Integrative Multi-omics Analysis Identifies Genetic Variants Contributing to Non-syndromic Cleft Lip with or without Cleft Palate.

OBJECTIVE: To provide novel insights into the aetiology of non-syndromic cleft lip with or without cleft palate (NSCL/P) by integrating multi-omics data and exploring susceptibility genes associated with NSCL/P. METHODS: A two-stage genome-wide association study (GWAS) of NSCL/P was performed, involving a total of 1,069 cases and 1,724 controls. Using promoter capture Hi-C (pCHi-C) datasets in human embryonic stem cells (hESC) and chromatin immunoprecipitation sequencing (ChIP-seq) in craniofacial tissues, we filtered out single nucleotide polymorphisms (SNPs) with active cis-regulation and their target genes. Additionally, we employed expression quantitative trait loci (eQTL) analysis to identify candidate genes. RESULTS: Thirteen SNPs were identified as cis-regulation units associated with the risk of NSCL/P. Five of these were proven to be active in chromatin states in early human craniofacial development (rs7218002: odds ratio [OR] 1.50, P = 8.14E-08; rs835367: OR 0.78, P = 3.48E- 05; rs77022994: OR 0.55, P = 1.05E-04; rs961470: OR 0.73, P = 1.38E-04; rs17314727: OR 0.73, P = 1.85E-04). Additionally, pCHi-C and eQTL analysis prioritised three candidate genes (rs7218002: NTN1, rs835367: FGGY, LINC01135). NTN1 and FGGY were expressed in mouse orofacial development. Deficiencies in NTN1, FGGY and LINC01135 were associated with cleft palate and cleft lip, abnormal facial shape and bifid uvula, and abnormality of the face, respectively. CONCLUSION: Our study identified five SNPs (rs7218002, rs835367, rs77022994, rs961470 and rs17314727) and three susceptibility genes (NTN1, FGGY and LINC01135) associated with NSCL/P. These findings contribute to a better understanding of the genetic factors involved.

Exploration of Genetic Variants of Non-syndromic Cleft Lip with or without Palate and Underlying Mechanisms.

Non-syndromic cleft lip with/without cleft palate (NSCL/P) is one of the most common birth defects in humans with an overall prevalence of one per 1000 live births. Due to genetic and environmental influences, the fusion of the lips or palate may be interrupted at any stage and cause a cleft. Over decades, dozens of susceptible genes and loci have been identified using multiple genetic approaches. Our group has collected samples of NSCL/P patients since 2008 and established the biobank. We discovered numerous susceptible loci related to the occurrence of NSCL/P in the Chinese population, such as 16p13.3, 1q32.2, 10q25.3 and 17p13.1. In addition, we performed functional studies on related loci and genes by using molecular biology, cell biology, animal models and other methods to provide a basis for the construction of the NSCL/P genetic map in the Chinese population and help to implement individualised prophylaxis and treatment. Future efforts will focus on identifying functional variants, investigating pathways and other interactions, and including phenotypic and ethnic diversity in research.

A Novel Classification of Relationship Between Nasal Septum and Inferior Turbinate Associated With Nasal Airway Obstruction in Patients With Unilateral Alveolar Cleft.

OBJECTIVE: This study aims to investigate nasal morphologies associated with nasal airway obstruction in unilateral alveolar cleft patients. METHODS: A total of 234 unilateral alveolar cleft cases were performed cone beam computed tomography scans. The digital imaging and communication in medicine data were imported into Simplant Pro software. The radiographic features including nasal septum deviation and inferior turbinate hypertrophy as well as nasal airway volume and sinusitis were analyzed. RESULTS: A new radiographic classification of relationship between nasal septum and inferior turbinate (NS-IT) on the cleft side was proposed and three types of NS-IT relationship (type I, II and III) were identified in 234 cases. The statistical analysis revealed that the nasal airway volume on non-cleft side was significantly higher than that on cleft side in each of three types (P  < 0.0001), while no difference of nasal airway volume on non-cleft side was found among three types. In addition, the nasal airway volume on non-cleft side in type I and II was significantly higher than that in type III (P < 0.0001). Also, type III presented higher rate of maxillary sinusitis (P = 0.0154) and ethmoid sinusitis on cleft side (P = 0.0490) than type I and II. The other indexes including clinical variances were not significant among three types. CONCLUSIONS: Unilateral alveolar cleft patients with type III NS-IT relationship could have nasal airway obstruction and higher rate of maxillary and ethmoid sinusitis on cleft side, which may be taken into account at primary cleft repair and alveolar bone grafting treatment.

