By Peter G. Barr-Gillespie, Ph.D.

Hearing loss occurs when sensory hair cells of the inner ear (cochlea) are damaged or die. The goal of the Hearing Restoration Project (HRP) is to develop therapeutic methods to convert the cells that remain after damage into new, completely functional sensory hair cells, restoring hearing. We know that in most species—but not mammals, like humans and mice—hair cells robustly regenerate on their own after damage to the auditory system. The HRP is tasked with uncovering how to replicate this regeneration process in humans.

Here are the funded HRP projects for the coming year. Thank you for your ongoing support.

Integrative Systems Biology of Hearing Restoration 
Seth Ament, Ph.D.
University of Maryland School of Medicine

Year 3  | The broad premise of the HRP is to identify molecules that could control hair cell regeneration. To do this, we are studying cell types and regenerative processes in multiple contexts and species, then integrating these data together to identify mechanisms that could potentially be turned on in the mouse cochlea to drive transdifferentiation (activating the correct set of hair cell–promoting genes in supporting cells). The role of this systems biology project is to provide the necessary data integration “glue,” binding together the results from the data generation projects. We will combine much of the data that is being generated by the HRP to advance our knowledge of hair cells, supporting cells, conversion of one cell type to another, and the potential for regeneration. By modeling all of the available HRP data, we will identify regulatory molecules that may contribute to regeneration.

Comparison of Three Reprogramming Cocktails in the Organ of Corti: Cells, Transcriptomes, and Epigenomes
Andy Groves, Ph.D.
Baylor College of Medicine

Year 3  | Each cell type in the human body is defined by its activation of a unique combination of genes that endow each cell type with unique properties. The activation of these genes is achieved by special proteins known as transcription factors, or “switches,” responsible for switching on appropriate genes in one cell type and preventing inappropriate genes from being activated. In recent years, investigators have identified a number of these transcription factors that cause the formation of hair cells. The goal this year is to examine why these cocktails of transcription factors are able to “reprogram” nonsensory cells, but not supporting cells of the inner ear, to become hair cells.

Detection of Transcriptome Changes in Single Cells After Aminoglycoside-Induced Hair Cell Loss in the Chicken Basilar Papilla 
Stefan Heller, Ph.D.
Stanford University

Year 4 | Birds robustly regenerate their cochlear hair cells through the conversion of dormant supporting cells into new hair cells. Our project uses selective, high-sensitivity methods to reveal the molecular changes in supporting cells after their activation by, for example, ototoxic drugs that cause hair cell death. By examining the responses of many single cells, we have begun to identify triggers that initiate, execute, sustain, and ultimately terminate the regenerative process. Recent experiments have confirmed what we already knew, that the two halves of the chicken cochlea (neural and abneural) predominantly use different regeneration mechanisms. Using bioinformatics methods to process the resulting data, this year we are focusing on analyzing chicken cochlea cell populations isolated at various time points during hair cell regeneration and specifically characterizing the two distinct responses. By examining regeneration in an animal that replaces hair cells after damage, we will be able to find triggers that may be activated in mammals to reverse hair cell loss.

Epigenetics Analysis of Maturation and Regenerative Responses in the Mouse Organ of Corti and Utricle 
Neil Segil, Ph.D.
University of Southern California
Andy Groves, Ph.D.
Baylor College of Medicine

Year 4 | Surprisingly, newborn mice have a limited ability to regenerate hair cells, although this capability disappears within the first few weeks of life. Because of this transition, we can address experimentally the failure of hair cell regeneration in mammals. Our project is investigating changes in the genetic material, the chromatin, that are responsible for orchestrating the differentiation of new hair cells within the newborn organ of Corti in the inner ear and the changes in the chromatin that lead to the failure of regeneration in the adult mammalian inner ear. This year we will focus on changes to the chromatin that occur after the loss of hair cell function and will test methods for activating hair cell regeneration by direct modification of the chromatin.

Implementing the gEAR for Data Sharing Within the HRP
Ronna Hertzano, M.D., Ph.D.
University of Maryland School of Medicine

Year 4 | One of the successes of the HRP has been the development of the gEAR portal (gene Expression Analysis Resource, umgear.org). The gEAR has many public and private datasets, and these complex datasets can be compared by scientists without the need for sophisticated programming expertise. The gEAR is also the primary data sharing, visualization, and analysis tool for auditory researchers outside of the HRP, becoming a platform that supports the hearing research community at large. This year we will build on past successes, continuing to support data upload, develop new visualization tools, and further enable the greater research community to exploit this resource. 

Mouse Model Systems to Interrogate Candidate Genes for Sensory Hair Cell Regeneration
John Brigande, Ph.D.
Oregon Health & Science University

Year 6 | As HRP scientists detect and characterize genes that are hypothesized to participate in the activation or inhibition of hair cell regeneration, methods for altering or disrupting those genes are critical to the demonstration of their importance. This project aims to couple together two sophisticated methods for manipulating genes in mice, the so-called CRISPR-READI and i-GONAD methods. CRISPR-READI enables efficient, large gene edits, and i-GONAD simplifies the delivery of reagents for gene editing. Together, the proposed CRISPR-READI-GO method should allow for rapid and efficient gene editing to be put to use by HRP investigators.

HRP scientific director Peter G. Barr-Gillespie, Ph.D., is a professor of otolaryngology and the chief research officer and executive vice president at Oregon Health & Science University. For more, see hhf.org/hrp.