Insights into the Biology of Hearing and Deafness Revealed by Single-Cell RNA Sequencing

• Published in: Cell reports (Cambridge) Vol. 26; no. 11; pp. 3160 - 3171.e3
• Main Authors: Ranum, Paul T., Goodwin, Alexander T., Yoshimura, Hidekane, Kolbe, Diana L., Walls, William D., Koh, Jin-Young, He, David Z.Z., Smith, Richard J.H.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 12.03.2019; Elsevier
• Subjects: alternative splicing; Animals; auditory; cochlea; Deafness - genetics; Female; gene expression; Gene Expression Profiling; hair cells; hearing; isoforms; Male; Mice; Organ of Corti - growth & development; Organ of Corti - metabolism; RNA sequencing; RNA-seq; scRNA-seq; Single-Cell Analysis; single-cell RNA-seq; sorcin; splicing; Transcriptome; RNA sequencing; cochlea; alternative splicing; single-cell RNA-seq; isoforms; hair cells; scRNA-seq; RNA-seq; auditory; hearing; splicing; sorcin; gene expression
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2019.02.053

Single-cell RNA sequencing is a powerful tool by which to characterize the transcriptional profile of low-abundance cell types, but its application to the inner ear has been hampered by the bony labyrinth, tissue sparsity, and difficulty dissociating the ultra-rare cells of the membranous cochlea. Herein, we present a method to isolate individual inner hair cells (IHCs), outer hair cells (OHCs), and Deiters’ cells (DCs) from the murine cochlea at any post-natal time point. We harvested more than 200 murine IHCs, OHCs, and DCs from post-natal days 15 (p15) to 228 (p228) and leveraged both short- and long-read single-cell RNA sequencing to profile transcript abundance and structure. Our results provide insights into the expression profiles of these cells and document an unappreciated complexity in isoform variety in deafness-associated genes. This refined view of transcription in the organ of Corti improves our understanding of the biology of hearing and deafness. [Display omitted] •Single-cell RNA-seq identifies inner and outer hair cell defining genes by AUC-ROC•Sorcin, a key component for cardiac excitation-contraction, is a top marker of OHCs•Analysis of deafness-associated genes identifies heretofore unrecognized exons•Nanopore long-read RNA-seq reveals splicing diversity and isoform abundance Single-cell RNA-seq of inner and outer auditory hair cells facilitates the identification of cell type-defining genes across a range of expression levels. Full-length reverse transcription with long-read sequencing identifies novel exons and unappreciated splicing diversity among deafness-associated genes.