Inner ear manifestations in CHARGE: Abnormalities, treatments, animal models, and progress toward treatments in auditory and vestibular structures

CHARGE syndrome in a child with a CHD7 variant and a novel pathogenic SOX2 variant: A case report

CHARGE syndrome is a clinically heterogeneous condition that typically presents with a loss-of-function mutation in CHD7. SOX2 anophthalmia syndrome is a rare condition associated with hypogonadism and hearing loss. Herein, we describe the case of a Japanese boy presenting with a micropenis, bilateral cryptorchidism, cupped ear, right facial nerve palsy, and bilateral hearing loss, clinically meeting the diagnostic criteria for CHARGE syndrome, but with optic nerve hypoplasia, which is atypical for the syndrome. Therefore, a genetic analysis (next-generation sequencing) was performed. In addition to the missense variant p.[Arg1940Cys] in CHD7, a novel nonsense variant, p. [Tyr110*] in SOX2 was identified. Although most features, including genital abnormalities and hearing loss, were clinically compatible with CHARGE syndrome caused by a CHD7 variant, optic nerve hypoplasia may have been caused by a pathogenic SOX2 variant. Prior research has shown that SOX2 is related to the development of male genitalia and the inner ear. Therefore, the genital abnormalities and hearing loss in this patient may be attributed to both the CHD7 and SOX2 variants. Furthermore, the interactions between SOX2 and CHD7 may have affected symptoms independently or reciprocally.

Computed tomography multi-planar and 3D image assessment protocol for detailed analysis of inner ear malformations in patients undergoing cochlear implantation counseling

<b><br>Introduction:</b> Congenital inner ear malformations resulting from embryogenesis may be visualized in radiological scans. Many attempts have been made to describe and classify the defects of the inner ear based on anatomical and radiological findings.</br> <b><br>Aim:</b> The aim was to propose and discuss computed tomography multi-planar and 3D image assessment protocols for detailed analysis of inner ear malformations in patients undergoing cochlear implantation counseling.</br> <b><br>Material and methods:</b> A retrospective analysis of 22 malformed inner ears. CT scans were analyzed using the Multi-Planar Reconstruction (MPR) option and 3D reconstruction.</br> <b><br>Results:</b> The protocol of image interpretation was developed to allow reproducibility for evaluating each set of images. The following malformations were identified: common cavity, cochlear hypoplasia type II, III, and IV, incomplete partition type II and III, and various combinations of vestibule labyrinth malformations. All anomalies have been presented and highlighted in figures with appropriate descriptions for easier identification. Figures of normal inner ears were also included for comparison. 3D reconstructions for each malformation were presented, adding clinical value to the detailed analysis.</br> <b><br>Conclusions:</b> Properly analyzing CT scans in cochlear implantation counseling is a necessary and beneficial tool for appropriate candidate selection and preparation for surgery. As proposed in this study, the unified scans evaluation scheme simplifies the identification of malformations and reduces the risk of omitting particular anomalies. Multi-planar assessment of scans provides most of the necessary details. The 3D reconstruction technique is valuable in addition to diagnostics influencing the decision-making process. It can minimize the risk of misdiagnosis. Disclosure of the inner ear defect and its precise imaging provides detailed anatomical knowledge of each ear, enabling the selection of the appropriate cochlear implant electrode and the optimal surgical technique.</br>.

ATP-Dependent Chromatin Remodellers in Inner Ear Development

During transcription, DNA replication and repair, chromatin structure is constantly modified to reveal specific genetic regions and allow access to DNA-interacting enzymes. ATP-dependent chromatin remodelling complexes use the energy of ATP hydrolysis to modify chromatin architecture by repositioning and rearranging nucleosomes. These complexes are defined by a conserved SNF2-like, catalytic ATPase subunit and are divided into four families: CHD, SWI/SNF, ISWI and INO80. ATP-dependent chromatin remodellers are crucial in regulating development and stem cell biology in numerous organs, including the inner ear. In addition, mutations in genes coding for proteins that are part of chromatin remodellers have been implicated in numerous cases of neurosensory deafness. In this review, we describe the composition, structure and functional activity of these complexes and discuss how they contribute to hearing and neurosensory deafness.

