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Rad A, Bartsch O, Bakhtiari S, Zhu C, Xu Y, Monteiro FP, Kok F, Vulto-van Silfhout AT, Kruer MC, Bowl MR, Vona B. Expanding the spectrum of phenotypes for MPDZ: Report of four unrelated families and review of the literature. Clin Genet 2024; 106:413-426. [PMID: 38857973 DOI: 10.1111/cge.14563] [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: 02/22/2024] [Revised: 04/24/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024]
Abstract
MPDZ, a gene with diverse functions mediating cell-cell junction interactions, receptor signaling, and binding multivalent scaffold proteins, is associated with a spectrum of clinically heterogeneous phenotypes with biallelic perturbation. Despite its clinical relevance, the mechanistic underpinnings of these variants remain elusive, underscoring the need for extensive case series and functional investigations. In this study, we conducted a systematic review of cases in the literature through two electronic databases following the PRISMA guidelines. We selected nine studies, including 18 patients, with homozygous or compound heterozygous variants in MPDZ and added five patients from four unrelated families with novel MPDZ variants. To evaluate the role of Mpdz on hearing, we analyzed available auditory electrophysiology data from a knockout murine model (Mpdzem1(IMPC)J/em1(IMPC)J) generated by the International Mouse Phenotyping Consortium. Using exome and genome sequencing, we identified three families with compound heterozygous variants, and one family with a homozygous frameshift variant. MPDZ-related disease is clinically heterogenous with hydrocephaly, vision impairment, hearing impairment and cardiovascular disease occurring most frequently. Additionally, we describe two unrelated patients with spasticity, expanding the phenotypic spectrum. Our murine analysis of the Mpdzem1(IMPC)J/em1(IMPC)J allele showed severe hearing impairment. Overall, we expand understanding of MPDZ-related phenotypes and highlight hearing impairment and spasticity among the heterogeneous phenotypes.
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Affiliation(s)
- Aboulfazl Rad
- Department of Otolaryngology - Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Oliver Bartsch
- Medical Care Centre Section Human Genetics and Institute of Human Genetics, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, Arizona, USA
- Department of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, USA
| | - Changlian Zhu
- Center for Brain Repair and Rehabilitation, Institute of Neuroscience and Physiology, University of Gothenburg, Göteborg, Sweden
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yiran Xu
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, Institute of Neuroscience and Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | | | - Fernando Kok
- Medical Department, Mendelics Genomic Analysis, Sao Paulo, Brazil
- Neurogenetics, Neurology Department, Hospital das Clínicas da Universidade de São Paulo, São Paulo, Brazil
| | - Anneke T Vulto-van Silfhout
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, Arizona, USA
- Department of Child Health, Cellular and Molecular Medicine, Genetics, and Neurology, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, USA
| | - Michael R Bowl
- UCL Ear Institute, University College London, London, UK
| | - Barbara Vona
- Department of Otolaryngology - Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
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2
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Jarysta A, Tadenev ALD, Day M, Krawchuk B, Low BE, Wiles MV, Tarchini B. Inhibitory G proteins play multiple roles to polarize sensory hair cell morphogenesis. eLife 2024; 12:RP88186. [PMID: 38651641 PMCID: PMC11037916 DOI: 10.7554/elife.88186] [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: 04/25/2024] Open
Abstract
Inhibitory G alpha (GNAI or Gαi) proteins are critical for the polarized morphogenesis of sensory hair cells and for hearing. The extent and nature of their actual contributions remains unclear, however, as previous studies did not investigate all GNAI proteins and included non-physiological approaches. Pertussis toxin can downregulate functionally redundant GNAI1, GNAI2, GNAI3, and GNAO proteins, but may also induce unrelated defects. Here, we directly and systematically determine the role(s) of each individual GNAI protein in mouse auditory hair cells. GNAI2 and GNAI3 are similarly polarized at the hair cell apex with their binding partner G protein signaling modulator 2 (GPSM2), whereas GNAI1 and GNAO are not detected. In Gnai3 mutants, GNAI2 progressively fails to fully occupy the sub-cellular compartments where GNAI3 is missing. In contrast, GNAI3 can fully compensate for the loss of GNAI2 and is essential for hair bundle morphogenesis and auditory function. Simultaneous inactivation of Gnai2 and Gnai3 recapitulates for the first time two distinct types of defects only observed so far with pertussis toxin: (1) a delay or failure of the basal body to migrate off-center in prospective hair cells, and (2) a reversal in the orientation of some hair cell types. We conclude that GNAI proteins are critical for hair cells to break planar symmetry and to orient properly before GNAI2/3 regulate hair bundle morphogenesis with GPSM2.
