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Liu Q, Zhang L, Chen Z, He Y, Huang Y, Qiu C, Zhu C, Zhou D, Gan Z, Gao X, Wan G. Metabolic Profiling of Cochlear Organoids Identifies α-Ketoglutarate and NAD + as Limiting Factors for Hair Cell Reprogramming. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2308032. [PMID: 38993037 DOI: 10.1002/advs.202308032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 04/11/2024] [Indexed: 07/13/2024]
Abstract
Cochlear hair cells are the sensory cells responsible for transduction of acoustic signals. In mammals, damaged hair cells do not regenerate, resulting in permanent hearing loss. Reprogramming of the surrounding supporting cells to functional hair cells represent a novel strategy to hearing restoration. However, cellular processes governing the efficient and functional hair cell reprogramming are not completely understood. Employing the mouse cochlear organoid system, detailed metabolomic characterizations of the expanding and differentiating organoids are performed. It is found that hair cell differentiation is associated with increased mitochondrial electron transport chain (ETC) activity and reactive oxidative species generation. Transcriptome and metabolome analyses indicate reduced expression of oxidoreductases and tricyclic acid (TCA) cycle metabolites. The metabolic decoupling between ETC and TCA cycle limits the availability of the key metabolic cofactors, α-ketoglutarate (α-KG) and nicotinamide adenine dinucleotide (NAD+). Reduced expression of NAD+ in cochlear supporting cells by PGC1α deficiency further impairs hair cell reprogramming, while supplementation of α-KG and NAD+ promotes hair cell reprogramming both in vitro and in vivo. These findings reveal metabolic rewiring as a central cellular process during hair cell differentiation, and highlight the insufficiency of key metabolites as a metabolic barrier for efficient hair cell reprogramming.
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Affiliation(s)
- Qing Liu
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
- Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, 210008, China
| | - Linqing Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
| | - Zhen Chen
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
| | - Yihan He
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
| | - Yuhang Huang
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
| | - Cui Qiu
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
| | - Chengwen Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
- Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, 210008, China
| | - Danxia Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
| | - Zhenji Gan
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
| | - Xia Gao
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
- Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, 210008, China
| | - Guoqiang Wan
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Medical School, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study and Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center of Medical School, Nanjing University, Nanjing, 210032, China
- Research Institute of Otolaryngology, No. 321 Zhongshan Road, Nanjing, 210008, China
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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 2024; 40:963-980. [PMID: 38015350 PMCID: PMC11250760 DOI: 10.1007/s12264-023-01149-z] [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: 06/27/2023] [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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3
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Fisch KM, Rosenthal SB, Mark A, Sasik R, Nasamran CA, Clifford R, Derebery MJ, Boussaty E, Jepsen K, Harris J, Friedman RA. The genomic landscape of Ménière's disease: a path to endolymphatic hydrops. BMC Genomics 2024; 25:646. [PMID: 38943082 PMCID: PMC11212243 DOI: 10.1186/s12864-024-10552-3] [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: 02/10/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND Ménière's disease (MD) is a disorder of the inner ear that causes episodic bouts of severe dizziness, roaring tinnitus, and fluctuating hearing loss. To date, no targeted therapy exists. As such, we have undertaken a large whole genome sequencing study on carefully phenotyped unilateral MD patients with the goal of gene/pathway discovery and a move towards targeted intervention. This study was a retrospective review of patients with a history of Ménière's disease. Genomic DNA, acquired from saliva samples, was purified and subjected to whole genome sequencing. RESULTS Stringent variant calling, performed on 511 samples passing quality checks, followed by gene-based filtering by recurrence and proximity in molecular interaction networks, led to 481 high priority MD genes. These high priority genes, including MPHOSPH8, MYO18A, TRIOBP, OTOGL, TNC, and MYO6, were previously implicated in hearing loss, balance, and cochlear function, and were significantly enriched in common variant studies of hearing loss. Validation in an independent MD cohort confirmed 82 recurrent genes. Pathway analysis pointed to cell-cell adhesion, extracellular matrix, and cellular energy maintenance as key mediators of MD. Furthermore, the MD-prioritized genes were highly expressed in human inner ear hair cells and dark/vestibular cells, and were differentially expressed in a mouse model of hearing loss. CONCLUSION By enabling the development of model systems that may lead to targeted therapies and MD screening panels, the genes and variants identified in this study will inform diagnosis and treatment of MD.
