A comprehensive catalogue of the coding and non-coding transcripts of the human inner ear

Abstract

The mammalian inner ear consists of the cochlea and the vestibular labyrinth (utricle, saccule, and semicircular canals), which participate in both hearing and balance. Proper development and life-long function of these structures involves a highly complex coordinated system of spatial and temporal gene expression. The characterization of the inner ear transcriptome is likely important for the functional study of auditory and vestibular components, yet, primarily due to tissue unavailability, detailed expression catalogues of the human inner ear remain largely incomplete. We report here, for the first time, comprehensive transcriptome characterization of the adult human cochlea, ampulla, saccule and utricle of the vestibule obtained from patients without hearing abnormalities. Using RNA-Seq, we measured the expression of >50,000 predicted genes corresponding to approximately 200,000 transcripts, in the adult inner ear and compared it to 32 other human tissues. First, we identified genes preferentially expressed in the inner ear, and unique either to the vestibule or cochlea. Next, we examined expression levels of specific groups of potentially interesting RNAs, such as genes implicated in hearing loss, long non-coding RNAs, pseudogenes and transcripts subject to nonsense mediated decay (NMD). We uncover the spatial specificity of expression of these RNAs in the hearing/balance system, and reveal evidence of tissue specific NMD. Lastly, we investigated the non-syndromic deafness loci to which no gene has been mapped, and narrow the list of potential candidates for each locus. These data represent the first high-resolution transcriptome catalogue of the adult human inner ear. A comprehensive identification of coding and non-coding RNAs in the inner ear will enable pathways of auditory and vestibular function to be further defined in the study of hearing and balance. Expression data are freely accessible at https://www.tgen.org/home/research/research-divisions/neurogenomics/supplementary-data/inner-ear-transcriptome.aspx.

Keywords: Balance; Cochlea; Hearing; RNA-Seq; Transcriptome; Vestibule.

Figure 1

Heatmap showing the Euclidean distances between the 6 human tissues studied by RNA-Seq including 3 cochlear and 3 vestibular samples (ampulla, saccule and utricle). Cochlear and vestibular tissue transcriptional environment can be clearly distinguished from each other. Regularized log transformation of counts generated in HTSeq were used to create this plot.

Figure 2

Differentially expressed known hearing/balance disorder genes between the cochlea and vestibular system of the inner ear (p_adj < 0.05). Ward's minimum variance method was used for hierarchical clustering. This plot shows Regularized log transformation of counts generated in HTSeq.

Figure 3

Nonsense mediated decay may be regulated in a tissue specific manner. A. Transcripts annotated as “nonsense mediated decay” that show >10 fold difference in expression between cochlea and other samples. B. Heat map of 1,133 transcripts that correspond to the same genes as transcripts in A, but are not annotated as “nonsense mediated decay”. All annotations are based on GENCODE V19 annotation of the human genome. Count and Value on the key scale reflect the count of features fitting that value (bright blue line in the key), and the color code of the expression value used in the heatmap, respectively. Plot is based on FPKM values.

Figure 4

Genome wide significant protein coding genes expressed significantly higher in the inner ear compared to 32 other human tissues (p_adj < 0.05). The 20 genes with the highest difference in expression level between the inner ear and other tissues (DESeq2), and with a mean normalized count of at least 5 are shown here. Ward's minimum variance method was used for hierarchical clustering. This plot shows Regularized log transformation of counts generated in HTSeq.

Figure 5

Expression of hearing loss related genes in the inner ear. Expression of principal versus total gene expression, for hearing loss related genes (red) and all expressed genes (grey). Hearing loss genes, for which the principle isoform accounts for less than 50% of the total expression are named. Plot is based on FPKM values.