Gene expression profiling of the developing mouse inner ear

Jing Geng, Samin Sajan and Michael Lovett, Department of Genetics, Washington University School of Medicine.

Hearing loss and/or balance disorders affect ~10% of the human population, and congenital deafness occurs with a frequency of about ~3 per 1,000 live births. Most human deafness occurs later in life, and is caused by a combination of environmental factors and genetic predisposition. The vast majority of this later onset hearing loss results from sensorineural deafness; damage to sensory hair cells (the mechanosensory transducers of sound) and/or the nerves of the inner ear. Once damaged, these structures cannot be regenerated. All mammals must maintain these specialized cell types, without replenishment, from embryogenesis to death. To better understand how these cell types might be induced to proliferate or regenerate it is important to understand how they normally develop. Unfortunately, we know very little about the genetic program that underlies the development of the inner ear, partly because the structures are small, complex and inaccessible. The majority of inner ear developmental genetics has yet to be explored. In order to identify genes and pathways that may play important roles in ear development, we embarked upon the first large-scale gene expression profile of the developing mouse inner ear. We micro-dissected inner ears from four different stages of mouse embryogenesis covering stages E9 to E13.5 (the latter being when the development of true hair cells initiates). The inner ear comprises the cochlea and vestibular organs that detect sound and movement, respectively. Therefore, we separately dissected these structures whenever possible. Gene expression profiles were derived using Affymetrix gene chips that interrogate ~30,000 mouse genes. Two litters of embryos per developmental stage were obtained, the structures were dissected and duplicate gene-chips were hybridized. Expression data were analyzed by a number of statistical clustering methods. Genes were selected that were reproducibly differentially expressed by at least 1.5-fold between any two stages, and self-organizing maps were created to identify genes with similar expression patterns. Approximately 600 genes were differentially expressed across the time course, 10% of which had been shown to be expressed in the inner ear previously. Genes with high expression at early stages (E9-E9.5) included Dachshund 2, Choroidermia, Kinesin family member 1B, and NeuroD6. Among those that are highly expressed later at E13.5 and beyond are GATA3, FGF-20, Aryl hydrocarbon receptor, Neuronatin, and Otogelin. This study provides new candidate pathways for further investigation in inner ear development and in the genetics of hearing loss.