Cellular reprogramming with ATOH1, GFI1, and POU4F3 implicate epigenetic changes and cell-cell signaling as obstacles to hair cell regeneration in mature mammals

Deciphering enhancers of hearing loss genes for efficient and targeted gene therapy of hereditary deafness

Hereditary hearing loss accounts for about 60% of congenital deafness. Although adeno-associated virus (AAV)-mediated gene therapy shows substantial potential for treating genetic hearing impairments, there remain significant concerns regarding the specificity and safety of AAV vectors. The sophisticated nature of the cochlea further complicates the challenge of precisely targeting gene delivery. Here, we introduced an AAV-reporter-based in vivo transcriptional enhancer reconstruction (ARBITER) workflow, enabling efficient and reliable dissection of enhancers. With ARBITER, we successfully demonstrated that the conserved non-coding elements (CNEs) within the gene locus collaboratively regulate the expression of Slc26a5, which was further validated using knockout mouse models. We also assessed the potential of identified enhancers to treat hereditary hearing loss by conducting gene therapy in Slc26a5 mutant mice. Based on the original Slc26a5 enhancer with limited efficiency, we engineered a highly efficient and outer hair cell (OHC)-specific enhancer, B8, which successfully restored hearing of Slc26a5 knockout mice.

AAV-Sparcl1 promotes hair cell regeneration by increasing supporting cell plasticity

Sensorineural hearing deficiency caused by hair cell damage represents a prevalent sensory deficit disorder. In mammals, age-related reduction in plasticity of inner ear supporting cells (recognized as hair cell precursors) compromises their trans-differentiation capacity, resulting in impaired spontaneous hair cell regeneration post-injury. Therapeutic reprogramming of supporting cells to functionally replace damaged hair cells has emerged as a promising strategy for sensorineural hearing loss treatment. In this study, we demonstrate that the secretory protein Sparcl1 enhances supporting cell reprogramming and hair cell regeneration in both in vitro and in vivo models. Through the adeno-associated virus (AAV)-mediated overexpression system, we successfully achieved in vivo expansion of inner ear organoids accompanied by hair cell differentiation. RNA-seq analysis revealed that Sparcl1 overexpression stimulates supporting cell proliferation via follistatin (Fst) activation and extracellular matrix (ECM) remodeling. Notably, both AAV-ie-Sparcl1 delivery and recombinant Sparcl1 protein administration effectively induced supporting cell differentiation into hair cells in vivo. Collectively, our findings establish Sparcl1 as a potent positive regulator of hair cell regeneration and elucidate mechanisms by which secretory proteins regulate supporting cell plasticity.

Conditional Overexpression of Net1 Enhances the Trans-Differentiation of Lgr5+ Progenitors into Hair Cells in the Neonatal Mouse Cochlea

Sensorineural hearing loss is mainly caused by damage to hair cells (HC), which cannot be regenerated spontaneously in adult mammals once damaged. Cochlear Lgr5+ progenitors are characterised by HC regeneration capacity in neonatal mice, and we previously screened several new genes that might induce HC regeneration from Lgr5+ progenitors. Net1, a guanine nucleotide exchange factor, is one of the screened new genes and is particularly active in cancer cells and is involved in cell proliferation and differentiation. Here, to explore in vivo roles of Net1 in HC regeneration, Net1 loxp/loxp mice were constructed and crossed with Lgr5 CreER/+ mice to conditionally overexpress (cOE) Net1 in cochlear Lgr5+ progenitors. We observed a large number of ectopic HCs in Lgr5 CreER/+ Net1 loxp/loxp mouse cochlea, which showed a dose-dependent effect. Moreover, the EdU assay was unable to detect any EdU+/Sox2+ supporting cells, while lineage tracing showed significantly more regenerated tdTomato+ HCs in Lgr5 CreER/+ Net1 loxp/loxp tdTomato mice, which indicated that Net1 cOE enhanced HC regeneration by inducing the direct trans-differentiation of Lgr5+ progenitors rather than mitotic HC regeneration. Additionally, qPCR results showed that the transcription factors related to HC regeneration, including Atoh1, Gfi1 and Pou4f3, were significantly upregulated and are probably the mechanism behind the HC regeneration induced by Net1. In conclusion, our study provides new evidence for the role of Net1 in enhancing HC regeneration in the neonatal mouse cochlea.

Gfi1 in the inner ear: A retrospective review

Gfi1 plays an important role in the development of hair cells (HCs), as indicated by its ability to regulate the expression of HC-related genes while the organ of Corti is developing. Given that the HCs and the supporting cells (SCs) are coming from a common stem/progenitor cell pool, it is conceivable to regenerate HCs from SCs that ectopically express Gfi1. The focus of this review was to elucidate the role of Gfi1 in controlling the development of HCs by dissecting the phenotypes of the inner ear in Gfi1-mutated mouse lines. In addition, we reviewed studies of regeneration in the mammalian inner ear, by which we discussed the novel function of Gfi1 as an essential factor in guiding non-HCs toward an HC destiny in coordination with Atoh1 and Pou4f3. Finally, we summarized the known Gfi1-specific Cre/CreER/reporter mouse lines and highlighted the pros and cons of each line, with the aim of providing insights for use in future studies. In summary, a better understanding of Gfi1 and its diverse roles is beneficial for advancing studies of HC regeneration in the inner ear.

