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

Mechanisms of pathogenicity and the quest for genetic modifiers of kidney disease in branchiootorenal syndrome

Backgound

Branchiootorenal (BOR) syndrome is an autosomal dominant disorder caused by pathogenic EYA1 variants and clinically characterized by auricular malformations with hearing loss, branchial arch anomalies, and congenital anomalies of the kidney and urinary tract. BOR phenotypes are highly variable and heterogenous. While random monoallelic expression is assumed to explain this phenotypic heterogeneity, the potential role of modifier genes has not yet been explored.

Methods

Through thorough phenotyping and exome sequencing, we studied one family with disease presentation in at least four generations in both clinical and genetic terms. Functional investigation of the single associated EYA1 variant c.1698+1G>A included splice site analysis and assessment of EYA1 distribution in patient-derived fibroblasts. The candidate modifier gene CYP51A1 was evaluated by histopathological analysis of murine Cyp51+/- and Cyp51-/- kidneys. As the gene encodes the enzyme lanosterol 14α-demethylase, we assessed sterol intermediates in patient blood samples as well.

Results

The EYA1 variant c.1698+1G>A resulted in functional deletion of the EYA domain by exon skipping. The EYA domain mediates protein-protein interactions between EYA1 and co-regulators of transcription. EYA1 abundance was reduced in the nuclear compartment of patient-derived fibroblasts, suggesting impaired nuclear translocation of these protein complexes. Within the affected family, renal phenotypes spanned from normal kidney function in adulthood to chronic kidney failure in infancy. By analyzing exome sequencing data for variants that potentially play roles as genetic modifiers, we identified a canonical splice site alteration in CYP51A1 as the strongest candidate variant.

Conclusion

In this study, we demonstrate pathogenicity of EYA1 c.1698+1G>A, propose a mechanism for dysfunction of mutant EYA1, and conjecture CYP51A1 as a potential genetic modifier of renal involvement in BOR syndrome.

A Novel EYA1 Mutation Causing Alternative RNA Splicing in a Chinese Family With Branchio-Oto Syndrome: Implications for Molecular Diagnosis and Clinical Application

OBJECTIVES

Branchio-oto syndrome (BOS) primarily manifests as hearing loss, preauricular pits, and branchial defects. EYA1 is the most common pathogenic gene, and splicing mutations account for a substantial proportion of cases. However, few studies have addressed the structural changes in the protein caused by splicing mutations and potential pathogenic factors, and several studies have shown that middle-ear surgery has limited effectiveness in improving hearing in these patients. BOS has also been relatively infrequently reported in the Chinese population. This study explored the genetic etiology in the family of a proband with BOS and provided clinical treatment to improve the patient's hearing.

METHODS

We collected detailed clinical features and peripheral blood samples from the patients and unaffected individuals within the family. Pathogenic mutations were identified by whole-exome sequencing and cosegregation analysis and classified according to the American College of Medical Genetics and Genomics guidelines. Alternative splicing was verified through a minigene assay. The predicted three-dimensional protein structure and biochemical experiments were used to investigate the pathogenicity of the mutation. The proband underwent middle-ear surgery and was followed up at 1 month and 6 months postoperatively to monitor auditory improvement.

RESULTS

A novel heterozygous EYA1 splicing variant (c.1050+4 A>C) was identified and classified as pathogenic (PVS1(RNA), PM2, PP1). Skipping of exon 11 of the EYA1 pre-mRNA was confirmed using a minigene assay. This mutation may impair EYA1-SIX1 interactions, as shown by an immunoprecipitation assay. The EYA1-Mut protein exhibited cellular mislocalization and decreased protein expression in cytological experiments. Middle-ear surgery significantly improved hearing loss caused by bone-conduction abnormalities in the proband.

CONCLUSION

We reported a novel splicing variant of EYA1 in a Chinese family with BOS and revealed the potential molecular pathogenic mechanism. The significant hearing improvement observed in the proband after middle-ear surgery provides a reference for auditory rehabilitation in similar patients.

