2.1 Summary of microarray datasets
Public microarray repositories were curated to search through the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo) using the keywords “ouabain” and “hearing loss”. We found three datasets in the search results and GSE59416 was used for the subsequent bioinformatics analysis. The overall design of GSE59416 was as follows: An ouabain solution was administered in the round window niche of the right ear, while the left ears (i.e., contralateral) were not surgically manipulated and were used as controls. Mice were allowed to recover for 3 days or 7 days following treatments. The cochleas were prepared for RNA extraction and the subsequent global gene expression analysis.
2.2 DEGs enrichment analysis and its visualization of the datasets
R tools was used in this study. Quality control was performed using the ‘simpleaffy’ ‘affyPLM’ packages. After quality control, unqualified sample data were removed. The datasets were then normalized on the base-2 logarithm using the Robust Multi-Array Average and Linear Models for Microarray packages and annotated by converting different probe IDs to gene IDs. Genes significantly dysregulated in acute SGN injury mice as compared to matched data in control samples were defined by an adjusted p-value < 0.01 and log2 fold change of > 2 (upregulated genes) or < − 2 (downregulated genes). Finally, gene ontology enrichment analysis and Kyoto encyclopedia of genes and genomes enrichment analysis were performed using the ‘GOstats’ and ‘GeneAnswers’ packages. We used the ‘Clusterfiler’ and ‘pheatmap’ packagex to visualize the statistical analysis.
2.3 Animals and experimental design
Animal experiments were carried out following the National Institute of Health Guide for the Care and Use of Laboratory Animals. The study protocol was approved by the Animal Subjects Review Board of the Hangzhou Normal University School of Medicine (permit no. 2019175). Surgeries were carried out under sodium pentobarbital anesthesia.
Mongolian gerbils (2–3 mouths, weighing 60–80 g) were obtained from the Laboratory Animal Centre of Hangzhou Normal University. All animals had free access to both food and water and were kept maintained in cages with a 12 h light: dark cycle at a temperature and humidity of 21–24 ℃ and 40–70%, respectively.
2.4 Neural deafness model and neuritin treatment
Gerbils were assigned to an experimental and control group. First, ouabain (Sigma, O3125, St Louis, MO, USA) was dissolved in normal saline (NS). Next, the cochlear bulla was exposed through a retro-auricular approach followed by creating a small hole in the bulla to expose the round window and the ouabain (20 µL, 1mM) solution was positioned onto the round window membrane of the cochlea. The solution was then incubated for 30 min at 37 ℃, after which small cubes (1 mm3) of gelfoam were soaked in 16/32 µL of a 1 mg/mL solution of neuritin dissolved in NS that positioned onto the round window membrane. The control group received NS instead of neuritin. Hearing was measured weekly after administration using the auditory brainstem response (ABR). Subsequently, the gerbils in each group were euthanized, and the cochlear samples were isolated and taken out for immunofluorescence detection
2.5 Cochlear samples collection
In order to clarify the correlation between neuritin and auditory function, we examined its expression changes in the cochlea of gerbils. Specifically, neuritin mRNA and protein expression from cochlear tissue of gerbils at different developmental stages was assessed by western blot and qPCR, respectively. After euthanasia, cochlear tissue samples (E20, P0-1, P7-10, P21, P56) were separated and stored in liquid nitrogen.
In order to further clarify the relationship between neuritin and ouabain-induced hearing impairment in gerbils, neuritin mRNA and protein expression in the control group and at 6 h and 3, 7, and 56 days after injury were detected by western blot and qPCR respectively. After euthanasia, the gerbil cochlea injured by ouabain was extracted, and the cochlea tissue samples were separated and stored in liquid nitrogen.
The cochlear tissue of the gerbils in the normal group and at 7 days were next assessed by immunofluorescence to detect the expression of neuritin in the cochlea.
2.6 Organotypic culture of the cochleae
Gerbil cochlear organotypic cultures were prepared as previously described [25]. Briefly, a mixture of rat-tail collagen (9:1:1 ratio of Type 1 collagen (BD Biosciences, #4236, Bedford, MA, USA), 10 × basal medium eagle (Sigma, #B9638), and 2% sodium carbonate was prepared, and 10 µL of the mixture was placed in the center of a 35 mm diameter culture dish (Falcon 1008, Becton Dickinson) for 30 min until the mixture solidified. Then, 1.3 mL of serum-free medium [2 g bovine serum albumin (BSA, Sigma A-4919), 2 mL serum-free supplement (Sigma, #I-188), 4.8 mL of 20% glucose (Sigma G-2020), 0.4 mL penicillin G (Sigma P-3414), 2 mL of 200 mM glutamine (Sigma G-6392), and 190.8 mL of 1 × BME (Sigma B-1522)] were added to the culture dish.
On postnatal day 3, gerbil pups were euthanized by carbon dioxide asphyxiation and decapitated. The temporal bones were removed, and the whole basilar membrane containing the organ of Corti and SGNs was carefully dissected out in Hank's balanced salt solution and placed on the surface of the collagen gel in the culture dish. The culture dish was then placed in an incubator for 1 h at 37 ℃ an 5% CO2 to allow the cochlear explants to attach to the surface of the gel. After, 0.7 mL of serum-free medium was added to the explants, and the culture dish was returned to the incubator overnight. On the second day, the culture medium was removed, and medium containing specific concentrations of ouabain (200 µM) was added to the culture dish. Meanwhile, the explants were treated with or without 16/32 µg/mL neuritin for 3 days and then subjected to immunofluorescence staining and western blotting analysis.
