1
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Wang S, Chakraborty S, Fu Y, Lee MP, Liu J, Waldhaus J. 3D reconstruction of the mouse cochlea from scRNA-seq data suggests morphogen-based principles in apex-to-base specification. Dev Cell 2024:S1534-5807(24)00196-5. [PMID: 38593801 DOI: 10.1016/j.devcel.2024.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 04/03/2023] [Accepted: 03/13/2024] [Indexed: 04/11/2024]
Abstract
In the mammalian auditory system, frequency discrimination depends on numerous morphological and physiological properties of the organ of Corti, which gradually change along the apex-to-base (tonotopic) axis of the organ. For example, the basilar membrane stiffness changes tonotopically, thus affecting the tuning properties of individual hair cells. At the molecular level, those frequency-specific characteristics are mirrored by gene expression gradients; however, the molecular mechanisms controlling tonotopic gene expression in the mouse cochlea remain elusive. Through analyzing single-cell RNA sequencing (scRNA-seq) data from E12.5 and E14.5 time points, we predicted that morphogens, rather than a cell division-associated mechanism, confer spatial identity in the extending cochlea. Subsequently, we reconstructed the developing cochlea in 3D space from scRNA-seq data to investigate the molecular pathways mediating positional information. The retinoic acid (RA) and hedgehog pathways were found to form opposing apex-to-base gradients, and functional interrogation using mouse cochlear explants suggested that both pathways jointly specify the longitudinal axis.
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Affiliation(s)
- Shuze Wang
- Department of Otolaryngology-Head and Neck Surgery, Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Saikat Chakraborty
- Department of Otolaryngology-Head and Neck Surgery, Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yujuan Fu
- Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, USA
| | - Mary P Lee
- Department of Otolaryngology-Head and Neck Surgery, Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jie Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joerg Waldhaus
- Department of Otolaryngology-Head and Neck Surgery, Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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2
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Waldhaus J, Jiang L, Liu L, Liu J, Duncan RK. Mapping the developmental potential of mouse inner ear organoids at single-cell resolution. iScience 2024; 27:109069. [PMID: 38375227 PMCID: PMC10875570 DOI: 10.1016/j.isci.2024.109069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/20/2023] [Accepted: 01/25/2024] [Indexed: 02/21/2024] Open
Abstract
Inner ear organoids recapitulate development and are intended to generate cell types of the otic lineage for applications such as basic science research and cell replacement strategies. Here, we use single-cell sequencing to study the cellular heterogeneity of late-stage mouse inner ear organoid sensory epithelia, which we validated by comparison with datasets of the mouse cochlea and vestibular epithelia. We resolved supporting cell sub-types, cochlear-like hair cells, and vestibular type I and type II-like hair cells. While cochlear-like hair cells aligned best with an outer hair cell trajectory, vestibular-like hair cells followed developmental trajectories similar to in vivo programs branching into type II and then type I extrastriolar hair cells. These results highlight the transcriptional accuracy of the organoid developmental program but will also inform future strategies to improve synaptic connectivity and regional specification.
