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Thulasiram MR, Yamamoto R, Olszewski RT, Gu S, Morell RJ, Hoa M, Dabdoub A. Molecular differences between neonatal and adult stria vascularis from organotypic explants and transcriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590986. [PMID: 38712156 PMCID: PMC11071502 DOI: 10.1101/2024.04.24.590986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Summary The stria vascularis (SV), part of the blood-labyrinth barrier, is an essential component of the inner ear that regulates the ionic environment required for hearing. SV degeneration disrupts cochlear homeostasis, leading to irreversible hearing loss, yet a comprehensive understanding of the SV, and consequently therapeutic availability for SV degeneration, is lacking. We developed a whole-tissue explant model from neonatal and adult mice to create a robust platform for SV research. We validated our model by demonstrating that the proliferative behaviour of the SV in vitro mimics SV in vivo, providing a representative model and advancing high-throughput SV research. We also provided evidence for pharmacological intervention in our system by investigating the role of Wnt/β-catenin signaling in SV proliferation. Finally, we performed single-cell RNA sequencing from in vivo neonatal and adult mouse SV and revealed key genes and pathways that may play a role in SV proliferation and maintenance. Together, our results contribute new insights into investigating biological solutions for SV-associated hearing loss. Significance Hearing loss impairs our ability to communicate with people and interact with our environment. This can lead to social isolation, depression, cognitive deficits, and dementia. Inner ear degeneration is a primary cause of hearing loss, and our study provides an in depth look at one of the major sites of inner ear degeneration: the stria vascularis. The stria vascularis and associated blood-labyrinth barrier maintain the functional integrity of the auditory system, yet it is relatively understudied. By developing a new in vitro model for the young and adult stria vascularis and using single cell RNA sequencing, our study provides a novel approach to studying this tissue, contributing new insights and widespread implications for auditory neuroscience and regenerative medicine. Highlights - We established an organotypic explant system of the neonatal and adult stria vascularis with an intact blood-labyrinth barrier. - Proliferation of the stria vascularis decreases with age in vitro , modelling its proliferative behaviour in vivo . - Pharmacological studies using our in vitro SV model open possibilities for testing injury paradigms and therapeutic interventions. - Inhibition of Wnt signalling decreases proliferation in neonatal stria vascularis.- We identified key genes and transcription factors unique to developing and mature SV cell types using single cell RNA sequencing.
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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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Khan S, Singh A, Nain N, Gulati S, Kukreti S. Sequence-specific recognition of a coding segment of human DACH1 gene via short pyrimidine/purine oligonucleotides. RSC Adv 2021; 11:40011-40021. [PMID: 35494143 PMCID: PMC9044637 DOI: 10.1039/d1ra06604h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/03/2021] [Indexed: 12/18/2022] Open
Abstract
With growing in vivo evidence of the roles of triplexes in biological processes, oligonucleotide-directed targeting of double-helical DNA for selective modulation of gene functions has become imperative in their therapeutic aspects. This study comprises a comparative investigation of 17-mer Py- and Pu-TFO for the formation of an intermolecular triplex with a 27-bp genomic homopurine–homopyrimidine track present in the transcriptional element of the human DACH1 gene. The biochemical and biophysical studies have revealed that triplex formation takes place only with Py-TFO and not with its Pu-counterpart. Non-denaturating gel electrophoresis indicated the formation of an intermolecular triplex in Py-motif with an increasing amount of Py-TFO, whereas no such interaction was observed for the Pu-counterpart. UV-thermal melting (Tm), circular dichroism (CD) and thermal difference spectra (TDS) studies confirmed the pyrimidine motif triplex formation, which was observed to be significantly pH-dependent and stable at acidic pH (5.2) in the presence of 100 mM Na+ ions. Contrarily, Pu-TFO was not found to bind to the target predominantly, owing to its self-association properties. Further studies have revealed that the GA-rich Pu-TFO adopts a homoduplex structure leading to a limit in its availability for triplex formation. These results may add to our understanding of sequence-specific gene targeting and give insight into designing more specific TFOs depending on genomic targets. Schematic representation of the proposed model of intermolecular triplex and homoduplex of used DNA sequences.![]()
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Affiliation(s)
- Shoaib Khan
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
| | - Anju Singh
- Department of Chemistry, Ramjas College, University of Delhi Delhi-110007 India
| | - Nishu Nain
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
| | - Srishty Gulati
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
| | - Shrikant Kukreti
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
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Miwa T, Ito N, Ohta K. Tsukushi is essential for the formation of the posterior semicircular canal that detects gait performance. J Cell Commun Signal 2021; 15:581-594. [PMID: 34061311 DOI: 10.1007/s12079-021-00627-1] [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: 01/27/2021] [Accepted: 05/25/2021] [Indexed: 11/27/2022] Open
Abstract
Tsukushi is a small, leucine-rich repeat proteoglycan that interacts with and regulates essential cellular signaling cascades in the chick retina and murine subventricular zone, hippocampus, dermal hair follicles, and the cochlea. However, its function in the vestibules of the inner ear remains unknown. Here, we investigated the function of Tsukushi in the vestibules and found that Tsukushi deficiency in mice resulted in defects in posterior semicircular canal formation in the vestibules, but did not lead to vestibular hair cell loss. Furthermore, Tsukushi accumulated in the non-prosensory and prosensory regions during the embryonic and postnatal developmental stages. The downregulation of Tsukushi altered the expression of key genes driving vestibule differentiation in the non-prosensory regions. Our results indicate that Tsukushi interacts with Wnt2b, bone morphogenetic protein 4, fibroblast growth factor 10, and netrin 1, thereby controlling semicircular canal formation. Therefore, Tsukushi may be an essential component of the molecular pathways regulating vestibular development.