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Affiliation(s)
- Kathleen M Fisch
- Center for Computational Biology & Bioinformatics, University of California, San Diego, La Jolla, CA, USA.
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
| | - Sara Brin Rosenthal
- Center for Computational Biology & Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Adam Mark
- Center for Computational Biology & Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Roman Sasik
- Center for Computational Biology & Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Chanond A Nasamran
- Center for Computational Biology & Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Royce Clifford
- Department of Otolaryngology, Head & Neck Surgery, University of California, San Diego, La Jolla, CA, USA
- Research Department, VA Hospitals, San Diego, CA, USA
| | | | - Ely Boussaty
- Department of Otolaryngology, Head & Neck Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jeffrey Harris
- Department of Otolaryngology, Head & Neck Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Rick A Friedman
- Department of Otolaryngology, Head & Neck Surgery, University of California, San Diego, La Jolla, CA, USA.
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Zafeer MF, Ramzan M, Duman D, Mutlu A, Seyhan S, Kalcioglu T, Fitoz S, DeRosa BA, Guo S, Dykxhoorn DM, Tekin M. Human Organoids for Rapid Validation of Gene Variants Linked to Cochlear Malformations. RESEARCH SQUARE 2024:rs.3.rs-4474071. [PMID: 38947059 PMCID: PMC11213182 DOI: 10.21203/rs.3.rs-4474071/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Developmental anomalies of the hearing organ, the cochlea, are diagnosed in approximately one-fourth of individuals with congenital deafness. Most patients with cochlear malformations remain etiologically undiagnosed due to insufficient knowledge about underlying genes or the inability to make conclusive interpretations of identified genetic variants. We used exome sequencing for genetic evaluation of hearing loss associated with cochlear malformations in three probands from unrelated families. We subsequently generated monoclonal induced pluripotent stem cell (iPSC) lines, bearing patient-specific knockins and knockouts using CRISPR/Cas9 to assess pathogenicity of candidate variants. We detected FGF3 (p.Arg165Gly) and GREB1L (p.Cys186Arg), variants of uncertain significance in two recognized genes for deafness, and PBXIP1(p.Trp574*) in a candidate gene. Upon differentiation of iPSCs towards inner ear organoids, we observed significant developmental aberrations in knockout lines compared to their isogenic controls. Patient-specific single nucleotide variants (SNVs) showed similar abnormalities as the knockout lines, functionally supporting their causality in the observed phenotype. Therefore, we present human inner ear organoids as a tool to rapidly validate the pathogenicity of DNA variants associated with cochlear malformations.
