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van der Valk WH, van Beelen ESA, Steinhart MR, Nist-Lund C, Osorio D, de Groot JCMJ, Sun L, van Benthem PPG, Koehler KR, Locher H. A single-cell level comparison of human inner ear organoids with the human cochlea and vestibular organs. Cell Rep 2023; 42:112623. [PMID: 37289589 PMCID: PMC10592453 DOI: 10.1016/j.celrep.2023.112623] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/21/2023] [Accepted: 05/23/2023] [Indexed: 06/10/2023] Open
Abstract
Inner ear disorders are among the most common congenital abnormalities; however, current tissue culture models lack the cell type diversity to study these disorders and normal otic development. Here, we demonstrate the robustness of human pluripotent stem cell-derived inner ear organoids (IEOs) and evaluate cell type heterogeneity by single-cell transcriptomics. To validate our findings, we construct a single-cell atlas of human fetal and adult inner ear tissue. Our study identifies various cell types in the IEOs including periotic mesenchyme, type I and type II vestibular hair cells, and developing vestibular and cochlear epithelium. Many genes linked to congenital inner ear dysfunction are confirmed to be expressed in these cell types. Additional cell-cell communication analysis within IEOs and fetal tissue highlights the role of endothelial cells on the developing sensory epithelium. These findings provide insights into this organoid model and its potential applications in studying inner ear development and disorders.
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Affiliation(s)
- Wouter H van der Valk
- OtoBiology Leiden, Department of Otorhinolaryngology and Head & Neck Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA; F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA 02115, USA.
| | - Edward S A van Beelen
- OtoBiology Leiden, Department of Otorhinolaryngology and Head & Neck Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Matthew R Steinhart
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA; F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Carl Nist-Lund
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA; F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; Program in Neuroscience, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Osorio
- Research Computing, Department of Information Technology, Boston Children's Hospital, Boston, MA 02115, USA
| | - John C M J de Groot
- OtoBiology Leiden, Department of Otorhinolaryngology and Head & Neck Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Liang Sun
- Research Computing, Department of Information Technology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Peter Paul G van Benthem
- OtoBiology Leiden, Department of Otorhinolaryngology and Head & Neck Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Karl R Koehler
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA; F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA; Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Plastic and Oral Surgery, Boston Children's Hospital, Boston, MA 02115, USA.
| | - Heiko Locher
- OtoBiology Leiden, Department of Otorhinolaryngology and Head & Neck Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, 2333 ZA Leiden, the Netherlands.
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Single-cell transcriptomic landscapes of the otic neuronal lineage at multiple early embryonic ages. Cell Rep 2022; 38:110542. [PMID: 35320729 DOI: 10.1016/j.celrep.2022.110542] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 12/03/2021] [Accepted: 02/25/2022] [Indexed: 11/20/2022] Open
Abstract
Inner ear vestibular and spiral ganglion neurons (VGNs and SGNs) are known to play pivotal roles in balance control and sound detection. However, the molecular mechanisms underlying otic neurogenesis at early embryonic ages have remained unclear. Here, we use single-cell RNA sequencing to reveal the transcriptomes of mouse otic tissues at three embryonic ages, embryonic day 9.5 (E9.5), E11.5, and E13.5, covering proliferating and undifferentiated otic neuroblasts and differentiating VGNs and SGNs. We validate the high quality of our studies by using multiple assays, including genetic fate mapping analysis, and we uncover several genes upregulated in neuroblasts or differentiating VGNs and SGNs, such as Shox2, Myt1, Casz1, and Sall3. Notably, our findings suggest a general cascaded differentiation trajectory during early otic neurogenesis. The comprehensive understanding of early otic neurogenesis provided by our study holds critical implications for both basic and translational research.
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Sun Y, Zhang Y, Zhang D, Wang G, Song L, Liu Z. In vivo CRISPR-Cas9-mediated DNA chop identifies a cochlear outer hair cell-specific enhancer. FASEB J 2022; 36:e22233. [PMID: 35225354 DOI: 10.1096/fj.202100421rr] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 02/06/2022] [Accepted: 02/14/2022] [Indexed: 01/18/2023]
Abstract
Cochlear outer hair cells (OHCs) are essential for hearing. A short, OHC-specific enhancer is necessary but not yet available for gene therapeutic applications in OHC damage. Such damage is a major cause of deafness. Prestin is a motor protein exclusively expressed in OHCs. We hypothesized that the cis-regulatory DNA fragment deletion of Slc26a5 would affect its expression. We tested this hypothesis by conducting CRISPR/Cas9-mediated large DNA fragment deletion of mouse Slc26a5 intron regions. First, starting from a ~13 kbp fragment, step-by-step, we narrowed down the sequence to a 1.4 kbp segment. By deleting either a 13 kbp or 1.4 kbp fragment, we observed delayed Prestin expression. Second, we showed that 1.4 kbp was an OHC-specific enhancer because enhanced green fluorescent protein (EGFP) was highly and specifically expressed in OHCs in a transgenic mouse where EGFP was driven by the 1.4 kbp segment. More importantly, specific EGFP was also driven by its homologous 398 bp fragment in human Slc26a5. This suggests that the enhancer is likely to be evolutionarily conserved across different species.
