Novel likely pathogenic variant in the EYA1 gene causing Branchio oto renal syndrome and the exploration of pathogenic mechanisms

OBJECTIVE

Branchio-oto-renal syndrome (BOR, OMIM#113,650) is a rare autosomal dominant disorder that presents with a variety of symptoms, including hearing loss (sensorineural, conductive, or mixed), structural abnormalities affecting the outer, middle, and inner ear, branchial fistulas or cysts, as well as renal abnormalities.This study aims to identify the pathogenic variants by performing genetic testing on a family with Branchio-oto-renal /Branchio-otic (BO, OMIM#602,588) syndrome using whole-exome sequencing, and to explore possible pathogenic mechanisms.

METHODS

The family spans 4 generations and consists of 9 individuals, including 4 affected by the BOR/BO syndrome. Phenotypic information, including ear malformation and branchial cleft, was collected from family members. Audiological, temporal bone imaging, and renal ultrasound examinations were also performed. Whole-exome sequencing was conducted to identify candidate pathogenic variants and explore the underlying molecular etiology of BOR/BO syndrome by minigene experiments.

RESULTS

Intra-familial variability was observed in the clinical phenotypes of BOR/BO syndrome in this family. The severity and nature of hearing loss varied in family members, with mixed or sensorineural hearing loss. The proband, in particular, had profound sensorineural hearing loss on the left and moderate conductive hearing loss on the right. Additionally, the proband exhibited developmental delay, and her mother experienced renal failure during pregnancy and terminated the pregnancy prematurely. Genetic testing revealed a novel heterozygous variant NM_000503.6: c.639 + 3 A > C in the EYA1 gene in affected family members. In vitro minigene experiments demonstrated its effect on splicing. According to the American College of Medical Genetics (ACMG) guidelines, this variant was classified as likely pathogenic.

CONCLUSION

This study highlights the phenotypic heterogeneity within the same family, reports the occurrence of renal failure and adverse pregnancy outcomes in a female patient at reproductive age with BOR syndrome, and enriches the mutational spectrum of pathogenic variants in the EYA1 gene.

Genetic research progress in branchiooto syndrome/ branchiootorenal syndrome

Branchio-oto syndrome (BOS)/branchio-oto-renal syndrome (BORS) is a kind of autosomal dominant heterogeneous disorder. These diseases are mainly characterized by hearing impairment and abnormal phenotype of ears, accompanied by renal malformation and branchial cleft anomalies including cyst or fistula, with an incidence of 1/40 000 in human population. Otic anormalies are one of the most obvious clinical manifestations of BOS/BORS, including deformities of external, middle, inner ears and hearing loss with conductive, sensorineural or mix, ranging from mild to profound loss. Temporal bone imaging could assist in the diagnosis of middle ear and inner ear malformations for clinicians. Multiple methods including direct sequencing combined with next generation sequencing (NGS), multiplex ligation-dependent probe amplification (MLPA), or array-based comparative genomic hybridization (aCGH) can effectively screen and identify pathogenic genes and/or variation types of BOS/BORS. About 40% of patients with BOS/BORS carry aberrations of EYA1 gene which is the most important cause of BOS/BORS. A total of 240 kinds of pathogenic variations of EYA1 have been reported in different populations so far, including frameshift, nonsense, missense, aberrant splicing, deletion and complex rearrangements. Human Endogenous Retroviral sequences (HERVs) may play an important role in mediating EYA1 chromosomal fragment deletion mutations caused by non-allelic homologous recombination. EYA1 encodes a phosphatase-transactivator cooperated with transcription factors of SIX1, participates in cranial sensory neurogenesis and development of branchial arch-derived organs, then regulates the morphological and functional differentiation of the outer ear, middle ear and inner ear toward normal tissues. In addition, pathogenic mutations of SIX1 and SIX5 genes can also cause BOS/BORS. Variations of these genes mentioned above may cause disease by destroying the bindings between SIX1-EYA1, SIX5-EYA1 or SIX1-DNA. However, the role of SIX5 gene in the pathogenesis of BORS needs further verification.