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Affiliation(s)
| | | | - Duygu Duman
- Ankara University Faculty of Health Sciences
| | | | | | | | | | | | - Shengru Guo
- University of Miami Miller School of Medicine
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5
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Novoa JJ, Westra IM, Steeneveld E, Fonseca Neves N, Arendzen CH, Rajaei B, Grundeken E, Yildiz M, van der Valk W, Salvador A, Carlotti F, Dijkers PF, Locher H, van den Berg CW, Raymond KI, Kirkeby A, Mummery CL, Rabelink TJ, Freund C, Meij P, Wieles B. Good Manufacturing Practice-compliant human induced pluripotent stem cells: from bench to putative clinical products. Cytotherapy 2024; 26:556-566. [PMID: 38483359 DOI: 10.1016/j.jcyt.2024.02.021] [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: 11/07/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND AIMS Few human induced pluripotent stem cell (hiPSC) lines are Good Manufacturing Practice (GMP)-compliant, limiting the clinical use of hiPSC-derived products. Here, we addressed this by establishing and validating an in-house platform to produce GMP-compliant hiPSCs that would be appropriate for producing both allogeneic and autologous hiPSC-derived products. METHODS Our standard research protocol for hiPSCs production was adapted and translated into a GMP-compliant platform. In addition to the generation of GMP-compliant hiPSC, the platform entails the methodology for donor recruitment, consent and screening, donor material procurement, hiPSCs manufacture, in-process control, specific QC test validation, QC testing, product release, hiPSCs storage and stability testing. For platform validation, one test run and three production runs were performed. Highest-quality lines were selected to establish master cell banks (MCBs). RESULTS Two MCBs were successfully released under GMP conditions. They demonstrated safety (sterility, negative mycoplasma, endotoxins <5.0 EU/mL and negative adventitious agents), cell identity (>75% of cells expressing markers of undifferentiated state, identical STR profile, normal karyotype in >20 metaphases), purity (negative residual vectors and no plasmid integration in the genome) and potency (expression of at least two of the three markers for each of the three germ layers). In addition, directed differentiation to somitoids (skeletal muscle precursors) and six potential clinical products from all three germ layers was achieved: pancreatic islets (endoderm), kidney organoids and cardiomyocytes (mesoderm), and keratinocytes, GABAergic interneurons and inner-ear organoids (ectoderm). CONCLUSIONS We successfully developed and validated a platform for generating GMP-compliant hiPSC lines. The two MCBs released were shown to differentiate into clinical products relevant for our own and other regenerative medicine interests.
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Affiliation(s)
- Juan J Novoa
- Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Inge M Westra
- Center for Cell and Gene Therapy, Leiden University Medical Center, Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands
| | - Esther Steeneveld
- Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Natascha Fonseca Neves
- Center for Cell and Gene Therapy, Leiden University Medical Center, Leiden, The Netherlands
| | - Christiaan H Arendzen
- LUMC hiPSC Hotel, Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands
| | - Bahareh Rajaei
- Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Esmée Grundeken
- LUMC hiPSC Hotel, Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands
| | - Mehmet Yildiz
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands
| | - Wouter van der Valk
- OtoBiology Leiden, Department of Otorhinolaryngology and Head & Neck Surgery, Leiden University Medical Center, Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands
| | - Alison Salvador
- Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Françoise Carlotti
- Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Pascale F Dijkers
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands
| | - Heiko Locher
- OtoBiology Leiden, Department of Otorhinolaryngology and Head & Neck Surgery, Leiden University Medical Center, Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands
| | - Cathelijne W van den Berg
- Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands
| | - Karine I Raymond
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands
| | - Agnete Kirkeby
- Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Christine L Mummery
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands
| | - Ton J Rabelink
- Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands.
| | - Christian Freund
- LUMC hiPSC Hotel, Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands
| | - Pauline Meij
- Center for Cell and Gene Therapy, Leiden University Medical Center, Leiden, The Netherlands; The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, The Netherlands
| | - Brigitte Wieles
- Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
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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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7
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Wang H, Guan L, Wu X, Guan J, Li J, Li N, Wu K, Gao Y, Bing D, Zhang J, Lan L, Shi T, Li D, Wang W, Xie L, Xiong F, Shi W, Zhao L, Wang D, Yin Y, Wang Q. Clinical and genetic architecture of a large cohort with auditory neuropathy. Hum Genet 2024; 143:293-309. [PMID: 38456936 PMCID: PMC11043192 DOI: 10.1007/s00439-024-02652-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/25/2024] [Indexed: 03/09/2024]
Abstract
Auditory neuropathy (AN) is a unique type of language developmental disorder, with no precise rate of genetic contribution that has been deciphered in a large cohort. In a retrospective cohort of 311 patients with AN, pathogenic and likely pathogenic variants of 23 genes were identified in 98 patients (31.5% in 311 patients), and 14 genes were mutated in two or more patients. Among subgroups of patients with AN, the prevalence of pathogenic and likely pathogenic variants was 54.4% and 56.2% in trios and families, while 22.9% in the cases with proband-only; 45.7% and 25.6% in the infant and non-infant group; and 33.7% and 0% in the bilateral and unilateral AN cases. Most of the OTOF gene (96.6%, 28/29) could only be identified in the infant group, while the AIFM1 gene could only be identified in the non-infant group; other genes such as ATP1A3 and OPA1 were identified in both infant and non-infant groups. In conclusion, genes distribution of AN, with the most common genes being OTOF and AIFM1, is totally different from other sensorineural hearing loss. The subgroups with different onset ages showed different genetic spectrums, so did bilateral and unilateral groups and sporadic and familial or trio groups.
