Cross-species analysis and comparison of the inner ear between chickens and mice

The inner ear of mammals includes the cochlea and vestibule, which house specialized hair cells that are responsible for hearing and balance, respectively. While cochlear hair cells fail to regenerate following damage, those of the utricle, which is part of the vestibular apparatus, show partial regeneration. In birds, the macula lagena, a unique ear structure in this clade, has the ability to regenerate hair cells similarly to the utricle. Many studies have sought to explain regeneration in terms of evolution and species differences. However, it remains unclear what the cellular and molecular basis is behind the differences in inner ear structures and between avians and mammals. In the present study, we first investigated the anatomical structures of the inner ear of both chickens and rodents. We then performed RNA sequencing (RNA-Seq) and made cross-species analyses of the expression of homologous genes obtained from the inner ear tissue from both chickens and mice. Finally, we focused on the lagena, the basilar papilla, and the utricle in chickens and identified differentially expressed genes between tissues and determined the expression patterns of genes involved in inner ear structure formation by single-cell RNA sequencing and bulk RNA-Seq. We concluded that the cellular and molecular composition of the lagena is more similar to that of the utricle than the cochlea. Taken together, our study provides a valuable resource for the study of inner ear evolution and development.

Exploring the Expression and Function of cTyro3, a Candidate Zika Virus Receptor, in the Embryonic Chicken Brain and Inner Ear

The transmembrane protein Axl was proposed as an entry receptor for Zika virus (ZIKV) infection in vitro, but conflicting results from in vivo studies have made it difficult to establish Axl as a physiologically relevant ZIKV receptor. Both the functional redundancy of receptors and the experimental model used can lead to variable results. Therefore, it can be informative to explore alternative animal models to analyze ZIKV receptor candidates as an aid in discovering antivirals. This study used chicken embryos to examine the role of chicken Tyro3 (cTyro3), the equivalent of human Axl. Results show that endogenous cTyro3 mRNA expression overlaps with previously described hot spots of ZIKV infectivity in the brain and inner ear. We asked if ectopic expression or knockdown of cTyro3 influenced ZIKV infection in embryos. Tol2 vectors or replication-competent avian retroviruses were used in ovo to introduce full-length or truncated (presumed dominant-negative) cTyro3, respectively, into the neural tube on embryonic day two (E2). ZIKV was delivered to the brain 24 h later. cTyro3 manipulations did not alter ZIKV infection or cell death in the E5/E6 brain. Moreover, delivery of truncated cTyro3 variants to the E3 otocyst had no effect on inner ear formation on E6 or E10.

Comparative study of ionic currents and exocytosis in hair cells of the basilar and amphibian papilla in bullfrogs

Hearing organs in the peripheral of different vertebrate species are extremely diverse in shape and function. In particular, while the basilar papilla (BP) is elongated and covers the sounds of both low and high frequencies in turtles and birds, it is round and responds to high frequencies only in frogs, leaving the low frequencies to the amphibian papilla (AP). In this study, we performed patch-clamp recordings in hair cells of both hearing organs in bullfrogs and conducted a comparative study of their ionic currents and exocytosis. Compared to hair cells in AP with a large tetraethylammonium (TEA)-sensitive slow-activating K⁺ current (I _K), those in BP exhibited a small 4-aminopyridine (4-AP)-sensitive fast-inactivating K⁺ current (I _A). Furthermore, hair cells in BP exhibited a significantly smaller Ca²⁺ current with a more positive half-activation voltage (V_half) and a slower slope of voltage dependency (k). In response to step depolarization, exocytosis (ΔC_m) in BP hair cells was also significantly smaller, but the Ca²⁺ efficiency, assessed with the ratio between ΔC_m and Ca²⁺ charge (Q_Ca), was comparable to that of AP hair cells. Finally, we applied a paired-step depolarization and varied the interval in between, and we found that the replenishment of synaptic vesicles was significantly slower in BP hair cells. Together, our findings suggest that hair cells tuned to high frequencies in bullfrogs release less synaptic vesicles and recycle synaptic vesicles more slowly, allowing them to cope well with the large DC component found in their receptor potentials in vivo.

