title: Laser-capture micro dissection combined with next-generation sequencing analysis of cell type-specific deafness gene expression in the mouse cochlea.
abstract: Cochlear implantation (CI), which directly stimulates the cochlear nerves, is the most effective and widely used medical intervention for patients with severe to profound sensorineural hearing loss. The etiology of the hearing loss is speculated to have a major influence of CI outcomes, particularly in cases resulting from mutations in genes preferentially expressed in the spiral ganglion region. To elucidate precise gene expression levels in each part of the cochlea, we performed laser-capture micro dissection in combination with next-generation sequencing analysis and determined the expression levels of all known deafness-associated genes in the organ of Corti, spiral ganglion, lateral wall, and spiral limbs. The results were generally consistent with previous reports based on immunocytochemistry or in situ hybridization. As a notable result, the genes associated with many kinds of syndromic hearing loss (such as Clpp, Hars2, Hsd17b4, Lars2 for Perrault syndrome, Polr1c and Polr1d for Treacher Collins syndrome, Ndp for Norrie Disease, Kal for Kallmann syndrome, Edn3 and Snai2 for Waardenburg Syndrome, Col4a3 for Alport syndrome, Sema3e for CHARGE syndrome, Col9a1 for Sticker syndrome, Cdh23, Cib2, Clrn1, Pcdh15, Ush1c, Ush2a, Whrn for Usher syndrome and Wfs1 for Wolfram syndrome) showed higher levels of expression in the spiral ganglion than in other parts of the cochlea. This dataset will provide a base for more detailed analysis in order to clarify gene functions in the cochlea as well as predict CI outcomes based on gene expression data.
authors.affiliation: Department of Otorhinolaryngology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto 390-8621, Japan; Department of Hearing Implant Sciences, Shinshu University School of Medicine 3-1-1 Asahi, Matsumoto 390-8621, Japan.
authors.forename: Shin-Ya
authors.initials: SY
authors.lastname: Nishio
authors.affiliation: Department of Otorhinolaryngology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto 390-8621, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Takumi
authors.affiliation: Department of Otorhinolaryngology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto 390-8621, Japan; Department of Hearing Implant Sciences, Shinshu University School of Medicine 3-1-1 Asahi, Matsumoto 390-8621, Japan. Electronic address: usami@shinshu-u.ac.jp.
authors.forename: Shin-Ichi
authors.initials: SI
authors.lastname: Usami
mesh_terms: D000818:Animals; D003051:Cochlea / Q000378:metabolism*; D019929:Cochlear Implantation / Q000009:adverse effects; D003638:Deafness / Q000175:diagnosis / Q000235:genetics*; D004195:Disease Models, Animal; D020869:Gene Expression Profiling; D059014:High-Throughput Nucleotide Sequencing; D007150:Immunohistochemistry; D017403:In Situ Hybridization; D061346:Laser Capture Microdissection; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D013136:Spiral Ganglion / Q000473:pathology*; D052245:Usher Syndromes / Q000235:genetics