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Affiliation(s)
- Joerg Waldhaus
- Department of Otolaryngology–Head and Neck Surgery, Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI, USA
| | - Linghua Jiang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Liqian Liu
- Department of Otolaryngology–Head and Neck Surgery, Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI, USA
| | - Jie Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Robert Keith Duncan
- Department of Otolaryngology–Head and Neck Surgery, Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI, USA
- Ann Arbor Department of Veterans Affairs Medical Center, Ann Arbor, MI, USA
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3
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Pan Y, Li S, He S, Wang G, Li C, Liu Z, Xiang M. Fgf8 P2A-3×GFP/+: A New Genetic Mouse Model for Specifically Labeling and Sorting Cochlear Inner Hair Cells. Neurosci Bull 2023; 39:1762-1774. [PMID: 37233921 PMCID: PMC10661496 DOI: 10.1007/s12264-023-01069-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/08/2023] [Indexed: 05/27/2023] Open
Abstract
The cochlear auditory epithelium contains two types of sound receptors, inner hair cells (IHCs) and outer hair cells (OHCs). Mouse models for labelling juvenile and adult IHCs or OHCs exist; however, labelling for embryonic and perinatal IHCs or OHCs are lacking. Here, we generated a new knock-in Fgf8P2A-3×GFP/+ (Fgf8GFP/+) strain, in which the expression of a series of three GFP fragments is controlled by endogenous Fgf8 cis-regulatory elements. After confirming that GFP expression accurately reflects the expression of Fgf8, we successfully obtained both embryonic and neonatal IHCs with high purity, highlighting the power of Fgf8GFP/+. Furthermore, our fate-mapping analysis revealed, unexpectedly, that IHCs are also derived from inner ear progenitors expressing Insm1, which is currently regarded as an OHC marker. Thus, besides serving as a highly favorable tool for sorting early IHCs, Fgf8GFP/+ will facilitate the isolation of pure early OHCs by excluding IHCs from the entire hair cell pool.
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Affiliation(s)
- Yi Pan
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Shuting Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shunji He
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, 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, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, 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, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
| | - Mingliang Xiang
- Department of Otolaryngology and Head and Neck Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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4
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Ma X, Guo J, Tian M, Fu Y, Jiang P, Zhang Y, Chai R. Advance and Application of Single-cell Transcriptomics in Auditory Research. Neurosci Bull 2023:10.1007/s12264-023-01149-z. [PMID: 38015350 DOI: 10.1007/s12264-023-01149-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/03/2023] [Indexed: 11/29/2023] Open
Abstract
Hearing loss and deafness, as a worldwide disability disease, have been troubling human beings. However, the auditory organ of the inner ear is highly heterogeneous and has a very limited number of cells, which are largely uncharacterized in depth. Recently, with the development and utilization of single-cell RNA sequencing (scRNA-seq), researchers have been able to unveil the complex and sophisticated biological mechanisms of various types of cells in the auditory organ at the single-cell level and address the challenges of cellular heterogeneity that are not resolved through by conventional bulk RNA sequencing (bulk RNA-seq). Herein, we reviewed the application of scRNA-seq technology in auditory research, with the aim of providing a reference for the development of auditory organs, the pathogenesis of hearing loss, and regenerative therapy. Prospects about spatial transcriptomic scRNA-seq, single-cell based genome, and Live-seq technology will also be discussed.
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Affiliation(s)
- Xiangyu Ma
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, 210096, China
| | - Jiamin Guo
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, 210096, China
| | - Mengyao Tian
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, 210096, China
| | - Yaoyang Fu
- Department of Psychiatry, Affiliated Hangzhou First People's Hospital, Zhejiang University school of Medicine, Hangzhou, 310030, China
| | - Pei Jiang
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, 210096, China
| | - Yuan Zhang
- Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical School, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing, China
- Research Institute of Otolaryngology, Nanjing, 210008, China
| | - Renjie Chai
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, 210096, China.
- Department of Otolaryngology Head and Neck Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610072, China.
- Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Science, Beijing, 101408, China.
- Beijing Key Laboratory of Neural Regeneration and Repair, Capital Medical University, Beijing, 100069, China.
