The genetic and phenotypic landscapes of Usher syndrome: from disease mechanisms to a new classification

Abstract

Usher syndrome (USH) is the most common cause of deaf-blindness in humans, with a prevalence of about 1/10,000 (~ 400,000 people worldwide). Cochlear implants are currently used to reduce the burden of hearing loss in severe-to-profoundly deaf patients, but many promising treatments including gene, cell, and drug therapies to restore the native function of the inner ear and retinal sensory cells are under investigation. The traditional clinical classification of Usher syndrome defines three major subtypes-USH1, 2 and 3-according to hearing loss severity and onset, the presence or absence of vestibular dysfunction, and age at onset of retinitis pigmentosa. Pathogenic variants of nine USH genes have been initially reported: MYO7A, USH1C, PCDH15, CDH23, and USH1G for USH1, USH2A, ADGRV1, and WHRN for USH2, and CLRN1 for USH3. Based on the co-occurrence of hearing and vision deficits, the list of USH genes has been extended to few other genes, but with limited supporting information. A consensus on combined criteria for Usher syndrome is crucial for the development of accurate diagnosis and to improve patient management. In recent years, a wealth of information has been obtained concerning the properties of the Usher proteins, related molecular networks, potential genotype-phenotype correlations, and the pathogenic mechanisms underlying the impairment or loss of hearing, balance and vision. The advent of precision medicine calls for a clear and more precise diagnosis of Usher syndrome, exploiting all the existing data to develop a combined clinical/genetic/network/functional classification for Usher syndrome.

Fig. 1

Anatomy of the mammalian ear, and the balance and hearing sensory organs in the inner ear. A The mammalian ear consists of 3 compartments: the outer, middle and inner ear. B The inner ear contains the vestibule (balance organ), and the cochlea (hearing organ). C, D The vestibular (C) and auditory (D) sensory epithelia are composed of the hair cells, associated innervation, and various types of supporting cells. In the vestibule, type I and type II vestibular hair cells (VHCs) sense head and body motion. In the cochlea, hearing results from the processing of sound waves by the hair cells, which are of two types: the inner hair cells (IHCs), which are the genuine auditory sensory cells responsible for signaling to the brain, and the outer hair cells (OHCs), which act as mechanical amplifiers, conferring on the mammalian cochlea its high sensitivity, and frequency discrimination capacity (low frequencies at the apex (20 Hz)-high frequencies at the base (20 kHz) in humans). The scanning electron micrographs illustrate the staircase pattern of the highly organized hair bundles, arranged in different shapes in different types of hair cell (C, D). In mammals, only the vestibular hair bundle retains the kinocilium (artificially colored in green in C), a true cilium that stands at the tallest edge of the hair bundle. Scale bar = 1 μm

Fig. 2

Anatomy of the eye, the retinal layers and the light-sensitive rod and cone photoreceptor cells. A The retina is a neural layer lining the back of the eye and containing retinal pigment epithelium cells (RPE) together with rod and cone photoreceptor cells. The photoreceptors are connected to various horizontal cells, bipolar cells, amacrine cells and ganglion cells present in the inner retina. Müller cells are glial cells that span all cell layers of the retina. B Schematic diagram illustrating the apical region of the photoreceptor cells. B1. Despite differences in their morphological architecture, the rod and cone photoreceptor cells have the same apical organization: a connecting cilium with an axoneme connects the light-sensitive outer segment consisting of tightly packed membrane disks with the inner segment containing all the organelles required for energy and protein synthesis. The connecting cilium and the periciliary ridge region form the periciliary membrane complex. B2. In some species (e.g., amphibians, non-human primates and primates), microvillus-like structures emerge from the top of the inner segment and form a collar around the base of the photoreceptor outer segment. These finger-like structures, visible on the scanning electron micrograph, are known as calyceal processes. Scale bar = 1 μm. ONL, outer nuclear layer; INL, inner nuclear layer, GCL, ganglion cell layer; OPL, outer plexiform layer; and INL, inner plexiform layer