Hearing restoration through hair cell regeneration: A review of recent advancements and current limitations

Hearing loss is extremely common, yet limited treatment options are available to restore hearing, and those that are available provide incomplete recovery of hearing detection. For patients who are born with normal hearing, the most common cause of hearing loss is the loss of the sensory hair cells located in the cochlea of the inner ear. Non-mammals, including birds, fish, and amphibians, naturally regenerate new hair cells after damage and this natural process results in functional recovery. While some limited hair cell regeneration also occurs in the immature cochlea of mice, the mature mammalian cochlea does not naturally produce replacement hair cells, and thus hearing loss is permanent. Since the late 1980s, researchers have been investigating mechanisms to convert supporting cells, the cells that remain once hair cells have been killed, into new replacement hair cells. Here we review the current status of hair cell regeneration in the adult cochlea, highlighting recent achievements, as well as challenges that have yet to be resolved.

Conditional Overexpression of Serpine2 Promotes Hair Cell Regeneration from Lgr5+ Progenitors in the Neonatal Mouse Cochlea

Neonatal cochlear Lgr5+ progenitors retain limited hair cells (HCs) regenerative capacity, but the regulatory network remains incompletely defined. Serpin family E member 2 (Serpine2) is shown to participate in regulating proliferation and differentiation of cochlear Lgr5+ progenitors in the previous in vitro study. Here, the expression pattern and in vivo roles of Serpine2 in HC regeneration are explored by transgenic mice. It is found that Serpine2 is expressed in the mouse cochlea after birth with a downward trend as the mice age. In addition, Serpine2 conditional overexpression in vivo in Lgr5+ progenitors of neonatal mice cochlea results in an increased number of ectopic HCs in a dose-dependent manner. Serpine2 knockdown ex vivo and in vivo can inhibit HC regeneration. EdU assay and lineage tracing assay demonstrate these ectopic HCs likely originate from Lgr5+ progenitors through direct transdifferentiation rather than through mitotic regeneration. Moreover, single-nucleus RNA sequencing analysis and mRNA level validation reveal that conditionally overexpressed Serpine2 likely induces HC regeneration via inhibiting sonic hedgehog (SHH) signal pathway and inducing Atoh1 and Pou4f3 transcription factor. In brief, these data indicate that Serpine2 plays a pivotal role in HC regeneration from Lgr5+ progenitors in the neonatal mouse cochlea, and this suggests a new avenue for future research into HC regeneration.

The Notch ligand Jagged1 plays a dual role in cochlear hair cell regeneration

Hair cells (HCs) within the inner ear cochlea are specialized mechanoreceptors required for hearing. Cochlear HCs are not regenerated in mammals, and their loss is a leading cause of deafness in humans. Cochlear supporting cells (SCs) in newborn mice have the capacity to regenerate HCs, but persistent Notch signaling, presumably activated by SC-specific Notch ligand Jagged1 (JAG1), prevents SCs from converting into HCs. Here, employing an organoid platform, we show that while JAG1 participates in HC-fate repression, JAG1's primary function is to preserve the "progenitor-like characteristics" of cochlear SCs. Transcriptomic and mechanistic studies reveal that JAG1/Notch signaling maintains the expression of progenitor and metabolic genes in cochlear SCs and sustains pro-growth pathways, including PI3K-Akt-mTOR signaling, a function that is mediated by Notch1 and Notch2. Finally, we show that JAG1/Notch signaling stimulation with JAG1-Fc peptide enhances the HC-forming capacity of cochlear SCs undergoing maturation in cochlear explants and in vivo .

Extent of genetic and epigenetic factor reprogramming via a single viral vector construct in deaf adult mice

In the adult mammalian cochlea, hair cell loss is irreversible and causes deafness. The basic helix-loop transcription factor Atoh1 is essential for normal hair cell development in the embryonic ear. Over-expression of Atoh1 in the adult cochlea by gene therapy can convert supporting cells (cells that underlie hair cells) into a hair cell lineage. However, the regeneration outcomes can be inconsistent. Given that hair cell development is regulated by multiple signalling and transcriptional factors in a temporal and spatial manner, a more complex combinatorial approach targeting additional transcription factors may be required for efficient hair cell regeneration. There is evidence that epigenetic factors are responsible for the lack in regenerative capacity of the deaf adult cochlea. This study aimed to develop a combined gene therapy approach to reprogram both the genome and epigenome of supporting cells to improve the efficiency of hair cell regeneration. Adult Pou4f3-DTR mice were used in which the administration of diphtheria toxin was used to ablate hair cells whilst leaving supporting cells relatively intact. A single adeno-associated viral construct was used to express human Atoh1, Pou4f3 and short hairpin RNA against Kdm1a (regeneration gene therapy) at two weeks following partial or severe hair cell ablation. The average transduction of the inner supporting cells, as measured by the control AAV2.7m8-GFP vector in the deaf cochlea, was only 8 % while transduction in the outer sensory region was <1 %. At 4- and 6-weeks post-treatment the number of Myo+ hair cells in the control and regeneration gene therapy-treated mice were not significantly different. Of note, although both control and regeneration gene therapy treated cochleae contained supporting cells that co-expressed the hair cell marker Myo7a and the supporting cell marker Sox2, the regeneration gene therapy treated cochleae had significantly higher numbers of these cells (p < 0.05). Furthermore, among these treated cochleae, those that had more hair cell loss had a higher number of Myo7a positive supporting cells (R2=0.33, Pearson correlation analysis, p < 0.001). Overall, our results indicate that the adult cochlea possesses limited intrinsic spontaneous regenerative capacity, that can be further enhanced by genetic and epigenetic reprogramming.