Inherited glomerular diseases in the gilded age of genomic advancements

The synchronized advent of high-throughput next-generation sequencing technology and knowledge of the human genome has rendered exponential contributions to our understanding of the pathophysiology of glomerular kidney diseases. A genetic diagnosis can now be made or confirmed in about two-thirds of the suspected inherited glomerular diseases. Next-generation sequencing is adept at identifying single nucleotide variations and small insertions or deletions that constitute majority of the disease-causing mutations. Description of the complete mutation spectrum in syndromic glomerulopathies may require the use of both sequencing and cytogenetic methods to detect large structural DNA variation in addition to single nucleotide changes. The enthusiastic application of genetic and genomic knowledge to inherited glomerular diseases has uncovered anticipated and unforeseen challenges mainly related to the biological interpretation of variants of uncertain significance and the limited benefit on clinical management for the individual patient when a diagnosis is obtained. To attain the ultimate goal of transforming clinical decision-making based on accurate genetic diagnosis using genomic information, these challenges need to be addressed. Till then, the glory of genomic medicine stands the test of time in this gilded age of genomic advancements.

Branchio-oculo-facial syndrome in a newborn caused by a novel TFAP2A mutation

We present an 18-day old boy with bilateral cervical cutaneous defect in the retroauricular region, low-set and posteriorly rotated ears, bilateral microphtalmia and bilateral pseudocleft of the upper lip. Histopathological evaluation of cervical cutaneous defect showed ulceration on the surface and ectopic thymus tissue in the deep dermis with cortex, medulla and Hassal's corpuscles. Clinical findings led to the diagnosis of Branchio-oculo-facial syndrome, characterized by branchial defects (erythematous cutaneous defects in cervical region), ocular anomalies (microphthalmia, anophthalmia, lacrimal duct obstruction, coloboma, cataract, ptosis) and facial defects (cleft lip and/or palate, pseudocleft or abnormal philtrum). DNA sequencing showed a novel heterozygous mutation, c.731T>C (p.L244P), in TFAP2A gene confirming the diagnosis of this rare autosomal dominant developmental disorder with variable clinical findings.

Middle and inner ear malformations in mutation-proven branchio-oculo-facial (BOF) syndrome: case series and review of the literature

Hearing impairment is common in individuals with branchio-oculo-facial (BOF) syndrome. The majority of described individuals have conductive hearing impairment due to malformed ossicles and/or external canal stenosis or atresia, although a sensorineural component to the hearing impairment in BOF syndrome is increasingly being reported. Sophisticated computed tomography (CT) of the temporal bone has revealed middle and inner ear malformations in three previous reports. We present middle and inner ear abnormalities in three additional individuals with mutation-proven BOF syndrome. We suggest that temporal bone CT imaging be included in the medical workup of a child with BOF syndrome, in order to guide management.

Catweasel mice: a novel role for Six1 in sensory patch development and a model for branchio-oto-renal syndrome

Large-scale mouse mutagenesis initiatives have provided new mouse mutants that are useful models of human deafness and vestibular dysfunction. Catweasel is a novel N-ethyl-N-nitrosourea (ENU)-induced mutation. Heterozygous catweasel mutant mice exhibit mild headtossing associated with a posterior crista defect. We mapped the catweasel mutation to a critical region of 13 Mb on chromosome 12 containing the Six1, -4 and -6 genes. We identified a basepair substitution in exon 1 of the Six1 gene that changes a conserved glutamic acid (E) at position 121 to a glycine (G) in the Six1 homeodomain. Cwe/Cwe animals lack Preyer and righting reflexes, display severe headshaking and have severely truncated cochlea and semicircular canals. Cwe/Cwe animals had very few hair cells in the utricle, but their ampullae and cochlea were devoid of any hair cells. Bmp4, Jag1 and Sox2 expression were largely absent at early stages of sensory development and NeuroD expression was reduced in the developing vestibulo-acoustic ganglion. Lastly we show that Six1 genetically interacts with Jag1. We propose that the catweasel phenotype is due to a hypomorphic mutation in Six1 and that catweasel mice are a suitable model for branchio-oto-renal syndrome. In addition Six1 has a pivotal role in early sensory patch development and may act in the same genetic pathway as Jag1.

A novel frameshift mutation in the EYA1 gene in a Korean family with branchio-oto-renal syndrome

Branchio-oto-renal (BOR) syndrome is an autosomal dominant disorder characterized by branchial cleft fistulae or cysts, preauricular pits, ear malformations, hearing loss, and renal anomalies. Mutations in the human homologue of the Drosophilia eyes absent gene (EYA1) are the most common cause of BOR syndrome. In this study, we found a Korean family showing clinical features of the disease. Mutation analysis of the EYA1 gene revealed a novel one-base-pair deletion resulting in truncated protein (c.321delT; p.Ala107fs). This is the first report of BOR syndrome caused by deletion mutation of the EYA1 gene in Korea.