Loss of the chromatin remodeler CHD7 impacts glial cells and myelination in the mouse cochlear spiral ganglion

CHARGE syndrome is a multiple anomaly developmental disorder characterized by a variety of sensory deficits, including sensorineural hearing loss of unknown etiology. Most cases of CHARGE are caused by heterozygous pathogenic variants in CHD7, the gene encoding Chromodomain DNA-binding Protein 7 (CHD7), a chromatin remodeler important for the development of neurons and glial cells. Previous studies in the Chd7^Gt/+ mouse model of CHARGE syndrome showed substantial neuron loss in the early stages of the developing inner ear that are compensated for by mid-gestation. In this study, we sought to determine if early developmental delays caused by Chd7 haploinsufficiency affect neurons, glial cells, and inner hair cell innervation in the mature cochlea. Analysis of auditory brainstem response recordings in Chd7^Gt/+ adult animals showed elevated thresholds at 4 kHz and 16 kHz, but no differences in ABR Wave I peak latency or amplitude compared to wild type controls. Proportions of neurons in the Chd7^Gt/+ adult spiral ganglion and densities of nerve projections from the spiral ganglion to the organ of Corti were not significantly different from wild type controls. Inner hair cell synapse formation also appeared unaffected in mature Chd7^Gt/+ cochleae. However, histological analysis of adult Chd7^Gt/+ cochleae revealed diminished satellite glial cells and hypermyelinated Type I spiral ganglion axons. We characterized the expression of CHD7 in developing inner ear glia and found CHD7 to be expressed during a tight window of inner ear development at the Schwann cell precursor stage at E9.5. While cochlear neurons appear to differentiate normally in the setting of Chd7 haploinsufficiency, our results suggest an important role for CHD7 in glial cells in the inner ear. This study highlights the dynamic nature of CHD7 activity during inner ear development in mice and contributes to understanding CHARGE syndrome pathology.

CHD7 regulates otic lineage specification and hair cell differentiation in human inner ear organoids

Mutations in CHD7 cause CHARGE syndrome, affecting multiple organs including the inner ear in humans. We investigate how CHD7 mutations affect inner ear development using human pluripotent stem cell-derived organoids as a model system. We find that loss of CHD7 or its chromatin remodeling activity leads to complete absence of hair cells and supporting cells, which can be explained by dysregulation of key otic development-associated genes in mutant otic progenitors. Further analysis of the mutant otic progenitors suggests that CHD7 can regulate otic genes through a chromatin remodeling-independent mechanism. Results from transcriptome profiling of hair cells reveal disruption of deafness gene expression as a potential underlying mechanism of CHARGE-associated sensorineural hearing loss. Notably, co-differentiating CHD7 knockout and wild-type cells in chimeric organoids partially rescues mutant phenotypes by restoring otherwise severely dysregulated otic genes. Taken together, our results suggest that CHD7 plays a critical role in regulating human otic lineage specification and hair cell differentiation.

Evaluation and Nonsurgical Treatment of Neonatal Ear Anomalies: A Case Report

BACKGROUND

Inspection and evaluation of the neonate's ears are important parts of the neonatal examination. Neonates display a wide variety of ear size and configuration. In many cases, ear molding techniques obviate the need for future surgical correction. This article provides a review of the fetal ear development and describes common physical examination findings of the newborn's external ear. A case report reviews a successful nonsurgical treatment of a minor ear deformity.

CLINICAL FINDINGS

Newborn infant with near absent to very thin bilateral helical rims and otherwise normal bilateral ear shape and structures.

PRIMARY DIAGNOSIS

Bilateral Stahl's ear deformity.

INTERVENTIONS

The EarBuddies product was applied to bilateral ears in an outpatient pediatric plastic surgery clinic. This product remained in place for 8 weeks.

OUTCOMES

The family was pleased with the overall progress and shape of their child's ears. At 18 months of age, the family has no desire to pursue surgical correction of their child's ears.

PRACTICE RECOMMENDATIONS

Assessment of the newborn's external ear is part of a routine admission examination. Careful attention to abnormal or unusual findings allows for prompt evaluation and nonsurgical intervention.

