Genetic Interactions in Nonsyndromic Orofacial Clefts in Europe—EUROCRAN Study

Unilateral Cleft lip and Palate: Long-Term Results of the Malek Technique

To review at 18 years-old the results of surgery and follow-up of children born in our hospital with unilateral cleft lip and palate (uCLP). They were operated at the time by the same surgeon, following the same primary surgical procedure (Malek).

Retrospective cohort study.

Tertiary Children's Hospital.

All children born with uCLP between 1996 and 2001 and operated in our hospital. Syndromic children were excluded.

Results of the primary surgery, ear-nose-throat interventions, maxillo-facial surgery and final phonatory results.

Seventy-nine files of children born with a cleft were reviewed: 34 were taken into consideration for uCLP: 15 right and 19 left. They were operated in two stages, following the inverse Malek procedure. Sixty per cent had a fistula. Eighty-eight percent had grommets. Ninety-seven percent had an alveolar graft at a median age of nine (5-10) and 22% underwent a Le Fort osteotomy. Seven percent were operated for a pharyngeal flap, 29% for a secondary lip surgery at a mean age of 12.8 and 29% for a late rhinoplasty at a mean age of 14.8 years. A median of 5.7 multidisciplinary consultations was realized with a median number of general anesthesia of 7.1 (4-13).

This retrospective study shows that the Malek procedure for children born with uCLP is related to a high risk of fistula but good long-term phonatory results. Twenty percent of children were operated for a Le Fort procedure and one-third for a secondary lip procedure and rhinoplasty.

The presence and distribution of various genes in postnatal CLP-affected palatine tissue

BACKGROUND

Worldwide cleft lip with or without a cleft palate (CL/P) is the most common craniofacial birth defect. Apart from changes in facial appearance, additionally affected individuals often suffer from various associated comorbidities requiring complex multidisciplinary treatment with overall high expenses. Understanding the complete pathogenetic mechanisms of CL/P might aid in developing new preventative strategies and therapeutic approaches, help with genetic counselling, and improve quality of life. Many genes have been associated with the development of orofacial clefts; however, the majority require further research. Based on the role of PAX7, PAX9, SHH, SOX3, WNT3A, and WNT9B in orofacial development, the intention was to use chromogenic in situ hybridization to detect the six genes in postnatal CLP-affected palatine tissue and compare their distribution within the tissue samples.

RESULTS

Statistically significant differences in the distribution of PAX7, PAX9, WNT3A, and WNT9B were observed. In total, 19 pairs of moderate to very strong positive correlations were noted.

CONCLUSIONS

Changes in the cleft-affected palatine epithelium primarily seem to be associated with the PAX7 gene; however, PAX9, WNT3A, WNT9B, and SOX3 role seems to be more limited. Whilst connective tissue changes seem to depend on PAX7 only, SHH seems to participate individually and indistinctly. Numerous positive correlations reflect the complicating interactions of the pathways and their components in the orofacial cleft morphopathogenesis.

MSX1 Gene Polymorphisms in Patients with non-Syndromic Cleft lip and Palate: A Tertiary Care Centre Based Case-Control Study from Central Kerala

OBJECTIVE

The purpose of this study was to investigate the contribution of MSX1 gene polymorphisms to the risk of developing NSCLP.

DESIGN

Case-Control Study.

SETTING

A tertiary care centre.

PATIENTS/PARTICIPANTS

The sample consisted of 200 subjects (100 cases and 100 controls).

INTERVENTIONS

None.

MAIN OUTCOME MEASURE(S)

Genotyping was performed by restriction fragment length polymorphism. Allele and genotype frequencies were calculated between patients and controls and analyzed using online Web Tools such as SISA and SNPstats. The MSX1 gene polymorphisms c. 799 GT, c.458 CA can be risk factors in the development of orofacial clefts.

RESULTS

In the cases, an association was found between NSCLP and c.799 and c.458 of the MSX1 gene when compared with the control. The dominant and overdominant models, c. 799 GT, c.458 CA genotypes and c. 799 T, c.458 A alleles in the population are said to be the main risk factors to develop the NSCLP in our study population. The genotype variation of c 799 G/T and c.458 C/A are revealed to be specifically contributing to an NSCLP-type Cleft lip and Palate. It is worth noting that NSCLP females in the study population showed a stronger association with heterozygous genotypes of c.799 and c.458. However, further investigation with a larger cohort is necessary to confirm these findings.

