Current concepts in genetics of nonsyndromic clefts

Increased susceptibility for nonsyndromic cleft lip with or without cleft palate by SLC19A1 80G>A genetic variation

BACKGROUND

The disruption of craniofacial developmental pathways during early embryogenesis can lead to conditions such as nonsyndromic cleft lip with or without cleft palate (NSCL/P). Several lines of evidence indicate that inadequate maternal nutrition causes low folate levels during the periconceptional period, resulting in NSCL/P. Although substantial research has been conducted on the possible link between SLC19A1 genetic variants and NSCL/P, the association between SLC19A1 80G>A (rs1051266) and NSCL/P remains unclear. In the present study, the associations of SLC19A1 80G>A with NSCL/P risk were assessed by calculating the pooled odds ratios (ORs) and 95% confidence intervals (CIs) by meta-analyses.

METHODS

Following the PRISMA guidelines, a meta-analysis was conducted on 10 studies assessing the NSCL/P risk associated with SLC19A1 80G>A variant. To ascertain the degree of relationship between the SLC19A1 80G>A genetic variant and the risk of NSCL/P, data were analyzed in allelic, recessive and dominant genetic models. CI of OR for each study and the pooled data were obtained. All statistical analyses were conducted utilizing the MetaGenyo software tool, which integrates the adjustment of P values for multiple testing through the Bonferroni method.

RESULTS

The pooled analysis showed that SLC19A1 80G>A variant significantly increased the NSCL/P risk in the allelic model (OR 1.39; 95% CI 1.00-1.92), recessive model (OR 1.37; 95% CI 1.03-1.82) and dominant models (OR 1.7; 95% CI 1.05-2.90). Publication bias was not observed.

CONCLUSIONS

This study supports that the SLC19A1 80G>A genetic variant is associated with NSCL/P risk.

CHDH, a key mitochondrial enzyme, plays a diagnostic role in metabolic disorders diseases and tumor progression

Human choline dehydrogenase (CHDH) is a transmembrane protein located in mitochondria. CHDH has been shown to be one of the important catalytic enzymes that catalyze the oxidation of choline to betaine and is involved in mitochondrial autophagy after mitochondrial damage. In recent years, an increasing number of studies have focused on CHDH and found a close association with the pathogenesis of various diseases, including tumor prognosis. Here we summarized the genomic localization, protein structure and basic functions of CHDH and discuss the progress of CHDH research in metabolic disorders and other diseases. Moreover, we described the regulatory role of CHDH on the progression of different types of malignant tumors. In addition, major pathogenic mechanisms of CHDH in multiple diseases may be associated with single nucleotide polymorphism (SNP). We look forward to providing new strategies and basis for clinical diagnosis and prognosis prediction of diseases by diagnosing SNP loci of CHDH genes. Our work evaluates the feasibility of CHDH as a molecular marker relevant to the diagnosis of some metabolic disorders diseases and tumors, which may provide new targets for the treatment of related diseases and tumors.

Epidemiological and Spatiotemporal Descriptive Analysis of Patients with Nonsyndromic Cleft Lip and/or Palate: A 12-Year Retrospective Study in Southern Iran

Objectives

The current study is aimed at evaluating epidemiological characteristics and spatiotemporal distribution of cleft lip and/or palate (CL/P) in the south of Iran.

Methods

Data were extracted from the 1840 medical records of patients who were referred to the Cleft Lip and Palate Center of Shiraz University of Medical Sciences, from January 1, 2011, to September 1, 2022. The collected variables included demographic data (gender, birth date and season, place, birth order, and weight), cleft types and the subtypes, parental information (health status, education level, marital status, and age during the pregnancy), and other basic parameters. The chi-square test at a significance level of 0.05 was used to analyze collected data. The geographic information system (GIS) analysis was also used for analyzing the spatial distribution of CL/P patients.

Results

Based on our inclusion criteria, 1281 nonsyndromic patients were included in this study. The most common type was cleft lip and palate (CLP) with 48.32%, whereas cleft palate (CP) and cleft lip (CL) accounted for 40.75% and 10.93% of the patients, respectively. There was a progressive increase in the frequency of all types of clefts, and most of them were male (P ≤ 0.001). The urban population outnumbered the rural ones in all provinces. Parents were mostly healthy (>80%) with low educational status (47.5%). Most born CL/P patients were from consanguineous marriages (58.9%), especially between first-degree relatives. A majority of CL/P patients (73.1%) were born in the first two gestations with a birth weight of 2500-4000 g (77.4%). Most infants with CL/P (84.3%) were born from mothers who had at least one of the predisposing factors.

Conclusion

In this study, the frequency of cleft types and subtypes was similar to the existing literature. However, high rate of consanguineous marriage, especially between first-degree relatives, was the most notable feature of this population.

Genetic markers for non-syndromic orofacial clefts in populations of European ancestry: a meta-analysis

To date, the involvement of various genetic markers in the aetiopathogenesis of non-syndromic orofacial cleft (nsOFC) has been extensively studied. In the present study, we focused on studies performed on populations of European ancestry to systematically review the available literature to define relevant genetic risk factors for nsOFC. Eligible studies were obtained by searching Ovid Medline and Ovid Embase. We gathered the genetic markers from population-based case–control studies on nsOFC, and conducted meta-analysis on the repeatedly reported markers. Whenever possible, we performed stratified analysis based on different nsOFC phenotypes, using allelic, dominant, recessive and overdominant genetic models. Effect sizes were expressed as pooled odds ratios (ORs) with 95% confidence intervals (CIs), and p ≤ 0.05 were considered statistically significant. A total of 84 studies were eligible for this systematic review, with > 700 markers included. Of these, 43 studies were included in the meta-analysis. We analysed 47 genetic variants in 30 genes/loci, which resulted in 226 forest plots. There were statistically significant associations between at least one of the nsOFC phenotypes and 19 genetic variants in 13 genes/loci. These data suggest that IRF6, GRHL3, 8q24, VAX1, TGFA, FOXE1, ABCA4, NOG, GREM1, AXIN2, DVL2, WNT3A and WNT5A have high potential as biomarkers of nsOFC in populations of European descent. Although other meta-analyses that included European samples have been performed on a limited number of genetic variants, this study represents the first meta-analysis of all genetic markers that have been studied in connection with nsOFC in populations of European ancestry.