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5
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Ragazzini R, Boeing S, Zanieri L, Green M, D'Agostino G, Bartolovic K, Agua-Doce A, Greco M, Watson SA, Batsivari A, Ariza-McNaughton L, Gjinovci A, Scoville D, Nam A, Hayday AC, Bonnet D, Bonfanti P. Defining the identity and the niches of epithelial stem cells with highly pleiotropic multilineage potency in the human thymus. Dev Cell 2023; 58:2428-2446.e9. [PMID: 37652013 PMCID: PMC10957394 DOI: 10.1016/j.devcel.2023.08.017] [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: 01/04/2022] [Revised: 09/19/2022] [Accepted: 08/09/2023] [Indexed: 09/02/2023]
Abstract
Thymus is necessary for lifelong immunological tolerance and immunity. It displays a distinctive epithelial complexity and undergoes age-dependent atrophy. Nonetheless, it also retains regenerative capacity, which, if harnessed appropriately, might permit rejuvenation of adaptive immunity. By characterizing cortical and medullary compartments in the human thymus at single-cell resolution, in this study we have defined specific epithelial populations, including those that share properties with bona fide stem cells (SCs) of lifelong regenerating epidermis. Thymic epithelial SCs display a distinctive transcriptional profile and phenotypic traits, including pleiotropic multilineage potency, to give rise to several cell types that were not previously considered to have shared origin. Using here identified SC markers, we have defined their cortical and medullary niches and shown that, in vitro, the cells display long-term clonal expansion and self-organizing capacity. These data substantively broaden our knowledge of SC biology and set a stage for tackling thymic atrophy and related disorders.
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Affiliation(s)
- Roberta Ragazzini
- Epithelial Stem Cell Biology & Regenerative Medicine Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Pears Building, Rosslyn Hill, London NW3 2PP, UK
| | - Stefan Boeing
- Bioinformatics & Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Luca Zanieri
- Epithelial Stem Cell Biology & Regenerative Medicine Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Pears Building, Rosslyn Hill, London NW3 2PP, UK
| | - Mary Green
- Experimental Histopathology Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Giuseppe D'Agostino
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Plasticell Limited, Stevenage Bioscience Catalyst, Gunnels Wood Road, Stevenage SG1 2FX, UK
| | - Kerol Bartolovic
- Flow Cytometry Core, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ana Agua-Doce
- Flow Cytometry Core, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Maria Greco
- Single Cell Facility, MRC WIMM, University of Oxford, Oxford OX3 9DS, UK
| | - Sara A Watson
- Epithelial Stem Cell Biology & Regenerative Medicine Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Antoniana Batsivari
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Linda Ariza-McNaughton
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Asllan Gjinovci
- Epithelial Stem Cell Biology & Regenerative Medicine Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Pears Building, Rosslyn Hill, London NW3 2PP, UK
| | | | - Andy Nam
- NanoString Technologies Inc., Seattle, WA, USA
| | - Adrian C Hayday
- Immunosurveillance Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Peter Gorer Department of Immunobiology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Dominique Bonnet
- Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Paola Bonfanti
- Epithelial Stem Cell Biology & Regenerative Medicine Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Institute of Immunity & Transplantation, Division of Infection & Immunity, UCL, Pears Building, Rosslyn Hill, London NW3 2PP, UK.
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6
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Doolittle ML, Khosla S, Saul D. Single-Cell Integration of BMD GWAS Results Prioritize Candidate Genes Influencing Age-Related Bone Loss. JBMR Plus 2023; 7:e10795. [PMID: 37808401 PMCID: PMC10556272 DOI: 10.1002/jbm4.10795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 05/17/2023] [Accepted: 06/19/2023] [Indexed: 10/10/2023] Open
Abstract
The regulation of bone mineral density (BMD) is highly influenced by genetics and age. Although genome-wide association studies (GWAS) for BMD have uncovered many genes through their proximity to associated variants (variant nearest-neighbor [VNN] genes), the cell-specific mechanisms of each VNN gene remain unclear. This is primarily due to the inability to prioritize these genes by cell type and age-related expression. Using age-related transcriptomics, we found that the expression of many VNN genes was upregulated in the bone and marrow from aged mice. Candidate genes from GWAS were investigated using single-cell RNA-sequencing (scRNA-seq) datasets to enrich for cell-specific expression signatures. VNN candidate genes are highly enriched in osteo-lineage cells, osteocytes, hypertrophic chondrocytes, and Lepr+ mesenchymal stem cells. These data were used to generate a "blueprint" for Cre-loxp mouse line selection for functional validation of candidate genes and further investigation of their role in BMD maintenance throughout aging. In VNN-gene-enriched cells, Sparc, encoding the extracellular matrix (ECM) protein osteonectin, was robustly expressed. This, along with expression of numerous other ECM genes, indicates that many VNN genes likely have roles in ECM deposition by osteoblasts. Overall, we provide data supporting streamlined translation of GWAS candidate genes to potential novel therapeutic targets for the treatment of osteoporosis. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Madison L. Doolittle
