• Corrigendum: Transcriptomic profiling of zebrafish hair cells using RiboTag [Front. Cell Dev. Biol., 6, 47, (2018)] doi: 10.3389/fcell.2018.00047

      Matern, M.S.; Beirl, A.; Ogawa, Y. (Frontiers Media S.A., 2018)
      Although the reported fold change values and statistics were accurate, there was a mistake in the CPM values shown in Supplementary Dataset 1 in the original article. This mistake has been corrected and it has resulted in a slight change in the number of transcripts meeting the CPM cutoff for expression (n = 17,164), enrichment (n = 2,379), and depletion (n = 2,258). These corrected numbers of expressed, enriched and depleted transcripts are now reflected in the text, as well as in Figure 3a. The gene ontology and ZEOGS analyses have been redone and changes have been made to Tables 1-3, and Supplementary Table 2. The genes chosen for validation now fall within the top 100 enriched transcripts rather than the top 50; therefore, Supplementary Table 3 has been changed to show the top 100 enriched transcripts. The scientific conclusions made from these analyses have not changed in any way. Copyright 2018 Matern, Beirl, Ogawa, Song, Paladugu, Kindt and Hertzano.
    • Magnetic nanoparticle mediated steroid delivery mitigates cisplatin induced hearing loss

      Ramaswamy, B.; Roy, S.; Apolo, A.B. (Frontiers Media S.A., 2017)
      Cisplatin (cis-diamminedichloroplatinum) is widely used as a chemotherapeutic drug for genitourinary, breast, lung and head and neck cancers. Though effective in inducing apoptosis in cancer cells, cisplatin treatment causes severe hearing loss among patients. Steroids have been shown to mitigate cisplatin-induced hearing loss. However, steroids may interfere with the anti-cancer properties of cisplatin if administered systemically, or are rapidly cleared from the middle and inner ear and hence lack effectiveness when administered intra-tympanically. In this work, we deliver prednisolone-loaded nanoparticles magnetically to the cochlea of cisplatin-treated mice. This magnetic delivery method substantially reduced hearing loss in treated animals at high frequency compared to control animals or animals that received intra-tympanicmethylprednisolone. The method also protected the outer hair cells from cisplatin-mediated ototoxicity. Copyright 2017 Ramaswamy, Roy, Apolo, Shapiro and Depireux.
    • Transcriptomic profiling of zebrafish hair cells using RiboTag

      Matern, M.S.; Beirl, A.; Ogawa, Y. (Frontiers Media S.A., 2018)
      The zebrafish inner ear organs and lateral line neuromasts are comprised of a variety of cell types, including mechanosensitive hair cells. Zebrafish hair cells are evolutionarily homologous to mammalian hair cells, and have been particularly useful for studying normal hair cell development and function. However, the relative scarcity of hair cells within these complex organs, as well as the difficulty of fine dissection at early developmental time points, makes hair cell-specific gene expression profiling technically challenging. Cell sorting methods, as well as single-cell RNA-Seq, have proved to be very informative in studying hair cell-specific gene expression. However, these methods require that tissues are dissociated, the processing for which can lead to changes in gene expression prior to RNA extraction. To bypass this problem, we have developed a transgenic zebrafish model to evaluate the translatome of the inner ear and lateral line hair cells in their native tissue environment; the Tg(myo6b:RiboTag) zebrafish. This model expresses both GFP and a hemagglutinin (HA) tagged rpl10a gene under control of the myo6b promoter (myo6b:GFP-2A-rpl10a-3xHA), resulting in HA-tagged ribosomes expressed specifically in hair cells. Consequently, intact zebrafish larvae can be used to enrich for actively translated hair cell mRNA via an immunoprecipitation protocol using an antibody for the HA-tag (similar to the RiboTag mice). We demonstrate that this model can be used to reliably enrich for actively translated zebrafish hair cell mRNA. Additionally, we perform a global hair cell translatome analysis using RNA-Seq and show enrichment of known hair cell expressed transcripts and depletion of non-hair cell expressed transcripts in the immunoprecipitated material compared with mRNA extracted from whole fish (input). Our results show that our model can identify novel hair cell expressed genes in intact zebrafish, without inducing changes to gene expression that result from tissue dissociation and delays during cell sorting. Overall, we believe that this model will be highly useful for studying changes in zebrafish hair cell-specific gene expression in response to developmental progression, mutations, as well as hair cell damage by noise or ototoxic drug exposure. Copyright 2018 Matern, Beirl, Ogawa, Song, Paladugu, Kindt and Hertzano.