Association between PTCH1 and RAD54B Single-Nucleotide Polymorphisms and Non-syndromic Orofacial Clefts in the Northeast Population of Iran

Background

Non-Syndromic Cleft Lip with or without cleft Palate (NSCL/P) is a common developmental disorder of the head and neck with a multifactorial etiology. The current study aimed to evaluate the potential association of PTCH1 (rs10512248) and RAD54B (rs12681366) polymorphisms with NSCL/P in the Northeast Iranian population.

Methods

In the present study, blood samples were taken from 122 subjects with NSCL/P and 161 healthy controls. Polymerase Chain Reaction (PCR) followed by Restriction Fragment Length Polymorphism (RFLP) were used to conduct genotyping of single-nucleotide polymorphisms.

Results

Although differences were observed between cases and controls in rs10512248 and rs12681366, our data did not support a significant association of these polymorphisms with NSCL/P in our population.

Conclusion

Our findings suggest that polymorphisms of rs10512248 and rs12681366 may not be potential risk factors for NSCL/P in the Northeast Iranian population due to the multifactorial and multiethnicity characteristics of some genes.

Genetic variations at 10q26 regions near FGFR2 gene and its association with non-syndromic cleft lip with or without cleft palate

OBJECTIVES

In our study, we focussed on three SNPs in the non-coding regions near FGFR2 gene, as studies on non-coding variants in the genome are the novel trends to identify the susceptible loci for nonsyndromic cleft lip with or without cleft palate (NSCL/P). FGFR2 gene is selected as a candidate gene based on knock out animal models and the role played in syndromic forms of clefting. FGFR2 gene also plays an important role in FGF signaling pathway during craniofacial development.

METHODS

In the present study 148 case-parent triads were assessed for three SNPs rs10749408, rs11199874 and rs10788165 near FGFR2 gene by using TaqMan allelic discrimination method. Transmission disequilibrium test (TDT) was used to find the allelic association. Linkage disequilibrium (LD) between the markers was analysed using Haploview program 4.2. Haplotype transmission effects were estimated using FAMHAP package. The possible parent-of-origin effects were assessed by likelihood based approach.

RESULTS

TDT analysis of three SNPs failed to show significant transmission disortion from heterozygous parents to the affected child and are not associated with NSCL/P. Linkage disequilibrium analysis showed strong LD between rs11199874 and rs10788165 SNPs. In the haplotype TDT analysis, GG haplotype of rs11199874-rs10788165 showed significant undertransmission to affected child. No significant parent-of-origin effects were observed.

CONCLUSION

The present study on noncoding variants near FGFR2 gene is not associated with NSCL/P. As the numbers of triads included in the study are less, further studies are needed including large sample size to find association with NSCL/P.

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.

Single-nucleotide polymorphisms of methylenetetrahydrofolate reductase gene in a South Indian cohort with nonsyndromic cleft lip with or without palate

Objective:

Clefts of the lip, with or without cleft palate and cleft palate only, collectively called as orofacial clefts (OFCs) are one of the most common congenital malformations with varying degrees of penetrance and phenotype expressions. The aim of this study was to investigate the association between methylenetetrahydrofolate reductase (MTHFR) cytosine-to-thymine (c. 677 C>T), adenine-to-cytosine (c.1298 A>C) single- nucleotide polymorphisms (SNPs) and South Indian patients with the nonsyndromic cleft lip with or without palate (NSCL ± P).

Methods:

A cohort consisting of 25 cases of NSCL ± P and 18 controls from a South Indian cohort were included in this case–control study. Genetic analysis of c.677C>T and c.1298A C polymorphisms in the MTHFR gene was carried out using Sanger sequencing and analyzed from chromatogram profiles. Data interpretation was done using statistical software MedCalc Statistical Software version 16.2 and the Statistical Package for the Social Sciences (SPSS version 22.0).

Results:

DNA sequence analysis of the MTHFR gene revealed c. 677C>T and c. 1298A>C polymorphisms in 16% and 76% of NSCL ± P cases, respectively. Heterozygous variant in MTHFR c. 1298A>C polymorphism was found to be a significant risk factor (P = 0.0164) for NSCL ± P in South Indian ethnic population. c.677C>T polymorphism, in particular, was apparently dormant overall in the study population. These results offer certain novelty in terms of the distinctive pattern in SNPs of genotypes observed in the study.

Conclusion:

NSCL ± P is one of the most common and challenging congenital malformations with complex etiological basis. Common risk factors such as MTHFR SNPs, namely c.677C>T and c.1298A>C, are subjected to variations in terms of ethnic group, geographic region and micro/macro-environmental factors. Overall, our study has explored part of South Indian ethnic population and revealed a different and unique distribution of mutations in this sample population.

Association of MAPK4 and SOX1-OT gene polymorphisms with cleft lip palate in multiplex families: A genetic study

Background. Cleft lip and palate (CLP) is a common congenital anomaly. Many genes, like MAPK4 and SOX-1OT, are associated with its etiology in different populations. High-risk markers on these gene sreported in other populations were not studied in our population. Hence, the study aimed to determine the association of MAPK4 and SOX-1OT polymorphisms in CLP in multiplex families.

Methods. Based on inclusion and exclusion criteria, we selected 20 multiplex CLP families for this case‒control study, in which the affected individuals and healthy controls selected from these families were compared. Fifty subjects affected with cleft and 38 unaffected subjects were included in the study. The polymorphisms studied for the association consisted of rs726455 and rs2969972 in the genes SOX-1 OT and MAPK4, respectively. DNA was isolated and sent for genotyping using the MassArray method. Plink, a whole-genome association analysis toolset, was used for statistical analysis.

Results. Both polymorphisms followed Hardy–Weinberg equilibrium. The rs726455 of SOX-1OT yielded a P-value of 0.983 and an allelic odds ratio (OR) of 0.983. For rs2969972 of MAPK4, the P-value was 0.04 (significant), and the allelic OR was 0.51. Minor allele frequency (MAF) in the unaffected subjects was more than the MAF in the affected subjects for rs2969972.