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
| | - Sundeep Khosla
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
| | - Dominik Saul
- Division of EndocrinologyMayo ClinicRochesterMinnesotaUSA
- Robert and Arlene Kogod Center on AgingMayo ClinicRochesterMinnesotaUSA
- Department for Trauma and Reconstructive SurgeryBG Clinic, University of TuebingenTuebingenGermany
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7
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Sun Y, Liu Z. Recent advances in molecular studies on cochlear development and regeneration. Curr Opin Neurobiol 2023; 81:102745. [PMID: 37356371 DOI: 10.1016/j.conb.2023.102745] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/06/2023] [Accepted: 05/25/2023] [Indexed: 06/27/2023]
Abstract
The auditory organ cochlea harbors two types of sound receptors, inner hair cells (IHCs) and outer hair cells (OHCs), which are innervated by spiral (auditory) ganglion neurons (SGNs). Recent transcriptomic, epigenetic, and genetic studies have started to reveal various aspects of cochlear development, including how prosensory progenitors are specified and diversified into IHCs or OHCs, as well as the heterogeneity among SGNs and how SGN subtypes are formed. Here, we primarily review advances in this line of research over the past five years and discuss a few key studies (from the past two years) to elucidate (1) how prosensory progenitors are specified; (2) the cis-regulatory control of Atoh1 expression and the synergistic interaction between Atoh1 and Pou4f3; and (3) the essential roles of Insm1 and Ikzf2 in OHC development and Tbx2 in IHC development. Moreover, we highlight the contribution of recent molecular studies on cochlear development toward the goal of regenerating IHCs and OHCs, which holds considerable potential for application in treating human deafness. Lastly, we briefly summarize the most recent progress on uncovering when and how SGN diversity is generated.
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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, 200031, 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, 200031, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
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8
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Cox B, Walters BJ. Post-transcriptional & post-translational control of gene expression in the inner ear. Hear Res 2023; 436:108823. [PMID: 37329863 DOI: 10.1016/j.heares.2023.108823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Affiliation(s)
- Brandon Cox
- Department of Pharmacology, Southern Illinois University, School of Medicine 801 N. Rutledge Street, Springfield, IL 62702
| | - Bradely J Walters
- Department of Otolaryngology - Head and Neck Surgery, The University of Mississippi Medical Center, 2500 North State Street Jackson, MS 39216, USA
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9
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Li S, He S, Lu Y, Jia S, Liu Z. Epistatic genetic interactions between Insm1 and Ikzf2 during cochlear outer hair cell development. Cell Rep 2023; 42:112504. [PMID: 37171961 DOI: 10.1016/j.celrep.2023.112504] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/17/2023] [Accepted: 04/27/2023] [Indexed: 05/14/2023] Open
Abstract
The cochlea harbors two types of sound receptors, outer hair cells (OHCs) and inner hair cells (IHCs). OHCs transdifferentiate into IHCs in Insm1 mutants, and OHCs in Ikzf2-deficient mice are dysfunctional and maintain partial IHC gene expression. Insm1 potentially acts as a positive but indirect regulator of Ikzf2, considering that Insm1 is expressed earlier than Ikzf2 and primarily functions as a transcriptional repressor. However, direct evidence of this possibility is lacking. Here, we report the following results: first, Insm1 overexpression in IHCs leads to ectopic Ikzf2 expression. Second, Ikzf2 expression is repressed in Insm1-deficient OHCs, and forced expression of Ikzf2 mitigates the OHC abnormality in Insm1 mutants. Last, dual ablation of Insm1 and Ikzf2 generates a similar OHC phenotype as does Insm1 ablation alone. Collectively, our findings reveal the transcriptional cascade from Insm1 to Ikzf2, which should facilitate future investigation of the molecular mechanisms underlying OHC development and regeneration.