Inducible, virus-free direct lineage reprogramming enhances scalable generation of human inner ear hair cell-like cells

Mammalian inner ear sensory hair cells are highly sensitive to environmental stress and do not regenerate, making hearing loss progressive and permanent. The paucity and extreme inaccessibility of these cells hinder the development of regenerative and otoprotective strategies, Direct lineage reprogramming to generate large quantities of hair cell-like cells in vitro offers a promising approach to overcome these experimental bottlenecks. Previously, we identified four transcription factors-Six1, Atoh1, Pou4f3, and Gfi1 (SAPG)-capable of converting mouse embryonic fibroblasts, adult tail tip fibroblasts, and postnatal mouse supporting cells into induced hair cell-like cells through retroviral or lentiviral transduction (Menendez et al., 2020). Here, we developed a virus-free, inducible system using a stable human induced pluripotent stem (iPS) cell line carrying doxycycline-inducible SAPG. Our inducible system significantly increases reprogramming efficiency compared to retroviral methods, achieving a ~19-fold greater conversion to a hair cell fate in half the time. Immunostaining, Western blot, and single-nucleus RNA-seq analyses confirm the expression of hair cell-specific markers and activation of hair cell gene networks in reprogrammed cells. The reprogrammed hair cells closely resemble developing fetal hair cells, as evidenced by comparison with a human fetal inner ear dataset. Electrophysiological analysis reveals that the induced hair cell-like cells exhibit diverse voltage-dependent ion currents, including robust, quick-activating, slowly inactivating currents characteristic of primary hair cells. This virus-free approach improves scalability, reproducibility, and the modeling of hair cell differentiation, offering significant potential for hair cell regenerative strategies and preclinical drug discovery targeting ototoxicity and otoprotection.

Co-overexpression of Atoh1, Pou4f3, and Gfi1 enhances the transdifferentiation of supporting cells into hair cells in the neonatal mouse utricle

Hair cells (HCs) are essential for vestibular function, and irreversible damage to vestibular HCs in mammals is closely associated with vertigo. The stimulation of HC regeneration through exogenous gene delivery represents an ideal therapeutic approach for restoring vestibular function. Overexpression of Atoh1, Pou4f3, and Gfi1 (collectively referred to as APG) has demonstrated efficacy in promoting HC regeneration in the cochlea. However, the effects of APG on vestibular HC regeneration remain unclear. Here, we used adeno-associated virus-inner ear (AAVie) as a carrier to deliver APG to the utricles of neonatal mice and assessed the morphology and number of HCs and supporting cells (SCs) by immunofluorescence staining. GLASTCreERT;Rosa26tdTomato mouse line was used to trace SCs. The results showed that APG overexpression resulted in substantial SC transdifferentiation into HCs in the neonatal mouse utricle. Furthermore, APG overexpression maintained SC number by facilitating SC proliferation. Continuous Atoh1 overexpression caused stereocilia damage, which was alleviated by APG overexpression. This study highlights the potential of regulating multiple transcription factors to promote vestibular HC regeneration.

The cochlea phenotypically differs from the vestibule in the Gfi1GFP/GFP mouse

BACKGROUND

Previous studies with Gfi1-mutated lines have shown that Gfi1 is essential for hair cell maturation and survival.

RESULTS

We analyzed the phenotype of another Gfi1-mutated line Gfi1GFP/GFP in the inner ears of neonates at P5-7 and found that the cochlea phenotypically differed from the vestibule in the Gfi1GFP/GFP mouse. Specifically, there was a marked reduction in hair cells in the cochlea, which was characterized by greater reductions in the outer hair cells but far less reductions (mainly in the basal turn) in the inner hair cells, whereas the vestibular hair cells remained unaffected. These results were consistent with findings from previous studies. Unexpectedly, the number of cochlear non-sensory supporting cells significantly decreased. However, the vestibular supporting cells did not demonstrate any abnormalities in number.

CONCLUSION

Gfi1 exhibits different functions in the cochlea and vestibule during inner ear development.