Conclusion. The results suggested that polymorphism rs726455 on SOX-1OT was not associated with familial cases of CLP. Since MAF in the unaffected subjects was more than the MAF-affected subjects, rs2969972 on MAPK4 is protective in the multiplex families.

Anatomical patterns of cleft lip and palate deformities among neonates in Mekelle, Tigray, Ethiopia; implication of environmental impact

Background

Cleft lip and palate deformities are considered one of the most common birth defects of the head and neck that pose significant medical, psychosocial and financial burdens on the affected individuals and families, especially in low income communities. The etiology and pathogenesis of cleft lip and palate is complex and is known to involve genetic and/or environmental factors.

Objective

To assess the patterns of anatomical cleft lip and palate deformities among neonates in Mekelle and Ayder Comprehensive Specialized hospitals, Tigray, Northern Ethiopia.

Methods

A hospital-based retrospective study was conducted from May 2017 to June 2017 at Mekelle and Ayder Comprehensive Specialized hospitals, both in Mekelle city. Data was collected from all medical charts of neonates registered from 2011 to 2016 and analyzed using SPSS version 21.0 and OpenEpi software. Results were presented using tables and graphs; Chi-square test was used to look for an association between variables, odds ratio to determine the strength of association of selected variables using multinomial logistic regression model, while Fisher Exact (Clopper-Pearson) was used to compare yearly prevalence.

Results

Of 37,152 neonatal charts analyzed, 119 (0.32%) cases were identified as having cleft deformities. 38.7, 17.6, and 43.7% of this figure had cleft lips, cleft palates and both cleft lip and palate respectively. 46 (38.7%) neonates had lateral patterns of cleft lip deformities with 56.5% located unilaterally on the right and 43.5% unilaterally on the left. Of 52 (43.7%) neonates with cleft lip and palate deformities, 40.4% were located bilaterally while 38.5 and 21.2% were located unilaterally on the left and right, respectively. Associated malformations were: cardiac (3.4%), central nervous system (1.7%) and limb deformities (5.9%). The overall prevalence of cleft deformities was found to be 3.11 per 1000 live births.

Conclusion

The study showed a higher prevalence of cleft deformities than that reported in Addis Ababa and some other African countries. A higher occurrence of left unilateral pattern of cleft lip and palate was observed whereas a higher right unilateral pattern of cleft lip was identified. The higher prevalence of cleft lip and palate recorded in this region of Ethiopia may reflect an environmental impact.

MSX1 gene polymorphisms and non-syndromic cleft lip with or without palate (NSCL/P): A meta-analysis

OBJECTIVE

Non-syndromic cleft lip, with or without cleft palate (NSCL/P), is a common craniofacial birth defect, the risk of which is influenced from multiple genetic loci. Association study outcomes between single nucleotide polymorphisms (SNPs) near the muscle segment homeobox gene 1 (MSX1) and NSCL/P have been inconsistent. This compels a meta-analysis to obtain more precise estimates.

METHODS

From 15 publications, we examined 12 SNPs under six groups (SG), based on linkage disequilibrium. Pooled odds ratios and 95% confidence intervals were calculated under the standard genetic models. The pooled effects were subjected to subgroup, outlier, sensitivity, and funnel plot (publication bias) analyses.

RESULTS

Three of the six SGs showed significant associations. SG1 and SG4 effects indicated reduced risks. SG1 outcomes were attributed to outlier treatment, which the Asian outcomes validated. In contrast, increased risks were observed in SG3. All these significant outcomes were deemed robust by sensitivity analysis with no evidence of publication bias.

CONCLUSIONS

Our study shows eight MSX1 SNPs associated with risk of NSCL/P. SG1 and SG4 carriers are protected (up to 23%), but SG3 carriers are 1.3-fold susceptible. Outlier treatment unmasked the significant associations in SG1. Non-heterogeneity and robustness helped elevate the level of evidence in our significant findings.

The Electrical Activity of Masseter and Anterior Temporal Muscles in Patients With Unilateral Cleft Lip and Palate

This study aimed to determine the electrical activity of masseter and anterior temporal muscles in patients with unilateral cleft lip and palate (CLP) and compare it with healthy volunteers. The study involved 20 female patients (mean age 20 ± 4 years) with unilateral cleft lip and palate who had undergone lip and palate surgery in childhood and finished the first-phase orthodontic therapy with level and align teeth. Twenty age- and sex-matched volunteers with no cleft lip and palate were involved as controls. Electromyographic (EMG) signals of masseter and anterior temporal muscles were recorded at rest position, during swallowing and during maximum bite force (MBF). EMG signals at different test conditions were compared between the cleft and noncleft sides of CLP patients and between CLP patients and healthy individuals. The EMG potentials of masseter (rest, swallowing, MBF) and temporal (rest, MBF) muscles were significantly higher in the cleft than the noncleft side of CLP patients (P value <0.001). Generally, patients with unilateral cleft lip and palate experienced a significant increase in the electrical activity of the masseter and temporal muscles in both sides compared to the control group (P <0.05). In conclusion, patients with unilateral cleft lip and palate exhibit overall greater masticatory muscle activity compared to healthy individuals. The asymmetric masticatory function in subjects with unilateral cleft lip and palate may be associated with severe consequences such as asymmetric facial growth, implying the importance of early diagnosis and orthodontic treatment to achieve a favorable environment for balanced facial growth in CLP affected patients.

Associated Malformations in Children with Orofacial Clefts in Portugal: A 31-Year Study

Background:

Orofacial clefts are among the most common congenital craniofacial malformations and may be associated with other birth defects. However, the proportion and type of additional anomalies vary greatly between studies. This study assessed the prevalence and type of associated congenital malformations in children with orofacial clefts, who attended the largest cleft lip and palate tertiary referral center in Portugal.

Methods:

Consecutive children with orofacial clefts who attended at least 1 consultation in our Clefts Unit between 1981 and 2012 were studied. Demographic and clinical data regarding the number and type of associated malformations were retrospectively collected and analyzed.