CONCLUSION

Overall the results of the study revealed that MSX1 c 799 G > T and c.458 C > A can be considered as one of the genetic risk factors in the formation of Non-Syndromic Cleft Lip and Palate in the study population.

Risk Assessment of the Increased Occurrence of Congenital Cardiac and Non-Cardiac Defects in Fetuses with a Normal Karyotype after Assisted Fertilization in Comparison to Natural Fertilization Based on Ultrasound Diagnostics

The goal of the study was to assess changes in parameters based on ultrasound examinations—these were Crown Rump Length (CRL), Nuchal Translucency (NT), Fetal Heart Rate (FHR), and Pulsatility Index for Ductus Venosus (DV-PI)—in the first trimester of pregnancy in women in which there was a natural initiation of the pregnancy due to spontaneous ovulation, women in which the pregnancy was initiated as a result of stimulated ovulation, as well as in the group in which pregnancy was achieved through the use of In-Vitro Fertilization (IVF)-assisted reproduction. A total of 1581 women became pregnant without the use of assisted reproduction methods. Out of 283 pregnancies, in 178 patients, induced ovulation was utilized. Next, 137 women had sexual intercourse and became pregnant; 41 of them became pregnant through Intrauterine Insemination (IUI) as a result of Artificial Insemination by Husband (AIH), and 13 became pregnant after Artificial Insemination by Donor (AID). The third group consisted of 105 women subjected to Controlled Ovarian Hyperstimulation (COH). In this group of pregnant women, 53 pregnancies were resultant of Intracytoplasmic Sperm Injection (ICSI), and 52 pregnancies were the result of Intracytoplasmic Morphologically selected Sperm Injection (IMSI). The obtained results did not indicate that the chosen method of fertilization or the chosen ovulation method had a statistically significant effect on the development risk of congenital heart or non-heart defects in the fetus.

MTHFR promoter methylation might mitigate the effect of smoking at the level of LINE-1 in cleft lip tissues: A preliminary study

BACKGROUND

The medial and maxillary aspects of the upper lip originate at separate embryonic stages and therefore may experience different maternal exposure patterns which may affect methylation. Based on this hypothesis, we investigated the level of methylation of the methylene tetrahydrofolate reductase promoter gene (mMTHFR) in tissues from cleft lip, and mMTHFR levels by MTHFR c.677C > T genotype. We further investigated whether mMTHFR mitigates the effect of smoking on long interspersed nuclear element (LINE-1) methylation in these tissues.

METHODS

DNA extracted from medial and lateral tissues of 26 infants with nonsyndromic cleft lip with or without cleft palate (nsCL/P) was bisulfite converted and mMTHFR was measured on a pyrosequenser. LINE-1 methylation and MTHFR c.677C > T genotype data were obtained in our previous study.

RESULTS

There was no substantial difference in mMTHFR (p = .733) and LINE-1 (p = .148) between the two tissues. mMTHFR was not influenced by MTHFR c.677C > T genotype, but there was suggestive evidence that the difference was larger among infants exposed to maternal smoking compared to nonexposed. LINE-1 methylation differences were significant (p = .025) in infants born to nonsmoking mothers, but this was not apparent (p = .872) in infants born to mothers who smoked. Our Pearson's correlation analysis suggested a weak inverse association between mMTHFR and LINE-1 (r = -.179, p = .381).

CONCLUSION

Our preliminary observation of differences in patterns of mMTHFR levels in lip tissue suggests the interplay of gene and environment in the establishment of methylation in tissues at both sides of cleft lip. This requires investigation in a larger cohort, integrated with metabolic assessment.

Folate intake, markers of folate status and oral clefts: An updated set of systematic reviews and meta-analyses

BACKGROUND

There has been a longstanding debate about the role of folate in the etiology of orofacial clefts (OFCs). Studies of different measures of nutritional intake or folate status have been done to investigate the possible role of folate in the prevention of OFC. Only one knowledge synthesis has attempted to bring together different types of evidence. The aim of the present work was to update it.