Single-cell atlas comparison across vertebrates reveals auditory cell evolution and mechanisms for hair cell regeneration

Mammals suffer permanent hearing impairment from the loss of auditory hair cells due to their inability to regenerate. In contrast, lower vertebrates exhibit extraordinary capacity for hair cell regeneration and hearing restoration, but the mechanisms remain unclear. Here we characterize the single-cell atlas of Xenopus laevis inner ear and perform a comprehensive comparison with mouse model. An exceptionally conserved inner ear neuronal cell type is discovered. The results reveal that the outer hair cells (OHCs) exist exclusively in mammals. Importantly, our analyses reveal an orchestrated gene expression program in Xenopus, characterized by upregulation of hair cell regeneration-related genes, coupled with downregulation of proliferation inhibitory genes. These findings unveil a natural feature of regenerative capacity in Xenopus, and provide molecular and evolutionary evidences for differential regenerative capacities across vertebrates. This work offers insights from amphibians into developing strategies to solve the challenges of hair cell regeneration in humans.

Genetic and pharmacologic alterations of claudin9 levels suffice to induce functional and mature inner hair cells

Hearing loss is the most common form of sensory deficit. It occurs predominantly due to hair cell (HC) loss. Mammalian HCs are terminally differentiated by birth, making HC loss challenging to replace. Here, we show the pharmacogenetic downregulation of Cldn9, a tight junction protein, generates robust supernumerary inner HCs (IHCs) in mice. The ectopic IHC shared functional and synaptic features akin to typical IHCs and were surprisingly and remarkably preserved for at least fifteen months >50% of the mouse's life cycle. In vivo, Cldn9 knockdown using shRNA on postnatal days (P) P2-7 yielded analogous functional ectopic IHCs that were equally durably conserved. The findings suggest that Cldn9 levels coordinate embryonic and postnatal HC differentiation, making it a viable target for altering IHC development pre- and post-terminal differentiation.

Jag1 represses Notch activation in lateral supporting cells and inhibits an outer hair cell fate in the medial cochlea

Notch signaling patterns the cochlear organ of Corti, and individuals with the JAG1/NOTCH2-related genetic disorder Alagille syndrome can thus experience hearing loss. We investigated the function of Jag1 in cochlear patterning and signaling using Jag1Ndr/Ndr mice, which are a model of Alagille syndrome. Jag1Ndr/Ndr mice exhibited expected vestibular and auditory deficits, a dose-dependent increase in ectopic inner hair cells, and a reduction in outer hair cells. Single cell RNA sequencing of the organ of Corti demonstrated a global dysregulation of genes associated with inner ear development and deafness. Analysis of individual cell types further revealed that Jag1 represses Notch activation in lateral supporting cells and demonstrated a function for Jag1 in gene regulation and development of outer hair cells. Surprisingly, ectopic 'outer hair cell-like' cells were present in the medial compartment and pillar cell region of Jag1Ndr/Ndr cochleae, yet they exhibited location-dependent expression of the inner hair cell fate-determinant Tbx2, suggesting Jag1 is required for Tbx2 to drive inner hair cell commitment. This study thus identifies new roles for Jag1 in supporting cells, and in outer hair cell specification and positioning.

Pharmacological Approaches to Hearing Loss

Hearing disorders pose significant challenges to individuals experiencing them and their overall quality of life, emphasizing the critical need for advanced pharmacological approaches to address these conditions. Current treatment options often focus on amplification devices, cochlear implants, or other rehabilitative therapies, leaving a substantial gap regarding effective pharmacological interventions. Advancements in our understanding of the molecular and cellular mechanisms involved in hearing disorders induced by noise, aging, and ototoxicity have opened new avenues for drug development, some of which have led to numerous clinical trials, with promising results. The development of optimal drug delivery solutions in animals and humans can also enhance the targeted delivery of medications to the ear. Moreover, large genome studies contributing to a genetic understanding of hearing loss in humans combined with advanced molecular technologies in animal studies have shown a great potential to increase our understanding of the etiologies of hearing loss. The auditory system exhibits circadian rhythms and temporal variations in its physiology, its vulnerability to auditory insults, and its responsiveness to drug treatments. The cochlear clock rhythms are under the control of the glucocorticoid system, and preclinical evidence suggests that the risk/benefit profile of hearing disorder treatments using chronopharmacological approaches would be beneficial. If translatable to the bedside, such approaches may improve the outcome of clinical trials. Ongoing research into the molecular and genetic basis of auditory disorders, coupled with advancements in drug formulation and delivery as well as optimized timing of drug administration, holds great promise of more effective treatments. SIGNIFICANCE STATEMENT: Hearing disorders pose significant challenges to individuals and their overall quality of life, emphasizing the critical need for advanced pharmacological approaches to address these conditions. Ongoing research into the molecular and genetic basis of auditory disorders, coupled with advancements in drug delivery procedures and optimized timing of drug administration, holds the promise of more effective treatments.

