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A single-cell level comparison of human inner ear organoids with the human cochlea and vestibular organs

ABSTRACT: In this study, we generated a human inner ear atlas containing three stages of inner ear development. This atlas was used to evaluate the differentiation approach of human pluripotent stem cells in to complex inner ear tissue, known as inner ear organoids. The primary goal of this single-nucleus RNA-sequencing analysis was to capture the cell type diversity of the human inner ear at different stages of development. The secondary goal was to define the similarity of organoid-derived inner ear cell types with the atlas-derived human inner ear cell types and to determine the developmental stage of the organoid-derived inner ear cell types.

ORGANISM(S): Homo sapiens

PROVIDER: GSE213796 | GEO | 2023/06/05

REPOSITORIES: GEO

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A single-cell level comparison of human inner ear organoids with the human cochlea and vestibular organs

Project description:In this study, we used a differentiation approach for guiding human pluripotent stem cells in to complex inner ear tissue, known as inner ear organoids. The primary goal of this single-cell and single-nucleus RNA-sequencing analyses was to define the cellular composition of the inner ear organoids, which we have shown and confirmed by histology. The secondary goal was to determine whether the inner ear organoids generated using different cell lines (WA01 hESCs, two reporter lines from the parental line GM25256, and LUMC0004iCtrl10 hiPSCs) contain similar cell types.

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A Single Cell RNA-seq Atlas of Developing Inner Ear Organoids

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scRNA-seq of P2 mouse cochlea

Project description:Purpose and Methods: Cochlear sensory hair cells (HCs) are essential for our sense of hearing. They are embedded in the organ of Corti that lacks regenerative capacity, which is a major cause of hearing loss. However, some neonatal non-sensory cells in the organ of Corti display a limited regenerative ability. We used fluorescence-activated cell sorting (FACS) to isolate different cochlear cell types from postnatal day 2 (P2) mice to assess the individual cell groups’ potential to grow organoids and to generate new HCs. Single-cell RNAseq validated the composition of the cell types in the sorted cell groups. Results and Conclusions: The greater epithelial ridge (GER), a transient tissue that only exists in the neonatal inner ear, harbored the most potent organoid-forming cells. GER-derived organoids expanded into large colonies when cultured adherently and gave rise to new hair cell marker-expressing cells in a sensory epithelia-resembling organization. The organoid forming ability of GER cells was synergistically enhanced when they were cultured at increasing density. The synergistic effect relied on direct cell-to-cell contact rather than released soluble factors.

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Expression data from chick cochlea and utricle

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Project description:We collected single cell transcriptome profiles of inner ear organoids from passage 2 (day 8) in expansion medium, differentiated day 5, and differentiated day 25. Cells from the three time points were divided into 5 distinct clusters by UMAP, indicating the presence of the basic cell types of the organ of Corti in cochlear organoid model. Deafness-related gene expression in differentiated day 25 organoid showed that the cell-type specificity related to genetic auditory disease was preserved in the organoids, and dynamic gene expression changes were observed along lineage trajectories form progenitors to mature cell types, similar to in vivo developmental process. These results showed that cochlea organoid can be used as a useful model for deciphering the effects of deafness gene mutations and understanding inner ear development.

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Expression data from chick cochlea and utricle

Project description:Inner ear auditory and vestibular tissues differ in their responses to mechanical stimuli. Chick cochlea and utricle sensory epithelia were microdissected at E20-E21. RNA was extracted and cRNA hybridized to Affymetrix microarrays.

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Tbx1-nmf219/nmf219 inner ear Transcriptomes

Project description:Purpose: The goal of this study is to compare the expression profile of wild type and Tbx1-nmf219/nmf219 mice with NGS-derived inner ear transcriptome profiling (RNA-seq) Methods: inner ear mRNA profiles of E16.5 wild-type (WT) and Tbx1-nmf219/nmf219mice were generated by RNA-seq Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome and identified transcripts in the inner ear of WT and Tbx1nmf219/nmf219 mice. Approximately 10% of the transcripts showed differential expression between the WT and Tbx1nmf219/nmf219 inner ear, with a fold change ≥1.5 and p value <0.05. Conclusions: Our study represents the detailed analysis of inner ear transcriptomes, with biologic replicates, generated by RNA-seq technology.

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