Results:

Of the 701 patients studied, 219 (31.2%) had associated congenital malformations. These malformations were more frequent in children with cleft palate (43.4%) than in children with cleft lip and palate (27.5%) or with cleft lip only (19.4%). Within the group with associated anomalies, 73 cases (33.3%) had conditions related with known chromosomal defects, monogenic syndromes or sequences, and 146 cases (66.7%) had multiple congenital anomalies of unknown origin. From those, head and neck malformations were the most common (60.3%), followed by malformations in the cardiovascular (28.3%) and musculoskeletal systems (26%).

Conclusions:

The overall prevalence of associated malformations of nearly 1 in 3 children with orofacial clefts stressed the need for a comprehensive evaluation of these patients by a multidisciplinary cleft team. Moreover, one-third of the children had multiple congenital anomalies of known origins. Thus, early routine screening for other malformations and genetic counseling might be valuable for orofacial clefts management.

Transmission analysis of TGFB1 gene polymorphisms in non-syndromic cleft lip with or without cleft palate

OBJECTIVES

Transforming growth factor beta1 (TGF-β1) plays a significant role in craniofacial development. Previous linkage studies reported that the TGF-β1-locus at 19q13.1 harbour predisposing genes for non-syndromic oral clefts. In the present study case parents triads were evaluated to find the transmission effects of genetic variants in TGF- β1 towards non-syndromic cleft lip or palate (NSCL/P).

METHODS

Using allelic discrimination method148 families (case-parent triads) were assessed for single nucleotide polymorphisms (SNPs) in TGF-β1 gene. The SNPs were checked for mendelian errors and Hardy-Weinberg equilibrium (HWE). Transmission disequilibrium test and haplotype frequencies were estimated.

RESULTS

The TGF-β1 SNPs showed very low minor allele frequencies (MAFs) and observed heterozygosity (Hobs). The transmission disequilibrium test (TDT) and parent-of-origin likelihood ratio tests (PO-LRT) were not significant for any of the SNPs tested. Strong linkage disequilibrium (r² = 0.722) was found between rs1800469 and rs1800470 SNPs. Haplotype analysis ignoring parent of origin showed strong evidence of excess transmission but it is not significant (p-value = 0.293).

CONCLUSION

Transmission of minor alleles were not observed from either parent indicating that the TGF-β1 gene polymorphisms by themselves do not confer risk for non-syndromic oral clefts but, rather, modify the stability and the activation process of TGF-β1. As the number of families included in the study are less, results must be considered still preliminary and require replication using more families.

Sonic hedgehog regulation of Foxf2 promotes cranial neural crest mesenchyme proliferation and is disrupted in cleft lip morphogenesis

Cleft lip is one of the most common human birth defects, yet our understanding of the mechanisms that regulate lip morphogenesis is limited. Here, we show in mice that sonic hedgehog (Shh)-induced proliferation of cranial neural crest cell (cNCC) mesenchyme is required for upper lip closure. Gene expression profiling revealed a subset of Forkhead box (Fox) genes that are regulated by Shh signaling during lip morphogenesis. During cleft pathogenesis, reduced proliferation in the medial nasal process mesenchyme paralleled the domain of reduced Foxf2 and Gli1 expression. SHH ligand induction of Foxf2 expression was dependent upon Shh pathway effectors in cNCCs, while a functional GLI-binding site was identified downstream of Foxf2 Consistent with the cellular mechanism demonstrated for cleft lip pathogenesis, we found that either SHH ligand addition or FOXF2 overexpression is sufficient to induce cNCC proliferation. Finally, analysis of a large multi-ethnic human population with cleft lip identified clusters of single-nucleotide polymorphisms in FOXF2 These data suggest that direct targeting of Foxf2 by Shh signaling drives cNCC mesenchyme proliferation during upper lip morphogenesis, and that disruption of this sequence results in cleft lip.

Clinical relevance of breast and gastric cancer-associated polymorphisms as potential susceptibility markers for oral clefts in the Brazilian population

BACKGROUND

Epidemiological studies have indicated a higher incidence of breast and gastric cancer in patients with nonsyndromic cleft lip with or without cleft palate (NSCL ± P) and their relatives, which can be based on similar genetic triggers segregated within family with NSCL ± P.

METHODS

This multicenter study evaluated the association of 9 single nucleotide polymorphisms (SNP) in AXIN2 and CDH1, representing genes consistently altered in breast and gastric tumors, with NSCL ± P in 223 trios (father, mother and patient with NSCL ± P) by transmission disequilibrium test (TDT).

RESULTS

Our results showed that the minor A allele of rs7210356 (p = 0.01) and the T-G-G-A-G haplotype formed by rs7591, rs7210356, rs4791171, rs11079571 and rs3923087 SNPs (p = 0.03) in AXIN2 were significantly under-transmitted to patients with NSCL ± P. In CDH1 gene, the C-G-A-A and A-G-A-G haplotypes composed by rs16260, rs9929218, rs7186053 and rs4783573 polymorphisms were respectively over-transmitted (p = 0.01) and under-transmitted (p = 0.008) from parents to the children with NSCL ± P.

CONCLUSIONS

The results suggest that polymorphic variants in AXIN2 and CDH1 may be associated with NSCL ± P susceptibility, and reinforce the putative link between cancer and oral clefts.

Tooth agenesis and orofacial clefting: genetic brothers in arms?

Tooth agenesis and orofacial clefts represent the most common developmental anomalies and their co-occurrence is often reported in patients as well in animal models. The aim of the present systematic review is to thoroughly investigate the current literature (PubMed, EMBASE) to identify the genes and genomic loci contributing to syndromic or non-syndromic co-occurrence of tooth agenesis and orofacial clefts, to gain insight into the molecular mechanisms underlying their dual involvement in the development of teeth and facial primordia. Altogether, 84 articles including phenotype and genotype description provided 9 genomic loci and 26 gene candidates underlying the co-occurrence of the two congenital defects: MSX1, PAX9, IRF6, TP63, KMT2D, KDM6A, SATB2, TBX22, TGFα, TGFβ3, TGFβR1, TGFβR2, FGF8, FGFR1, KISS1R, WNT3, WNT5A, CDH1, CHD7, AXIN2, TWIST1, BCOR, OFD1, PTCH1, PITX2, and PVRL1. The molecular pathways, cellular functions, tissue-specific expression and disease association were investigated using publicly accessible databases (EntrezGene, UniProt, OMIM). The Gene Ontology terms of the biological processes mediated by the candidate genes were used to cluster them using the GOTermMapper (Lewis-Sigler Institute, Princeton University), speculating on six super-clusters: (a) anatomical development, (b) cell division, growth and motility, (c) cell metabolism and catabolism, (d) cell transport, (e) cell structure organization and (f) organ/system-specific processes. This review aims to increase the knowledge on the mechanisms underlying the co-occurrence of tooth agenesis and orofacial clefts, to pave the way for improving targeted (prenatal) molecular diagnosis and finally to reflect on therapeutic or ultimately preventive strategies for these disabling conditions in the future.