Reprogramming with Atoh1, Gfi1, and Pou4f3 promotes hair cell regeneration in the adult organ of Corti

Cochlear hair cells can be killed by loud noises, ototoxic drugs, and natural aging. Once lost, mammalian hair cells do not naturally regenerate, leading to permanent hearing loss. Since the mammalian cochlea lacks any intrinsic ability to regenerate, genetic reprogramming of cochlear supporting cells that lie adjacent to hair cells is a potential option for hearing restoration therapies. We targeted cochlear supporting cells with three hair cell transcription factors: Atoh1, or Atoh1 + Gfi1, or Atoh1 + Gfi1 + Pou4f3 and found that 1- and 2-factor reprogramming is not sufficient to reprogram adult supporting cells into hair cells. However, activation of all three hair cell transcription factors reprogrammed some adult supporting cells into hair cell-like cells. We found that killing endogenous hair cells significantly improved the ability of supporting cells to be reprogrammed and regenerated numerous hair cell-like cells throughout the length of the cochlea. These regenerated hair cell-like cells expressed myosin VIIa and parvalbumin, as well as the mature outer hair cell protein prestin, were innervated, expressed proteins associated with ribbon synapses, and formed rudimentary stereociliary bundles. Finally, we demonstrate that supporting cells remained responsive to transcription factor reprogramming for at least 6 weeks after hair cell damage, suggesting that hair cell reprogramming may be effective in the chronically deafened cochlea.

Roles of supporting cells in the maintenance and regeneration of the damaged inner ear: A literature review

The inner ear sensory epithelium consists of two major types of cells: hair cells (HCs) and supporting cells (SCs). Critical functions of HCs in the perception of mechanical stimulation and mechanosensory transduction have long been elucidated. SCs are indispensable components of the sensory epithelia, and they maintain the structural integrity and ionic environment of the inner ear. Once delicate inner ear epithelia sustain injuries (for example, due to ototoxic drugs or noise exposure), SCs respond immediately to serve as repairers of the epithelium and as adapters to become HC progenitors, aiming at morphological and functional recovery of the inner ear. This regenerative process is extensive in non-mammals, but is limited in the mammalian inner ear, especially in the mature cochlea. This review aimed to discuss the important roles of SCs in the repair of the mammalian inner ear.

Advance and Application of Single-cell Transcriptomics in Auditory Research

Hearing loss and deafness, as a worldwide disability disease, have been troubling human beings. However, the auditory organ of the inner ear is highly heterogeneous and has a very limited number of cells, which are largely uncharacterized in depth. Recently, with the development and utilization of single-cell RNA sequencing (scRNA-seq), researchers have been able to unveil the complex and sophisticated biological mechanisms of various types of cells in the auditory organ at the single-cell level and address the challenges of cellular heterogeneity that are not resolved through by conventional bulk RNA sequencing (bulk RNA-seq). Herein, we reviewed the application of scRNA-seq technology in auditory research, with the aim of providing a reference for the development of auditory organs, the pathogenesis of hearing loss, and regenerative therapy. Prospects about spatial transcriptomic scRNA-seq, single-cell based genome, and Live-seq technology will also be discussed.

Murine cochlear damage models in the context of hair cell regeneration research

Understanding the complex pathologies associated with hearing loss is a significant motivation for conducting inner ear research. Lifelong exposure to loud noise, ototoxic drugs, genetic diversity, sex, and aging collectively contribute to human hearing loss. Replicating this pathology in research animals is challenging because hearing impairment has varied causes and different manifestations. A central aspect, however, is the loss of sensory hair cells and the inability of the mammalian cochlea to replace them. Researching therapeutic strategies to rekindle regenerative cochlear capacity, therefore, requires the generation of animal models in which cochlear hair cells are eliminated. This review discusses different approaches to ablate cochlear hair cells in adult mice. We inventoried the cochlear cyto- and histo-pathology caused by acoustic overstimulation, systemic and locally applied drugs, and various genetic tools. The focus is not to prescribe a perfect damage model but to highlight the limitations and advantages of existing approaches and identify areas for further refinement of damage models for use in regenerative studies.

Sensory cells in tunicates: insights into mechanoreceptor evolution

Tunicates, the sister group of vertebrates, offer a unique perspective for evolutionary developmental studies (Evo-Devo) due to their simple anatomical organization. Moreover, the separation of tunicates from vertebrates predated the vertebrate-specific genome duplications. As adults, they include both sessile and pelagic species, with very limited mobility requirements related mainly to water filtration. In sessile species, larvae exhibit simple swimming behaviors that are required for the selection of a suitable substrate on which to metamorphose. Despite their apparent simplicity, tunicates display a variety of mechanoreceptor structures involving both primary and secondary sensory cells (i.e., coronal sensory cells). This review encapsulates two decades of research on tunicate mechanoreception focusing on the coronal organ's sensory cells as prime candidates for understanding the evolution of vertebrate hair cells of the inner ear and the lateral line organ. The review spans anatomical, cellular and molecular levels emphasizing both similarity and differences between tunicate and vertebrate mechanoreception strategies. The evolutionary significance of mechanoreception is discussed within the broader context of Evo-Devo studies, shedding light on the intricate pathways that have shaped the sensory system in chordates.

