Animals
Sprague–Dawley rats were obtained from Dae Han Bio Link Co., Ltd. (Chungbuk, Korea). All procedures involving animals were approved by the institutional review board of Ajou University School of Medicine (AJIRB-MED-SMP-11-002; Suwon, South Korea).
Organ of Corti explants
After making an incision in the neck of Sprague–Dawley rats, the skin and mandibular bone were removed and the skull was opened. Then, the brain was removed, and the temporal bone was collected in a sterile 60-mm petri dish containing phosphate-buffered saline (PBS). The lateral wall and spiral ganglion neurons (SGNs) were removed using fine forceps and the organ of Corti was placed in a tissue culture plate and cultured overnight in Dulbecco’s modified Eagle’s medium (Gibco-BRL, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (Gibco-BRL) and 0.06 mg/mL penicillin (Sigma-Aldrich, Steinheim, Germany) at 37°C with 5% CO2.
Drug treatment
After 24 h in culture, the cochlea was randomly divided into four groups. We used 10 μM of the γ-secretase inhibitor, N-[N-(3,5-difluorophenacetyl)-L-alanyl]-(S)-phenylglycine t-butyl ester (DAPT; Calbiochem, Darmstadt, Germany), and 5 µM of the Wnt activator, CHIR-99021 (Sigma-Aldrich), for transdifferentiation. LDN-57444 (Selleckchem, Houston, TX, USA), a specific UCHL1 inhibitor, was used at a concentration of 5 μM. The explant was treated with 48 mM gentamicin (Sigma-Aldrich) for 24 h to induce damage to the HCs, followed by treatment with 2.5 nM rapamycin (Sigma-Aldrich), a mammalian target of rapamycin (mTOR) inhibitor. The culture medium was replaced once every 3 days after drug treatment.
Quantitative polymerase chain reaction
Total cochlear RNA was extracted using RNAiso Plus (TaKaRa, Shiga, Japan), and cDNA was synthesized using a reverse transcription kit (TaKaRa) according to the manufacturer’s instructions. Quantitative PCR (qPCR) measurements were performed using the ABI Prism 7000 Sequence Detection System (Bio-Rad, Hercules, CA, USA) and the SYBR Green I qPCR Kit (NanoHelix, Daejeon, Korea) according to the manufacturer’s instructions. The qPCR primers were as follows: Uchl1 (F) 5’- GAT TAA CCC CGA GAT GCT GA -3’, Uchl1 (R) 5’- CTG AGC CCA GAG TCT CCT CC -3’; myosin VIIA (Myo7a) (F) 5’- GAG CTG CTG TGG CTG TGG ACA GGC C -3’, Myo7a (R) 5’- CAC CAG GTG TGG AGG GTA CTT C -3’; Brn3c (F) 5’- GTC TCA GCG ATG TGG AGT CA -3’, Brn3c (R) 5’- GCG ACA GGG TAA GAG ACT CG -3’; SRY-box 2 (Sox2) (F) 5’- GGG AAA TGG GGA GGG GTG CAA AAG AGG, Sox2 (R) 5’- TTG CGT GAG TGT GGA TGG GAT TGG TG -3’; and Gapdh (F) 5’- AAC GAC CCC TTC ATT GAC C -3’, Gapdh (R) 5’- TCC ACG ACA TAC TCA GCA CC -3’. After normalization to Gapdh, relative gene expression was analyzed by threshold cycle method. The expression of the gene of interest was expressed as fold-change relative to the control group.
Immunohistochemistry
The dissected cochleae were fixed in 4% paraformaldehyde and stored overnight at 4°C. Then, they were washed with PBS and decalcified in Calci-Clear Rapid Decalcifying Solution (National Diagnostics, Atlanta, GA, USA) for 3 days. For immunofluorescent histological analysis, the cochleae were embedded in paraffin using a specialized automated tissue processing system. The paraffin-sectioned slide was deparaffinized, rehydrated with grade alcohol, and processed for antigen retrieval using citrate buffer (pH 6.0) at 95°C for 15 min. After cooling, endogenous peroxidase was blocked in 3% hydrogen peroxide in methanol at room temperature for 10 min. The slide was blocked in 1% bovine serum albumin (BSA; GenDEPOT, Barker, TX, USA) for 1 h, and then incubated overnight at 4°C with the following primary antibodies: anti-UCHL1 (1:1,000; #13179; Cell Signaling Technology [CST], Danvers, MA, USA), anti-SOX2 (1:1,000; #4900; CST), and anti-MYO7A (1:1,000; #25-6790; Proteus Biosciences, Ramona, CA, USA). After washing, the slide was incubated at room temperature for 1 h with fluorescein isothiocyanate (FITC)- or cyanine 3 (Cy3)-conjugated secondary antibody. The nuclei were counterstained with 4′6,-diamidino-2-phenylindole (1:10,000; DAPI; Invitrogen, Paisley, UK). Images were taken with the Zeiss LSM 710 confocal microscope (Carl Zeiss Meditec, Jena, Germany).