Position Specific Alternative Splicing and Gene Expression Profiles Along the Tonotopic Axis of Chick Cochlea

Alternative splicing (AS) refers to the production of multiple mRNA isoforms from a single gene due to alternative selection of exons or splice sites during pre-mRNA splicing. It is a primary mechanism of gene regulation in higher eukaryotes and significantly expands the functional complexity of eukaryotic organisms, contributing to animal development and disease. Recent studies have shown that AS also influences functional diversity by affecting the transcriptomic and proteomic profiles in a position-dependent manner in a single organ. The peripheral hearing organ, the cochlea, is organized to detect sounds at different frequencies depending on its location along the longitudinal axis. This unique functional configuration, the tonotopy, is known to be facilitated by differential gene expression along the cochlear duct. We profiled transcriptome-wide gene expression and AS changes that occur within the different positions of chick cochlea. These analyses revealed distinct gene expression profiles and AS, including a splicing program that is unique to tonotopy. Changes in the expression of splicing factors PTBP3, ESRP1, and ESRP2 were demonstrated to contribute to position-specific AS. RNA-binding motif enrichment analysis near alternatively spliced exons provided further insight into the combinatorial regulation of AS at different positions by different RNA-binding proteins. These data, along with gene ontology (GO) analysis, represent a comprehensive analysis of the dynamic regulation of AS at different positions in chick cochlea.

Initiation of Supporting Cell Activation for Hair Cell Regeneration in the Avian Auditory Epithelium: An Explant Culture Model

Sensorineural hearing loss is a common disability often caused by the loss of sensory hair cells in the cochlea. Hair cell (HCs) regeneration has long been the main target for the development of novel therapeutics for sensorineural hearing loss. In the mammalian cochlea, hair cell regeneration is limited, but the auditory epithelia of non-mammalian organisms retain the capacity for hair cell regeneration. In the avian basilar papilla (BP), supporting cells (SCs), which give rise to regenerated hair cells, are usually quiescent. Hair cell loss induces both direct transdifferentiation and mitotic division of supporting cells. Here, we established an explant culture model for hair cell regeneration in chick basilar papillae and validated it for investigating the initial phase of hair cell regeneration. The histological assessment demonstrated hair cell regeneration via direct transdifferentiation of supporting cells. Labeling with 5-ethynyl-2′-deoxyuridine (EdU) revealed the occurrence of mitotic division in the supporting cells at specific locations in the basilar papillae, while no EdU labeling was observed in newly generated hair cells. RNA sequencing indicated alterations in known signaling pathways associated with hair cell regeneration, consistent with previous findings. Also, unbiased analyses of RNA sequencing data revealed novel genes and signaling pathways that may be related to the induction of supporting cell activation in the chick basilar papillae. These results indicate the advantages of our explant culture model of the chick basilar papillae for exploring the molecular mechanisms of hair cell regeneration.

Infrasonic hearing in birds: a review of audiometry and hypothesized structure-function relationships