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Affiliation(s)
- Hongyang Wang
- Senior Department of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, The Sixth Medical Center of Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, People's Republic of China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, People's Republic of China
| | - Liping Guan
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Shijiazhuang, 050000, People's Republic of China
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
| | - Xiaonan Wu
- Senior Department of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, The Sixth Medical Center of Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, People's Republic of China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, People's Republic of China
| | - Jing Guan
- Senior Department of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, The Sixth Medical Center of Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, People's Republic of China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, People's Republic of China
| | - Jin Li
- Senior Department of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, The Sixth Medical Center of Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, People's Republic of China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, People's Republic of China
| | - Nan Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
| | - Kaili Wu
- Senior Department of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, The Sixth Medical Center of Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, People's Republic of China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, People's Republic of China
| | - Ya Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
| | - Dan Bing
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Jianguo Zhang
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Shijiazhuang, 050000, People's Republic of China
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
| | - Lan Lan
- Senior Department of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, The Sixth Medical Center of Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, People's Republic of China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, People's Republic of China
| | - Tao Shi
- Senior Department of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, The Sixth Medical Center of Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, People's Republic of China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, People's Republic of China
| | - Danyang Li
- Senior Department of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, The Sixth Medical Center of Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, People's Republic of China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, People's Republic of China
| | - Wenjia Wang
- Senior Department of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, The Sixth Medical Center of Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, People's Republic of China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, People's Republic of China
| | - Linyi Xie
- Senior Department of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, The Sixth Medical Center of Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, People's Republic of China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, People's Republic of China
| | - Fen Xiong
- Senior Department of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, The Sixth Medical Center of Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, People's Republic of China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, People's Republic of China
| | - Wei Shi
- Senior Department of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, The Sixth Medical Center of Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, People's Republic of China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, People's Republic of China
| | - Lijian Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
- Medical Technology College, Hebei Medical University, Shijiazhuang, 050000, People's Republic of China
| | - Dayong Wang
- Senior Department of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, The Sixth Medical Center of Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, People's Republic of China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, People's Republic of China
| | - Ye Yin
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, People's Republic of China
| | - Qiuju Wang
- Senior Department of Otolaryngology Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, The Sixth Medical Center of Chinese PLA General Hospital, Medical School of Chinese PLA, 28 Fuxing Road, Beijing, 100853, People's Republic of China.
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, People's Republic of China.
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8
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Strepay D, Olszewski RT, Nixon S, Korrapati S, Adadey S, Griffith AJ, Su Y, Liu J, Vishwasrao H, Gu S, Saunders T, Roux I, Hoa M. Transgenic Tg(Kcnj10-ZsGreen) fluorescent reporter mice allow visualization of intermediate cells in the stria vascularis. Sci Rep 2024; 14:3038. [PMID: 38321040 PMCID: PMC10847169 DOI: 10.1038/s41598-024-52663-7] [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: 09/27/2023] [Accepted: 01/22/2024] [Indexed: 02/08/2024] Open
Abstract
The stria vascularis (SV) is a stratified epithelium in the lateral wall of the mammalian cochlea, responsible for both endolymphatic ion homeostasis and generation of the endocochlear potential (EP) critical for normal hearing. The SV has three layers consisting predominantly of basal, intermediate, and marginal cells. Intermediate and marginal cells form an intricate interdigitated network of cell projections making discrimination of the cells challenging. To enable intermediate cell visualization, we engineered by BAC transgenesis, reporter mouse lines expressing ZsGreen fluorescent protein under the control of Kcnj10 promoter and regulatory sequences. Kcnj10 encodes KCNJ10 protein (also known as Kir4.1 or Kir1.2), an ATP-sensitive inwardly-rectifying potassium channel critical to EP generation, highly expressed in SV intermediate cells. In these transgenic mice, ZsGreen fluorescence mimics Kcnj10 endogenous expression in the cochlea and was detected in the intermediate cells of the SV, in the inner phalangeal cells, Hensen's, Deiters' and pillar cells, in a subset of spiral ganglion neurons, and in glial cells. We show that expression of the transgene in hemizygous mice does not alter auditory function, nor EP. These transgenic Tg(Kcnj10-ZsGreen) mice allow live and fixed tissue visualization of ZsGreen-expressing intermediate cells and will facilitate future studies of stria vascularis cell function.
