ABSTRACT: This article presents data on genes associated with cleft palate (CP), retrieved through both a full-text systematic review and a mouse genome informatics (MGI) database search. In order to group CP-associated genes according to function, pathway, biological process, and cellular component, the genes were analyzed using category enrichment bioinformatics tools, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO). This approach provides invaluable opportunities for the identification of candidate pathways and genes in CP research.
Project description:Plasma microRNAs (miRNAs) have recently emerged as a new class of regulatory molecules that influence many biological functions. However, the expression profile of plasma microRNAs in nonsyndromic cleft palate (NSCP) or nonsyndromic cleft lip with cleft palate (NSCLP) remains poorly investigated. In this study, we used Agilent human miRNA microarray chips to monitor miRNA levels in three NSCP plasma samples (mixed as the CP group), three NSCLP plasma samples (mixed as the CLP group) and three normal plasma samples (mixed as the Control group). Six selected plasma miRNAs were validated in samples from an additional 16 CP, 33 CLP and 8 healthy children using qRT-PCR. Using Venn diagrams, distinct and overlapping dysregulated miRNAs were identified. Their respective target genes were further assessed using gene ontology and pathway analysis. The results show that distinct or overlapping biological processes and signalling pathways were involved in CP and CLP. Our study showed that the common key gene targets reflected functional relationships to the Notch, Wnt, phosphatidylinositol and Hedgehog signalling pathways. Further studies should examine the mechanism of the potential target genes, which may provide new avenues for future clinical prevention and therapy.
Project description:The Chinese sturgeon (Acipenser sinensis) is anadromous fish distributed in Yangtze River and East China Sea. In this study, we reported cleft-palate Chinese sturgeons in artificial population for the first time. In order to explore the genetic basis of palate malformation in A. sinensis, Illumina RNA-seq technology was used to analyze the transcriptome data of normal and cleft-palate individuals in farmed Chinese sturgeons. Raw reads were obtained and assembled into 808,612 unigenes, with an average length of 509.33 bp and an N50 of 574 bp. Sequence similarity analyses against four public databases (Nr, Uniprot, KEGG and COGs) found 158,642 unigenes that can be annotated. GABAergic synapse and TGF-β signal pathway were the most two enriched pathways with high Richfactor in the analyses of different expressed genes. In these two signal pathways, six genes (GABRA4, GS, GNS, S6K, PITX2, and BMP8) were found as cleft-palate genes in Chinese sturgeon. These findings contribute to our understanding of the genetic basis of cleft palate in sturgeon, while simultaneously adding to our knowledge about craniofacial development. Overall design: Palate RNA profiles of 3 noncleft-palate (NCP) and 3 cleft-palate (CP) were used for deep sequecing.
Project description:Cleft palate (CP) is one of the most common craniofacial birth defects, impacting about 1 in 800 births in the USA. Tgf-?3 plays a critical role in regulating murine palate development, and Tgf-?3 null mutants develop cleft palate with 100% penetrance. In this study, we compared global palatal transcriptomes of wild type (WT) and Tgf-?3 -/- homozygous (HM) mouse embryos at the crucial palatogenesis stages of E14.5, and E16.5, using RNA-seq data. We found 1,809 and 2,127 differentially expressed genes at E16.5 vs. E14.5 in the WT and HM groups, respectively (adjusted p?<?0.05; |fold change|>?2.0). We focused on the genes that were uniquely up/downregulated in WT or HM at E16.5 vs. E14.5 to identify genes associated with CP. Systems biology analysis relating to cell behaviors and function of WT and HM specific genes identified functional non-Smad pathways and preference of apoptosis to epithelial-mesenchymal transition. We identified 24 HM specific and 11 WT specific genes that are CP-related and/or involved in Tgf-?3 signaling. We validated the expression of 29 of the 35 genes using qRT-PCR and the trend of mRNA expression is similar to that of RNA-seq data . Our results enrich our understanding of genes associated with CP that are directly or indirectly regulated via TGF-?.