Branchio-oto-renal syndrome

Branchio-oto-renal syndrome, a phenotype consisting of hearing loss, auricular malformations, branchial arch remnants, and renal anomalies is now recognized as one of the more common forms of autosomal dominant syndromic hearing impairment. Three loci known to be associated with the BOR phenotype have been identified and two genes that act in a regulatory network have been cloned, EYA1 and SIX1. EYA1 and SIX1 are homologous to genes involved in Drosophila eye development, eyes absent gene (eya), and sine oculis (so), respectively. EYA1, a transcriptional co-activator has a conserved, 271-amino acid, C-terminal known as the Eya Domain (ED). SIX1 has two highly conserved domains; a homeodomain (HD) and a specific Six-domain (SD) whose products function as transcription factors with specific DNA-binding activity that are crucial for protein-protein interaction. To determine the molecular basis for the organ defects that occur in BOR syndrome, many studies have focused on the effects of mutations to EYA and effects of mutations of the EYA-SIX regulatory system. However, over 60% of BOR syndrome patients do not have known mutations in EYA1 and relatively little is known about mutations to SIX1. Further evaluation of SIX1 and its related target genes may provide a better understanding of the pathophysiology of BOR syndrome and offer greater clues to the disease mechanisms.

Branchio-oto-renal syndrome: detection of EYA1 and SIX1 mutations in five out of six Danish families by combining linkage, MLPA and sequencing analyses

The branchio-oto-renal (BOR) syndrome is an autosomal-dominant disorder characterized by hearing loss, branchial and renal anomalies. BOR is genetically heterogeneous and caused by mutations in EYA1 (8q13.3), SIX1 (14q23.1), SIX5 (19q13.3) and in an unidentified gene on 1q31. We examined six Danish families with BOR syndrome by assessing linkage to BOR loci, by performing EYA1 multiplex ligation-dependent probe amplification (MLPA) analysis for deletions and duplications and by sequencing of EYA1, SIX1 and SIX5. We identified four EYA1 mutations (c.920delG, IVS10-1G>A, IVS12+4A>G and p.Y591X) and one SIX1 mutation (p.W122R), providing a molecular diagnosis in five out of the six families (83%). The present, yet preliminary, observation that renal and temporal bone malformations are less frequent in SIX1-related disease suggests a slightly different clinical profile compared to EYA1-related disease. Unidentified mutations impairing mRNA expression or further genetic heterogeneity may explain the lack of mutation finding in one family despite LOD score indications of EYA1 involvement.

Bilateral dermal thymus of neck in branchio-oculo-facial syndrome

Dermal thymus in bilateral sides of neck is very rare, probably unique anomaly of branchio-oculo-facial syndrome (BOF). We report a case of BOF with cleft lip and non-healing erosions on bilateral sides of neck. The thymus of neck in our case showed unusual clinical course that appeared at 1 year and half of age after the repair of cleft lip deformity. The lesions of neck were completely excised, and the histopathologic examination for neck lesion confirmed ectopic dermal thymus. Ectopic thymus can be excised completely after careful evaluation of haematologic, immunologic status if normal thymic shadow cannot be identified on chest X-p.

A novel nonsense mutation in the EYA1 gene associated with branchio-oto-renal/branchiootic syndrome in an Afrikaner kindred

Branchio-oto-renal (BOR) syndrome is an autosomal dominant disorder characterized by the associations of hearing loss, branchial arch defects and renal anomalies. Branchiootic (BO) syndrome is a related disorder that presents without the highly variable characteristic renal anomalies of BOR syndrome. Dominant mutations in the human homologue of the Drosophila eyes absent gene (EYA1) are frequently the cause of both BOR and BO syndromes. We report a South African family of Afrikaner descent with affected individuals presenting with pre-auricular abnormalities and either hearing loss or bilateral absence of the kidneys. Genetic analysis of the pedigree detected a novel EYA1 heterozygous nonsense mutation in affected family members but not in unaffected family members or a random DNA panel. Through mutational analysis, we conclude that this particular mutation is the cause of BOR/BO syndrome in this family as a result of a truncation of the EYA1 protein that ablates the critical EYA homologous region. To the best of our knowledge, this is the first case of BOR/BO syndrome reported in Africa or in those of the Afrikaner descent.