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Affiliation(s)
- Dillon Strepay
- Auditory Development and Restoration Program, Neurotology Branch, National Institute On Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892-3745, USA
| | - Rafal T Olszewski
- Auditory Development and Restoration Program, Neurotology Branch, National Institute On Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892-3745, USA
| | - Sydney Nixon
- Auditory Development and Restoration Program, Neurotology Branch, National Institute On Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892-3745, USA
| | - Soumya Korrapati
- Auditory Development and Restoration Program, Neurotology Branch, National Institute On Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892-3745, USA
| | - Samuel Adadey
- Auditory Development and Restoration Program, Neurotology Branch, National Institute On Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892-3745, USA
| | - Andrew J Griffith
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Yijun Su
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Jiamin Liu
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Harshad Vishwasrao
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Shoujun Gu
- Auditory Development and Restoration Program, Neurotology Branch, National Institute On Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892-3745, USA
| | - Thomas Saunders
- Transgenic Animal Model Core, Biomedical Research Core Facility, University of Michigan, Ann Arbor, MI, USA
| | - Isabelle Roux
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA
| | - Michael Hoa
- Auditory Development and Restoration Program, Neurotology Branch, National Institute On Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, 35 Convent Dr., Room 1F-226, Bethesda, MD, 20892-3745, USA.
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9
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Norton B, Quirk A, Matsuoka AJ. Unraveling the Mechanisms of Vestibular Neuron Formation from Human Induced Pluripotent Stem Cells. Tissue Eng Part A 2024; 30:131-143. [PMID: 37917115 DOI: 10.1089/ten.tea.2023.0166] [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] [Indexed: 11/03/2023] Open
Abstract
The development of in vitro models that accurately recapitulate the complex cellular and molecular interactions of the inner ear is crucial for understanding inner ear development, function, and disease. In this study, we utilized a customized microfluidic platform to generate human induced pluripotent stem cell (hiPSC)-derived three-dimensional otic sensory neurons (OSNs). hiPSC-derived otic neuronal progenitors (ONPs) were cultured in hydrogel-embedded microfluidic channels over a 40-day period. Careful modulation of Wnt and Shh signaling pathways was used to influence dorsoventral patterning and direct differentiation toward a vestibular neuron lineage. After validating the microfluidic platform, OSN spheroid transcription factor and protein expression were assessed using real-time quantitative polymerase chain reaction (RT-qPCR), immunocytochemistry, and flow cytometry. The results demonstrated the successful differentiation of hiPSCs into ONPs and subsequent divergent differentiation into vestibular neuronal lineages, as evidenced by the expression of characteristic markers. Overall, our microfluidic platform provides a physiologically relevant environment for the culture and differentiation of hiPSCs, offering a valuable tool for studying inner ear development, disease and drug screening, and regenerative medicine applications.
