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Gao J, Skidmore JM, Cimerman J, Ritter KE, Qiu J, Wilson LMQ, Raphael Y, Kwan KY, Martin DM. CHD7 and SOX2 act in a common gene regulatory network during mammalian semicircular canal and cochlear development. Proc Natl Acad Sci U S A 2024; 121:e2311720121. [PMID: 38408234 PMCID: PMC10927591 DOI: 10.1073/pnas.2311720121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 01/19/2024] [Indexed: 02/28/2024] Open
Abstract
Inner ear morphogenesis requires tightly regulated epigenetic and transcriptional control of gene expression. CHD7, an ATP-dependent chromodomain helicase DNA-binding protein, and SOX2, an SRY-related HMG box pioneer transcription factor, are known to contribute to vestibular and auditory system development, but their genetic interactions in the ear have not been explored. Here, we analyzed inner ear development and the transcriptional regulatory landscapes in mice with variable dosages of Chd7 and/or Sox2. We show that combined haploinsufficiency for Chd7 and Sox2 results in reduced otic cell proliferation, severe malformations of semicircular canals, and shortened cochleae with ectopic hair cells. Examination of mice with conditional, inducible Chd7 loss by Sox2CreER reveals a critical period (~E9.5) of susceptibility in the inner ear to combined Chd7 and Sox2 loss. Data from genome-wide RNA-sequencing and CUT&Tag studies in the otocyst show that CHD7 regulates Sox2 expression and acts early in a gene regulatory network to control expression of key otic patterning genes, including Pax2 and Otx2. CHD7 and SOX2 directly bind independently and cooperatively at transcription start sites and enhancers to regulate otic progenitor cell gene expression. Together, our findings reveal essential roles for Chd7 and Sox2 in early inner ear development and may be applicable for syndromic and other forms of hearing or balance disorders.
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Affiliation(s)
- Jingxia Gao
- Department of Pediatrics, The University of Michigan, Ann Arbor, MI48109
| | | | - Jelka Cimerman
- Department of Pediatrics, The University of Michigan, Ann Arbor, MI48109
| | - K. Elaine Ritter
- Department of Pediatrics, The University of Michigan, Ann Arbor, MI48109
| | - Jingyun Qiu
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ08854
- Keck Center for Collaborative Neuroscience, Stem Cell Research Center, Rutgers University, Piscataway, NJ08854
| | - Lindsey M. Q. Wilson
- Medical Scientist Training Program, The University of Michigan, Ann Arbor, MI48109
| | - Yehoash Raphael
- Department of Otolaryngology-Head and Neck Surgery, The University of Michigan, Ann Arbor, MI48109
| | - Kelvin Y. Kwan
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ08854
- Keck Center for Collaborative Neuroscience, Stem Cell Research Center, Rutgers University, Piscataway, NJ08854
| | - Donna M. Martin
- Department of Pediatrics, The University of Michigan, Ann Arbor, MI48109
- Department of Human Genetics, The University of Michigan, Ann Arbor, MI48109
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Kagoshima H, Ohnishi H, Yamamoto R, Yasumoto A, Tona Y, Nakagawa T, Omori K, Yamamoto N. EBF1 Limits the Numbers of Cochlear Hair and Supporting Cells and Forms the Scala Tympani and Spiral Limbus during Inner Ear Development. J Neurosci 2024; 44:e1060232023. [PMID: 38176908 PMCID: PMC10869149 DOI: 10.1523/jneurosci.1060-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/12/2023] [Accepted: 12/13/2023] [Indexed: 01/06/2024] Open
Abstract
Early B-cell factor 1 (EBF1) is a basic helix-loop-helix transcription factor essential for the differentiation of various tissues. Our single-cell RNA sequencing data suggest that Ebf1 is expressed in the sensory epithelium of the mouse inner ear. Here, we found that the murine Ebf1 gene and its protein are expressed in the prosensory domain of the inner ear, medial region of the cochlear duct floor, otic mesenchyme, and cochleovestibular ganglion. Ebf1 deletion in mice results in incomplete formation of the spiral limbus and scala tympani, increased number of cells in the organ of Corti and Kölliker's organ, and aberrant course of the spiral ganglion axons. Ebf1 deletion in the mouse cochlear epithelia caused the proliferation of SOX2-positive cochlear cells at E13.5, indicating that EBF1 suppresses the proliferation of the prosensory domain and cells of Kölliker's organ to facilitate the development of appropriate numbers of hair and supporting cells. Furthermore, mice with deletion of cochlear epithelium-specific Ebf1 showed poor postnatal hearing function. Our results suggest that Ebf1 is essential for normal auditory function in mammals.