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Affiliation(s)
- Shuting Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shunji He
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ying Lu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shiqi Jia
- The First Affiliated Hospital, Jinan University, Guangzhou 510630, 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 200031, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai 201210, China.
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10
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Reagor CC, Velez-Angel N, Hudspeth AJ. Depicting pseudotime-lagged causality across single-cell trajectories for accurate gene-regulatory inference. PNAS NEXUS 2023; 2:pgad113. [PMID: 37113980 PMCID: PMC10129065 DOI: 10.1093/pnasnexus/pgad113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 04/29/2023]
Abstract
Identifying the causal interactions in gene-regulatory networks requires an accurate understanding of the time-lagged relationships between transcription factors and their target genes. Here we describe DELAY (short for Depicting Lagged Causality), a convolutional neural network for the inference of gene-regulatory relationships across pseudotime-ordered single-cell trajectories. We show that combining supervised deep learning with joint probability matrices of pseudotime-lagged trajectories allows the network to overcome important limitations of ordinary Granger causality-based methods, for example, the inability to infer cyclic relationships such as feedback loops. Our network outperforms several common methods for inferring gene regulation and, when given partial ground-truth labels, predicts novel regulatory networks from single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) data sets. To validate this approach, we used DELAY to identify important genes and modules in the regulatory network of auditory hair cells, as well as likely DNA-binding partners for two hair cell cofactors (Hist1h1c and Ccnd1) and a novel binding sequence for the hair cell-specific transcription factor Fiz1. We provide an easy-to-use implementation of DELAY under an open-source license at https://github.com/calebclayreagor/DELAY.
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Affiliation(s)
| | - Nicolas Velez-Angel
- Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY 10065, USA
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11
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Wu S, Schmitz U. Single-cell and long-read sequencing to enhance modelling of splicing and cell-fate determination. Comput Struct Biotechnol J 2023; 21:2373-2380. [PMID: 37066125 PMCID: PMC10091034 DOI: 10.1016/j.csbj.2023.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Single-cell sequencing technologies have revolutionised the life sciences and biomedical research. Single-cell sequencing provides high-resolution data on cell heterogeneity, allowing high-fidelity cell type identification, and lineage tracking. Computational algorithms and mathematical models have been developed to make sense of the data, compensate for errors and simulate the biological processes, which has led to breakthroughs in our understanding of cell differentiation, cell-fate determination and tissue cell composition. The development of long-read (a.k.a. third-generation) sequencing technologies has produced powerful tools for investigating alternative splicing, isoform expression (at the RNA level), genome assembly and the detection of complex structural variants (at the DNA level). In this review, we provide an overview of the recent advancements in single-cell and long-read sequencing technologies, with a particular focus on the computational algorithms that help in correcting, analysing, and interpreting the resulting data. Additionally, we review some mathematical models that use single-cell and long-read sequencing data to study cell-fate determination and alternative splicing, respectively. Moreover, we highlight the emerging opportunities in modelling cell-fate determination that result from the combination of single-cell and long-read sequencing technologies.