Otological manifestations in branchiootorenal spectrum disorder: A systematic review and meta-analysis

Branchiootorenal spectrum disorder (BORSD) is a group of rare autosomal dominant entities characterized by branchiogenic malformations, hearing loss (HL) and renal anomalies. It comprises branchiootorenal syndrome and branchiootic syndrome, distinguished by the presence or absence of renal abnormalities. Pathogenic variants have been discovered in the following genes: EYA1, SIX5, SIX1 and SALL1. As the otological phenotype in BORSD is inconsistently reported, we performed a systematic review to provide an up-to-date overview, correlated with the genotype. Forty publications were included, describing 295 individual patients. HL was diagnosed in 95%, usually bilateral and mixed-type, and differed among the different genes involved. Mixed moderate-to-severe HL was the predominant finding in patients with EYA1 involvement, regardless of the presence of renal abnormalities. The sensorineural HL of profound severity was more prevalent in patients with SIX1 mutations. No significant differences among different mutation types or location within the genes could be observed. Structural otological manifestations, ranging from periauricular to inner ear anomalies, were common in both genes. Especially periauricular anomalies were more common and more severe in EYA1. In summary, otological differences among the different genes involved in BORSD are observed, so the molecular analysis is strongly advised.

Nephron number, hypertension, and CKD: physiological and genetic insight from humans and animal models

The kidneys play a vital role in the excretion of waste products and the regulation of electrolytes, maintenance of acid-base balance, regulation of blood pressure, and production of several hormones. Any alteration in the structure of the nephron (basic functional unit of the kidney) can have a major impact on the kidney's ability to work efficiently. Progressive decline in kidney function can lead to serious illness and ultimately death if not treated by dialysis or transplantation. While there have been numerous studies that implicate lower nephron numbers as being an important factor in influencing susceptibility to developing hypertension and chronic kidney disease, a direct association has been difficult to establish because of three main limitations: 1) the large variation in nephron number observed in the human population; 2) no established reliable noninvasive methods to determine nephron complement; and 3) to date, nephron measurements have been done after death, which doesn't adequately account for potential loss of nephrons with age or disease. In this review, we will provide an overview of kidney structure/function, discuss the current literature for both humans and other species linking nephron deficiency and cardio-renal complications, as well as describe the major molecular signaling factors involved in nephrogenesis that modulate variation in nephron number. As more detailed knowledge about the molecular determinants of nephron development and the role of nephron endowment in the cardio-renal system is obtained, it will hopefully provide clinicians the ability to accurately identify people at risk to develop CKD/hypertension and lead to a shift in patient care from disease treatment to prevention.

Anatomical Changes and Audiological Profile in Branchio-oto-renal Syndrome: A Literature Review

Introduction Branchio-oto-renal (BOR) syndrome is an autosomal-dominant genetic condition with high penetrance and variable expressivity, with an estimated prevalence of 1 in 40,000. Approximately 40% of the patients with the syndrome have mutations in the gene EYA1, located at chromosomal region 8q13.3, and 5% have mutations in the gene SIX5 in chromosome region 19q13. The phenotype of this syndrome is characterized by preauricular fistulas; structural malformations of the external, middle, and inner ears; branchial fistulas; renal disorders; cleft palate; and variable type and degree of hearing loss.

Aim Hearing loss is part of BOR syndrome phenotype. The aim of this study was to present a literature review on the anatomical aspects and audiological profile of BOR syndrome.

Data Synthesis Thirty-four studies were selected for analysis. Some aspects when specifying the phenotype of BOR syndrome are controversial, especially those issues related to the audiological profile in which there was variability on auditory standard, hearing loss progression, and type and degree of the hearing loss. Mixed loss was the most common type of hearing loss among the studies; however, there was no consensus among studies regarding the degree of the hearing loss.