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Affiliation(s)
| | | | - Matthew Day
- The Jackson LaboratoryBar HarborUnited States
| | | | | | | | - Basile Tarchini
- The Jackson LaboratoryBar HarborUnited States
- Tufts University School of MedicineBostonUnited States
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3
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Buswinka CJ, Rosenberg DB, Simikyan RG, Osgood RT, Fernandez K, Nitta H, Hayashi Y, Liberman LW, Nguyen E, Yildiz E, Kim J, Jarysta A, Renauld J, Wesson E, Wang H, Thapa P, Bordiga P, McMurtry N, Llamas J, Kitcher SR, López-Porras AI, Cui R, Behnammanesh G, Bird JE, Ballesteros A, Vélez-Ortega AC, Edge ASB, Deans MR, Gnedeva K, Shrestha BR, Manor U, Zhao B, Ricci AJ, Tarchini B, Basch ML, Stepanyan R, Landegger LD, Rutherford MA, Liberman MC, Walters BJ, Kros CJ, Richardson GP, Cunningham LL, Indzhykulian AA. Large-scale annotated dataset for cochlear hair cell detection and classification. Sci Data 2024; 11:416. [PMID: 38653806 PMCID: PMC11039649 DOI: 10.1038/s41597-024-03218-y] [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: 10/30/2023] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Our sense of hearing is mediated by cochlear hair cells, of which there are two types organized in one row of inner hair cells and three rows of outer hair cells. Each cochlea contains 5-15 thousand terminally differentiated hair cells, and their survival is essential for hearing as they do not regenerate after insult. It is often desirable in hearing research to quantify the number of hair cells within cochlear samples, in both pathological conditions, and in response to treatment. Machine learning can be used to automate the quantification process but requires a vast and diverse dataset for effective training. In this study, we present a large collection of annotated cochlear hair-cell datasets, labeled with commonly used hair-cell markers and imaged using various fluorescence microscopy techniques. The collection includes samples from mouse, rat, guinea pig, pig, primate, and human cochlear tissue, from normal conditions and following in-vivo and in-vitro ototoxic drug application. The dataset includes over 107,000 hair cells which have been identified and annotated as either inner or outer hair cells. This dataset is the result of a collaborative effort from multiple laboratories and has been carefully curated to represent a variety of imaging techniques. With suggested usage parameters and a well-described annotation procedure, this collection can facilitate the development of generalizable cochlear hair-cell detection models or serve as a starting point for fine-tuning models for other analysis tasks. By providing this dataset, we aim to give other hearing research groups the opportunity to develop their own tools with which to analyze cochlear imaging data more fully, accurately, and with greater ease.