Imaging of inner ear malformations: a primer for radiologists

In the multidisciplinary management of patients with inner ear malformations (IEMs), the correct diagnosis makes the differences in terms of clinical and surgical treatment. The complex anatomical landscape of the inner ear, comprising several small structures, makes imaging of this region particularly challenging for general radiologists. Imaging techniques are important for identifying the presence and defining the type of IEM and the cochlear nerve condition. High-resolution magnetic resonance imaging (MRI) sequences and high-resolution computed tomography (HRCT) are the mainstay imaging techniques in this area. Dedicated MRI and HRCT protocols play an important role in the diagnosis and treatment of patients with inner ear disease. The most suitable technique should be selected depending on the clinical setting. However, in cases of congenital malformation of the inner ear, these techniques should be considered complementary. Since prompt intervention has a positive impact on the treatment outcomes, early diagnosis of IEMs is very important in the management of deaf patients. This article reviews the key concepts of IEMs for clinical radiologists by focusing on recent literature updates, discusses the principal imaging findings and clinical implications for every IEM subgroup, thus providing a practical diagnostic approach.

Chromatin remodeler CHD7 is critical for cochlear morphogenesis and neurosensory patterning

Epigenetic regulation of gene transcription by chromatin remodeling proteins has recently emerged as an important contributing factor in inner ear development. Pathogenic variants in CHD7, the gene encoding Chromodomain Helicase DNA binding protein 7, cause CHARGE syndrome, which presents with malformations in the developing ear. Chd7 is broadly expressed in the developing mouse otocyst and mature auditory epithelium, yet the pathogenic effects of Chd7 loss in the cochlea are not well understood. Here we characterized cochlear epithelial phenotypes in mice with deletion of Chd7 throughout the otocyst (using Foxg1^Cre/+ and Pax2Cre), in the otic mesenchyme (using TCre), in hair cells (using Atoh1Cre), in developing neuroblasts (using NgnCre), or in spiral ganglion neurons (using Shh^Cre/+). Pan-otic deletion of Chd7 resulted in shortened cochleae with aberrant projections and axonal looping, disorganized, supernumerary hair cells at the apical turn and a narrowed epithelium with missing hair cells in the middle region. Deletion of Chd7 in the otic mesenchyme had no effect on overall cochlear morphology. Loss of Chd7 in hair cells did not disrupt their formation or organization of the auditory epithelium. Similarly, absence of Chd7 in spiral ganglion neurons had no effect on axonal projections. In contrast, deletion of Chd7 in developing neuroblasts led to smaller spiral ganglia and disorganized cochlear neurites. Together, these observations reveal dosage-, tissue-, and time-sensitive cell autonomous roles for Chd7 in cochlear elongation and cochlear neuron organization, with minimal functions for Chd7 in hair cells. These studies provide novel information about roles for Chd7 in development of auditory neurons.

Phenotypic Spectrum of Idiopathic Hypogonadotropic Hypogonadism Patients With CHD7 Variants From a Large Chinese Cohort

PURPOSE

Idiopathic hypogonadotropic hypogonadism (IHH) and CHARGE (C, coloboma; H, heart abnormalities; A, choanal atresia, R, retardation of growth and/or development; G, gonadal defects; E, ear deformities and deafness) syndrome are 2 distinct developmental disorders sharing features of hypogonadism and/or impaired olfaction. CHD7 variants contribute to >60% CHARGE syndrome and ~10% IHH patients. A variety of extended CHARGE-like features are frequently reported in CHARGE patients harboring CHD7 variants. In this study, we aimed to systematically analyze the diagnostic CHARGE features and the extended CHARGE-like features in patients with IHH with CHD7 variants.

METHODS

Rare sequencing variants (RSVs) in CHD7 were identified through exome sequencing in 177 IHH probands. Detailed phenotyping was performed in the IHH patients harboring CHD7 variants and their available family members.

RESULTS

CHD7 RSVs were identified in 10.2% (18/177) of the IHH probands. Two diagnostic CHARGE features, hearing loss and ear deformities, were significantly enriched in patients with CHD7 variants. Furthermore, CHD7 variants were significantly associated with a panel of extended CHARGE-like phenotypes, including mild ocular defects, dyspepsia/gastroesophageal reflux disease and skeletal defects. We also developed a predictive model for prioritizing CHD7 genetic testing in IHH patients.

CONCLUSION

CHD7 variants rarely cause isolated IHH. Surveillance of symptoms in CHARGE syndrome-affected organs will facilitate the proper treatment for these patients. Certain clinical features can be useful for prioritizing CHD7 genetic screening.