Project description:To investigate malformations associated with cleft lip and cleft palate, we conducted surveys at neonatal intensive care units (NICUs) and other non-NICU facilities and to determine whether there are differences among facilities. The regional survey investigated NICU facilities located in Oita Prefecture, including 92 patients with cleft lip and palate (CLP) or cleft palate (CP) that occurred between 2004 and 2013, and the national survey investigated oral surgery, plastic surgery, and obstetrics and gynecology facilities located in Japan, including 16,452 patients with cleft lip (CL), CLP, or CP that occurred since 2000. The incidence per 10,000 births was 4.2, 6.2, and 2.8 for CL, CLP, and CP, respectively, according to the national survey, and 6.3 and 2.9 for CLP and CP, respectively according to the regional survey. These results indicated comparable incidences between the two surveys. In contrast, when the survey results on malformations associated with CLP and CP according to the ICD-10 classification were compared between the national survey conducted at oral surgery or plastic surgery facilities and the regional survey conducted at NICU facilities, the occurrence of associated malformations was 19.8% vs. 41.3% for any types of associated malformation, 6.8% vs. 21.7% for congenital heart disease, and 0.5% vs. 16.3% for chromosomal abnormalities. These results indicated that the incidences of all of these associated malformations were significantly greater in the survey conducted at NICU facilities and similar to the findings from international epidemiological surveys. When comparing the survey conducted at obstetrics facilities vs. NICU facilities, the occurrence of associated malformations was similar results as above. The incidence of CLP and CP was not different between surveys conducted at NICU facilities vs. non-NICU facilities; however, when conducting surveys on associated malformations, it is possible to obtain accurate epidemiological data by investigating NICU facilities where detailed examinations are thoroughly performed.
Project description:Cleft palate (CP) is the most prevalent craniofacial deformity, with ethnic and geographic variation in prevalence in humans. Mice have been used as an animal model to study the cause(s) of CP by several approaches, including genetic and chemical-induced approaches. Mouse genetic approaches revealed that significant amounts of genes are involved in the CP pathology. The aim of this study was to identify common features of CP-associated genes and to explore the roles of microRNAs (miRNAs) as important post-transcriptional regulators that may be involved in the regulation of CP genes. To generate an accurate list of genes associated with CP, we first conducted systematic literature searches through main databases such as Medline, Embase, and PubMed, as well as other sources such as Scopus and Mouse Genome Informatics. We found that 195 mouse strains with single-gene mutations and 140 mouse strains with compound-gene mutations were reported to have CP. The CP genes were categorized by functions and pathways using the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology annotations, highlighting the contribution of cellular metabolism to CP. A total of 18 miRNAs were involved in the regulation of multiple CP genes. Human genotype-phenotype analysis revealed that variants in five human homologous CP genes (IRF6, FOXE1, VAX1, WNT9B, and GAD1) significantly contributed to the human CP phenotype. Thus, our results suggest that cellular metabolism and miRNAs play an important role in the regulation of genetic pathways and networks crucial for palatal formation.
Project description:Whether treatment of cleft palate (CP) associated with Robin sequence (RS) should attain outcomes similar to those of isolated cleft palate (ICP) remains unknown. This study compares treatment and outcomes in both conditions and delineates predictors of long-term outcome.<h4>Methods</h4>This retrospective case series of consecutive syndromic and isolated RS- and ICP-patients (1990-2016) includes indications and outcomes of straight-line repair with intravelar veloplasty (SLIV) or Furlow repair depending on cleft and airway characteristics.<h4>Results</h4>Seventy-five RS and 83 ICP patients underwent CP repair. Velopharyngeal insufficiency (VPI) occurred in 41% of RS versus 17% of ICP patients (<i>P</i> = 0.012), and in 60% of patients with syndromic RS versus 16% with isolated RS (<i>P</i> = 0.005). In multivariable logistic regression analysis, wider and more severe CP anatomy was the only factor independently associated with VPI (<i>P</i> = 0.028), in contrast to age at repair, syndromic RS compared with isolated RS, and isolated RS compared with ICP and initial tongue-lip adhesion. Secondary Furlow after primary SLIV was used to treat VPI in all groups, and more frequently in syndromic versus isolated RS patients (<i>P</i> = 0.025).<h4>Conclusions</h4>Variability of RS anatomy and airway compromise necessitates individualized treatment protocols. Despite differing CP etiology and other variables, our findings demonstrate cleft anatomy as the only independent variable predictive of VPI comparing RS and ICP patients. Patients with isolated RS should ultimately attain similar VPI outcomes compared with ICP patients. Obstructive speech operations in RS patients can be avoided without compromising speech outcome by reserving the prsocedure for secondary cases.
Project description:Cleft lip and/or palate (CL/P) is a common congenital malformation with a complex etiology which is not fully elucidated yet. Epidemiological studies point to different etiologies in the cleft lip and palate subgroups, isolated cleft lip (CL), isolated cleft palate (CP) and combined cleft lip and palate (CLP). In order to understand the biological basis in these cleft lip and palate subgroups better we studied the expression profiles in human tissue from patients with CL/P. In each of the CL/P subgroups, samples were obtained from three patients and gene expression analysis was performed. Moreover, selected differentially expressed genes were analyzed by quantitative RT-PCR, and by immunohistochemical staining of craniofacial tissue from human embryos. Osteopontin (SPP1) and other immune related genes were significantly higher expressed in palate tissue from patients with CLP compared to CP and immunostaining in palatal shelves against SPP1, chemokine receptor 4 (CXCR4) and serglycin (PRG1) in human embryonic craniofacial tissue were positive, supporting a role for these genes in palatal development. However, gene expression profiles are subject to variations during growth and therefore we recommend that future gene expression in CL/P studies should use tissue from the correct embryonic time and place if possible, to overcome the biases in the presented study.
