Utilizing Single Cell RNA-Sequencing to Implicate Cell Types and Therapeutic Targets for SSNHL in the Adult Cochlea

Abstract

Objective: To identify genes implicated in sudden sensorineural hearing loss (SSNHL) and localize their expression in the cochlea to further explore potential pathogenic mechanisms and therapeutic targets.

Study design: Systematic literature review and bioinformatics analysis.

Data sources: The following sources were searched from inception through July 2, 2020: PubMed-NCBI, MEDLINE, Embase, CINAHL, Cochrane Library, ClinicalTrials.gov, OpenGrey, GreyNet, GreyLiterature Report, and European Union Clinical Trials Registry. PubMed-NCBI and MEDLINE were additionally searched for human temporal bone histopathologic studies related to SSNHL.

Methods: Literature review of candidate SSNHL genes was conducted according to PRISMA guidelines. Existing temporal bone studies from SSNHL patients were analyzed to identify the most commonly affected inner ear structures. Previously published single-cell and single-nucleus RNA-Seq datasets of the adult mouse stria vascularis, as well as postnatal day 7 and 15 mouse cochlear hair cells and supporting cells, were utilized for localization of the SSNHL-related genes curated through literature review.

Conclusions: We report 92 unique single nucleotide polymorphisms (SNPs) in 76 different genes that have been investigated in relation to SSNHL in the literature. We demonstrate that a subset of these genes are expressed by cell types in the adult mouse stria vascularis and organ of Corti, consistent with findings from temporal bone studies in human subjects with SSNHL. We highlight several potential genetic targets relevant to current and possible future SSNHL treatments.

Trial registration: ClinicalTrials.gov NCT03325790.

Conflict of interest statement

The authors disclose no conflicts of interest.

Copyright © 2021, Otology & Neurotology, Inc.

Figures

Figure 1.. PRISMA Flow Diagram for Systematic Literature Review of SSNHL-Implicated Genes

Flow diagram illustrates the literature review and study selection process conducted according to PRISMA reporting guidelines for published studies investigating genes related to SSNHL. A total of 63 studies satisfied inclusion criteria and were included in the final review.

Figure 2.. Distribution of Inner Ear Cell Type Abnormalities Identified in Human Temporal Bone Studies

Published temporal bone studies reporting histopathological findings from patients with SSNHL were analyzed to determine the distribution of inner ear cell types found to have structural abnormalities. Graph displays inner ear cell types along the horizontal axis and percentage of abnormal cells on the vertical axis. Cell types include supporting cells (SC), hair cells (HC), stria vascularis (SV), spiral ganglion (SG), tectorial membrane (TM), and spiral limbus (S). Percentage of abnormal cells was calculated by dividing the number of abnormal samples by the total number of analyzed subjects for each cell type. Subjects from studies that did not report findings for particular cell types were excluded from the analysis. Cell type abnormality was defined by criteria that varied by study and included metrics such as significantly decreased cell count and/or presence of structural degeneration or atrophy in SSNHL patient samples compared to controls. Cell type-specific definitions for abnormality are provided in the methods.

Figure 3A.. Expression of SSNHL-investigated genes in the adult mouse stria vascularis utilizing a single cell RNA-Seq adult mouse stria vascularis dataset (Korrapati, Taukulis et al., 2019).

Heatmap displays cells along the horizontal axis with cell types grouped by color and SSNHL-investigated genes along the vertical axis. The darker the bar the more highly expressed the gene is in a given cell. Cell types include SV cell types (marginal cells in pink, intermediate cells in green, basal cells in light blue), cells at the boundary of the SV (spindle-root cells in gold, fibrocytes in light green), as well as immune cells (macrophages in purple, B cells in blue, and neutrophils in magenta). Spindle and root cell profiles were not distinguishable from each other in this dataset.

Figure 3B.. Expression of SSNHL-investigated genes in the adult mouse stria vascularis utilizing a single nucleus RNA-Seq adult mouse stria vascularis dataset (Korrapati, Taukulis et al., 2019).

Heatmap displays cells along the horizontal axis with cell types grouped by color and SSNHL-investigated genes along the vertical axis. The darker the bar the more highly expressed the gene is in a given cell. Cell types include SV cell types (marginal cells in pink, intermediate cells in green, basal cells in light blue), cells at the boundary of the SV (spindle cells in gold, root cells in dark green, fibrocytes in light green), as well as immune cells (macrophages in purple, B cells in blue, and neutrophils in magenta).

Figure 4.. Expression of SSNHL-investigated genes in P7 mouse organ of Corti utilizing a single cell RNA-Seq P7 mouse organ of Corti dataset (Kolla et al., 2020).

Heatmap displays cells along the horizontal axis with cell types grouped by color and SSNHL-investigated genes along the vertical axis. The darker the bar the more highly expressed the gene is in a given cell. Cell types in the organ of Corti analyzed for this heatmap include inner hair cells (IHC) in pastel green, outer hair cells (OHC) in gray, pillar cells in midnight blue, and Deiters cells in forest green.

Figure 5.. Expression of SSNHL-investigated genes in P15 mouse organ of Corti utilizing a single cell RNA-Seq P15 mouse organ of Corti dataset (Ranum et al., 2019).

Heatmap displays cells along the horizontal axis with cell types grouped by color and SSNHL-investigated genes along the vertical axis. The darker the bar the more highly expressed the gene is in a given cell. Cell types in the organ of Corti available for analysis include inner hair cells (IHC) in blue, outer hair cells (OHC) in gold, and Deiters cells in green.