The perception of airborne infrasound (sounds below 20 Hz, inaudible to humans except at very high levels) has been documented in a handful of mammals and birds. While animals that produce vocalizations with infrasonic components (e.g. elephants) present conspicuous examples of potential use of infrasound in the context of communication, the extent to which airborne infrasound perception exists among terrestrial animals is unclear. Given that most infrasound in the environment arises from geophysical sources, many of which could be ecologically relevant, communication might not be the only use of infrasound by animals. Therefore, infrasound perception could be more common than currently realized. At least three bird species, each of which do not communicate using infrasound, are capable of detecting infrasound, but the associated auditory mechanisms are not well understood. Here we combine an evaluation of hearing measurements with anatomical observations to propose and evaluate hypotheses supporting avian infrasound detection. Environmental infrasound is mixed with non-acoustic pressure fluctuations that also occur at infrasonic frequencies. The ear can detect such non-acoustic pressure perturbations and therefore, distinguishing responses to infrasound from responses to non-acoustic perturbations presents a great challenge. Our review shows that infrasound could stimulate the ear through the middle ear (tympanic) route and by extratympanic routes bypassing the middle ear. While vibration velocities of the middle ear decline towards infrasonic frequencies, whole-body vibrations - which are normally much lower amplitude than that those of the middle ear in the 'audible' range (i.e. >20 Hz) - do not exhibit a similar decline and therefore may reach vibration magnitudes comparable to the middle ear at infrasonic frequencies. Low stiffness in the middle and inner ear is expected to aid infrasound transmission. In the middle ear, this could be achieved by large air cavities in the skull connected to the middle ear and low stiffness of middle ear structures; in the inner ear, the stiffness of round windows and cochlear partitions are key factors. Within the inner ear, the sizes of the helicotrema and cochlear aqueduct are expected to play important roles in shunting low-frequency vibrations away from low-frequency hair-cell sensors in the cochlea. The basilar papilla, the auditory organ in birds, responds to infrasound in some species, and in pigeons, infrasonic-sensitive neurons were traced back to the apical, abneural end of the basilar papilla. Vestibular organs and the paratympanic organ, a hair cell organ outside of the inner ear, are additional untested candidates for infrasound detection in birds. In summary, this review brings together evidence to create a hypothetical framework for infrasonic hearing mechanisms in birds and other animals.

Diverse Mechanisms of Sound Frequency Discrimination in the Vertebrate Cochlea

Discrimination of different sound frequencies is pivotal to recognizing and localizing friend and foe. Here, I review the various hair cell-tuning mechanisms used among vertebrates. Electrical resonance, filtering of the receptor potential by voltage-dependent ion channels, is ubiquitous in all non-mammals, but has an upper limit of ~1 kHz. The frequency range is extended by mechanical resonance of the hair bundles in frogs and lizards, but may need active hair-bundle motion to achieve sharp tuning up to 5 kHz. Tuning in mammals uses somatic motility of outer hair cells, underpinned by the membrane protein prestin, to expand the frequency range. The bird cochlea may also use prestin at high frequencies, but hair cells <1 kHz show electrical resonance.

Reciprocal Matched Filtering in the Inner Ear of the African Clawed Frog (Xenopus laevis)

Anurans (frogs and toads) are the most vocal amphibians. In most species, only males produce advertisement calls for defending territories and attracting mates. Female vocalizations are the exceptions among frogs, however in the African clawed frog (Xenopus laevis) both males and females produce distinct vocalizations. The matched filter hypothesis predicts a correspondence between peripheral auditory tuning of receivers and properties of species-specific acoustic signals, but few studies have assessed this relationship between the sexes. Measuring hearing sensitivity with a binaural recording of distortion product otoacoustic emissions, we have found that the ears of the males of this species are tuned to the dominant frequency of the female's calls, whereas the ears of the females are tuned close to the dominant frequency of the male's calls. Our findings provide support for the matched filter hypothesis extended to include male-female calling. This unique example of reciprocal matched filtering ensures that males and females communicate effectively in high levels of background noise, each sex being most sensitive to the frequencies of the other sex's calls.

The role of Wnt/β-catenin signaling in proliferation and regeneration of the developing basilar papilla and lateral line