Project description:Nonsyndromic orofacial clefts are a common complex birth defect caused by genetic and environmental factors and/or their interactions. A previous genome-wide linkage scan discovered a novel locus for cleft lip with or without cleft palate (CL/P) at 9q22-q33. To identify the etiologic gene, we undertook an iterative and complementary fine mapping strategy using family-based CL/P samples from Colombia, USA and the Philippines. Candidate genes within 9q22-q33 were sequenced, revealing 32 new variants. Concurrently, 397 SNPs spanning the 9q22-q33 2-LOD-unit interval were tested for association. Significant SNP and haplotype association signals (P = 1.45E - 08) narrowed the interval to a 200 kb region containing: FOXE1, C9ORF156 and HEMGN. Association results were replicated in CL/P families of European descent and when all populations were combined the two most associated SNPs, rs3758249 (P = 5.01E - 13) and rs4460498 (P = 6.51E - 12), were located inside a 70 kb high linkage disequilibrium block containing FOXE1. Association signals for Caucasians and Asians clustered 5' and 3' of FOXE1, respectively. Isolated cleft palate (CP) was also associated, indicating that FOXE1 plays a role in two phenotypes thought to be genetically distinct. Foxe1 expression was found in the epithelium undergoing fusion between the medial nasal and maxillary processes. Mutation screens of FOXE1 identified two family-specific missense mutations at highly conserved amino acids. These data indicate that FOXE1 is a major gene for CL/P and provides new insights for improved counseling and genetic interaction studies.
Project description:The identification of the genetic risk factors in patients with isolated cleft palate by whole genome sequencing analysis. Pathogenic or likely pathogenic variants were discovered in genes associated with CP (TBX22, COL2A1, FBN1, PCGF2, and KMT2D) in five patients; hence, rare disease variants were identified in 17% of patients with non-syndromic isolated CP. Our results are relevant to routine genetic counselling practice and genetic testing recommendations.
Project description:In humans, cleft palate (CP) accounts for one of the largest number of birth defects with a complex genetic and environmental etiology. TGF?3 has been established as an important regulator of palatal fusion in mice and it has been shown that TGF?3-null mice exhibit CP without any other major deformities. However, the genes that regulate cellular decisions and molecular mechanisms maintained by the TGF?3 pathway throughout palatogenesis are predominantly unexplored. Our objective in this study was to analyze global transcriptome changes within the palate during different gestational ages within TGF?3 knockout mice to identify TGF?3-associated genes previously unknown to be associated with the development of cleft palate. We used deep sequencing technology, RNA-Seq, to analyze the transcriptome of TGF?3 knockout mice at crucial stages of palatogenesis, including palatal growth (E14.5), adhesion (E15.5), and fusion (E16.5).The overall transcriptome analysis of TGF?3 wildtype mice (C57BL/6) reveals that almost 6000 genes were upregulated during the transition from E14.5 to E15.5 and more than 2000 were downregulated from E15.5 to E16.5. Using bioinformatics tools and databases, we identified the most comprehensive list of CP genes (n = 322) in which mutations cause CP either in humans or mice, and analyzed their expression patterns. The expression motifs of CP genes between TGF?3+/- and TGF?3-/- were not significantly different from each other, and the expression of the majority of CP genes remained unchanged from E14.5 to E16.5. Using these patterns, we identified 8 unique genes within TGF?3-/- mice (Chrng, Foxc2, H19, Kcnj13, Lhx8, Meox2, Shh, and Six3), which may function as the primary contributors to the development of cleft palate in TGF?3-/- mice. When the significantly altered CP genes were overlaid with TGF? signaling, all of these genes followed the Smad-dependent pathway.Our study represents the first analysis of the palatal transcriptome of the mouse, as well as TGF?3 knockout mice, using deep sequencing methods. In this study, we characterized the critical regulation of palatal transcripts that may play key regulatory roles through crucial stages of palatal development. We identified potential causative CP genes in a TGF?3 knockout model, which may lead to a better understanding of the genetic mechanisms of palatogenesis and provide novel potential targets for gene therapy approaches to treat cleft palate.