design, the association between maternal genotypes for variants in 23 genes involved in folate/one-carbon metabolism and nonsyndromic cleft lip with or without cleft palate (NSCL/P) in a Chilean population. After applying several filters to an Illumina array, we extracted 175 single nucleotide polymorphisms (SNPs) from 150 mothers of NSCL/P cases and 150 control women. Association was evaluated using computed odds ratio (OR) with a 95% confidence interval (95% CI) in additive, recessive, and dominant models. After multiple comparison correction, only SNP rs4451422 (A>C), located 237 bp downstream of the gene encoding the human folylpolyglutamate synthetase (FPGS), maintained a significant association with NSCL/P in the offspring (OR 3.03; 95% CI 1.69-5.26). The variant rs4451422 is associated with a decrease in FPGS expression according to database annotation. Our results lead to a new hypothesis that a lower activity of FPGS enzyme reduces intracellular folate levels and increases the risk of an offspring having NSCL/P.

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.

Gene-Environment Interplay and MicroRNAs in Cleft Lip and Cleft Palate

Cleft lip (CL) with/without cleft palate (CP) (hereafter CL/P) is the second most common congenital birth defect, affecting 7.94 to 9.92 children per 10,000 live births worldwide, followed by Down syndrome. An increasing number of genes have been identified as affecting susceptibility and/or as causative genes for CL/P in mouse genetic and chemically-induced CL and CP studies, as well as in human genome-wide association studies and linkage analysis. While marked progress has been made in the identification of genetic and environmental risk factors for CL/P, the interplays between these factors are not yet fully understood. This review aims to summarize our current knowledge of CL and CP from genetically engineered mouse models and environmental factors that have been studied in mice. Understanding the regulatory mechanism(s) of craniofacial development may not only advance our understanding of craniofacial developmental biology, but could also provide approaches for the prevention of birth defects and for tissue engineering in craniofacial tissue regeneration.