Association of TFAP2A gene polymorphism with susceptibility to non-syndromic cleft lip with or without palate risk in south Indian population

The aetiology of non-syndromic cleft lip with or without cleft palate (NSCL/P) is complex involving multiple interacting genes and environmental factors. The primary objective of the present study was to investigate the role of TFAP2A gene single nucleotide polymorphisms (SNPs) in the pathogenesis of NSCL/P. In this study, 173 unrelated NSCL/P patients and 176 controls without clefts were genotyped with TFAP2A rs1675414 (Exon 1), rs3798691 (Intron 1), and rs303050 (Intron 4) variants by allele-specific amplification using the KASPar SNP genotyping system. The method of multifactor dimensionality reduction (MDR) was used to analyze gene-gene interactions. TFAP2A polymorphisms are not found to be associated with non-syndromic cleft lip with or without cleft palate (NSCL/P) at either the genotype or allele levels. No linkage disequilibrium (LD) was found between TFAP2A variants. MDR analysis did not show a significant effect of the TFAP2A gene polymorphisms on susceptibility to NSCL/P (p > 0.05). These results suggest that the analyzed variations in TFAP2A gene might not be associated with NSCL/P pathogenesis in south Indian population.

The old and new face of craniofacial research: How animal models inform human craniofacial genetic and clinical data

The craniofacial skeletal structures that comprise the human head develop from multiple tissues that converge to form the bones and cartilage of the face. Because of their complex development and morphogenesis, many human birth defects arise due to disruptions in these cellular populations. Thus, determining how these structures normally develop is vital if we are to gain a deeper understanding of craniofacial birth defects and devise treatment and prevention options. In this review, we will focus on how animal model systems have been used historically and in an ongoing context to enhance our understanding of human craniofacial development. We do this by first highlighting "animal to man" approaches; that is, how animal models are being utilized to understand fundamental mechanisms of craniofacial development. We discuss emerging technologies, including high throughput sequencing and genome editing, and new animal repository resources, and how their application can revolutionize the future of animal models in craniofacial research. Secondly, we highlight "man to animal" approaches, including the current use of animal models to test the function of candidate human disease variants. Specifically, we outline a common workflow deployed after discovery of a potentially disease causing variant based on a select set of recent examples in which human mutations are investigated in vivo using animal models. Collectively, these topics will provide a pipeline for the use of animal models in understanding human craniofacial development and disease for clinical geneticist and basic researchers alike.

Polymorphic variants near 1p22 and 20q11.2 loci and the risk of non-syndromic cleft lip and palate in South Indian population

BACKGROUND

Recent genome-wide association studies (GWAS) have reported multiple genetic risk loci for non-syndromic orofacial clefts (NSOFCs) in many populations. However, the contribution of these loci to NSOFC in India, which comprises one-fifth of the global population, is completely lacking. Our aim was to replicate the association of the SNPs located on 1p22 chromosomal loci (rs540026, rs481931) and 20q11.2 (rs13041247, rs11696257) in the aetiology of NSOFCs, in South Indian populations.

METHODS

The SNPs were genotyped by using KBiosciences KASPar SNP genotyping chemistry in 173 cases and 176 controls for NSOFCs in South India. To estimate the association between these SNPs and NSOFCs, chi-square test was adopted. Odds ratios (OR) with 95% confidence intervals (CI) were also calculated in order to assess the risk.

RESULTS

Single nucleotide polymorphisms located at chromosomal region 1p22 are not found to be associated with cleft lip with or without non-syndromic cleft palate (NSCL/P) and non-syndromic cleft palate only (NSCPO) at either the genotype or allele levels. Further, there is no LD observed between these variants. The polymorphic variants near 20q11.2 (rs13041247, rs11696257) are in complete linkage disequilibrium (LD) and are significantly associated with only NSCL/P in genotypic (p=0.013) and allelic models (p=0.029). In the genotypic model significance persisted even after Bonferroni correction (p<0.016).

CONCLUSION

These results suggest that 20q11.2 SNPs could play a contributory role in the pathophysiology and risk of NSCL/P, while the variations in 1p22 do not underlie the pathophysiology of NSOFCs in South Indian populations.

Systematic analysis of copy number variants of a large cohort of orofacial cleft patients identifies candidate genes for orofacial clefts

Orofacial clefts (OFCs) represent a large fraction of human birth defects and are one of the most common phenotypes affected by large copy number variants (CNVs). Due to the limited number of CNV patients in individual centers, CNV analyses of a large number of OFC patients are challenging. The present study analyzed 249 genomic deletions and 226 duplications from a cohort of 312 OFC patients reported in two publicly accessible databases of chromosome imbalance and phenotype in humans, DECIPHER and ECARUCA. Genomic regions deleted or duplicated in multiple patients were identified, and genes in these overlapping CNVs were prioritized based on the number of genes encompassed by the region and gene expression in embryonic mouse palate. Our analyses of these overlapping CNVs identified two genes known to be causative for human OFCs, SATB2 and MEIS2, and 12 genes (DGCR6, FGF2, FRZB, LETM1, MAPK3, SPRY1, THBS1, TSHZ1, TTC28, TULP4, WHSC1, WHSC2) that are associated with OFC or orofacial development. Additionally, we report 34 deleted and 24 duplicated genes that have not previously been associated with OFCs but are associated with the BMP, MAPK and RAC1 pathways. Statistical analyses show that the high number of overlapping CNVs is not due to random occurrence. The identified genes are not located in highly variable genomic regions in healthy populations and are significantly enriched for genes that are involved in orofacial development. In summary, we report a CNV analysis pipeline of a large cohort of OFC patients and identify novel candidate OFC genes.

