Towards a predictive model for vertebrate inner ear determination

Communication with each other and our environment through speech and hearing is fundamental for normal development of children as well as for healthy ageing. Worldwide, 1.64 babies per 1000 births are born deaf, making hearing impairment one of the most prevalent congenital defects. Likewise, more than 50% of the population over 60 is affected by hearing problems reducing their quality of life and mental and social well-being. Despite progress in identifying genes underlying ear defects in children and in understanding how sound sensing cells in the ageing or damaged ear degenerate, many of the genes responsible remain unknown; for those that are known, their interactions are poorly understood. This is because systematic studies are lacking, as is a unifying model for ear formation that integrates information about gene function from different animal models. Here we propose to construct such a model by combining a computational tool, systematic in vivo experiments and a new technology to monitor changes in up to 200 molecules in a single sample. To do this we have chosen a higher vertebrate model system, the chick, whose development closely resembles human development. We adapted state-of-the-art technology to make this project possible and have already generated a list of genes specific for cells that form the ear. Now, we will use this list together with data from the literature to construct a computer model that predicts how different molecules interact with each other and which molecules are most important to form the ear. We will then test these predictions using in vivo experiments by systematically removing the function of each important factor and measuring how all other components of the model behave. This information will then be fed back into the model for refinement. Repeating the cycle of experimental manipulation and computer modelling will generate a reliable model that replicates normal ear formation in the embryo, to explain the interactions between different molecules. This model will be useful to predict novel candidates for congenital and late-onset deafness, to predict the consequences of genetic mutations, and to design strategies to drive stem cells towards ear fate or to reactivate intrinsic stem cells in the normal ear to replace damaged structures. In addition, because of its predictive nature, it will be help to reduce and refine animal experiments in biomedical research.

Understanding how cell fate decisions are controlled has been a key objective of developmental biology over the past decades. Ultimately, the instructions for developmental programmes reside in the non-coding regulatory regions and their interacting factors. While many of these have been identified, the next major challenge is to integrate this information and to develop predictive models for normal development and disease. Gene regulatory networks are models to predict gene interactions and functional relationships. However, until now the bottleneck has been the lack of tools to measure different network components simultaneously after experimental perturbation in vivo. To overcome this we have adapted new technology to a well-studied amniote system, the chick: we have perfected expression profiling from small tissue samples, optimised temporal and spatial gene knockdown, quantification of up to 200 transcripts in a single sample and rapid identification and in vivo testing of enhancers. These advances put us into the unique position to address this challenge in a higher vertebrate. Because of its importance to human disease and its well-described embryonic development, we are studying the commitment of multipotent cells to the inner ear lineage. Having taken an unbiased approach to uncover novel ear specifiers we will now - construct a predictive gene regulatory network for ear specification from literature and our own data using computational tools - reiterate experimental model testing and modelling by systematic knockdown of predicted key components, measuring the behaviour of all genes within the network and feeding the results back into the model - verify predicted genetic interactions by in vivo enhancer analysis This will establish a dynamic gene regulatory network for inner ear specification, which predicts experimental outcomes and point to new candidates for human disease.

This project aims to establish a model for ear development as a basis to identify new candidate genes for congenital deafness and late-onset hearing impairment. It combines biological, bioinformatics and modelling approaches to create an interactive network of the genes and processes that commit multipotent sensory stem cells to otic identity. The data produced in this project will be made publically available, including an on-line, interactive network. We will seek different routes to engage with academics and medical professionals by publications and seminars and with the public by working with charities and schools. Once our data are presentable we aim to participate in the Royal Society Science Exhibition, which is visited by individuals and school classes. Who will benefit from this research? This research will benefit children born with hearing defects, their parents and medical professionals such as paediatricians, otolaryngologists and genetic counsellors. It will also benefit the general public interested in science, schools and 6th form students, as well as charities. Finally, because of its multidisciplinary nature it will also train early career scientists in innovative research strategies and provide them with transferrable skills. How will they benefit from this research? Childhood deafness causes problems with language, communication, literacy and can decrease a child's confidence throughout life, while age-related hearing impairment can lead to isolation and depression thus affecting both physical and mental well-being. The identification of new candidate genes for human deafness will improve diagnosis, genetic counselling and may ultimately lead to the development of new treatments or drugs. This will not only benefit the individuals affected, but also medical professionals engaged clinical aspects of deafness. Thus, in the long term our data will improve health in the UK and worldwide. We will provide an interactive model of ear development, which will be publically available as a virtual learning environment. This will help members of the general public to learn about the ear and the causes of deafness, as well as about general principles in development, in an interactive way. This will be useful for parents of children with hearing problems for better understanding of the disease, for interested individuals, but also as a resource for teachers to demonstrate the complexity of biological systems. Importantly, as our network can be viewed at different levels, individuals can zoom in as deep as they wish. Thus, the project contributes to education of the general public in scientific research. Two main charities in the UK, Deafness Research UK and RNID, are crucial supporters for deaf and hard of hearing people. Our data will be publically available and aid these charities to raise awareness as well as to attract donors to support basic and clinical research into deafness. As previous and current grant holder I have already established contact and will continue to provide material to promote their cause. Finally, multidisciplinary projects as this provide an excellent opportunity to train new professionals for a scientific career in academia, industry and elsewhere. Committed to excellence in teaching I make a special point of training incoming young scientist myself. This project provides them with a broad foundation for a career in science and equips them with transferrable skills useful to any profession. They will learn how to tackle complex questions systematically and acquire time management, multi-tasking, problem solving, presentation and communication skills, as well as obtain scientific training. In addition, we routinely host summer projects for 6th form students to introduce and engage them into science through first-hand experience. The project therefore contributes to education and professional development and thus benefits UK economy in the long term.