The development of an educational checklist for individuals with CHARGE syndrome

CHARGE syndrome is a rare genetic disorder which can impact every sensory system and is often associated with significant medical, communicative, developmental, and behavioral difficulties. Due to the rarity and complexity of CHARGE syndrome, educators often lack the expertise required to effectively understand and accommodate the needs of these students. Therefore, an educational checklist (i.e. "Checklist") was developed to provide a comprehensive tool that educators and related professionals can utilize to aid in the education of individuals with CHARGE syndrome. The Checklist was developed through collaboration with an international panel of experts; CHARGE Syndrome Research Lab at Central Michigan University (CMU); and a select group consisting of parents, professionals, and state deafblind project employees. The Checklist outlines major CHARGE characteristics, resulting educational needs, team members, consulting professionals, and suggested methods of accommodation. The Checklist may be utilized to develop and inform services for individuals with CHARGE syndrome in the schools.

Genes Involved in the Development and Physiology of Both the Peripheral and Central Auditory Systems

The genetic approach, based on the study of inherited forms of deafness, has proven to be particularly effective for deciphering the molecular mechanisms underlying the development of the peripheral auditory system, the cochlea and its afferent auditory neurons, and how this system extracts the physical parameters of sound. Although this genetic dissection has provided little information about the central auditory system, scattered data suggest that some genes may have a critical role in both the peripheral and central auditory systems. Here, we review the genes controlling the development and function of the peripheral and central auditory systems, focusing on those with demonstrated intrinsic roles in both systems and highlighting the current underappreciation of these genes. Their encoded products are diverse, from transcription factors to ion channels, as are their roles in the central auditory system, mostly evaluated in brainstem nuclei. We examine the ontogenetic and evolutionary mechanisms that may underlie their expression at different sites.

Approaches for the study of epigenetic modifications in the inner ear and related tissues

DNA methylation and histone modifications such as methylation, acetylation, and phosphorylation, are two types of epigenetic modifications that alter gene expression. These additions to DNA regulatory elements or to the tails of histones can be inherited or can also occur de novo. Since epigenetic modifications can have significant effects on various processes at both the cellular and organismal level, there has been a rapid increase in research on this topic throughout all fields of biology in recent years. However, epigenetic research is relativity new for the inner ear field, likely due to the limited number of cells present and their quiescent nature. Here, we provide an overview of methods used to detect DNA methylation and histone modifications with a focus on those that have been validated for use with limited cell numbers and a discussion of the strengths and limitations for each. We also provide examples for how these methods have been used to investigate the epigenetic landscape in the inner ear and related tissues.

Neural crest contributions to the ear: Implications for congenital hearing disorders

Congenital hearing disorders affect millions of children worldwide and can significantly impact acquisition of speech and language. Efforts to identify the developmental genetic etiologies of conductive and sensorineural hearing losses have revealed critical roles for cranial neural crest cells (NCCs) in ear development. Cranial NCCs contribute to all portions of the ear, and defects in neural crest development can lead to neurocristopathies associated with profound hearing loss. The molecular mechanisms governing the development of neural crest derivatives within the ear are partially understood, but many questions remain. In this review, we describe recent advancements in determining neural crest contributions to the ear, how they inform our understanding of neurocristopathies, and highlight new avenues for further research using bioinformatic approaches.

Single Cell Transcriptomics Reveal Abnormalities in Neurosensory Patterning of the Chd7 Mutant Mouse Ear

The chromatin remodeling protein CHD7 is critical for proper formation of the mammalian inner ear. Humans with heterozygous pathogenic variants in CHD7 exhibit CHARGE syndrome, characterized by hearing loss and inner ear dysplasia, including abnormalities of the semicircular canals and Mondini malformations. Chd7^Gt/+ heterozygous null mutant mice also exhibit dysplastic semicircular canals and hearing loss. Prior studies have demonstrated that reduced Chd7 dosage in the ear disrupts expression of genes involved in morphogenesis and neurogenesis, yet the relationships between these changes in gene expression and otic patterning are not well understood. Here, we sought to define roles for CHD7 in global regulation of gene expression and patterning in the developing mouse ear. Using single-cell multiplex qRT-PCR, we analyzed expression of 192 genes in FAC sorted cells from Pax2Cre;mT/mGFP wild type and Chd7^Gt/+ mutant microdissected mouse otocysts. We found that Chd7 haploinsufficient otocysts exhibit a relative enrichment of cells adopting a neuroblast (vs. otic) transcriptional identity compared with wild type. Additionally, we uncovered disruptions in pro-sensory and pro-neurogenic gene expression with Chd7 loss, including genes encoding proteins that function in Notch signaling. Our results suggest that Chd7 is required for early cell fate decisions in the developing ear that involve highly specific aspects of otic patterning and differentiation.