Evidence of the involvement of the polymorphisms near MSX1 gene in non-syndromic cleft lip with or without cleft palate

OBJECTIVE

Non-syndromic cleft lip, with or without cleft palate (NSCL/P) is a common craniofacial birth defect, characterised by an incomplete separation between nasal and oral cavities without any other congenital anomaly in humans. Several genes which play a role in cell differentiation, migration, growth and apoptosis, have been associated with clefting. The purpose of this study was to investigate the association between single-nucleotide polymorphisms (SNPs) near MSX1 gene and NSCL/P among South Indian population.

METHODS

A case-control analysis of five single nucleotide polymorphisms near MSX1 gene (rs11726039, rs868257, rs6446693, rs1907998 and rs6832405) was carried out in 173 patients with NSCL/P and 176 unaffected controls to determine their association with NSCL/P.

RESULTS

All SNPs were polymorphic in the study population. Comparisons of allele and genotype frequencies revealed that the C variant allele and the TC/CC genotypes of rs11726039 was significantly higher in controls than in the NSCL/P group (OR: 0.63; 95% CI: 0.41-0.097; p=0.037). However, neither of these findings remained significant after Bonferroni correction for multiple comparisons. The frequencies of rs868257, rs6446693, rs1907998 and rs6832405 minor alleles and genotypes were similar between the control and NSCL/P groups. No significant linkage disequilibrium (LD) was observed. Genotype-genotype interaction and the haplotype analysis did not reveal any significant association with NSCL/P.

CONCLUSIONS

The study results were suggestive of a positive association between MSX1 rs11726039 and NSCL/P in the South Indian population.

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.

MTHFD1 gene polymorphisms as risk factors involved in orofacial cleft: an independent case-control study and a meta-analysis

BACKGROUND

Orofacial clefts (OFCs) were among the most familiar birth defects in the world, which had been reported to be influenced by the folic acid ingestion in pregnancy previously. Methylenetetrahydrofolate dehydrogenase1 (MTHFD1) gene was associated with the susceptibility of OFCs through a complex metabolism correlate with folic acid. The aim of our study was to evaluate the correlation of five single-nucleotide polymorphisms (SNPs) within MTHFD1 related to the OFCs risk in a Chinese population.

METHODS

By the use of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), we genotyped 5 filtered SNPs (identified by Haploview 4.2 software with HapMap databases) on MTHFD1 gene: 118913T>C, 31136A>G, 58893A>G, 1958G>A and 61869T>C of 216 subjects (108 OFCs cases and 108 healthy controls) from a Chinese population. The association between these SNPs and OFCs risk was investigated by student t-test, one-way analysis of variance (ANOVA) and chi-square test with GraphPad Prism 5.0 software. Furthermore, we also performed a meta-analysis of relevant studies to investigate the association between MTHFD1 1958G>A and the susceptibility of OFCs.

RESULTS

Through the genotyping, the AA genotype was found significantly correlated with the susceptibility of OFCs compared with other SNPs on MTHFD1, yielding an OR of 2.71 (95% CI = 1.12-6.58, P = 0.025) under the homozygous model and an OR of 2.37 (95% CI = 1.06-5.30, P = 0.033) under the recessive model. While other selected SNPs 118913T>C and 31136A>G were also associated with an increased OFC risk, the results were not statistically significant (all P > 0.05). However, the overall result of meta-analysis did not support the conclusion that the 1958G>A variant could be a genetic susceptible factor for OFCs (A allele vs. G allele: OR = 1.02, 95% CI = 0.85-1.23, AA vs. GG: OR = 1.06, 95% CI = 0.69-1.63, GA vs. GG: OR = 1.02, 95% CI = 0.81-1.27, AA vs. GG+GA: OR = 0.94, 95% CI = 0.61-1.46, AA+GA vs. GG: OR = 0.94, 95% CI = 0.74-1.19).

CONCLUSIONS

The MTHFD1 1958G>A variant was significantly associated with the increased OFCs risk in Chinese population. However, this association was not supported by meta-analysis of all relevant studies. Further investigations about functional impact of this polymorphism were needed.

Isolated cleft lip with generalized aggressive periodontitis: A rare entity

Oro-facial clefts are one of the most common birth defects and may be associated with other genetic anomalies. Aggressive periodontitis is a rare condition that progresses rapidly, but affects only a small percentage of the population. Most of the cases of aggressive periodontitis are familial. Even though, literature has documented the association of various genetic disorders with aggressive periodontitis, the aggressive periodontitis in patients with isolated cleft lip (CL) have never been addressed. Here, we report a rare case of isolated CL with generalized aggressive periodontitis. The concomitant presentation of isolated CL with aggressive periodontitis in an individual has clinical significance for multi-disciplinary care.

Significant association of MTHFD1 1958G>A single nucleotide polymorphism with nonsyndromic cleft lip and palate in Indian population

Objectives: Nonsyndromic cleft lip and palate (NSCLP) is genetically distinct from those with syndromic clefts, and accounts for ~70% of cases with Oral clefts. Folate, or vitamin B9, is an essential nutrient in our diet. Allelic variants in genes involved in the folate pathway might be expected to have an impact on risk of oral clefts. Given the key role of methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) in folate metabolism, it would be of significant interest to assess its role in NSCLP etiology. Study Design: The present study aims at examining the association between MTHFD1 1958G>A polymorphism and NSCLP risk by conducting a case-control study in south Indian population. Our sample comprised of 142 cases with nonsyndromic clefts and 141 controls without clefts or family history of clefting. The MTHFD1 1958G>A polymorphism was genotyped using PCR-RFLP. Results: An increased risk was found for the heterozygous 1958GA (OR=2.44; P=0.020) and homozygous 1958AA (OR=2.45; P=0.012) genotypes in the children. When the dominant model (AG+AA vs GG) was applied the risk remained the same as co-dominant model, but the level of significance increased (OR=2.44; P=0.002). Conclusions: The results indicated the MTHFD1 1958G>A polymorphism to be one of the important genetic determinants of NSCLP risk in South Indian subjects.