METHODS

Evidence for associations between OFC and dietary folate, supplement use, folic acid fortification, biomarkers of folate status, and variants of MTHFR (C677T and A1298C) were included. Potentially eligible articles were systematically identified from PubMed, Medline, Embase, and Web of Science (2007-2020) and combined using random-effects meta-analysis when appropriate. Quality assessments were conducted using the Newcastle-Ottawa scale and Cochrane's risk of bias tool.

RESULTS

Sixty-four studies published since the previous knowledge synthesis were identified, with eight of these identified through a supplementary search from October, 2018 to August, 2020. There was an inverse association between folic acid-containing supplement use before or during pregnancy and cleft lip with or without cleft palate (CL/P) (OR 0.60, 95% CI 0.51-0.69), with considerable between-study heterogeneity. The prevalence of CL/P showed a small decline post-folic acid fortification in seven studies (OR 0.94, 95% CI 0.86-1.02). No association was found between OFC and genetic markers of folate status. The coronavirus-19 pandemic has threatened food availability globally and therefore there is a need to maintain and even enhance surveillance concerning maternal intake of folate and related vitamins.

CONCLUSIONS

The risk of non-syndromic OFC was reduced among pregnant women with folic acid-containing supplements during the etiologically relevant period. However, high heterogeneity between included studies, incomplete reporting of population characteristics and variation in timing of exposure and supplement types mean that conclusions should be drawn with caution.

Non-syndromic Cleft Palate: An Overview on Human Genetic and Environmental Risk Factors

The epithelial and mesenchymal cells involved in early embryonic facial development are guided by complex regulatory mechanisms. Any factor perturbing the growth, approach and fusion of the frontonasal and maxillary processes could result in orofacial clefts that represent the most common craniofacial malformations in humans. The rarest and, probably for this reason, the least studied form of cleft involves only the secondary palate, which is posterior to the incisive foramen. The etiology of cleft palate only is multifactorial and involves both genetic and environmental risk factors. The intention of this review is to give the reader an overview of the efforts made by researchers to shed light on the underlying causes of this birth defect. Most of the scientific papers suggesting potential environmental and genetic causes of non-syndromic cleft palate are summarized in this review, including genome-wide association and gene–environment interaction studies.

Extracellular Matrix Composition and Remodeling: Current Perspectives on Secondary Palate Formation, Cleft Lip/Palate, and Palatal Reconstruction

Craniofacial development comprises a complex process in humans in which failures or disturbances frequently lead to congenital anomalies. Cleft lip with/without palate (CL/P) is a common congenital anomaly that occurs due to variations in craniofacial development genes, and may occur as part of a syndrome, or more commonly in isolated forms (non-syndromic). The etiology of CL/P is multifactorial with genes, environmental factors, and their potential interactions contributing to the condition. Rehabilitation of CL/P patients requires a multidisciplinary team to perform the multiple surgical, dental, and psychological interventions required throughout the patient's life. Despite progress, lip/palatal reconstruction is still a major treatment challenge. Genetic mutations and polymorphisms in several genes, including extracellular matrix (ECM) genes, soluble factors, and enzymes responsible for ECM remodeling (e.g., metalloproteinases), have been suggested to play a role in the etiology of CL/P; hence, these may be considered likely targets for the development of new preventive and/or therapeutic strategies. In this context, investigations are being conducted on new therapeutic approaches based on tissue bioengineering, associating stem cells with biomaterials, signaling molecules, and innovative technologies. In this review, we discuss the role of genes involved in ECM composition and remodeling during secondary palate formation and pathogenesis and genetic etiology of CL/P. We also discuss potential therapeutic approaches using bioactive molecules and principles of tissue bioengineering for state-of-the-art CL/P repair and palatal reconstruction.

Exome sequencing of family trios from the National Birth Defects Prevention Study: Tapping into a rich resource of genetic and environmental data

BACKGROUND

The National Birth Defects Prevention Study (NBDPS) is a multisite, population-based, case-control study of genetic and nongenetic risk factors for major structural birth defects. Eligible women had a pregnancy affected by a birth defect or a liveborn child without a birth defect between 1997 and 2011. They were invited to complete a telephone interview to collect pregnancy exposure data and were mailed buccal cell collection kits to collect specimens from themselves, their child (if living), and their child's father. Over 23,000 families representing more than 30 major structural birth defects provided DNA specimens.