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Affiliation(s)
- Toru Miwa
- Department of Otolaryngology-Head and Neck Surgery, Kitano Hospital, Tazuke Kofukai Medical Research Institute, Ougimaci, Kita-ku, Osaka, Japan.
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, Japan.
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kumamoto University, Honjo, Kumamoto, Japan.
| | - Naofumi Ito
- Department of Developmental Neurobiology, Graduate School of Life Sciences, Kumamoto University, Honjo, Kumamoto, Japan
- K.K. Sciex Japan, Shinagawa, Tokyo, Japan
| | - Kunimasa Ohta
- Department of Stem Cell Biology, Faculty of Arts and Science, Kyushu University, Motooka, Nishi-ku, Fukuoka, Japan
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Miwa T, Wei FY, Tomizawa K. Cdk5 regulatory subunit-associated protein 1 knockout mice show hearing loss phenotypically similar to age-related hearing loss. Mol Brain 2021; 14:82. [PMID: 34001214 PMCID: PMC8130336 DOI: 10.1186/s13041-021-00791-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/12/2021] [Indexed: 11/10/2022] Open
Abstract
Mitochondrial dysfunction is associated with aging and age-related hearing loss (AHL). However, the precise mechanisms underlying the pathophysiology of hearing loss remain unclear. Cdk5 regulatory subunit-associated protein 1 (CDK5RAP1) enables efficient intramitochondrial translation by catalyzing the deposition of 2-methylthio modifications on mitochondrial tRNAs. Here we investigated the effect of defective mitochondrial protein translation on hearing and AHL in a Cdk5rap1 deficiency C57BL/6 mouse model. Compared to control C57BL/6 mice, Cdk5rap1-knockout female mice displayed hearing loss phenotypically similar to AHL from an early age. The premature hearing loss in Cdk5rap1-knockout mice was associated with the degeneration of the spiral ligament and reduction of endocochlear potentials following the loss of auditory sensory cells. Furthermore, cultured primary mouse embryonic fibroblasts displayed early onset of cellular senescence associated with high oxidative stress and cell death. These results indicate that the CDK5RAP1 deficiency-induced defective mitochondrial translation might cause early hearing loss through the induction of cellular senescence and cochlear dysfunction in the inner ear. Our results suggest that the accumulation of dysfunctional mitochondria might promote AHL progression. Furthermore, our findings suggest that mitochondrial dysfunction and dysregulated mitochondrial tRNA modifications mechanistically cause AHL. Understanding the mechanisms underlying AHL will guide future clinical investigations and interventions in the attempt to mitigate the consequences of AHL.
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Affiliation(s)
- Toru Miwa
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 6068507, Japan.
- Department of Otolaryngology-Head and Neck Surgery, Kitano Hospital, Tazuke Kofukai Medical Research Institute, 2-4-20 Ougimaci, Kita-ku, Osaka, 5308480, Japan.
| | - Fan-Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, 1-1-1- Honjo, Chuo-ku, Kumamoto, 8608556, Japan
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo, Aoba-ku, Sendai, Miyagi, 9808575, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, 1-1-1- Honjo, Chuo-ku, Kumamoto, 8608556, Japan
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Miwa T. Protective Effects of N 1-Methylnicotinamide Against High-Fat Diet- and Age-Induced Hearing Loss via Moderate Overexpression of Sirtuin 1 Protein. Front Cell Neurosci 2021; 15:634868. [PMID: 33889076 PMCID: PMC8055820 DOI: 10.3389/fncel.2021.634868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
Age-related hearing loss (ARHL) is the most common form of hearing loss and the predominant neurodegenerative disease associated with aging. Sirtuin 1 (SIRT1) is associated with the most complex physiological processes, including metabolism, cancer onset, and aging. SIRT1 protein levels are enhanced by the conversion of nicotinamide to N1-methylnicotinamide (MNAM), independent of its mRNA levels. Moreover, MNAM has implications in increased longevity achieved through its mitohormetic effects. Nicotinamide N-methyltransferase (Nnmt) is an enzyme involved in MNAM metabolism, and its level increases under caloric restriction (CR) conditions. The CR condition has implications in delaying ARHL onset. In this study, we aimed to determine the relationship between diet, hearing function, SIRT1 and SIRT3 expression levels in the inner ear, and cochlear morphology. Mice fed with a high-fat diet (HFD), HFD + 1% MNAM, and low-fat diet (LFD) were monitored for age-related auditory-evoked brainstem responses, and changes in cochlear histology, metabolism, and protein and mRNA expressions were analyzed. Our results revealed that the HFD- and aging-mediated downregulated expression of SIRT1 and SIRT3 promoted hearing loss that was obfuscated by MNAM supplementation-induced upregulated expression of cochlear SIRT1 and SIRT3. Thus, our results suggest that MNAM can be used as a therapeutic agent for preventing ARHL.