Comparative Outcomes of Block and Cancellous Iliac Bone Grafting in Older Unilateral Alveolar Cleft Patients.

OBJECTIVE: To compare osseous outcomes of block and cancellous iliac bone grafting in older unilateral alveolar cleft patients. DESIGN: Retrospective and observational follow-up study. SETTING: Cleft Lip and Palate Centre, Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, China. PATIENTS: Forty-five nonsyndromic patients with unilateral complete alveolar cleft were enrolled in this study (25 patients in block bone graft group and 20 patients in cancellous bone graft group). INTERVENTIONS: In cancellous bone graft group, the alveolar cleft was filled with iliac cancellous bone particulate. In group of block bone graft, the harvested bone block was trimmed and fixed in alveolar defect. MAIN OUTCOME MEASURES: A novel method was proposed to investigate the volume and density of residual bone graft at 1-week, 3- and 6-month, 1- and 2-year postoperatively based on cone beam computed tomography scans. RESULTS: No difference in bone graft volume was found between 2 groups at 1-week and 3-month postoperatively; however, the residual volume of block bone graft group was significantly larger than that of cancellous bone graft group at 6-month, 1- and 2-year postoperatively. The bone density of block bone graft group was lower at 1-week and 3-month postoperatively but was comparable at 6-month, 1- and 2-year postoperatively. Our method was reliable and accurate to identify the range of residual bone graft when the boundary of grafted bone could not be identified clearly. CONCLUSION: Block bone graft could achieve comparable bone density and retain a greater amount of residual bone comparing to cancellous bone graft.

[Msh homebox-1 polymorphisms and susceptibility to 198 sporadic tooth agenesis: a case-control study].

OBJECTIVE: To study the relationships between single nucleotide polymorphisms (SNP) of gene msh homebox-1 (MSX-1) (rs3821949, rs12532) and sporadic tooth agenesis by filtering the susceptibility genes in a Jiangsu province population. METHODS: DNA samples were extracted from 198 patients with sporadic tooth agenesis and 207 control subjects. Two MSX-1 gene polymorphisms were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. The association between the genetic polymorphism and risk of sporadic tooth agenesis was estimated by chi(2) and logistic regression. The Phase was used to determine the Hardy-Weinberg equilibrium and haplotype association. RESULTS: In the population, the allele frequency and genotype rates of the SNP rs3821949 were significant different between the patients with sporadic tooth agenesis and normal controls: the A allele frequency in the patients (43.2%) was significantly higher than that in the normal controls (31.4%, P = 0.008), and the AA genotype rate of the patients (14.7%) was significantly higher than that of the controls (12.6%, P = 0.030). However, There were no significant differences in the allele frequency and genotype rates of the SNP rs12532 between the patients with sporadic tooth agenesis and normal controls. Similar results were obtained between the mandibular incisor agenesis cases and controls. The haplotype frequencies of GA (27.9%) were significantly lower in non-mandibular incisor agenesis cases group than that in the control group (37.0%, P = 0.03, OR = 0.51). CONCLUSIONS: The results show that SNP rs3821949, which is located at 5';near region of the MSX-1 gene, is likely to have an influence on the transcriptional activity of this gene and be associated with sporadic tooth agenesis. The haplotypes constructed with these 2 SNP sites may be linked with the susceptibility gene of non-mandibular incisor agenesis.