METHODS

To evaluate their utility for exome sequencing (ES), specimens from 20 children with colonic atresia were studied. Evaluations were conducted on specimens collected using cytobrushes stored and transported in open versus closed packaging, on native genomic DNA (gDNA) versus whole genome amplified (WGA) products and on a library preparation protocol adapted to low amounts of DNA.

RESULTS

The DNA extracted from brushes in open packaging yielded higher quality sequence data than DNA from brushes in closed packaging. Quality metrics of sequenced gDNA were consistently higher than metrics from corresponding WGA products and were consistently high when using a low input protocol.

CONCLUSIONS

This proof-of-principle study established conditions under which ES can be applied to NBDPS specimens. Successful sequencing of exomes from well-characterized NBDPS families indicated that this unique collection can be used to investigate the roles of genetic variation and gene-environment interaction effects in birth defect etiologies, providing a valuable resource for birth defect researchers.

Speech Phenotyping in Unaffected Family Members of Individuals With Nonsyndromic Cleft Lip With or Without Palate

OBJECTIVE

Subclinical phenotypes of nonsyndromic cleft lip with or without cleft palate (CL ± P) may be identified from clinically "unaffected" relatives and could be associated with specific cleft-related gene mutations. It has been hypothesized that velopharyngeal insufficiency (VPI) may be a subclinical phenotype of interest in this population, but this has not been explored quantitatively with appropriate control cohorts. The aim of this case-control study was to compare VPI in at-risk clinically unaffected relatives of individuals with nonsyndromic CL ± P with a low-risk matched normative Australian cohort.

PARTICIPANTS

Clinically unaffected (ie, with no overt cleft) first-degree relatives of a proband with nonsyndromic CL ± P (n = 189) and noncleft controls (n = 207).

MAIN OUTCOME MEASURE(S)

Perceptual measures of VPI encompassing resonance, nasal emission, and articulation were evaluated using the Great Ormond Street Speech Assessment. Quantitative measures of VPI were obtained from the Nasometer II using standardized adult and pediatric speech stimuli.

RESULTS

Both perceptual and instrumental measures showed no significant difference (P > .01) between the VPI in unaffected relatives and the noncleft comparison group. Mean nasalance scores for both groups were calculated and reported according to speech stimuli, age, and sex.

CONCLUSIONS

Results suggest that VPI, measured through speech, is not a significant subclinical phenotype of nonsyndromic CL ± P. Therefore, further familial genetic investigations exploring VPI may not yield meaningful results. Exploration across multiple subclinical phenotypes in larger cohorts may enable researchers to better understand the multifaceted nature of this complex and heterogeneous anomaly.

Association between a common missense variant in LOXL3 gene and the risk of non-syndromic cleft palate

To investigate possible association between functional common variants in the lysyl oxidase like 3 gene and non-syndromic cleft palate we selected a common missense variant p.Ile615Phe (rs17010021), which was predicted to have a probably damaging effect on the lysyl oxidase like 3 enzyme. We genotyped 258 non-syndromic cleft palate case-parent triads of European origin and tested genetic association using the transmission disequilibrium test and log-linear regression analyses of genotypic relative risks and of parent-of-origin effects. The observed genotype frequency in parents was in Hardy-Weinberg equilibrium. Compared with wild-type Ile/Ile homozygotes, the relative risks for Phe/Phe homozygote infants was 6.87 (P value 3.0 × 10^-3 ), while that for Ile/Phe heterozygotes was not significant. Assuming an autosomal recessive model, the relative risks for Phe/Phe genotype resulted 10.54 (P value 2.9 × 10^-5 ), with a 3.6% population attributable risk. No parent-of-origin effect was observed. The identification in lysyl oxidase like 3 of a missense variant which under a recessive model associates with 10-fold increased risk of non-syndromic cleft palate supports the hypothesis that the genetic etiology of this congenital anomaly includes relatively uncommon recessive variants with moderate penetrance and located in genes which are also involved in syndromes that include cleft palate as part of the phenotype. Our findings require functional validation and replication in a larger independent genetic association study.

Integrated assessment of differentially expressed plasma microRNAs in subtypes of nonsyndromic orofacial clefts

BACKGROUND

Orofacial clefts include cleft lip only (CLO), cleft palate only (CPO), and cleft lip with palate (CLP). Previously, we reported the expression profile of plasma microRNAs in CLO, CPO, and CLP, respectively. However, the interaction of each subtype remains poorly investigated.