Fig. 3

Illustration of the differences between the three clinical forms of Usher syndrome and the Usher proteins. Usher syndrome (USH) is classified into three types—USH1 (A), USH2 (B) and USH3 (C)—on the basis of age at onset and severity of hearing loss, the presence or absence of vestibular deficits, and age at onset of retinitis pigmentosa. Based on genetic evidence and the functions of Usher proteins and phenotypic manifestations in disease models, there is good evidence for nine undisputed Usher syndrome genes: Five USH1 genes A MYO7A (myosin VIIa, responsible for USH1B), USH1C (harmonin, responsible for USH1C), CDH23 (cadherin-23, responsible for USH1D), PCDH15 (protocadherin-15, responsible for USH1F); three USH2 genes B USH2A (usherin, responsible for USH2A), ADGRV1 (ADGRV1, adhesion G protein-coupled receptor V1, responsible for USH2C), WHRN (whirlin, responsible for USH2D), and one USH3 gene C CLRN1 (clarin-1, responsible for USH3A). For more details on any USH gene, please refer to the references for the corresponding OMIM number, and < http://hereditaryhearingloss.org > . D The Usher network analysis using Cytoscape software. Among USH1 interactions, almost all interactions (5/7) were identified at least once using detection methods indicative of direct physical contact between proteins (purple edges). The blue, and green lines indicate the existence of experimental evidence for the involvement of these proteins in one 'physical association' or more 'association' complexes, respectively. Among the other proteins referred to as USH molecules (yellow boxes), several has no connection to the classic USH proteins

Fig. 4

Usher proteins in the hair bundle and the principal related pathogenic phenotypic features in the inner ear. A Developing and mature stages of the cochlear hair bundle illustrating the dynamic changes in the various types of hair-bundle link: the transient apical lateral links, ankle links, and kinocilial links disappear after bundle maturation, by P12, in mice. The top connectors develop late in differentiation and persist in the mature hair bundles. The tip link is a unique fibrous link that connects the tip of a stereocilium to the side of the adjacent stereocilium. It is present in both developing and mature hair bundles. In mammals, the kinocilium, with its 9 + 2 axoneme pattern and typical motile cilium structure, is absent from mature hair bundles. The middle close-up views illustrate the function of USH proteins in the hair bundle. Cadherin 23 homodimers and protocadherin 15 homodimers interact to form the tip links, with protocadherin 15 forming the lower component that gates the MET channels. Myosin VIIa, harmonin, and sans cross-link the stereociliary membrane to the core of actin filaments. USH2 proteins are the key components of the ankle links, which eventually disappear and are absent from mature auditory hair bundles. It remains unclear whether USH3A acts as an accessory protein of the MET channel complex. B Usher protein defects cause a wide range of physiological, morphological, and molecular abnormalities; the main phenotypic findings for USH1 are listed. The USH3 SEM micrograph is adapted from (Dulon et al. 2018). Scale bar = 1 μm

Fig. 5

Usher proteins in photoreceptor cells and the principal related pathogenic phenotypic features in the retina. A The functional assemblies of Usher proteins operating in the hair bundle also play analogous roles in the photoreceptor cells, notably in the periciliary ridge membrane complex (PMC) and the calyceal processes (when present). Based on their presence close to the vesicle loading point at the base of the PMC region, the USH2 proteins (along with myosin VIIa and sans) were thought to play a role in vesicle transport between the inner and outer segments of the photoreceptors. Recent evidence suggests that USH1 proteins play a key role at the interface between the inner and outer segments, probably controlling the size of newly produced membrane disks and contributing to their correct organization in the apical zone of the PMC region. B As in the inner ear, USH protein defects cause diverse phenotypic abnormalities in the retina, including decreased electroretinogram responses (ERGs), probably due to misshapen photoreceptor disks (as shown in Xenopus morphants, adapted from Schietroma et al. (2017)). Other abnormalities—opsin transport delay and melanosome mispositioning—are observed in absence of Myo7a. The precise distribution of clarin-1 in the retina is currently unknown, and there are no mouse USH3A models for the retinal phenotype, limiting the accuracy of extrapolations of USH3 function in the eye. Scale bar = 1 μm