Large Scale Gene Expression Profiles of Regenerating Inner Ear Sensory Epithelia

Abstract

Loss of inner ear sensory hair cells (HC) is a leading cause of human hearing loss and balance disorders. Unlike mammals, many lower vertebrates can regenerate these cells. We used cross-species microarrays to examine this process in the avian inner ear. Specifically, changes in expression of over 1700 transcription factor (TF) genes were investigated in hair cells of auditory and vestibular organs following treatment with two different damaging agents and regeneration in vitro. Multiple components of seven distinct known signaling pathways were clearly identifiable: TGFβ, PAX, NOTCH, WNT, NFKappaB, INSULIN/IGF1 and AP1. Numerous components of apoptotic and cell cycle control pathways were differentially expressed, including p27KIP and TFs that regulate its expression. A comparison of expression trends across tissues and treatments revealed identical patterns of expression that occurred at identical times during regenerative proliferation. Network analysis of the patterns of gene expression in this large dataset also revealed the additional presence of many components (and possible network interactions) of estrogen receptor signaling, circadian rhythm genes and parts of the polycomb complex (among others). Equal numbers of differentially expressed genes were identified that have not yet been placed into any known pathway. Specific time points and tissues also exhibited interesting differences: For example, 45 zinc finger genes were specifically up-regulated at later stages of cochlear regeneration. These results are the first of their kind and should provide the starting point for more detailed investigations of the role of these many pathways in HC recovery, and for a description of their possible interactions.

Gene-expression analysis of hair cell regeneration in the zebrafish lateral line

“…Work in birds has shed light on the mechanisms regulating sensory hair cell regeneration in vertebrates (2,4,(11)(12)(13)(14)(15)(16)(17)(18). For instance, during sensory hair cell regeneration in the chick, the majority of hair cells arise by proliferation of neighboring support cells (19).…”

“…Given that mammalian support cells do not respond to hair cell death by proliferating, molecular studies in chick have focused on identifying the mitogenic signals as well as the target genes that induce re-entering of the cell cycle in support cells (11,(20)(21)(22). For example, the transcription factors Atoh1 and Sox2 and the Wnt/β-catenin and Notch pathways have been shown to play crucial roles (23), and gene-expression analyses using microarrays have identified hundreds of genes involved in chick hair cell regeneration (18,24).…”

Epigenetic Influences on Sensory Regeneration: Histone Deacetylases Regulate Supporting Cell Proliferation in the Avian Utricle

“…In contrast, the ears of nonmammalian vertebrates can quickly regenerate hair cells after noise trauma or ototoxic injury (Corwin and Oberholtzer 1997). Microarray-based studies have identified numerous changes in gene expression that occur during sensory regeneration in the avian ear (Hawkins et al 2003(Hawkins et al , 2007. Similar changes in transcriptional activity have been demonstrated in the developing mammalian inner ear, suggesting certain commonalities between development and regeneration .…”

“…Replacement hair cells are generated by epithelial supporting cells, either through renewed proliferation or by direct phenotypic change (e.g., Raphael 1992; Roberson et al 2004;Weisleder and Rubel 1993). Both of these regenerative processes will require significant changes in gene expression (e.g., Hawkins et al 2007), but the possible involvement of epigenetic forms of regulation (e.g., histone acetylation) in regeneration has not been previously examined. In the present study, we show that pharmacological inhibition of histone deacetylases results in decreased proliferation of vestibular supporting cells, both in dissociated culture and in intact utricles.…”

“…It would be of great interest to identify genes that actively inhibit the proliferation of supporting cells since they may partially account for the qualitative differences in regenerative ability of the avian vs. mammalian ear. Several previous studies have utilized microarray methods to characterize gene expression in the regenerating avian ear (Hawkins et al 2003(Hawkins et al , 2007, and further studies should reveal the identity of genes in the avian ear whose expression is regulated by histone acetylation.…”