Branchio-oculo-facial syndrome with bilateral linear scars of the neck

A case of branchio-oculo-facial syndrome with bilateral linear scars affecting both sides of the neck is described. The disease occured in a male patient aged 20 years and presented with facial asymmetry, pre and postauricular pits, lip pits, microphthalmia, broad malformed nose, colobomas and dystrophic right kidney. In addition, there were bilateral linear hypertrophic scars on both sides of the neck. We believe that the latter lesions may represent the end stage of dermal thymus; a rare condition which has been reported so far in only four cases, two of which had branchio-oculo-facial syndrome.

Thymic tissue in the skin: a clue to the diagnosis of the branchio-oculo-facial syndrome: report of two cases

The branchio-oculo-facial (BOF) syndrome is a rare autosomal dominant disorder with a peculiar phenotype related to a combination of craniofacial abnormalities. Rare examples presenting with dermal thymic tissue have been described. We are reporting 2 children, 15 and 4 months old, respectively, with BOF syndrome in whom surgical repair/excision of skin cervical lesions showed thymic tissue. In the first patient the thymic tissue was exposed to the surface, without epithelial coverage and contained areas suggestive of all stages of thymus formation. A dermohypodermal nodule of fully developed thymic tissue superficially covered by nonkeratinizing squamous epithelium was found in the second patient. Since pharyngeal pouches are not exposed to the surface during normal embryogenesis and the thymus originates from the third pharyngeal pouch, both examples seem to indicate that in BOF syndrome there is a more complex malformation than simply ectopic thymus tissue. Thymic tissue at the skin appears to be unique for BOF syndrome and in a given case may provide the clue for the accurate diagnosis of the malformation complex.

Inner ear anomalies are frequent but nonobligatory features of the branchio-oto-renal syndrome

OBJECTIVE

To summarize the syndromic features and evaluate the presence of inner ear anomalies in 35 patients with branchio-oto-renal (BOR) syndrome from 6 families.

DESIGN

Retrospective evaluation of magnetic resonance imaging of the temporal bones and clinical features in patients with BOR syndrome.

SETTING

Tertiary referral center.

PATIENTS

The study population comprised 35 clinically affected patients with BOR syndrome from 6 families. Most of these families were followed for over 25 years.

MAIN OUTCOME MEASURES

Twenty-four patients underwent high-resolution, heavily T2-weighted 3-dimensional magnetic resonance imaging of the temporal bones for evaluation of inner ear anomalies. Special attention was paid to the endolymphatic duct and sac.

RESULTS

A total of 7 enlarged endolymphatic ducts and sacs (3 bilaterally and 4 unilaterally) and 5 enlarged endolymphatic ducts only (2 bilaterally and 3 unilaterally) were observed. Eight hypoplastic cochleas and 6 hypoplastic labyrinths were seen bilaterally. Seven family members had normal inner ears.

CONCLUSION

These findings suggest that inner ear anomalies are frequent but nonobligatory features of BOR syndrome.

Molecular effects of Eya1 domain mutations causing organ defects in BOR syndrome

Eya1 is a critical gene for mammalian organogenesis. Mutations in human EYA1 cause branchio-oto-renal (BOR) syndrome, an autosomal dominant disorder characterized by varying combinations of branchial, otic and renal anomalies, whereas deletion of mouse Eya1 results in the absence of multiple organ formation. Eya1 and other Eya gene products share a highly conserved 271 amino acid Eya domain that is required for protein-protein interaction. Recently, several point mutations that result in single amino acid substitutions in the conserved Eya domain region of EYA1 have been identified in BOR patients; however, the molecular and developmental basis of organ defects that occurred in BOR syndrome is unclear. To understand how these point mutations cause disease, we have analyzed the functional importance of these Eya domain missense mutations with respect to protein complex formation and cellular localization. We have demonstrated that these point mutations do not alter protein localization. However, four mutations are crucial for protein-protein interactions in both yeast and mammalian cells. Our results provide insights into the molecular mechanisms of organ defects detected in human syndromes.

The presence of a widened vestibular aqueduct and progressive sensorineural hearing loss in the branchio-oto-renal syndrome. A family study

OBJECTIVE

A new large family with the BOR syndrome is reported with special reference to the presence of a widened vestibular aqueduct and a progressive sensorineural component in the mixed hearing loss. A review of the BOR literature of 184 patients is given.

SETTING

University Hospitals.