2.7 Electrophysiological recordings
Gerbils were first anesthetized with an intraperitoneal injection of 0.01 g/mL pentobarbital sodium (100 mg/kg body weight). Next, the System 3 digital signal processing package of hardware and software (Tucker Davies Technologies (TDT), FL) was used to present click stimuli ranging from 90 to 10 dB at a rate of 20 s− 1 in decreasing 10 dB steps. Tone stimuli were presented as pure tone pips lasting 5 ms at 90 dB, at frequencies at 2, 4, 8, 16, and 32 kHz. The sounds were presented to the animal via a ‘closed field’ method a 3 mm diameter, 10 cm tube leading from the speaker was inserted into the auditory meatus until its tip was close to the tympanic membrane. ABR measurements were recorded using 27G subdermal needle electrodes placed at the vertex of the skull (recording electrode) and the ipsilateral mastoid process (reference electrode), with a ground electrode placed dorsally adjacent to the tail. The differential voltage induced by the presentation of the sound stimulus was thus recorded. Each stimulus was presented 1024 times, thus the wave generated represented an average response over this time. All experiments were carried out in a sound-proof, custom-made audiology booth. The ABR data were analyzed using GraphPad Prism 6 software.
2.8 RNA isolation and qPCR
To detect Neuritin mRNA levels, total RNA was isolated from cochlear Corti tissue samples using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.). Equivalent amounts of RNA from each sample were used for cDNA synthesis using the FastKing gDNA Dispelling RT SuperMix kit [Tiangen Biotech (Beijing) Co., Ltd.]. Subsequently, the cDNAs were used for qPCR analysis. The primers used were as follows: Neuritin (F) 5’-CGCGGTGCAAATAGCTTACC-3’; Neuritin (R) 5’-TGTTCGTCTTGTCGTCCAGG-3’; β-actin (F) 5’-CTGGCTCCTAGCACCATGAA-3’; β-actin (R) 5’-CGCAGCTCAGTAACAGTCCG-3’. The thermocycling conditions for Nrn1 mRNA were 95°C for 15 min, followed by 40 cycles at 95°C for 10 s, 60°C for 20 s, and 72°C for 30 s. The 2−ΔΔCt method was used to analyze the level of mRNA.
2.9 Western blot analysis
Neuritin protein levels in the cochlear tissues were detected by western blot analysis. Cells were lysed in RIPA lysis buffer (Beyotime Institute of Biotechnology) with 1% protease inhibitor cocktail (Beyotime Institute of Biotechnology), centrifuged for 10 min at 15,777 g and 4°C, and the supernatant was collected. The amount of total protein was determined using a BCA protein assay kit (Beyotime Institute of Biotechnology). Total protein was electrophoresed by 12.5% SDS-PAGE and transferred to PVDF membranes at 23 V for 43 min. Membranes were blocked with Tris-buffered saline/5% fat-free skim milk for 2 h at room temperature, and then incubated with rabbit anti-Neuritin monoclonal antibody (1:1,000; ab64186, Abcam) for 16 h at 4°C. The following day, the membranes were incubated with secondary goat anti-rabbit IgG-HRP antibody (1:2,500; ZB-2301, Zsgb-Bio) for 2 h at room temperature. Finally, proteins were detected using Clarity Western ECL substrates (Bio-Rad Laboratories, Inc.). β-actin (Zsgb-Bio) was used as an endogenous control. Adobe photoshop CC 2015 software was used for densitometry.
2.10 Histology
Cochlear tissues were fixed by immersion in 4% paraformaldehyde (PFA; pH 7.4) for 24–48 h at 4 ℃ and decalcified in 0.25 M ethylenediaminetetraacetic acid pH 8.0 for a week at 4 ℃. Samples were then immersed an ascending sucrose/PBS series (15% and 30%, several hours/overnight at each stage). Following embedding in Cryo-M-Bed medium (VWR, Lutterworth, U.K.), tissue was sectioned (12 µm) onto gelatin/ chrome alum-coated glass slides using a Bright cryostat. The tissue sections were defrosted, rehydrated, briefly re-fixed with 4% PFA, rinsed with 0.1% Triton/PBS, and blocked in 2% BSA before incubation overnight at 4 ℃ with the following antibodies: anti-MyoVIIA (1:1000, rabbit monoclonal, Abcam), anti-Neurofilament 200 (NF-200; 1:1000, rabbit monoclonal, Abcam), and anti-Tuj1(1:1000, mouse monoclonal, Abcam). Sections were then incubated with anti-chicken Alexa 633, anti-mouse Alexa 488, and anti-rabbit Alexa 568 (all from Life Technologies, Paisley, U.K.) for 2 h at room temperature and counter-stained with 4,6-diamidino-2-phenylindole (DAPI; Sigma) before mounting in Vectashield (Vector Laboratories, Peterborough, U.K.). Images were taken on a Zeiss Axiophot microscope using Axiovision software and figures assembled using Adobe Photoshop 7.0. Five visual fields were randomly selected in each group for quantitative statistics. The SGNs density was calculated as the number of SGNs per 0.01 mm2. The HCs and nerve fibers was calculated as the number of cells per 100µm.
2.11 Statistical analyses
For each experimental condition, at least three independent experiments were performed. Data were analyzed using GraphPad Prism 6 software and are presented as the means ± standard errors of the means. Two-tailed, unpaired Student's t tests were used to determine statistical significance when comparing two groups, and two-way ANOVA followed by a Bonferroni post-hoc test was used when comparing more than two groups. A value of P < 0.05 was considered statistically significant.