Canonical Wnt/β-catenin signaling has been implicated in multiple developmental events including the regulation of proliferation, cell fate, and differentiation. In the inner ear, Wnt/β-catenin signaling is required from the earliest stages of otic placode specification through the formation of the mature cochlea. Within the avian inner ear, the basilar papilla (BP), many Wnt pathway components are expressed throughout development. Here, using reporter constructs for Wnt/β-catenin signaling, we show that this pathway is active throughout the BP (E6-E14) in both hair cells (HCs) and supporting cells. To characterize the role of Wnt/β-catenin activity in developing HCs, we performed gain- and loss-of-function experiments in vitro and in vivo in the chick BP and zebrafish lateral line systems, respectively. Pharmacological inhibition of Wnt signaling in the BP and lateral line neuromasts during the periods of proliferation and HC differentiation resulted in reduced proliferation and decreased HC formation. Conversely, pharmacological activation of this pathway significantly increased the number of HCs in the lateral line and BP. Results demonstrated that this increase was the result of up-regulated cell proliferation within the Sox2-positive cells of the prosensory domains. Furthermore, Wnt/β-catenin activation resulted in enhanced HC regeneration in the zebrafish lateral line following aminoglycoside-induced HC loss. Combined, our data suggest that Wnt/β-catenin signaling specifies the number of cells within the prosensory domain and subsequently the number of HCs. This ability to induce proliferation suggests that the modulation of Wnt/β-catenin signaling could play an important role in therapeutic HC regeneration.

Spatial tuning curves along the chick basilar papilla in normal and sound-exposed ears

Intense sound exposure destroys chick short hair cells and damages the tectorial membrane. Within a few days postexposure, signs of repair appear resulting in nearly complete structural recovery of the inner ear. Tectorial membrane repair, however, is incomplete, leaving a permanent defect on the sensory surface. The consequences of this defect on cochlear function, and particularly frequency analysis, are unclear. The present study organizes the sound-induced discharge activity of cochlear nerve units to describe the distribution of neural activity along the tonotopic axis of the basilar papilla. The distribution of this activity is compared in 12-day postexposed and age-matched control groups. Spontaneous activity, tuning curves, and rate-intensity functions were measured in each unit. Discharge activity at 60 frequency and intensity combinations was identified in the tuning curves of hundreds of units. Activity at each of these criterion frequency/intensity combinations was plotted against the unit's characteristic frequency to construct spatial tuning curves (STCs). The STCs depict tone-driven cochlear nerve activity along the length of the papilla. Tuning sharpness, low- and high- frequency slopes, and the maximum response were quantified for each STC. The sharpness of tuning increased with increasing criterion frequency. However, within a frequency, increasing sound intensity yielded more broadly tuned STCs. Also, the high-frequency slope was consistently steeper than the low-frequency slope. The STCs of exposed ears exhibited slightly less frequency selectivity than control ears across all frequencies and larger maximum responses for STCs with criterion frequencies spanning the tectorial membrane defect. When rate-intensity types were segregated, differences were observed in the STCs between saturating and sloping-up units. We propose that STC shape may be determined by global mechanical events, as well as localized tuning and nonlinear processes associated with individual hair cells. The results indicated that 12 days after intense sound exposure, global and local contributions to spatially distributed neural activity are restored.

Identification of genes expressed in the Xenopus inner ear

Recent studies indicate that hearing loss in humans has strong hereditary components associated with expression of specific genes in the auditory apparatus of the inner ear. However, the inner ear poses challenges for molecular research because the amount of tissue that can be isolated is limited, and extraction procedures yield small quantities of RNA and protein. To begin to identity genes essential for auditory function, we synthesized a cDNA library using an RT-PCR protocol and total RNA isolated from eight Xenopus laevis inner ears. Sequence analysis of randomly selected clones demonstrated expression of both identified (calmodulin, SNARE protein, syndecan-2) and unidentified genes, and confirmed synthesis of full length transcripts. Confocal and scanning electron microscopy (SEM) were used to examine the structure of inner ear organs that serve as auditory receptors in amphibians: the sacculus, the amphibian papilla and the basilar papilla. SEM images illustrate the heterogeneity of bundle morphology and demonstrate the continuous appearance of stereociliary bundles in the X. laevis amphibian papilla during larval development and adult life. Investigations of gene expression in Xenopus auditory organs using clones recovered from inner ear cDNA libraries should provide insight regarding the molecular basis of hearing.