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Affiliation(s)
- Benjamin Norton
- Department of Otolaryngology and Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Analia Quirk
- Department of Otolaryngology and Head and Neck Surgery, University of California San Diego, La Jolla, California, USA
| | - Akihiro J Matsuoka
- Department of Otolaryngology and Head and Neck Surgery, University of California San Diego, La Jolla, California, USA
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10
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Wang SX, Streit A. Shared features in ear and kidney development - implications for oto-renal syndromes. Dis Model Mech 2024; 17:dmm050447. [PMID: 38353121 PMCID: PMC10886756 DOI: 10.1242/dmm.050447] [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] [Indexed: 02/16/2024] Open
Abstract
The association between ear and kidney anomalies has long been recognized. However, little is known about the underlying mechanisms. In the last two decades, embryonic development of the inner ear and kidney has been studied extensively. Here, we describe the developmental pathways shared between both organs with particular emphasis on the genes that regulate signalling cross talk and the specification of progenitor cells and specialised cell types. We relate this to the clinical features of oto-renal syndromes and explore links to developmental mechanisms.
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Affiliation(s)
- Scarlet Xiaoyan Wang
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Andrea Streit
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
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11
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Griffin C, Saint-Jeannet JP. In vitro modeling of cranial placode differentiation: Recent advances, challenges, and perspectives. Dev Biol 2024; 506:20-30. [PMID: 38052294 PMCID: PMC10843546 DOI: 10.1016/j.ydbio.2023.11.009] [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: 05/26/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/07/2023]
Abstract
Cranial placodes are transient ectodermal thickenings that contribute to a diverse array of organs in the vertebrate head. They develop from a common territory, the pre-placodal region that over time segregates along the antero-posterior axis into individual placodal domains: the adenohypophyseal, olfactory, lens, trigeminal, otic, and epibranchial placodes. These placodes terminally differentiate into the anterior pituitary, the lens, and contribute to sensory organs including the olfactory epithelium, and inner ear, as well as several cranial ganglia. To study cranial placodes and their derivatives and generate cells for therapeutic purposes, several groups have turned to in vitro derivation of placodal cells from human embryonic stem cells (hESCs) or induced pluripotent stem cells (hiPSCs). In this review, we summarize the signaling cues and mechanisms involved in cranial placode induction, specification, and differentiation in vivo, and discuss how this knowledge has informed protocols to derive cranial placodes in vitro. We also discuss the benefits and limitations of these protocols, and the potential of in vitro cranial placode modeling in regenerative medicine to treat cranial placode-related pathologies.
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Affiliation(s)
- Casey Griffin
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Jean-Pierre Saint-Jeannet
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA.
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12
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Pianigiani G, Roccio M. Inner Ear Organoids: Strengths and Limitations. J Assoc Res Otolaryngol 2024; 25:5-11. [PMID: 38334886 PMCID: PMC10907556 DOI: 10.1007/s10162-024-00929-2] [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: 11/27/2023] [Accepted: 01/15/2024] [Indexed: 02/10/2024] Open
Abstract
Inner ear organoids derived from differentiation of human pluripotent stem cells have recently gained momentum as tools to study inner ear development and developmental defects. An additional exciting aspect about this technology is represented by its translational potential, specifically, the use of organoids to validate therapeutics for hearing and balance restoration on human/patient-specific cells. This latter aspect will be briefly discussed here including opportunities and current limitations.
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Affiliation(s)
- Giulia Pianigiani
- Institute for Maternal and Child Health - I.R.C.C.S. "Burlo Garofolo", Trieste, Italy
| | - Marta Roccio
- Inner Ear Stem Cell Lab, Department Otorhinolaryngology, Head and Neck Surgery, University Hospital Zurich and University of Zurich, USZ Campus WAGI18, Wagistrasse 18, 8952, Schlieren, Switzerland.
