In Vivo Interplay between p27Kip1, GATA3, ATOH1, and POU4F3 Converts Non-sensory Cells to Hair Cells in Adult Mice

High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a co-reprogramming factor

In vivo direct conversion of differentiated cells holds promise for regenerative medicine; however, improving the conversion efficiency and producing functional target cells remain challenging. Ectopic Atoh1 expression in non-sensory supporting cells (SCs) in mouse cochleae induces their partial conversion to hair cells (HCs) at low efficiency. Here, we performed single-cell RNA sequencing of whole mouse sensory epithelia harvested at multiple time points after conditional overexpression of Atoh1. Pseudotemporal ordering revealed that converted HCs (cHCs) are present along a conversion continuum that correlates with both endogenous and exogenous Atoh1 expression. Bulk sequencing of isolated cell populations and single-cell qPCR confirmed 51 transcription factors, including Isl1, are differentially expressed among cHCs, SCs and HCs. In transgenic mice, co-overexpression of Atoh1 and Isl1 enhanced the HC conversion efficiency. Together, our study shows how high-resolution transcriptional profiling of direct cell conversion can identify co-reprogramming factors required for efficient conversion.

The ongoing ATOH1 gene therapy clinical trial offers promise for hearing restoration in humans. However, in animal models, Atoh1-mediated sensory regeneration is inefficient and incomplete. Here we performed high-resolution gene expression profiling of single cochlear cells at multiple time points in a mouse model whereby we discovered a continuous regeneration process that leads to the formation of immature sensory cells. We identified 51 key reprogramming transcription factors that may increase the efficiency and completion of the regeneration process and confirmed that Isl1 in transgenic mice promotes Atoh1-mediated sensory regeneration as a co-reprogramming factor. Our studies identify molecular mechanisms and novel co-reprogramming factors for sensory restoration in humans with irreversible hearing loss.

Regenerating hair cells in vestibular sensory epithelia from humans

Human vestibular sensory epithelia in explant culture were incubated in gentamicin to ablate hair cells. Subsequent transduction of supporting cells with ATOH1 using an Ad-2 viral vector resulted in generation of highly significant numbers of cells expressing the hair cell marker protein myosin VIIa. Cells expressing myosin VIIa were also generated after blocking the Notch signalling pathway with TAPI-1 but less efficiently. Transcriptomic analysis following ATOH1 transduction confirmed up-regulation of 335 putative hair cell marker genes, including several downstream targets of ATOH1. Morphological analysis revealed numerous cells bearing dense clusters of microvilli at the apical surfaces which showed some hair cell-like characteristics confirming a degree of conversion of supporting cells. However, no cells bore organised hair bundles and several expected hair cell markers genes were not expressed suggesting incomplete differentiation. Nevertheless, the results show a potential to induce conversion of supporting cells in the vestibular sensory tissues of humans.

The inner ear contains our balance system (the vestibular system) and our hearing organ (the cochlea). Their sensing units, the hair cells, detect movement or sound waves. A loss of hair cells is a major cause of inner ear disorders, such as dizziness, imbalance and deafness.

When hair cells die, supporting cells that surround them close the ‘wound’ to repair the tissue. In fish, amphibians, reptiles and birds, the supporting cells can replace lost hair cells, but in mammals – including humans – hair cells are unable to regenerate in the cochlea, so hearing loss is permanent. However, previous research has shown that in certain mammals, spontaneous replacement of lost hair cells in the vestibular system can occur, but not enough to lead to a full recovery.

Scientists have been able to convert supporting cells in the vestibular system of mice into hair cells by using either certain chemicals, or by introducing a specific gene into the supporting cells. In the mouse embryo, this gene, called Atoh1, switches on a signalling pathway in the inner ear, through which a non-specialised precursor cell becomes a hair cell. Inducing hair cell regeneration could be a therapy for inner ear disorders. Therefore, Taylor et al. wanted to find out if such procedures would work in inner ear tissue from humans.

The researchers collected intact tissue samples from the vestibular system of patients who had undergone surgery to have a tumour removed, which would normally destroy the inner ear. All existing hair cells were removed so that mainly supporting cells remained. Then, the tissue was either treated with chemicals that increased the production of hair cells or received the gene ATOH1. The results showed that the cells containing the gene were able to develop many features characteristic of hair cells. And a smaller number of hair cells treated with the chemicals also started to develop hair cell-like features. A gene analysis after the ATOH1 transfer revealed a number of active genes known to be markers of hair cells, but also several inactive ones. This suggests that additional factors are necessary for generating fully functional hair cells.

Dizziness and balance disorders present a major health care burden, particularly in the elderly population. Yet, they are often disregarded and overlooked. This study suggests that hair cell regeneration could be a feasible therapy for some forms of balance disorders linked to loss of vestibular hair cells. More research is needed to identify the other factors at play to test if hair cell regeneration in the cochlea could be used to treat hearing impairment.