Cellular studies of auditory hair cell regeneration in birds

A decade ago it was discovered that mature birds are able to regenerate hair cells, the receptors for auditory perception. This surprising finding generated hope in the field of auditory neuroscience that new hair cells someday may be coaxed to form in another class of warm-blooded vertebrates, mammals. We have made considerable progress toward understanding some cellular and molecular events that lead to hair cell regeneration in birds. This review discusses our current understanding of avian hair cell regeneration, with some comparisons to other vertebrate classes and other regenerative systems.

Coding of sound pressure level in the barn owl's auditory nerve

Rate-intensity functions, i.e., the relation between discharge rate and sound pressure level, were recorded from single auditory nerve fibers in the barn owl. Differences in sound pressure level between the owl's two ears are known to be an important cue in sound localization. One objective was therefore to quantify the discharge rates of auditory nerve fibers, as a basis for higher-order processing of sound pressure level. The second aim was to investigate the rate-intensity functions for cues to the underlying cochlear mechanisms, using a model developed in mammals. Rate-intensity functions at the most sensitive frequency mostly showed a well-defined breakpoint between an initial steep segment and a progressively flattening segment. This shape has, in mammals, been convincingly traced to a compressive nonlinearity in the cochlear mechanics, which in turn is a reflection of the cochlear amplifier enhancing low-level stimuli. The similarity of the rate-intensity functions of the barn owl is thus further evidence for a similar mechanism in birds. An interesting difference from mammalian data was that this compressive nonlinearity was not shared among fibers of similar characteristic frequency, suggesting a different mechanism with a more locally differentiated operation than in mammals. In all fibers, the steepest change in discharge rate with rising sound pressure level occurred within 10-20 dB of their respective thresholds. Because the range of neural thresholds at any one characteristic frequency is small in the owl, auditory nerve fibers were collectively most sensitive for changes in sound pressure level within approximately 30 dB of the best thresholds. Fibers most sensitive to high frequencies (>6-7 kHz) showed a smaller increase of rate above spontaneous discharge rate than did lower-frequency fibers.

Hair cells and supporting cells share a common progenitor in the avian inner ear

Sensory organs of the vertebrate inner ear contain two major cell types: hair cells (HCs) and supporting cells (SCs). To study the lineage relationships between these two populations, replication-defective retroviral vectors encoding marker genes were delivered to the otic vesicle of the chicken embryo. The resulting labeled clones were analyzed in the hearing organ of the chicken, called the basilar papilla (BP), after cellular differentiation. BPs were allowed to develop for 2 weeks after delivery of the retrovirus, were removed, and were processed histochemically as whole mounts to identify clones of cells. Clusters of labeled cells were evident in the sensory epithelium, the nonsensory epithelium, and in adjacent tissues. Labeled cell types included HCs, two morphologically distinct types of SCs, homogene cells, border cells, hyaline cells, ganglion cells, and connective tissue cells. Each clone was sectioned and cell-type identification was performed on sensory clones expressing retrovirally transduced beta-galactosidase. Cell composition was determined for 41 sensory clones, most of which contained both HCs and SCs. Clones containing one HC and one SC were observed, suggesting that a common progenitor exists that can remain bipotential up to its final mitotic division. The possibility that these two cell types may also arise from a mitotic precursor during HC regeneration in the mature basilar papilla is consistent with their developmental history.

Development of the Xenopus laevis VIIIth cranial nerve: increase in number and area of axons of the saccular and papillar branches