Immunofluorescence
Cochlea explant tissues were fixed in 4% paraformaldehyde (Biosesang, Gyeonggi-do, Korea) for 15 min at room temperature, washed, permeabilized, and blocked in 1% BSA (GenDEPOT). Then, the cochlea tissues were incubated overnight at 4°C with the following primary antibodies: anti-SOX2 (1:1000; CST), anti-MYO7A (1:1,000; Proteus Biosciences), and anti-BRN3C (1:0,00; sc-81980; Santa Cruz Biotechnology, Santa Cruz, CA, USA). Samples were thoroughly washed and incubated at room temperature for 1 h with FITC- or Cy3-conjugated secondary antibodies. Nuclei were counterstained with DAPI, and coverslips were mounted onto slides with mounting medium (Vector Laboratories, Burlingame, CA, USA). The immunostained tissues were observed by confocal laser scanning microscopy (LSM 710; Carl Zeiss Meditec) at the Three-Dimensional Immune System Imaging Core Facility of Ajou University.
Western blot analysis
Cochlea explant tissue was lysed in radioimmunoprecipitation buffer (25 mM Tris HCl, pH 8, 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, and 0.1% sodium dodecyl sulfate [SDS]) with a protease inhibitor cocktail (GenDEPOT). After extracting the proteins by centrifugation (13,000 rpm, 30 min), equal amounts of protein were loaded onto each lane of a gel, separated by SDS-polyacrylamide gel electrophoresis, and transferred to a polyvinylidene difluoride membrane (Millipore, Bedford, MA, USA) using an electroblotting apparatus. Membranes were blocked in 5% skim milk for 1 h and then incubated with primary antibodies at 4°C overnight. Then, the membranes were incubated with horseradish peroxidase-conjugated secondary antibodies (1:5,000; GenDEPOT) for 1 h at room temperature. After washing the membrane, the proteins were detected using Enhanced Chemiluminescence Western Blotting Substrate (Thermo Scientific, Pierce Biotechnology, Waltham, MA, USA) and quantitated with densitometry analysis using ImageJ software (National Institutes of Health, Bethesda, MD, USA). The following primary antibodies were used: anti-UCHL1 (1:1,000; CST), anti-BRN3C (1:1,000; Santa Cruz Biotechnology), anti-MYO7A (1:500; Proteus Biosciences), anti-SOX2 (1:500; CST), anti-phospho-P70S6 (p-P70S6) kinase (1:1,000; #97596; CST), anti-P70S6 kinase (1:1,000; sc-393967; Santa Cruz Biotechnology), and anti-β-actin (1:5,000, #4970; CST).
5-ethynyl-2′-deoxyuridine incorporation assay
5-ethynyl-2′-deoxyuridine (EdU) is a nucleoside analog of thymidine incorporated into DNA during active DNA synthesis. Cell proliferation was determined by the EdU incorporation assay using the Click-iT® EdU Imaging Kit (Invitrogen/Molecular Probes) according to the manufacturer’s protocol. Briefly, tissues were treated with 10 µM EdU for 5 days and then fixed in 4% paraformaldehyde (Biosesang) for 15 min at room temperature. After washing with PBS and permeabilizing with 0.5% Triton X-100, the Click-iT® reaction cocktail containing AlexaFluor® 555-azide was added to the cells for 30 min. Then immunofluorescence was performed for co-labeling with EdU and SOX2 or MYO7A.
Hematoxylin and eosin staining and histological analysis
Cochleae were harvested and fixed in 4% paraformaldehyde at 4°C for 2 days. Then, they were washed with PBS and decalcified for 5 days using the Calci-Clear Rapid high-speed decalcifier (National Diagnostics). Decalcified cochleae tissues were embedded in paraffin using an automated tissue processing system. The paraffin blocks were sliced into 5-μm-thick sections. The slides were dried for 30 min on a slide warmer at 60°C, deparaffinized, rehydrated in a graded alcohol series, and then stained with hematoxylin and eosin. The percentages of HCs, SGNs, and fibrocytes in the middle turn of the cochleae of at least five ears were scored, and the average was calculated.
Statistical analyses
All values are expressed as the mean ± standard deviation. The groups were compared by the Mann–Whitney U test using SPSS software (version 12.0; SPSS Inc., Chicago, IL, USA). P < 0.05 was considered statistically significant.