RESULTS

A BOR family with 17 affected members was studied. Fourteen of those 17 were still alive and 12 of those cooperated in this clinical study. Detailed radiological studies showed in three out of 12 affected family members a widened vestibular aqueduct and progressive sensorineural hearing loss. This raises the question whether there is a true correlation or whether those are coincidental.

CONCLUSION

In our family with the Branchio-Oto-Renal syndrome, a widened vestibular aqueduct and progressive hearing loss is found in a few affected family members. Imaging of the temporal bones and long-term audiometric follow-up could help to reveal whether the widened vestibular aqueduct is the cause for the progressive hearing loss.

Branchio-oto-renal syndrome: identification of a novel mutation in the EYA1 gene

Branchio-oto-renal (BOR) syndrome is an autosomal dominant disorder characterized by the association of branchial cysts or fistulae, external ear malformation and/or preauricular pits, hearing loss, and renal anomalies. Mutations in the EYA1 gene, a human homologue of the Drosophila 'eyes absent' gene, have been identified as cause of the syndrome. We report here two families with BOR syndrome. In one family, with the complete phenotype, a novel splice site mutation in exon 15 (1599 +1 G to A) is described. No mutations in the EYA1 gene were found in a second family presenting with ear pits, deafness, and renal anomalies, but lacking branchial fistulae. These and other findings from the literature suggest the existence of genetic heterogeneity of the BOR, BO, and other related phenotypes, with two or more genes involved.

Inner ear and kidney anomalies caused by IAP insertion in an intron of the Eya1 gene in a mouse model of BOR syndrome

A spontaneous mutation causing deafness and circling behavior was discovered in a C3H/HeJ colony of mice at the Jackson Laboratory. Pathological analysis of mutant mice revealed gross morphological abnormalities of the inner ear, and also dysmorphic or missing kidneys. The deafness and abnormal behavior were shown to be inherited as an autosomal recessive trait and mapped to mouse chromosome 1 near the position of the Eya1 gene. The human homolog of this gene, EYA1, has been shown to underly branchio-oto-renal (BOR) syndrome, an autosomal dominant disorder characterized by hearing loss with associated branchial and renal anomalies. Molecular analysis of the Eya1 gene in mutant mice revealed the insertion of an intracisternal A particle (IAP) element in intron 7. The presence of the IAP insertion was associated with reduced expression of the normal Eya1 message and formation of additional aberrant transcripts. The hypomorphic nature of the mutation may explain its recessive inheritance, if protein levels in homozygotes, but not heterozygotes, are below a critical threshold needed for normal developmental function. The new mouse mutation is designated Eya1(bor) to denote its similarity to human BOR syndrome, and will provide a valuable model for studying mutant gene expression and etiology.

Branchio-oto-renal syndrome with generalized microdontia: case report

Branchio-oto-renal syndrome, first defined in 1976, is an autosomal dominant disorder characterized by anomalies of the external, middle, and inner ear in association with preauricular sinuses, branchial cleft anomalies, and varying degrees of renal dysplasia, including aplasia. Less frequently expressed phenotypic abnormalities include lacrimal duct aplasia and stigmata of renal dysgenesis known as Potter facies. Although the precise incidence of the disorder is unknown, it may be more common than is generally appreciated, and it appears to be distinct from other autosomal dominant otobranchial syndromes. Moreover, not all features of the syndrome are expressed in all carriers of the gene. An unusual case of branchio-oto-renal syndrome with generalized microdontia of the permanent dentition is reported.

Branchio-oculo-facial syndrome with cleft lip and bilateral dermal thymus

OBJECTIVE

The objective of this study was to demonstrate that the branchiooculo-facial (BOF) syndrome is a cervicocephalic neural crest maldevelopment.

RESULTS

Using an embryologic study, we linked the clinical features and the level of the neural crest deficiency. We report here two cases of BOF syndrome with a particular branchial cleft presenting as bilateral supernumerary thymus glands on the surface of the skin; one of the cases was associated with tetralogy of Fallot. One patient underwent lip reconstruction at 4 months, combined with excision of bilateral auricular pits and superior labial fistula. The other patient had a surgical correction of the tetralogy of Fallot, and at 2 months, the two stages of the lip reconstruction were performed, combined with bilateral auricular pit excision. Both patients have shown normal developmental patterns to date.

CONCLUSION

The BOF syndrome must be considered as a neurocristopathy at different levels, with a tiny mesencephalo-prosencephalic lesion and a severe rhombencephalic lesion that includes seven consecutive hindbrain segments, from rhombomere 2 to rhombomere 8.