The cells of the sensory epithelium, and not the stria vascularis, are the main cochlear cells related to the genetic pathogenesis of age-related hearing loss

Age-related hearing loss (ARHL) is a major health concern among the elderly population. It is hoped that increasing our understanding of its underlying pathophysiological processes will lead to the development of novel therapies. Recent genome-wide association studies (GWASs) discovered a few dozen genetic variants in association with elevated risk for ARHL. Integrated analysis of GWAS results and transcriptomics data is a powerful approach for elucidating specific cell types that are involved in disease pathogenesis. Intriguingly, recent studies that applied such bioinformatics approaches to ARHL resulted in disagreeing findings as for the key cell types that are most strongly linked to the genetic pathogenesis of ARHL. These conflicting studies pointed either to cochlear sensory epithelial or to stria vascularis cells as the cell types most prominently involved in the genetic basis of ARHL. Seeking to resolve this discrepancy, we integrated the analysis of four ARHL GWAS datasets with four independent inner-ear single-cell RNA-sequencing datasets. Our analysis clearly points to the cochlear sensory epithelial cells as the key cells for the genetic predisposition to ARHL. We also explain the limitation of the bioinformatics analysis performed by previous studies that led to missing the enrichment for ARHL GWAS signal in sensory epithelial cells. Collectively, we show that cochlear epithelial cells, not stria vascularis cells, are the main inner-ear cells related to the genetic pathogenesis of ARHL.

Expression of Atoh1, Gfi1, and Pou4f3 in the mature cochlea reprograms nonsensory cells into hair cells

Mechanosensory hair cells of the mature mammalian organ of Corti do not regenerate; consequently, loss of hair cells leads to permanent hearing loss. Although nonmammalian vertebrates can regenerate hair cells from neighboring supporting cells, many humans with severe hearing loss lack both hair cells and supporting cells, with the organ of Corti being replaced by a flat epithelium of nonsensory cells. To determine whether the mature cochlea can produce hair cells in vivo, we reprogrammed nonsensory cells adjacent to the organ of Corti with three hair cell transcription factors: Gfi1, Atoh1, and Pou4f3. We generated numerous hair cell-like cells in nonsensory regions of the cochlea and new hair cells continued to be added over a period of 9 wk. Significantly, cells adjacent to reprogrammed hair cells expressed markers of supporting cells, suggesting that transcription factor reprogramming of nonsensory cochlear cells in adult animals can generate mosaics of sensory cells like those seen in the organ of Corti. Generating such sensory mosaics by reprogramming may represent a potential strategy for hearing restoration in humans.

Stem Cell-Based Hair Cell Regeneration and Therapy in the Inner Ear

Hearing loss has become increasingly prevalent and causes considerable disability, thus gravely burdening the global economy. Irreversible loss of hair cells is a main cause of sensorineural hearing loss, and currently, the only relatively effective clinical treatments are limited to digital hearing equipment like cochlear implants and hearing aids, but these are of limited benefit in patients. It is therefore urgent to understand the mechanisms of damage repair in order to develop new neuroprotective strategies. At present, how to promote the regeneration of functional hair cells is a key scientific question in the field of hearing research. Multiple signaling pathways and transcriptional factors trigger the activation of hair cell progenitors and ensure the maturation of newborn hair cells, and in this article, we first review the principal mechanisms underlying hair cell reproduction. We then further discuss therapeutic strategies involving the co-regulation of multiple signaling pathways in order to induce effective functional hair cell regeneration after degeneration, and we summarize current achievements in hair cell regeneration. Lastly, we discuss potential future approaches, such as small molecule drugs and gene therapy, which might be applied for regenerating functional hair cells in the clinic.

Advanced Omics Techniques for Understanding Cochlear Genome, Epigenome, and Transcriptome in Health and Disease

Advanced genomics, transcriptomics, and epigenomics techniques are providing unprecedented insights into the understanding of the molecular underpinnings of the central nervous system, including the neuro-sensory cochlea of the inner ear. Here, we report for the first time a comprehensive and updated overview of the most advanced omics techniques for the study of nucleic acids and their applications in cochlear research. We describe the available in vitro and in vivo models for hearing research and the principles of genomics, transcriptomics, and epigenomics, alongside their most advanced technologies (like single-cell omics and spatial omics), which allow for the investigation of the molecular events that occur at a single-cell resolution while retaining the spatial information.

Nissl Granules, Axonal Regeneration, and Regenerative Therapeutics: A Comprehensive Review

Nissl granules, traditionally recognized for their pivotal role in protein synthesis within neuronal cell bodies, are emerging as intriguing components with far-reaching implications in the realm of regenerative therapeutics. This abstract encapsulates the essence of a comprehensive review, exploring the nexus between Nissl granules, axonal regeneration, and their transformative applications in regenerative medicine. The molecular intricacies of Nissl granules form the foundation of this exploration, unraveling their dynamic role in orchestrating cellular responses, particularly in the context of axonal regeneration. As we delve into the interplay between Nissl granules and regenerative processes, this review highlights the diverse mechanisms through which these granules contribute to neuronal repair and recovery. Beyond their conventional association with neurobiology, recent advancements underscore the translational potential of Nissl granules as therapeutic agents. Insights into their involvement in enhancing axonal regeneration prompt a reconsideration of these granules as key players in the broader field of regenerative medicine. The abstract encapsulates evidence suggesting that modulating Nissl granule-related pathways holds promise for augmenting tissue regeneration, extending their applicability beyond the confines of the nervous system. This review aims to serve as a valuable resource for medical professionals, researchers, and clinicians seeking to comprehend the multifaceted role of Nissl granules in regenerative therapeutics. By illuminating the intricate connections between Nissl granules, axonal regeneration, and therapeutic applications, this work aspires to catalyze further research and innovation, ultimately contributing to the evolution of regenerative strategies that harness the innate reparative capacities within cellular constituents.

