OBJECTIVE: To explore the clinical feature and genetic etiology of a patient with Craniofacial nasal syndrome (CNFS). METHODS: A patient with CNFS who had presented at the Guiyang Maternal and Child Health Care Hospital on November 13, 2021 was selected as the study subject. Clinical data of the patient were collected. Peripheral venous blood samples were collected from the patient and her parents and subjected to trio-whole exome sequencing (trio-WES). Candidate variants were verified by Sanger sequencing and bioinformatic analysis. RESULTS: The patient, a 15-year-old female, had predominantly featured forehead bulging, hypertelorism, wide nasal dorsum and bifid nasal tip. Genetic testing revealed that she has harbored a heterozygous missense c.473T>C (p.M158T) variant of the EFNB1 gene, which was detected in either of her parents. By bioinformatic analysis, the variant has not been recorded in the HGMD and ClinVar databases, and no population frequency was recorded in the 1000 Genomes, ExAC, gnomAD and Shenzhou Genome Data Cloud databases. As predicted by the REVEL online software, the variant can confer deleterious effects on the gene or its product. Analysis using UGENE software showed the corresponding amino acid to be highly conserved among various species. Analysis with AlphaFold2 software suggested that the variant may affect the 3D structure and function of the Ephrin-B1 protein. Based on the American College of Medical Genetics and Genomics (ACMG) standards and guidelines and recommendation of Clinical Genome Resource (ClinGen), the variant was rated as pathogenic. CONCLUSION Combining the patient's clinical features and genetic finding, the diagnosis of CNFS was confirmed. The heterozygous c.473T>C (p.M158T) missense variant of the EFNB1 gene probably underlay the disease in this patient. Above finding has provided a basis for the genetic counseling and prenatal diagnosis for her family.
Humans ; Child ; Female ; Pregnancy ; Adolescent ; Ephrin-B1/genetics* ; China ; Computational Biology ; Family ; Mutation

Due to advances in omics technologies, numerous genome-wide studies on human samples have been published, and most of the omics data with the associated clinical information are available in public repositories, such as Gene Expression Omnibus and ArrayExpress. While analyzing several public datasets, we observed that errors in gender information occur quite often in public datasets. When we analyzed the gender description and the methylation patterns of gender-specific probes (glucose-6-phosphate dehydrogenase [G6PD], ephrin-B1 [EFNB1], and testis specific protein, Y-linked 2 [TSPY2]) in 5,611 samples produced using Infinium 450K HumanMethylation arrays, we found that 19 samples from 7 datasets were erroneously described. We also analyzed 1,819 samples produced using the Affymetrix U133Plus2 array using several gender-specific genes (X (inactive)-specific transcript [XIST], eukaryotic translation initiation factor 1A, Y-linked [EIF1AY], and DEAD [Asp-Glu-Ala-Asp] box polypeptide 3, Y-linked [DDDX3Y]) and found that 40 samples from 3 datasets were erroneously described. We suggest that the users of public datasets should not expect that the data are error-free and, whenever possible, that they should check the consistency of the data.
Dataset* ; DNA Methylation ; Ephrin-B1 ; Gender Identity ; Gene Expression ; Humans ; Methylation ; Microarray Analysis ; Oxidoreductases ; Peptide Initiation Factors ; Testis

Recent studies showed that Eph/Ephrin tyrosine kinase family plays an important role in the development and functional maintenance of the nervous system, but its function in the sympathetic nervous system is still obscure. In the present study, we examined the effect of Eph/Ephrin-B1 signaling on the whole-cell currents mediated by either alpha7 or alpha3-nicotinic acetylcholine receptors (nAChRs) in acutly dissociated ciliary ganglion (CG) neurons. Firstly, we detected the effect of Ephrin-B1 on nAChRs currents. The neurons were randomly divided into control group, Ephrin-B1Fc-treated group that was stimulated by recombinant Ephrin-B1Fc, IgG-treated group, and Ephrin-B1-treated group. Secondly, we studied the regulatory mechanism of Ephrin-B1Fc on nAChRs currents. The neurons were randomly divided into control group, Ephrin-B1Fc-treated group, PP2 (inhibitor of Src tyrosine kinase) or PD98095 (antagonist of mitogen-activated protein kinase)-treated group, Ephrin-B1Fc + PP2 or PD98095-treated group. The results showed that there was no significant difference between the currents in control group, IgG-treated group and Ephrin-B1-treated group, but Ephrin-B1Fc significantly suppressed both alpha3-nAChRs and alpha7-nAChRs-mediated currents (P=0.002, P=0.003). Pretreatment with PP2 or PD98095 could partially rescue the Ephrin-B1Fc-induced suppression of currents mediated by alpha3-nAChRs or alpha7-nAChRs respectively. These results suggest that the Eph/Ephrin-B1 signaling may inhibit alpha3-nAChRs and alpha7-nAChRs-mediated currents on CG neurons, involving Src tyrosine kinase and mitogen-activated protein kinase signaling in the regulation of sympathetic nervous system.
Ephrin-B1 ; metabolism ; Ganglia, Parasympathetic ; enzymology ; Mitogen-Activated Protein Kinases ; metabolism ; Neurons ; enzymology ; Receptors, Nicotinic ; metabolism ; Signal Transduction ; alpha7 Nicotinic Acetylcholine Receptor ; metabolism ; src-Family Kinases ; metabolism