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13
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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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14
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Strepay D, Olszewski RT, Nixon S, Korrapati S, Adadey S, Griffith AJ, Su Y, Liu J, Vishwasrao H, Gu S, Saunders T, Roux I, Hoa M. Transgenic Tg(Kcnj10-ZsGreen) Fluorescent Reporter Mice Allow Visualization of Intermediate Cells in the Stria Vascularis. RESEARCH SQUARE 2023:rs.3.rs-3393161. [PMID: 37886521 PMCID: PMC10602146 DOI: 10.21203/rs.3.rs-3393161/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The stria vascularis (SV) is a stratified epithelium in the lateral wall of the mammalian cochlea, responsible for both endolymphatic ion homeostasis and generation of the endocochlear potential (EP) critical for normal hearing. The SV has three layers consisting predominantly of basal, intermediate, and marginal cells. Intermediate and marginal cells form an intricate interdigitated network of cell projections making discrimination of the cells challenging. To enable intermediate cell visualization, we engineered by BAC transgenesis, reporter mouse lines expressing ZsGreen fluorescent protein under the control of Kcnj10 promoter and regulatory sequences. Kcnj10 encodes KCNJ10 protein (also known as Kir4.1 or Kir1.2), an ATP-sensitive inwardly-rectifying potassium channel critical to EP generation, highly expressed in SV intermediate cells. In these transgenic mice, ZsGreen fluorescence mimics Kcnj10 endogenous expression in the cochlea and was detected in the intermediate cells of the SV, in the inner phalangeal cells, Hensen's, Deiters' and pillar cells, in a subset of spiral ganglion neurons, and in glial cells. We show that expression of the transgene in hemizygous mice does not alter auditory function, nor EP These transgenic Tg(Kcnj10-ZsGreen) mice allow live and fixed tissue visualization of ZsGreen-expressing intermediate cells and will facilitate future studies of stria vascularis cell function.
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Affiliation(s)
- Dillon Strepay
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health
| | - Rafal T Olszewski
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health
| | - Sydney Nixon
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health
| | - Soumya Korrapati
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health
| | - Samuel Adadey
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health
| | - Andrew J Griffith
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health
| | - Yijun Su
- Advanced Imaging and Microscopy Resource, National Institutes of Health
| | - Jiamin Liu
- Advanced Imaging and Microscopy Resource, National Institutes of Health
| | | | - Shoujun Gu
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health
| | - Thomas Saunders
- Transgenic Animal Model Core, Biomedical Research Core Facility, University of Michigan
| | - Isabelle Roux
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health
| | - Michael Hoa
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health
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15
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Doda D, Alonso Jimenez S, Rehrauer H, Carreño JF, Valsamides V, Di Santo S, Widmer HR, Edge A, Locher H, van der Valk WH, Zhang J, Koehler KR, Roccio M. Human pluripotent stem cell-derived inner ear organoids recapitulate otic development in vitro. Development 2023; 150:dev201865. [PMID: 37791525 PMCID: PMC10565253 DOI: 10.1242/dev.201865] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/01/2023] [Indexed: 10/05/2023]
Abstract
Our molecular understanding of the early stages of human inner ear development has been limited by the difficulty in accessing fetal samples at early gestational stages. As an alternative, previous studies have shown that inner ear morphogenesis can be partially recapitulated using induced pluripotent stem cells directed to differentiate into inner ear organoids (IEOs). Once validated and benchmarked, these systems could represent unique tools to complement and refine our understanding of human otic differentiation and model developmental defects. Here, we provide the first direct comparisons of the early human embryonic otocyst and fetal sensory organs with human IEOs. We use multiplexed immunostaining and single-cell RNA-sequencing to characterize IEOs at three key developmental steps, providing a new and unique signature of in vitro-derived otic placode, epithelium, neuroblasts and sensory epithelia. In parallel, we evaluate the expression and localization of crucial markers at these equivalent stages in human embryos. Together, our data indicate that the current state-of-the-art protocol enables the specification of bona fide otic tissue, supporting the further application of IEOs to inform inner ear biology and disease.