DNA methylation in the mouse cochlea promotes maturation of supporting cells and contributes to the failure of hair cell regeneration

Mammalian hair cells do not functionally regenerate in adulthood but can regenerate at embryonic and neonatal stages in mice by direct transdifferentiation of neighboring supporting cells into new hair cells. Previous work showed loss of transdifferentiation potential of supporting cells is in part due to H3K4me1 enhancer decommissioning of the hair cell gene regulatory network during the first postnatal week. However, inhibiting this decommissioning only partially preserves transdifferentiation potential. Therefore, we explored other repressive epigenetic modifications that may be responsible for this loss of plasticity. We find supporting cells progressively accumulate DNA methylation at promoters of developmentally regulated hair cell genes. Specifically, DNA methylation overlaps with binding sites of Atoh1, a key transcription factor for hair cell fate. We further show that DNA hypermethylation replaces H3K27me3-mediated repression of hair cell genes in mature supporting cells, and is accompanied by progressive loss of chromatin accessibility, suggestive of facultative heterochromatin formation. Another subset of hair cell loci is hypermethylated in supporting cells, but not in hair cells. Ten-eleven translocation (TET) enzyme-mediated demethylation of these hypermethylated sites is necessary for neonatal supporting cells to transdifferentiate into hair cells. We also observe changes in chromatin accessibility of supporting cell subtypes at the single-cell level with increasing age: Gene programs promoting sensory epithelium development loses chromatin accessibility, in favor of gene programs that promote physiological maturation and function of the cochlea. We also find chromatin accessibility is partially recovered in a chronically deafened mouse model, which holds promise for future translational efforts in hearing restoration.

Recent advances in molecular studies on cochlear development and regeneration

The auditory organ cochlea harbors two types of sound receptors, inner hair cells (IHCs) and outer hair cells (OHCs), which are innervated by spiral (auditory) ganglion neurons (SGNs). Recent transcriptomic, epigenetic, and genetic studies have started to reveal various aspects of cochlear development, including how prosensory progenitors are specified and diversified into IHCs or OHCs, as well as the heterogeneity among SGNs and how SGN subtypes are formed. Here, we primarily review advances in this line of research over the past five years and discuss a few key studies (from the past two years) to elucidate (1) how prosensory progenitors are specified; (2) the cis-regulatory control of Atoh1 expression and the synergistic interaction between Atoh1 and Pou4f3; and (3) the essential roles of Insm1 and Ikzf2 in OHC development and Tbx2 in IHC development. Moreover, we highlight the contribution of recent molecular studies on cochlear development toward the goal of regenerating IHCs and OHCs, which holds considerable potential for application in treating human deafness. Lastly, we briefly summarize the most recent progress on uncovering when and how SGN diversity is generated.

Defining developmental trajectories of prosensory cells in human inner ear organoids at single-cell resolution

The inner ear sensory epithelia contain mechanosensitive hair cells and supporting cells. Both cell types arise from SOX2-expressing prosensory cells, but the mechanisms underlying the diversification of these cell lineages remain unclear. To determine the transcriptional trajectory of prosensory cells, we established a SOX2-2A-ntdTomato human embryonic stem cell line using CRISPR/Cas9, and performed single-cell RNA-sequencing analyses with SOX2-positive cells isolated from inner ear organoids at various time points between differentiation days 20 and 60. Our pseudotime analysis suggests that vestibular type II hair cells arise primarily from supporting cells, rather than bi-fated prosensory cells in organoids. Moreover, ion channel- and ion-transporter-related gene sets were enriched in supporting cells versus prosensory cells, whereas Wnt signaling-related gene sets were enriched in hair cells versus supporting cells. These findings provide valuable insights into how prosensory cells give rise to hair cells and supporting cells during human inner ear development, and may provide a clue to promote hair cell regeneration from resident supporting cells in individuals with hearing loss or balance disorders.

The role of epigenetic modifications in sensory hair cell development, survival, and regulation

The cochlea is the sensory organ in the periphery, and hair cells are its main sensory cells. The development and survival of hair cells are highly controlled processes. When cells face intracellular and environmental stimuli, epigenetic regulation controls the structure and function of the genome in response to different cell fates. During sensory hair cell development, different histone modifications can induce normal numbers of functional hair cells to generate. When individuals are exposed to environmental-related hair cell damage, epigenetic modification also plays a significant role in the regulation of hair cell fate. Since mammalian hair cells cannot regenerate, their loss can cause permanent sensorineural hearing loss. Many breakthroughs have been achieved in recent years in understanding the signaling pathways that determine hair cell regeneration, and it is fascinating to note that epigenetic regulation plays a significant role in hair cell regeneration. In this review, we discuss the role of epigenetics in inner ear cell development, survival and regeneration and the significant impact on hearing protection.

