Exclusion of the branchio-oto-renal syndrome locus (EYA1) from patients with branchio-oculo-facial syndrome

Systematic target function annotation of human transcription factors

Background

Transcription factors (TFs), the key players in transcriptional regulation, have attracted great experimental attention, yet the functions of most human TFs remain poorly understood. Recent capabilities in genome-wide protein binding profiling have stimulated systematic studies of the hierarchical organization of human gene regulatory network and DNA-binding specificity of TFs, shedding light on combinatorial gene regulation. We show here that these data also enable a systematic annotation of the biological functions and functional diversity of TFs.

Result

We compiled a human gene regulatory network for 384 TFs covering the 146,096 TF–target gene (TF–TG) relationships, extracted from over 850 ChIP-seq experiments as well as the literature. By integrating this network of TF–TF and TF–TG relationships with 3715 functional concepts from six sources of gene function annotations, we obtained over 9000 confident functional annotations for 279 TFs. We observe extensive connectivity between TFs and Mendelian diseases, GWAS phenotypes, and pharmacogenetic pathways. Further, we show that TFs link apparently unrelated functions, even when the two functions do not share common genes. Finally, we analyze the pleiotropic functions of TFs and suggest that the increased number of upstream regulators contributes to the functional pleiotropy of TFs.

Conclusion

Our computational approach is complementary to focused experimental studies on TF functions, and the resulting knowledge can guide experimental design for the discovery of unknown roles of TFs in human disease and drug response.

Electronic supplementary material

The online version of this article (doi:10.1186/s12915-017-0469-0) contains supplementary material, which is available to authorized users.

Treatment of otorhinolaryngological manifestations of three rare genetic syndromes: Branchio-Oculo-Facial (BOF), Ectrodactyly Ectodermal dysplasia Clefting (EEC) and focal dermal hypoplasia (Goltz syndrome)

Genetic background and characteristic symptoms of three children with rare genetic syndromes: Ectrodactyly Ectodermal dysplasia Clefting (EEC), Branchio-Oculo-Facial (BOF) and focal dermal hypoplasia (Goltz syndrome) were outlined. All patients presented common otorhinolaryngological features of bilateral hearing impairment and dermal problems. Diagnostic protocol and treatment strategies for all three syndromes were presented and discussed. Skin lesions of the head and neck and degree of hearing loss were identified in clinical examination and by audiological methods. Treatment of hypoacousis and skin disorders were the primary issues in presented cases. In both the EEC syndrome and FDH our priority was to achieve and maintain hearing at the level of social efficiency. Patient with the Branchio-Oculo-Facial syndrome received a cochlear implant at the age of 12 months and was surgically treated for bilateral retroauricular fistulas. In both cases of dysplasia conservative treatment and otosurgery were applied. Results of treatment after 12 months are presented. In all patients hearing result provided good social skills in communication and a good local condition was achieved. Possibilities for future interventions were mentioned and necessity for medical follow-up and rehabilitation were stressed as key issues in maintaining results achieved with treatment presented in this study. Patient with FDH underwent CO(2) laser treatment for papillomatous lesions on her face and neck. Good aesthetic result without recurrence in follow-up examinations was achieved. Baby with the Branchio-Oculo-Facial syndrome is rehabilitated in our Cochlear Implant Center and the fistulas have healed without complications. Due to the rarity and multiplicity of symptoms in presented syndromes a standard therapy has not been established yet. However, it is of crucial importance in such cases to focus on hearing improvement in order to reach and maintain hearing at the level of social communication.

TFAP2A mutations result in branchio-oculo-facial syndrome

Branchio-oculo-facial syndrome (BOFS) is a rare autosomal-dominant cleft palate-craniofacial disorder with variable expressivity. The major features include cutaneous anomalies (cervical, infra- and/or supra-auricular defects, often with dermal thymus), ocular anomalies, characteristic facial appearance (malformed pinnae, oral clefts), and, less commonly, renal and ectodermal (dental and hair) anomalies. The molecular basis for this disorder is heretofore unknown. We detected a 3.2 Mb deletion by 500K SNP microarray in an affected mother and son with BOFS at chromosome 6p24.3. Candidate genes in this region were selected for sequencing on the basis of their expression patterns and involvement in developmental pathways associated with the clinical findings of BOFS. Four additional BOFS patients were found to have de novo missense mutations in the highly conserved exons 4 and 5 (basic region of the DNA binding domain) of the TFAP2A gene in the candidate deleted region. We conclude BOFS is caused by mutations involving TFAP2A. More patients need to be studied to determine possible genetic heterogeneity and to establish whether there are genotype-phenotype correlations.

Branchio-oculo-facial syndrome with the atresia of external ear

We report an 8-year-old child with branchio-oculo-facial syndrome. He showed atresia of external ear, preauricular pit, maxillar and mandibular hypoplasia, mild ptosis on the left side, lacrimal duct obstruction, unilateral branchial cyst, hypertrichosis of the neck, left foot showed mild syndactily of fourth and fifth toes and dental abnormalities. His mother had pseudocleft of the lip which led to the diagnosis. The importance of serial observations in patients with rare genetic disorders is emphasized.

Branchio-oculo-facial syndrome

Branchio-oculo-facial syndrome (BOFS) is a very rare autosomal dominant disorder with incomplete penetrance and variable expression; with phenotypic variation ranging from mild to severe forms, involving eye, ear, oral and craniofacial structure. We report three members of one family, showing great variability in its phenotypic expression and review the recent literature.

A family affected by branchio-oto syndrome with EYA1 mutations

Branchio-oto (BO) syndrome is complicated with congenital preauricular fistulae, branchial fistulae (cysts), and hearing loss (sensorineural, conductive or mixed). As well as branchio-oto-renal (BOR) syndrome. it is known to be an autosomal dominant hereditary disorder. Since mutations in the EYA1 gene have been identified in both BO and BOR syndromes, mutation screening of this gene has been drawing attention as a genetic test to diagnose BOR/BO syndromes. In this study, we genetically investigated the presence of EYA1 mutations in a BO syndrome family in which we observed congenital preauricular fistulae, branchial fistulae (cysts) and hearing loss in four generations. Whereas there was a variety of phenotype expressions in this family, all subjects tested had a nonsense mutation (R264X) in exon 8 of the EYA1 gene. The present report adds further examples to support the usefulness of molecular genetic testing for the diagnosis of patients with BO syndrome.