Key words:MTHFD1, orofacial cleft, SNP, genetics.

CBS c.844ins68 Polymorphism Frequencies in Control Populations: Implications on Nonsyndromic Cleft Lip With or Without Cleft Palate

INTRODUCTION

Nonsyndromic cleft lip with or without cleft palate (NSCLP) is a common birth defect with substantial clinical and social impact. Folate deficiency is one of the factors that have been associated with increased risk for NSCLP. Polymorphisms in folate and homocysteine pathway genes may act as susceptibility factors.

OBJECTIVE

The objective of this study was to evaluate prevalence estimates of cystathionine beta-synthase (CBS) insertion of 68-bp (c.844ins68) polymorphisms and their correlation with NSCLP.

MATERIAL AND METHODS

A total of 236 unrelated individuals from seven Indian populations and an additional 355 cases with NSCLP and 357 controls without NSCLP were included in this study. We investigated the CBS c.844ins68 polymorphism in all samples. Genotyping was performed with polymerase chain reaction and electrophoresis. The data were statistically analyzed using the chi-square test.

RESULTS

The CBS c.844ins68 allele is present in six of the seven populations analyzed, and allele frequencies range from 1.5% in Balija to 9.1% in Sugali populations. The CBS c.844ins68 polymorphism showed a significant protective effect on NSCLP at both genotype (WW versus WI: odds ratio [OR] = 0.54, 95% confidence interval [CI] = 0.31 to 0.95, P = .149) and allele levels (W versus I: OR = 0.56, 95% CI = 0.32 to 0.96, P = .033).

CONCLUSIONS

The current study observed significant differences in the frequency of the CBS 844ins68 allele across populations. There is a significant association between CBS c.844ins68 polymorphism and cleft lip and palate in the Indian population. Additional studies are warranted to identify the functional variants in the genes controlling homocysteine as etiological contributors to the formation of oral clefts.

Analysis of microsatellite polymorphisms in South Indian patients with non syndromic cleft lip and palate

Non syndromic cleft lip and/or palate (NSCLP) is a complex congenital anomaly with varying incidence among patients of different geographical origins. Multiple contributing factors are known to trigger the cleft formation. There are several genes involved in the aetiology of NSCLP and they are different in different populations. The genetic components of clefts that underlie the susceptibility to respond to the environment still remain unclear. In this study, five microsatellite polymorphisms from five candidate genes were employed to analyze the association between these genes and NSCLP in 83 patients and 90 controls. Genotyping was performed by separating and visualizing the fluorescently-labeled polymerase chain reaction (PCR) products. The association of the five microsatellite polymorphisms with NSCLP was tested by using the CLUMP v1.9 program that uses the Monte Carlo method. The genotypic distribution is in Hardy-Weinberg equilibrium in the control group for only the MSX1 and DLX3 genes. The RARA microsatellite was significantly associated with NSCLP. Our results suggest that the RARA gene is involved in pathogenesis of cleft lip and palate in South Indians.

Developmental profiles of the murine palatal methylome

BACKGROUND

Environmental factors contribute to the etiology of cleft palate (CP). Identification of genes that are methylated during development of the secondary palate will contribute to a better understanding of the gene-environment link contributing to CP.

METHODS

Genomic DNA fragments from secondary palate tissue from gestational days (GDs) 12 to 14 were subjected to Selective Enrichment of Methylated DNA (SEMD) and used to probe NimbleGen 2.1M mouse promoter arrays. Input (control) and SEMD samples were labeled with Cy3 and Cy5, respectively, and used for array hybridization (three arrays per GD). Data were analyzed using the Bioconductor package Ringo. Gene methylation was verified by pyrosequencing analysis and expression by quantitative real-time PCR.

RESULTS

A total of 5577 methylated genes were identified during palate development: (1) 74% of genes were methylated on all three GDs; (2) CpG islands accounted for only 30% of methylated regions of interest (MRIs); (3) location of MRIs was more often observed in gene bodies (73%) than in promoters; (4) evaluation of MRIs on GDs 12-14 revealed no significant differentially methylated regions; (5) DAVID analysis of MRIs revealed that the cadherin and Wnt signaling pathways, as well as pathways involved in proteoglycan synthesis, were significantly enriched for methylated genes.

CONCLUSIONS

Our prior studies identified differentially expressed mRNAs and microRNAs in the developing palate. The current study complements these studies by identifying genes whose expression may be altered as a result of DNA methylation.

An insight into genetics of non-syndromic cleft palate

Our proband is a 29-year-old man, who is affected with soft cleft palate and hypernasality. A study of about six generations of this family pedigree shows that cleft palate has repeatedly occurred in males, with probably a X-linked recessive pattern of inheritance. Interestingly, the sister of the proband is affected with hypernasality and she has an affected son. This is the first report of X-linked inheritance pattern of cleft palate in Iran.

No Evidence of Association between 8q24 and Susceptibility to Nonsyndromic Cleft Lip with or without Palate in Japanese Population

Objective

Recent genome-wide association studies identified susceptibility loci for nonsyndromic cleft lip with or without cleft palate (NSCL±P) on 8q24.21, 10q25.3, 13q31.1, 15q13.3, 17q22, and 18q22 in populations of European origin. The purpose of this study was to determine, using DNA samples, whether 8q24.21 was a susceptibility locus for the development of NSCL±P in Japanese patients.

Methods

We used DNA from 167 Japanese NSCL±P patients (45 cleft lip without cleft palate and 122 cleft lip with cleft palate patients) and 190 Japanese unaffected control individuals. We performed an association study using 13 single nucleotide polymorphisms (SNPs) selected on the 8q24.21 locus. Genotyping of each SNP was carried out by direct sequencing of genomic DNA. Additionally, a haplotype block was constructed using the selected SNPs.

Results

The 13 selected SNPs were successfully genotyped in 357 individuals. The p values obtained were not low enough to indicate a significant association between the haplotypes and the development of NSCL±P in this population.