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Affiliation(s)
- Toru Miwa
- Department of Otolaryngology and Head and Neck Surgery, Kitano Hospital, Tazuke Kofukai Medical Research Institute, Osaka, Japan.,Department of Otolaryngology and Head and Neck Surgery, Graduate of School of Medicine, Kyoto University, Kyoto, Japan
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Lipid nanoparticles-encapsulated brain-derived neurotrophic factor mRNA delivered through the round window niche in the cochleae of guinea pigs. Exp Brain Res 2020; 239:425-433. [PMID: 33215262 DOI: 10.1007/s00221-020-05970-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/21/2020] [Indexed: 01/10/2023]
Abstract
The treatment of sensorineural hearing loss (SNHL) may be achieved via the application of a cochlear implant (CI) that allows the electrical stimulation of spiral ganglion neurons (SGNs). Nevertheless, the efficacy of CIs is limited by the degeneration of SGNs following SNHL. Although the application of exogenous neurotrophic factors has been reported to decrease SGN degeneration, non-invasive targeted drug delivery systems are required to achieve effective results. In this study, an SS-cleavable proton-activated lipid-like material [ssPalm; a neutral lipid nanoparticle (LNP)], was loaded with mRNA, and the efficacy of this material as a delivery system was investigated. Our results showed that LNPssPalm carrying brain-derived neurotrophic factor (BDNF) mRNA was suitable for the treatment of inner ear diseases, preventing the degeneration of SGNs. In conclusion, this modern nanotechnology-based bioconjugation system, LNPssPalm, is a potential non-invasive targeted therapy allowing the delivering biomaterials to specific structures within the inner ear for the treatment of SHNL.
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Yamamoto R, Ohnishi H, Omori K, Yamamoto N. In silico analysis of inner ear development using public whole embryonic body single-cell RNA-sequencing data. Dev Biol 2020; 469:160-171. [PMID: 33131705 DOI: 10.1016/j.ydbio.2020.10.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 02/02/2023]
Abstract
The inner ear comprises four epithelial domains: the cochlea, vestibule, semicircular canals, and endolymphatic duct/sac. These structures are segregated at embryonic day 13.5 (E13.5). However, these four anatomical structures remain undefined at E10.5. Here, we aimed to identify lineage-specific genes in the early developing inner ear using published data obtained from single-cell RNA-sequencing (scRNA-seq) of embryonic mice. We downloaded 5000 single-cell transcriptome data, named 'auditory epithelial trajectory', from the Mouse Organogenesis Cell Atlas. The dataset was supposed to include otic epithelial cells at E9.5-13.5. We projected the 5000 cells onto a two-dimensional space encoding the transcriptional state and visualised the pattern of otic epithelial cell differentiation. We identified 15 clusters, which were annotated as one of the four components of the inner ear epithelium using known genes that characterise the four different tissues. Additionally, we classified 15 clusters into sub-regions of the four inner ear components. By comparing transcriptomes between these 15 clusters, we identified several candidates of lineage-specific genes. Characterising these new candidate genes will help future studies about inner ear development.
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Affiliation(s)
- Ryosuke Yamamoto
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, 54, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 6068507, Japan.
| | - Hiroe Ohnishi
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, 54, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 6068507, Japan.
| | - Koichi Omori
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, 54, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 6068507, Japan.
| | - Norio Yamamoto
- Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, 54, Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 6068507, Japan.
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First person – Toru Miwa. Biol Open 2019. [PMCID: PMC6737970 DOI: 10.1242/bio.046821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
First Person is a series of interviews with the first authors of a selection of papers published in Biology Open, helping early-career researchers promote themselves alongside their papers. Toru Miwa is first author on ‘Role of Dach1 revealed using a novel inner ear-specific Dach1-knockdown mouse model’, published in BiO. Toru conducted the research described in this article while a post-doc fellow of ENT in University of Southern California, in Takahiro Ohyama's lab at the Keck School of Medicine, USA. He is now a head physician specializing in ENT at JCHO Kumamoto General Hospital, Japan, investigating the inner ear.
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