A novel splice site mutation inEYA4 causes DFNA10 hearing loss

Nonsyndromic autosomal dominant sensorineural hearing loss (SNHL) at the DFNA10 locus was described in two families in 2001. Causative mutations that affect the EyaHR domain of the 'Eyes absent 4' (EYA4) protein were identified. We report on the clinical and genetic analyses of an Australian family with nonsyndromic SNHL. Screening of the EYA4 gene showed the novel polypyrimidine tract variation ca. 1,282-12T > A that introduces a new 3' splice acceptor site. This is the first report of a point mutation in EYA4 that is hypothesized to lead to aberrant pre-mRNA splicing and human disease. The DFNA10 family described is only the fourth to be identified. One individual presented with apparently the same phenotype as other affected members of the family. However, genotyping illustrated that he did not share the DFNA10 disease haplotype. Detailed clinical investigation showed differences in the onset and severity of his hearing loss and thus he is presumed to represent a phenocopy, perhaps resulting from long-term exposure to loud noise.

Identification of a novel mutation in the EYA1 gene in a Korean family with branchio-oto-renal (BOR) syndrome

The 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 on the chromosome band 8q13.3, the human homologue of the Drosophila eyes absent (eya) gene, have been identified to be the underlying genetic defects of the syndrome. We found a Korean family with BOR syndrome and identified a novel insertion mutation (c.1474_1475insC; R492PfsX40) in the EYA1 gene. To the best of our knowledge, this is the first report of genetically confirmed case of BOR syndrome in Korea.

The transcription factor Six2 activates expression of the Gdnf gene as well as its own promoter

The development of the metanephric kidney proceeds through reciprocal interactions between the metanephric mesenchyme and the ureteric bud. One important molecule mediating this interaction is the glial cell line-derived neurotrophic factor Gdnf, which is secreted by the mesenchymal cells. Regulation of Gdnf expression is largely unknown. We show here that a member of the Six family of homeobox containing transcription factors, namely Six2 activates Gdnf expression. We have identified two Six2 binding sites in the Gdnf promoter that show similarity to the consensus DNA binding sequences of other homeobox proteins and harbor short palindromic sequences. Furthermore, we have characterized the Six2 protein and show that Six2 possesses a transcriptional activation domain in the C-terminus and nuclear localization determinants in the Six domain. In order to identify factors which activate expression of Six2, particularly in the metanephric mesenchyme during early kidney development we have cloned and characterized a 930 bp fragment of the murine Six2 promoter. Transgenic mice harboring a construct in which the LacZ gene is driven by the Six2 promoter fragment revealed LacZ expression at multiple sites which overlap with endogenous Six2 expression. Surprisingly, Six2 bound and activated this 930 bp fragment. The architecture of the binding sites in the Six2 promoter, but not the binding sequence itself, is very similar to the one in the Gdnf promoter. The identification of two target genes and our biochemical characterization suggest a critical role for Six2 in kidney development.

Genetic disorders of human congenital anomalies of the kidney and urinary tract (CAKUT)

Congenital abnormalities of the kidney and urinary tract, CAKUT are common in humans, occurring at a frequency of approximately 1 in 500 fetal ultrasound examinations. CAKUT are major causes of chronic renal failure in infants and young children, but little is known about the molecular pathogenesis of these disorders. To date, several gene mutations have been identified as a cause of human CAKUT: these include PAX2, KAL, EYA1, AGTR2 and HNF-1beta. At present, there is only limited information regarding how mutations alter gene expression during development to cause some CAKUT. The most convincing information comes from the multiorgan malformation syndromes with specific gene mutations. However, these syndromes are relatively rare, and most CAKUT appear to occur in isolation. The goal of this review is to provide an overview of these genetic disorders for CAKUT. An understanding of the genetic aspects of human CAKUT will help to unravel the pathogenesis of these disorders and may facilitate the design of genetic screening tests for early diagnosis and appropriate genetic counseling. Moreover, a deeper insight into the relationship between abnormal genes and the pathogenesis of abnormalities of CAKUT will provide an etiological classification of CAKUT. In addition, the importance of developing a registry of patients with various forms of CAKUT is discussed. This information will allow us to combine molecular biology and classical epidemiologic methods, and to continue expanding our knowledge regarding CAKUT.