METHODS

In this study, we integrated the expression profiles of plasma miRNAs in these 3 subtypes, and assessed the distinct and overlapping dysregulated miRNAs using Venn diagrams. Their respective target genes reported in the literature were further analyzed using pathway analysis.

RESULTS AND CONCLUSION

The results showed that distinct or overlapping signaling pathways were involved in CLO, CPO, and CLP. The common key gene targets reflected functional relationships to the Wnt, Notch, TGF-beta, and Hedgehog signaling pathways. Further studies should examine the mechanism of the potential target genes, which may provide new avenues for future clinical prevention and therapy.

Application of high-resolution array platform for genome-wide copy number variation analysis in patients with nonsyndromic cleft lip and palate

BACKGROUND

Although more than 14 loci may be involved in the development of nonsyndromic cleft lip and palate (NSCLP), the etiology has not been fully elucidated due to genetic and environmental risk factor interactions. Despite advances in identifying genes associated with the NSCLP development using traditional genetic mapping strategies of candidate genes, genome-wide studies, and epidemiologic and linkage analysis, microarray techniques have become important complementary tools in the search for potential causative oral clefts genes in genetic studies. Microarray hybridization enables scanning of the whole genome and detecting copy number variants (CNVs). Although common benign CNVs are often smaller, with sizes smaller than 20 kb, here we reveal small exonic CNVs based on the importance of the encompassed genes in cleft lip and palate phenotype.

METHODS

Microarray hybridization analysis was performed in 15 individuals with NSCLP.

RESULTS

We identified 11 exonic CNVs affecting at least one exon of the candidate genes. Thirteen candidate genes (COL11A1-1p21; IRF6-1q32.3; MSX1-4p16.2; TERT-5p15.33; MIR4457-5p15.33; CLPTM1L-5p15.33; ESR1-6q25.1; GLI3-7p13; FGFR-8p11.23; TBX1-22q11.21; OFD-Xp22; PHF8-Xp11.22; and FLNA-Xq28) overlapped with the CNVs identified.

CONCLUSIONS

Considering the importance to NSCLP, the microdeletions that encompass MSX1, microduplications over TERT, MIR4457, CLPTM1L, and microduplication of PHF8 have been identified as small CNVs related to sequence variants associated with oral clefts susceptibility. Our findings represent a preliminary study on the clinical significance of small CNVs and their relationship with genes implicated in NSCLP.

Nonsyndromic cleft palate: An association study at GWAS candidate loci in a multiethnic sample

BACKGROUND

Nonsyndromic cleft palate only (nsCPO) is a common and multifactorial form of orofacial clefting. In contrast to successes achieved for the other common form of orofacial clefting, that is, nonsyndromic cleft lip with/without cleft palate (nsCL/P), genome wide association studies (GWAS) of nsCPO have identified only one genome wide significant locus. Aim of the present study was to investigate whether common variants contribute to nsCPO and, if so, to identify novel risk loci.

METHODS

We genotyped 33 SNPs at 27 candidate loci from 2 previously published nsCPO GWAS in an independent multiethnic sample. It included: (i) a family-based sample of European ancestry (n = 212); and (ii) two case/control samples of Central European (n = 94/339) and Arabian ancestry (n = 38/231), respectively. A separate association analysis was performed for each genotyped dataset, and meta-analyses were performed.

RESULTS

After association analysis and meta-analyses, none of the 33 SNPs showed genome-wide significance. Two variants showed nominally significant association in the imputed GWAS dataset and exhibited a further decrease in p-value in a European and an overall meta-analysis including imputed GWAS data, respectively (rs395572: P_MetaEU  = 3.16 × 10^-4 ; rs6809420: P_MetaAll  = 2.80 × 10^-4 ).

CONCLUSION

Our findings suggest that there is a limited contribution of common variants to nsCPO. However, the individual effect sizes might be too small for detection of further associations in the present sample sizes. Rare variants may play a more substantial role in nsCPO than in nsCL/P, for which GWAS of smaller sample sizes have identified genome-wide significant loci. Whole-exome/genome sequencing studies of nsCPO are now warranted.