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Affiliation(s)
- Daniela Doda
- Inner Ear Stem Cell Laboratory, Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Zurich (USZ), 8091 Zurich,Switzerland
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Zurich (UZH), 8006 Zurich, Switzerland
| | - Sara Alonso Jimenez
- Inner Ear Stem Cell Laboratory, Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Zurich (USZ), 8091 Zurich,Switzerland
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Zurich (UZH), 8006 Zurich, Switzerland
| | - Hubert Rehrauer
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Zurich (UZH), 8006 Zurich, Switzerland
- Functional Genomics Center Zurich (ETH Zurich and University of Zurich), 8092 Zurich, Switzerland
| | - Jose F. Carreño
- Inner Ear Stem Cell Laboratory, Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Zurich (USZ), 8091 Zurich,Switzerland
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Zurich (UZH), 8006 Zurich, Switzerland
- Functional Genomics Center Zurich (ETH Zurich and University of Zurich), 8092 Zurich, Switzerland
| | - Victoria Valsamides
- Inner Ear Stem Cell Laboratory, Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Zurich (USZ), 8091 Zurich,Switzerland
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Zurich (UZH), 8006 Zurich, Switzerland
| | - Stefano Di Santo
- Program for Regenerative Neuroscience, Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Hans R. Widmer
- Program for Regenerative Neuroscience, Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland
| | - Albert Edge
- Eaton Peabody Laboratory, Massachusetts Eye and Ear, Boston, MA 02114, USA
- Department of Otorhinolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, 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
| | - Wouter H. van der Valk
- OtoBiology Leiden, Department of Otorhinolaryngology and Head & Neck Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Jingyuan Zhang
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F.M. Kirby Neurobiology Center, Boston Children's Hospital,Boston, MA 02115, USA
| | - 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 Plastic and Oral Surgery, Boston Children's Hospital, Boston, MA 02115, USA
| | - Marta Roccio
- Inner Ear Stem Cell Laboratory, Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Zurich (USZ), 8091 Zurich,Switzerland
- Department of Otorhinolaryngology, Head and Neck Surgery, University of Zurich (UZH), 8006 Zurich, Switzerland
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16
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Steinhart MR, van der Valk WH, Osorio D, Serdy SA, Zhang J, Nist-Lund C, Kim J, Moncada-Reid C, Sun L, Lee J, Koehler KR. Mapping oto-pharyngeal development in a human inner ear organoid model. Development 2023; 150:dev201871. [PMID: 37796037 DOI: 10.1242/dev.201871] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/08/2023] [Indexed: 10/06/2023]
Abstract
Inner ear development requires the coordination of cell types from distinct epithelial, mesenchymal and neuronal lineages. Although we have learned much from animal models, many details about human inner ear development remain elusive. We recently developed an in vitro model of human inner ear organogenesis using pluripotent stem cells in a 3D culture, fostering the growth of a sensorineural circuit, including hair cells and neurons. Despite previously characterizing some cell types, many remain undefined. This study aimed to chart the in vitro development timeline of the inner ear organoid to understand the mechanisms at play. Using single-cell RNA sequencing at ten stages during the first 36 days of differentiation, we tracked the evolution from pluripotency to various ear cell types after exposure to specific signaling modulators. Our findings showcase gene expression that influences differentiation, identifying a plethora of ectodermal and mesenchymal cell types. We also discern aspects of the organoid model consistent with in vivo development, while highlighting potential discrepancies. Our study establishes the Inner Ear Organoid Developmental Atlas (IODA), offering deeper insights into human biology and improving inner ear tissue differentiation.
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Affiliation(s)
- 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
| | - Wouter H van der Valk
- 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
- OtoBiology Leiden, Department of Otorhinolaryngology and Head & Neck Surgery; Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW); Leiden University Medical Center, Leiden, 2333 ZA, the Netherlands
| | - Daniel Osorio
- Research Computing, Department of Information Technology; Boston Children's Hospital, Boston, MA 02115, USA
| | - Sara A Serdy
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA 02115, USA
- F. M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jingyuan Zhang
- 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
| | - 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
| | - Jin Kim
- 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
| | - Cynthia Moncada-Reid
- Speech and Hearing Bioscience and Technology (SHBT) Graduate Program, Harvard Medical School, Boston, MA 02115, USA
| | - Liang Sun
- Research Computing, Department of Information Technology; Boston Children's Hospital, Boston, MA 02115, USA
| | - Jiyoon Lee
- 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
| | - 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
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