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Affiliation(s)
- Hiroki Kagoshima
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Hiroe Ohnishi
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Ryosuke Yamamoto
- Biological Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario M4N 3M5, Canada
| | - Akiyoshi Yasumoto
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Yosuke Tona
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Takayuki Nakagawa
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Koichi Omori
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Norio Yamamoto
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Department of Otolaryngology, Kobe City Medical Center General Hospital, Hyogo 650-0047, Japan
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3
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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: 16] [Impact Index Per Article: 16.0] [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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4
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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: 21] [Impact Index Per Article: 10.5] [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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Schwarzer S, Rekhade DR, Machate A, Spieß S, Geffarth M, Ezhkova D, Hans S. Reactivation of the Neurogenic Niche in the Adult Zebrafish Statoacoustic Ganglion Following a Mechanical Lesion. Front Cell Dev Biol 2022; 10:850624. [PMID: 35372332 PMCID: PMC8964994 DOI: 10.3389/fcell.2022.850624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
Sensorineural hearing loss is caused by the loss of sensory hair cells and/or their innervating neurons within the inner ear and affects millions of people worldwide. In mammals, including humans, the underlying cell types are only produced during fetal stages making loss of these cells and the resulting consequences irreversible. In contrast, zebrafish produce sensory hair cells throughout life and additionally possess the remarkable capacity to regenerate them upon lesion. Recently, we showed that also inner ear neurogenesis continues to take place in the zebrafish statoacoustic ganglion (SAG) well into adulthood. The neurogenic niche displays presumptive stem cells, proliferating Neurod-positive progenitors and a high level of neurogenesis at juvenile stages. It turns dormant at adult stages with only a few proliferating presumptive stem cells, no proliferating Neurod-positive progenitors, and very low levels of newborn neurons. Whether the neurogenic niche can be reactivated and whether SAG neurons can regenerate upon damage is unknown. To study the regenerative capacity of the SAG, we established a lesion paradigm using injections into the otic capsule of the right ear. Upon lesion, the number of apoptotic cells increased, and immune cells infiltrated the SAG of the lesioned side. Importantly, the Neurod-positive progenitor cells re-entered the cell cycle displaying a peak in proliferation at 8 days post lesion before they returned to homeostatic levels at 57 days post lesion. In parallel to reactive proliferation, we observed increased neurogenesis from the Neurod-positive progenitor pool. Reactive neurogenesis started at around 4 days post lesion peaking at 8 days post lesion before the neurogenesis rate decreased again to low homeostatic levels at 57 days post lesion. Additionally, administration of the thymidine analog BrdU and, thereby, labeling proliferating cells and their progeny revealed the generation of new sensory neurons within 19 days post lesion. Taken together, we show that the neurogenic niche of the adult zebrafish SAG can indeed be reactivated to re-enter the cell cycle and to increase neurogenesis upon lesion. Studying the underlying genes and pathways in zebrafish will allow comparative studies with mammalian species and might provide valuable insights into developing cures for auditory and vestibular neuropathies.
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Bryant JP, Chandrashekhar V, Cappadona AJ, Lookian PP, Chandrashekhar V, Donahue DR, Munasinghe JB, Kim HJ, Vortmeyer AO, Heiss JD, Zhuang Z, Rosenblum JS. Multimodal Atlas of the Murine Inner Ear: From Embryo to Adult. Front Neurol 2021; 12:699674. [PMID: 34335453 PMCID: PMC8319626 DOI: 10.3389/fneur.2021.699674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/22/2021] [Indexed: 12/02/2022] Open
Abstract
The inner ear is a complex organ housed within the petrous bone of the skull. Its intimate relationship with the brain enables the transmission of auditory and vestibular signals via cranial nerves. Development of this structure from neural crest begins in utero and continues into early adulthood. However, the anatomy of the murine inner ear has only been well-characterized from early embryogenesis to post-natal day 6. Inner ear and skull base development continue into the post-natal period in mice and early adulthood in humans. Traditional methods used to evaluate the inner ear in animal models, such as histologic sectioning or paint-fill and corrosion, cannot visualize this complex anatomy in situ. Further, as the petrous bone ossifies in the postnatal period, these traditional techniques become increasingly difficult. Advances in modern imaging, including high resolution Micro-CT and MRI, now allow for 3D visualization of the in situ anatomy of organs such as the inner ear. Here, we present a longitudinal atlas of the murine inner ear using high resolution ex vivo Micro-CT and MRI.
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Affiliation(s)
- Jean-Paul Bryant
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Vikram Chandrashekhar
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.,Center for Imaging Science, Johns Hopkins University, Baltimore, MD, United States
| | - Anthony J Cappadona
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Pashayar P Lookian
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States.,Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | | | - Danielle R Donahue
- Mouse Imaging Facility, National Institute of Neurological Disorders and Stroke, Bethesda, MD, United States
| | - Jeeva B Munasinghe
- Mouse Imaging Facility, National Institute of Neurological Disorders and Stroke, Bethesda, MD, United States
| | - H Jeffrey Kim
- Department of Otolaryngology, Georgetown University School of Medicine, Washington, DC, United States.,Office of Clinical Director, National Institute on Deafness and Other Communication Disorders, Bethesda, MD, United States
| | - Alexander O Vortmeyer
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - John D Heiss
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Zhengping Zhuang
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Jared S Rosenblum
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States.,Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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