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Affiliation(s)
- Yuwei Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu Zhang
- Department of Otolaryngology-Head and Neck Surgery, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Di Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guangqin Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lei Song
- Department of Otolaryngology-Head and Neck Surgery, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyong Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
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Yamamoto R, Ohnishi H, Omori K, Yamamoto N. In silico analysis of inner ear development using public whole embryonic body single-cell RNA-sequencing data. Dev Biol 2020; 469:160-171. [PMID: 33131705 DOI: 10.1016/j.ydbio.2020.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 02/02/2023]
Abstract
The inner ear comprises four epithelial domains: the cochlea, vestibule, semicircular canals, and endolymphatic duct/sac. These structures are segregated at embryonic day 13.5 (E13.5). However, these four anatomical structures remain undefined at E10.5. Here, we aimed to identify lineage-specific genes in the early developing inner ear using published data obtained from single-cell RNA-sequencing (scRNA-seq) of embryonic mice. We downloaded 5000 single-cell transcriptome data, named 'auditory epithelial trajectory', from the Mouse Organogenesis Cell Atlas. The dataset was supposed to include otic epithelial cells at E9.5-13.5. We projected the 5000 cells onto a two-dimensional space encoding the transcriptional state and visualised the pattern of otic epithelial cell differentiation. We identified 15 clusters, which were annotated as one of the four components of the inner ear epithelium using known genes that characterise the four different tissues. Additionally, we classified 15 clusters into sub-regions of the four inner ear components. By comparing transcriptomes between these 15 clusters, we identified several candidates of lineage-specific genes. Characterising these new candidate genes will help future studies about inner ear development.
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Affiliation(s)
- Ryosuke Yamamoto
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, 54, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 6068507, Japan.
| | - Hiroe Ohnishi
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, 54, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 6068507, Japan.
| | - Koichi Omori
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, 54, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 6068507, Japan.
| | - Norio Yamamoto
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, 54, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 6068507, Japan.
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Gu S, Olszewski R, Taukulis I, Wei Z, Martin D, Morell RJ, Hoa M. Characterization of rare spindle and root cell transcriptional profiles in the stria vascularis of the adult mouse cochlea. Sci Rep 2020; 10:18100. [PMID: 33093630 PMCID: PMC7581811 DOI: 10.1038/s41598-020-75238-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/12/2020] [Indexed: 12/20/2022] Open
Abstract
The stria vascularis (SV) in the cochlea generates and maintains the endocochlear potential, thereby playing a pivotal role in normal hearing. Knowing transcriptional profiles and gene regulatory networks of SV cell types establishes a basis for studying the mechanism underlying SV-related hearing loss. While we have previously characterized the expression profiles of major SV cell types in the adult mouse, transcriptional profiles of rare SV cell types remained elusive due to the limitation of cell capture in single-cell RNA-Seq. The role of these rare cell types in the homeostatic function of the adult SV remain largely undefined. In this study, we performed single-nucleus RNA-Seq on the adult mouse SV in conjunction with sample preservation treatments during the isolation steps. We distinguish rare SV cell types, including spindle cells and root cells, from other cell types, and characterize their transcriptional profiles. Furthermore, we also identify and validate novel specific markers for these rare SV cell types. Finally, we identify homeostatic gene regulatory networks within spindle and root cells, establishing a basis for understanding the functional roles of these cells in hearing. These novel findings will provide new insights for future work in SV-related hearing loss and hearing fluctuation.
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Affiliation(s)
- Shoujun Gu
- Auditory Development and Restoration Program, National Institutes on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892, USA
| | - Rafal Olszewski
- Auditory Development and Restoration Program, National Institutes on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892, USA
| | - Ian Taukulis
- Auditory Development and Restoration Program, National Institutes on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892, USA
| | - Zheng Wei
- Biomedical Research Informatics Office, National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, 20892, USA
| | - Daniel Martin
- Biomedical Research Informatics Office, National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, 20892, USA
| | - Robert J Morell
- Computational Biology and Genomics Core, National Institutes on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael Hoa
- Auditory Development and Restoration Program, National Institutes on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892, USA.
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Yang LM, Stout L, Rauchman M, Ornitz DM. Analysis of FGF20-regulated genes in organ of Corti progenitors by translating ribosome affinity purification. Dev Dyn 2020; 249:1217-1242. [PMID: 32492250 DOI: 10.1002/dvdy.211] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Understanding the mechanisms that regulate hair cell (HC) differentiation in the organ of Corti (OC) is essential to designing genetic therapies for hearing loss due to HC loss or damage. We have previously identified Fibroblast Growth Factor 20 (FGF20) as having a key role in HC and supporting cell differentiation in the mouse OC. To investigate the genetic landscape regulated by FGF20 signaling in OC progenitors, we employ Translating Ribosome Affinity Purification combined with Next Generation RNA Sequencing (TRAPseq) in the Fgf20 lineage. RESULTS We show that TRAPseq targeting OC progenitors effectively enriched for RNA from this rare cell population. TRAPseq identified differentially expressed genes (DEGs) downstream of FGF20, including Etv4, Etv5, Etv1, Dusp6, Hey1, Hey2, Heyl, Tectb, Fat3, Cpxm2, Sall1, Sall3, and cell cycle regulators such as Cdc20. Analysis of Cdc20 conditional-null mice identified decreased cochlea length, while analysis of Sall1-null and Sall1-ΔZn2-10 mice, which harbor a mutation that causes Townes-Brocks syndrome, identified a decrease in outer hair cell number. CONCLUSIONS We present two datasets: genes with enriched expression in OC progenitors, and DEGs downstream of FGF20 in the embryonic day 14.5 cochlea. We validate select DEGs via in situ hybridization and in vivo functional studies in mice.
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Affiliation(s)
- Lu M Yang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lisa Stout
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael Rauchman
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - David M Ornitz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA
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