title: Characterization of transcriptomes of cochlear inner and outer hair cells.
abstract: Inner hair cells (IHCs) and outer hair cells (OHCs) are the two types of sensory receptor cells that are critical for hearing in the mammalian cochlea. IHCs and OHCs have different morphology and function. The genetic mechanisms that define their morphological and functional specializations are essentially unknown. The transcriptome reflects the genes that are being actively expressed in a cell and holds the key to understanding the molecular mechanisms of the biological properties of the cell. Using DNA microarray, we examined the transcriptome of 2000 individually collected IHCs and OHCs from adult mouse cochleae. We show that 16,647 and 17,711 transcripts are expressed in IHCs and OHCs, respectively. Of those genes, ∼73% are known genes, 22% are uncharacterized sequences, and 5.0% are noncoding RNAs in both populations. A total of 16,117 transcripts are expressed in both populations. Uniquely and differentially expressed genes account for <15% of all genes in either cell type. The top 10 differentially expressed genes include Slc17a8, Dnajc5b, Slc1a3, Atp2a3, Osbpl6, Slc7a14, Bcl2, Bin1, Prkd1, and Map4k4 in IHCs and Slc26a5, C1ql1, Strc, Dnm3, Plbd1, Lbh, Olfm1, Plce1, Tectb, and Ankrd22 in OHCs. We analyzed commonly and differentially expressed genes with the focus on genes related to hair cell specializations in the apical, basolateral, and synaptic membranes. Eighty-three percent of the known deafness-related genes are expressed in hair cells. We also analyzed genes involved in cell-cycle regulation. Our dataset holds an extraordinary trove of information about the molecular mechanisms underlying hair cell morphology, function, pathology, and cell-cycle control.
authors.affiliation: Neuroscience Center, Ningbo University School of Medicine, Ningbo 315211, China, and Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68178.
authors.forename: Huizhan
authors.initials: H
authors.lastname: Liu
authors.affiliation: Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68178.
authors.forename: Jason L
authors.initials: JL
authors.lastname: Pecka
authors.affiliation: Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68178.
authors.forename: Qian
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68178.
authors.forename: Garrett A
authors.initials: GA
authors.lastname: Soukup
authors.affiliation: Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68178.
authors.forename: Kirk W
authors.initials: KW
authors.lastname: Beisel
authors.affiliation: Neuroscience Center, Ningbo University School of Medicine, Ningbo 315211, China, and Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68178 hed@creighton.edu.
authors.forename: David Z Z
authors.identifier: http://orcid.org/0000-0001-8383-9634
authors.initials: DZ
authors.lastname: He
mesh_terms: D000818:Animals; D003051:Cochlea / Q000166:cytology* / Q000378:metabolism; D006199:Hair Cells, Auditory, Inner / Q000166:cytology / Q000378:metabolism*; D018072:Hair Cells, Auditory, Outer / Q000166:cytology / Q000378:metabolism*; D051379:Mice; D059467:Transcriptome
keywords: DNA microarray; inner hair cells; mouse; outer hair cells; transcriptome