Transcription factor induced conversion of human fibroblasts towards the hair cell lineage

Hearing loss is the most common sensorineural disorder, affecting over 5% of the population worldwide. Its most frequent cause is the loss of hair cells (HCs), the mechanosensory receptors of the cochlea. HCs transduce incoming sounds into electrical signals that activate auditory neurons, which in turn send this information to the brain. Although some spontaneous HC regeneration has been observed in neonatal mammals, the very small pool of putative progenitor cells that have been identified in the adult mammalian cochlea is not able to replace the damaged HCs, making any hearing impairment permanent. To date, guided differentiation of human cells to HC-like cells has only been achieved using either embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs). However, use of such cell types suffers from a number of important disadvantages, such as the risk of tumourigenicity if transplanted into the host´s tissue. We have obtained cells expressing hair cell markers from cultures of human fibroblasts by overexpression of GFI1, Pou4f3 and ATOH1 (GPA), three genes that are known to play a critical role in the development of HCs. Immunocytochemical, qPCR and RNAseq analyses demonstrate the expression of genes typically expressed by HCs in the transdifferentiated cells. Our protocol represents a much faster approach than the methods applied to ESCs and iPSCs and validates the combination of GPA as a set of genes whose activation leads to the direct conversion of human somatic cells towards the hair cell lineage. Our observations are expected to contribute to the development of future therapies aimed at the regeneration of the auditory organ and the restoration of hearing.

Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness

BACKGROUND

Hearing loss is a major cause of disability worldwide, impairing communication, health, and quality of life. Emerging methods of gene therapy aim to address this morbidity, which can be employed to fix a genetic problem causing hair cell dysfunction and to promote the proliferation of supporting cells in the cochlea and their transdifferentiation into hair cells. In order to extend the applicability of gene therapy, the scientific community is focusing on discovery of additional deafness genes, identifying new genetic variants associated with hearing loss, and revealing new factors that can be manipulated in a coordinated manner to improve hair cell regeneration. Here, we addressed these challenges via genome-wide measurement and computational analysis of transcriptional profiles of mouse cochlea and vestibule sensory epithelium at embryonic day (E)16.5 and postnatal day (P)0. These time points correspond to developmental stages before and during the acquisition of mechanosensitivity, a major turning point in the ability to hear.

RESULTS

We hypothesized that tissue-specific transcription factors are primarily involved in differentiation, while those associated with development are more concerned with proliferation. Therefore, we searched for enrichment of transcription factor binding motifs in genes differentially expressed between the tissues and between developmental ages of mouse sensory epithelium. By comparison with transcription factors known to alter their expression during avian hair cell regeneration, we identified 37 candidates likely to be important for regeneration. Furthermore, according to our estimates, only half of the deafness genes in human have been discovered. To help remedy the situation, we developed a machine learning classifier that utilizes the expression patterns of genes to predict how likely they are to be undiscovered deafness genes.

CONCLUSIONS

We used a novel approach to highlight novel additional factors that can serve as points of intervention for enhancing hair cell regeneration. Given the similarities between mouse and human deafness, our predictions may be of value in prioritizing future research on novel human deafness genes.

Regeneration of Cochlear Hair Cells and Hearing Recovery through Hes1 Modulation with siRNA Nanoparticles in Adult Guinea Pigs

Deafness is commonly caused by the irreversible loss of mammalian cochlear hair cells (HCs) due to noise trauma, toxins, or infections. We previously demonstrated that small interfering RNAs (siRNAs) directed against the Notch pathway gene, hairy and enhancer of split 1 (Hes1), encapsulated within biocompatible poly(lactic-co-glycolic acid) nanoparticles (PLGA NPs) could regenerate HCs within ototoxin-ablated murine organotypic cultures. In the present study, we delivered this sustained-release formulation of Hes1 siRNA (siHes1) into the cochleae of noise-injured adult guinea pigs. Auditory functional recovery was measured by serial auditory brainstem responses over a nine-week follow-up period, and HC regeneration was evaluated by immunohistological evaluations and scanning electron microscopy. Significant HC restoration and hearing recovery were observed across a broad tonotopic range in ears treated with siHes1 NPs, beginning at three weeks and extending out to nine weeks post-treatment. Moreover, both ectopic and immature HCs were uniquely observed in noise-injured cochleae treated with siHes1 NPs, consistent with de novo HC production. Our results indicate that durable cochlear HCs were regenerated and promoted significant hearing recovery in adult guinea pigs through reversible modulation of Hes1 expression. Therefore, PLGA-NP-mediated delivery of siHes1 to the cochlea represents a promising pharmacologic approach to regenerate functional and sustainable mammalian HCs in vivo.

Hearing Loss in the Elderly

Presbycusis, or age-related hearing loss (ARHL), is the result of physiologic and pathologic changes associated with advancing age. ARHL presents typically with a high-frequency hearing loss, which contributes to greater trouble hearing consonants within words. Consonants convey the bulk of meaning within a word, and this loss of linguistic information results in complaints associated with ARHL. Hearing aids and cochlear implants significantly improve the lives of older adults with hearing loss, in particular, those with depression and dementia. Successful current research in gene therapy, pharmacotherapy, and stems cells holds the promise of being able to restore native cochlear function.

Notch pathway inhibitor DAPT enhances Atoh1 activity to generate new hair cells in situ in rat cochleae

Atoh1 overexpression in cochlear epithelium induces new hair cell formation. Use of adenovirus-mediated Atoh1 overexpression has mainly focused on the rat lesser epithelial ridge and induces ectopic hair cell regeneration. The sensory region of rat cochlea is difficult to transfect, thus new hair cells are rarely produced in situ in rat cochlear explants. After culturing rat cochleae in medium containing 10% fetal bovine serum, adenovirus successfully infected the sensory region as the width of the supporting cell area was significantly increased. Adenovirus encoding Atoh1 infected the sensory region and induced hair cell formation in situ. Combined application of the Notch inhibitor DAPT and Atoh1 increased the Atoh1 expression level and decreased hes1 and hes5 levels, further promoting hair cell generation. Our results demonstrate that DAPT enhances Atoh1 activity to promote hair cell regeneration in rat cochlear sensory epithelium in vitro.