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12
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Szeto IYY, Chu DKH, Chen P, Chu KC, Au TYK, Leung KKH, Huang YH, Wynn SL, Mak ACY, Chan YS, Chan WY, Jauch R, Fritzsch B, Sham MH, Lovell-Badge R, Cheah KSE. SOX9 and SOX10 control fluid homeostasis in the inner ear for hearing through independent and cooperative mechanisms. Proc Natl Acad Sci U S A 2022; 119:e2122121119. [PMID: 36343245 PMCID: PMC9674217 DOI: 10.1073/pnas.2122121119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 09/10/2022] [Indexed: 11/09/2022] Open
Abstract
The in vivo mechanisms underlying dominant syndromes caused by mutations in SRY-Box Transcription Factor 9 (SOX9) and SOX10 (SOXE) transcription factors, when they either are expressed alone or are coexpressed, are ill-defined. We created a mouse model for the campomelic dysplasia SOX9Y440X mutation, which truncates the transactivation domain but leaves DNA binding and dimerization intact. Here, we find that SOX9Y440X causes deafness via distinct mechanisms in the endolymphatic sac (ES)/duct and cochlea. By contrast, conditional heterozygous Sox9-null mice are normal. During the ES development of Sox9Y440X/+ heterozygotes, Sox10 and genes important for ionic homeostasis are down-regulated, and there is developmental persistence of progenitors, resulting in fewer mature cells. Sox10 heterozygous null mutants also display persistence of ES/duct progenitors. By contrast, SOX10 retains its expression in the early Sox9Y440X/+ mutant cochlea. Later, in the postnatal stria vascularis, dominant interference by SOX9Y440X is implicated in impairing the normal cooperation of SOX9 and SOX10 in repressing the expression of the water channel Aquaporin 3, thereby contributing to endolymphatic hydrops. Our study shows that for a functioning endolymphatic system in the inner ear, SOX9 regulates Sox10, and depending on the cell type and target gene, it works either independently of or cooperatively with SOX10. SOX9Y440X can interfere with the activity of both SOXE factors, exerting effects that can be classified as haploinsufficient/hypomorphic or dominant negative depending on the cell/gene context. This model of disruption of transcription factor partnerships may be applicable to congenital deafness, which affects ∼0.3% of newborns, and other syndromic disorders.
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Affiliation(s)
- Irene Y. Y. Szeto
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Daniel K. H. Chu
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Peikai Chen
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Ka Chi Chu
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Tiffany Y. K. Au
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Keith K. H. Leung
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Yong-Heng Huang
- Genome Regulation Laboratory, CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Medical University, Guangzhou 511436, China
| | - Sarah L. Wynn
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Angel C. Y. Mak
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Ying-Shing Chan
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | - Wood Yee Chan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ralf Jauch
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
- Genome Regulation Laboratory, CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Medical University, Guangzhou 511436, China
| | - Bernd Fritzsch
- Department of Biology, College of Arts & Sciences, University of Iowa, Iowa City, IA 52242
- Department of Otolaryngology, College of Arts & Sciences, University of Iowa, Iowa City, IA 52242
| | - Mai Har Sham
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
| | | | - Kathryn S. E. Cheah
- School of Biomedical Sciences, The University of Hong Kong, Li Ka Shing Faculty of Medicine, Hong Kong, China
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Early S, Du E, Boussaty E, Friedman R. Genetics of noise-induced hearing loss in the mouse model. Hear Res 2022; 425:108505. [DOI: 10.1016/j.heares.2022.108505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 03/28/2022] [Accepted: 04/07/2022] [Indexed: 12/01/2022]
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Kwan KY, White PM. Understanding the differentiation and epigenetics of cochlear sensory progenitors in pursuit of regeneration. Curr Opin Otolaryngol Head Neck Surg 2021; 29:366-372. [PMID: 34374667 PMCID: PMC8452321 DOI: 10.1097/moo.0000000000000741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PURPOSE OF REVIEW Sensory hair cells (HCs) of the inner ear are responsible for our ability to hear and balance. Loss of these cells results in hearing loss. Stem cell replacement and in situ regeneration have the potential to replace lost HCs. Newly discovered contributions of transcription factor regulatory networks and epigenetic mechanisms in regulating HC differentiation and regeneration are placed into context of the literature. RECENT FINDINGS A wealth of new data has helped to define cochlear sensory progenitors in their developmental trajectories. This includes transcription factor networks, epigenetic manipulations, and cochlear HC subtype specification. SUMMARY Understanding how sensory progenitors differ and how HC subtypes arise will substantially inform efforts in hearing restoration.
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Affiliation(s)
- Kelvin Y. Kwan
- Department of Cell Biology & Neuroscience, Rutgers University, Piscataway, New Jersey
| | - Patricia M. White
- Department of Neuroscience, Ernest J. Del Monte Institute of Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
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