Conclusions

Our results suggest that the 8q24.21 locus is not associated with susceptibility to NSCL±P in Japanese patients and provide further evidence that ethnicity is a strong factor in determining susceptibility loci, albeit using a limited number of samples. Further studies are needed to identify regions involved in the development of NSCL±P in the Japanese population.

Developmental epigenetics of the murine secondary palate

Orofacial clefts occur with a frequency of 1 to 2 per 1000 live births. Cleft palate, which accounts for 30% of orofacial clefts, is caused by the failure of the secondary palatal processes--medially directed, oral projections of the paired embryonic maxillary processes--to fuse. Both gene mutations and environmental effects contribute to the complex etiology of this disorder. Although much progress has been made in identifying genes whose mutations are associated with cleft palate, little is known about the mechanisms by which the environment adversely influences gene expression during secondary palate development. An increasing body of evidence, however, implicates epigenetic processes as playing a role in adversely influencing orofacial development. Epigenetics refers to inherited changes in phenotype or gene expression caused by processes other than changes in the underlying DNA sequence. Such processes include, but are not limited to, DNA methylation, microRNA effects, and histone modifications that alter chromatin conformation. In this review, we describe our current understanding of the possible role epigenetics may play during development of the secondary palate. Specifically, we present the salient features of the embryonic palatal methylome and profile the expression of numerous microRNAs that regulate protein-encoding genes crucial to normal orofacial ontogeny.

Polymorphisms in CHDH gene and the risk of tooth agenesis

BACKGROUND

Tooth agenesis is one of the most common anomalies of human dentition and is due to a complex and not fully elucidated etiology. The purpose of this study was to evaluate the possibility that polymorphic variants of genes encoding the main folate and choline metabolism enzymes might be associated with the risk of hypodontia in the Polish population.

METHODS AND RESULTS

We analyzed 21 polymorphisms of 13 candidate genes and found that single nucleotide polymorphisms (SNPs) in the CHDH gene are significantly correlated with the risk of dental agenesis. The strongest association was found for the SNP located in the intronic sequence of CHDH. Individuals carrying one copy of the rs6445606 C allele had an over two-fold decreased risk of having hypodontia (odds ratio [OR]CTvsTT=0.434; 95% confidence interval [CI], 0.2724-0.6915; p=0.0004; pcorr=0.0084). A reduced risk of tooth agenesis was also observed in individuals with one or two copies of the rs6445606 C allele compared to T allele carriers (ORCT+CCvsTT=0.524; 95% CI, 0.3386-0.8097; p=0.0035; pcorr=0.0735). Moreover, the gene-gene interaction analysis revealed a significant epistatic interaction between CHDH (rs6445606) and PLD2 (rs3764897) in the susceptibility to hypodontia (p=0.004).

CONCLUSION

Our study identified CHDH and PLD2 as novel candidate genes, the nucleotide variants of which could be associated with the risk of tooth agenesis.

Polymorphisms located in the region containing BHMT and BHMT2 genes as maternal protective factors for orofacial clefts

Nonsyndromic cleft lip with or without cleft palate (NCL/P) is one of the most common craniofacial malformations; however, its aetiology is still unclear. Because the effects of maternal nutrition on fetal development are well known, we decided to pursue the question of whether polymorphic variants of genes encoding enzymes involved in choline metabolism might be associated with the maternal risk of having a baby with NCL/P. Analysis of 18 single nucleotide polymorphisms (SNPs) of betaine-homocysteine methyltransferase (BHMT), betaine-homocysteine methyltransferase-2 (BHMT2), choline dehydrogenase (CHDH), choline kinase (CHKA), dimethylglycine dehydrogenase (DMGDH), choline-phosphate cytidylyltransferase A (PCYT1A), and phosphatidylethanolamine N-methyltransferase (PEMT) provided evidence that polymorphisms located in the region containing BHMT and BHMT2 were protective factors against NCL/P affected pregnancies in our population. The strongest signal was found for the SNP located in the intronic sequence of BHMT2. Women carrying two copies of the rs625879 T allele had a significantly decreased risk of having offspring with orofacial clefts. These results were significant, even after correction for multiple comparisons. Moreover, the gene-gene interaction analysis revealed a significant epistatic interaction of BHMT2 (rs673752), PEMT (rs12325817), and PCYT1A (rs712012) with maternal NCL/P susceptibility. Altogether, our study identified a novel gene, the nucleotide variants of which were be associated with a decreased risk of having a baby with NCL/P.

Polymorphic variants of genes related to arginine metabolism and the risk of orofacial clefts

OBJECTIVE

Maternal mid-pregnancy low levels of symmetric dimethylarginine and newborn low levels of citrulline are suspected to be risk factors for orofacial clefts. This study was undertaken to investigate the involvement of polymorphic variants of genes related to arginine metabolism in the susceptibility of clefting.

DESIGN

PCR-RFLP and HRM analyses were used to analyze single nucleotide polymorphisms (SNPs) of ASS1, ASL, and SLC25A13 in 172 children with non-syndromic cleft lip with or without cleft palate (CL/P) and 188 controls without congenital anomalies. The differences in allele and genotype frequencies between cases and controls were determined using standard Chi-square and Fisher exact tests. The odds ratio (OR) and associated 95% confidence intervals (95% CI) for individuals with CL/P versus controls were also calculated. Associations between the investigated polymorphisms and the risk of being born with an orofacial cleft were tested using the nonparametric and genetic model-free Multifactor Dimensionality Reduction (MDR) approach.

RESULTS

Analysis of five SNPs of the ASS1 gene revealed that the G allele of rs7860909 is associated with increased CL/P risk. Compared to individuals with the AA genotype, the G allele carriers had an OR of 1.768 (95% CI: 1.133-2.759; p=0.012). For the remaining SNPs of all analysed genes, there was no overall evidence for cleft association considering the allele and genotype distribution. However, gene-by-gene interaction analysis conducted using the MDR approach revealed a significant interactive genetic effect of ASS1 (rs666174) and SLC25A13 (rs10252573) on the occurrence of clefting (p=0.002).

CONCLUSION

Our results demonstrate moderate evidence for the association of polymorphic variants of genes related to arginine metabolism with abnormal palatogenesis.