Development of three branches of the VIIIth cranial nerve was examined in the anuran, Xenopus laevis. Sectioned tissue from the saccular, amphibian papillar, and basilar papillar branches of stage 52 larvae, 1 day postmetamorphosis juveniles, and 2-year adult animals was analyzed under the light microscope with a digital image analysis system. Numbers and cross-sectional areas of myelinated axons were measured in five to six nerve sections at each developmental age for each of the three branches. In all three branches, results show a significant increase in axon numbers between larval stage 52 and juvenile ages and negligible increase in axon number between the juvenile and adult ages. There were differences in the average number of axons between the saccular (704.4 +/- 39.5; n = 5), amphibian papillar (508.4 +/- 35.0; n = 5), and basilar papillar (316.0 +/- 7.0; n = 5) branches of adult animals. Myelinated axons increase at an estimated rate of 11.7, 15.1, and 6.2 axons per day for the saccular, amphibian papillar, and basilar papillar branches, respectively. Axonal cross-sectional areas increased throughout the developmental ages of this study, with the greatest increase taking place between juvenile and adult ages. In adult animals, 98% of axons in all three branches have diameters between 2-10 microns. Ratios of axons to hair cells in adult animals were estimated at 0.3, 1.1, and 5.3 for the sacculus, amphibian papilla, and basilar papilla, respectively. The higher axon to hair cell ratio correlates with the increasing acoustical frequency sensitivity of the end organ.

Differential expression of bone morphogenetic proteins in the developing vestibular and auditory sensory organs

The genes responsible for the formation of various sensory organs in the inner ear are not known. There are eight sensory organs in the chick inner ear, and our previous study showed that all presumptive sensory organs initially express bone morphogenetic protein 4 (BMP4), a member of the transforming growth factor (TGF)-beta gene family. To address the potential role of BMPs in the patterning of different sensory organ structures, we investigated the expression of BMP4, BMP5, and BMP7 during sensory organ differentiation in the chick inner ear. The gene expression pattern of BMP5, although similar to that of BMP4, was transient and disappeared by embryonic day 3.5 (E3.5). In contrast, BMP7 gene expression was quite extensive, starting in the otic placode. By E5, gene expression patterns of BMP4 and BMP7 differed among vestibular and auditory sensory organs. In the vestibular sensory organs, BMP7 gene expression segregated from the main sensory tissue areas at the onset of differentiation, whereas BMP4 expression concentrated in supporting cells. In the cochlea, however, BMP7 gene expression became restricted to sensory tissue over time and eventually concentrated in supporting cells, whereas BMP4 gene expression was localized to hair cells. The different BMP expression patterns in developing auditory and vestibular sensory organs may help to shape each respective sensory structure. Furthermore, the expression of BMP4 in the cochlea also revealed an interesting pattern of sensory cell differentiation: the distal portion of the cochlea differentiates first, and the tall hair cells develop before the short hair cells.

Hair cell differentiation in chick cochlear epithelium after aminoglycoside toxicity: in vivo and in vitro observations

Inner ear epithelia of mature birds regenerate hair cells after ototoxic or acoustic insult. The lack of markers that selectively label cells in regenerating epithelia and of culture systems composed primarily of progenitor cells has hampered the identification of cellular and molecular interactions that regulate hair cell regeneration. In control basilar papillae, we identified two markers that selectively label hair cells (calmodulin and TUJ1 beta tubulin antibodies) and one marker unique for support cells (cytokeratin antibodies). Examination of regenerating epithelia demonstrated that calmodulin and beta tubulin are also expressed in early differentiating hair cells, and cytokeratins are retained in proliferative support cells. Enzymatic and mechanical methods were used to isolate sensory epithelia from mature chick basilar papillae, and epithelia were cultured in different conditions. In control cultures, hair cells are morphologically stable for up to 6 d, because calmodulin immunoreactivity and phalloidin labeling of filamentous actin are retained. The addition of an ototoxic antibiotic to cultures, however, causes complete hair cell loss by 2 d in vitro and generates cultures composed of calmodulin-negative, cytokeratin-positive support cells. These cells are highly proliferative for the first 2-7 d after plating, but stop dividing by 9 d. Calmodulin- or TUJ1-positive cells reemerge in cultures treated with antibiotic for 5 d and maintained for an additional 5 d without antibiotic. A subset of calmodulin-positive cells was also labeled with BrdU when it was continuously present in cultures, suggesting that some cells generated in culture begin to differentiate into hair cells.