Epistatic genetic interactions between Insm1 and Ikzf2 during cochlear outer hair cell development

The cochlea harbors two types of sound receptors, outer hair cells (OHCs) and inner hair cells (IHCs). OHCs transdifferentiate into IHCs in Insm1 mutants, and OHCs in Ikzf2-deficient mice are dysfunctional and maintain partial IHC gene expression. Insm1 potentially acts as a positive but indirect regulator of Ikzf2, considering that Insm1 is expressed earlier than Ikzf2 and primarily functions as a transcriptional repressor. However, direct evidence of this possibility is lacking. Here, we report the following results: first, Insm1 overexpression in IHCs leads to ectopic Ikzf2 expression. Second, Ikzf2 expression is repressed in Insm1-deficient OHCs, and forced expression of Ikzf2 mitigates the OHC abnormality in Insm1 mutants. Last, dual ablation of Insm1 and Ikzf2 generates a similar OHC phenotype as does Insm1 ablation alone. Collectively, our findings reveal the transcriptional cascade from Insm1 to Ikzf2, which should facilitate future investigation of the molecular mechanisms underlying OHC development and regeneration.

Regeneration of Hair Cells from Endogenous Otic Progenitors in the Adult Mammalian Cochlea: Understanding Its Origins and Future Directions

Sensorineural hearing loss is caused by damage to sensory hair cells and/or spiral ganglion neurons. In non-mammalian species, hair cell regeneration after damage is observed, even in adulthood. Although the neonatal mammalian cochlea carries regenerative potential, the adult cochlea cannot regenerate lost hair cells. The survival of supporting cells with regenerative potential after cochlear trauma in adults is promising for promoting hair cell regeneration through therapeutic approaches. Targeting these cells by manipulating key signaling pathways that control mammalian cochlear development and non-mammalian hair cell regeneration could lead to regeneration of hair cells in the mammalian cochlea. This review discusses the pathways involved in the development of the cochlea and the impact that trauma has on the regenerative capacity of the endogenous progenitor cells. Furthermore, it discusses the effects of manipulating key signaling pathways targeting supporting cells with progenitor potential to promote hair cell regeneration and translates these findings to the human situation. To improve hearing recovery after hearing loss in adults, we propose a combined approach targeting (1) the endogenous progenitor cells by manipulating signaling pathways (Wnt, Notch, Shh, FGF and BMP/TGFβ signaling pathways), (2) by manipulating epigenetic control, and (3) by applying neurotrophic treatments to promote reinnervation.

Future Pharmacotherapy for Sensorineural Hearing Loss by Protection and Regeneration of Auditory Hair Cells

Sensorineural hearing loss has been a global burden of diseases for decades. However, according to recent progress in experimental studies on hair cell regeneration and protection, clinical trials of pharmacotherapy for sensorineural hearing loss have rapidly progressed. In this review, we focus on recent clinical trials for hair cell protection and regeneration and outline mechanisms based on associated experimental studies. Outcomes of recent clinical trials provided valuable data regarding the safety and tolerability of intra-cochlear and intra-tympanic applications as drug delivery methods. Recent findings in molecular mechanisms of hair cell regeneration suggested the realization of regenerative medicine for sensorineural hearing loss in the near future.

Gene therapy: an emerging therapy for hair cells regeneration in the cochlea

Sensorineural hearing loss is typically caused by damage to the cochlear hair cells (HCs) due to external stimuli or because of one's genetic factors and the inability to convert sound mechanical energy into nerve impulses. Adult mammalian cochlear HCs cannot regenerate spontaneously; therefore, this type of deafness is usually considered irreversible. Studies on the developmental mechanisms of HC differentiation have revealed that nonsensory cells in the cochlea acquire the ability to differentiate into HCs after the overexpression of specific genes, such as Atoh1, which makes HC regeneration possible. Gene therapy, through in vitro selection and editing of target genes, transforms exogenous gene fragments into target cells and alters the expression of genes in target cells to activate the corresponding differentiation developmental program in target cells. This review summarizes the genes that have been associated with the growth and development of cochlear HCs in recent years and provides an overview of gene therapy approaches in the field of HC regeneration. It concludes with a discussion of the limitations of the current therapeutic approaches to facilitate the early implementation of this therapy in a clinical setting.

Advances in Understanding the Notch Signaling Pathway in the Cochlea

The cochlear structure is highly complex and specific, and its development is regulated by multiple signaling pathways. Abnormalities in cochlear development can lead to different degrees of loss of function. Hair cells (HCs), which are difficult to regenerate in the mature mammalian cochlea, are susceptible to damage from noise and ototoxic drugs, and damage to HCs can cause hearing loss to varying degrees. Notch, a classical developmental signaling molecule, has been shown to be closely associated with embryonic cochlear development and plays an important role in HC regeneration in mammals, suggesting that the Notch signaling pathway may be a potential therapeutic target for cochlear development and hearing impairment due to HC damage. In recent years, the important role of the Notch signaling pathway in the cochlea has received increasing attention. In this paper, we review the role of Notch signaling in cochlear development and HC regeneration, with the aim of providing new research ideas for the prevention and treatment of related diseases.