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Affiliation(s)
- Christopher J Buswinka
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
- Speech and Hearing Biosciences and Technology graduate program, Harvard University, Cambridge, MA, 02138, USA
| | - David B Rosenberg
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rubina G Simikyan
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
| | - Richard T Osgood
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - Katharine Fernandez
- Section on Sensory Cell Biology, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Hidetomi Nitta
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
| | - Yushi Hayashi
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
| | - Leslie W Liberman
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
| | - Emily Nguyen
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
| | - Erdem Yildiz
- Department of Otolaryngology, Head and Neck Surgery, Vienna General Hospital and Medical University of Vienna, 1090, Vienna, Austria
| | - Jinkyung Kim
- Department of Otolaryngology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Otolaryngology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Justine Renauld
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Ella Wesson
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
| | - Haobing Wang
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
| | - Punam Thapa
- The University of Mississippi Medical Center, Department of Otolaryngology - Head and Neck Surgery, Jackson, MS, 39216, USA
| | - Pierrick Bordiga
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
| | - Noah McMurtry
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Juan Llamas
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, 90033, USA
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery, University of Southern California, Los Angeles, CA, 90033, USA
| | - Siân R Kitcher
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - Ana I López-Porras
- Department of Physiology, University of Kentucky, Lexington, KY, 40536, USA
| | - Runjia Cui
- Section on Sensory Physiology and Biophysics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Ghazaleh Behnammanesh
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, 32610, USA
| | - Jonathan E Bird
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, 32610, USA
| | - Angela Ballesteros
- Section on Sensory Physiology and Biophysics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20814, USA
| | | | - Albert S B Edge
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
| | - Michael R Deans
- Department of Neurobiology, Spencer Fox Eccles School of Medicine at the University of Utah, Salt Lake City, UT, 84112, USA
- Department of Otolaryngology - Head & Neck Surgery, Spencer Fox Eccles School of Medicine at the University of Utah, Salt Lake City, UT, 84132, USA
| | - Ksenia Gnedeva
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, 90033, USA
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery, University of Southern California, Los Angeles, CA, 90033, USA
| | - Brikha R Shrestha
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
| | - Uri Manor
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093, USA
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Bo Zhao
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Anthony J Ricci
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Basile Tarchini
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
- Tufts University School of Medicine, Boston, 02111, MA, USA
- Graduate School of Biomedical Science and Engineering (GSBSE), University of Maine, Orono, ME, 04469, USA
| | - Martín L Basch
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Ruben Stepanyan
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Lukas D Landegger
- Department of Otolaryngology, Head and Neck Surgery, Vienna General Hospital and Medical University of Vienna, 1090, Vienna, Austria
- Department of Otolaryngology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Mark A Rutherford
- Department of Otolaryngology, Washington University, 660 S. Euclid Avenue, Campus Box 8115, St. Louis, MO, 63110, USA
| | - M Charles Liberman
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
- Speech and Hearing Biosciences and Technology graduate program, Harvard University, Cambridge, MA, 02138, USA
| | - Bradley J Walters
- The University of Mississippi Medical Center, Department of Otolaryngology - Head and Neck Surgery, Jackson, MS, 39216, USA
| | - Corné J Kros
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - Guy P Richardson
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - Lisa L Cunningham
- Section on Sensory Cell Biology, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Artur A Indzhykulian
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA.
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA.
- Speech and Hearing Biosciences and Technology graduate program, Harvard University, Cambridge, MA, 02138, USA.
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4
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Buswinka CJ, Rosenberg DB, Simikyan RG, Osgood RT, Fernandez K, Nitta H, Hayashi Y, Liberman LW, Nguyen E, Yildiz E, Kim J, Jarysta A, Renauld J, Wesson E, Thapa P, Bordiga P, McMurtry N, Llamas J, Kitcher SR, López-Porras AI, Cui R, Behnammanesh G, Bird JE, Ballesteros A, Vélez-Ortega AC, Edge AS, Deans MR, Gnedeva K, Shrestha BR, Manor U, Zhao B, Ricci AJ, Tarchini B, Basch M, Stepanyan RS, Landegger LD, Rutherford M, Liberman MC, Walters BJ, Kros CJ, Richardson GP, Cunningham LL, Indzhykulian AA. Large-scale annotated dataset for cochlear hair cell detection and classification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.30.553559. [PMID: 37693382 PMCID: PMC10491224 DOI: 10.1101/2023.08.30.553559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Our sense of hearing is mediated by cochlear hair cells, localized within the sensory epithelium called the organ of Corti. There are two types of hair cells in the cochlea, which are organized in one row of inner hair cells and three rows of outer hair cells. Each cochlea contains a few thousands of hair cells, and their survival is essential for our perception of sound because they are terminally differentiated and do not regenerate after insult. It is often desirable in hearing research to quantify the number of hair cells within cochlear samples, in both pathological conditions, and in response to treatment. However, the sheer number of cells along the cochlea makes manual quantification impractical. Machine learning can be used to overcome this challenge by automating the quantification process but requires a vast and diverse dataset for effective training. In this study, we present a large collection of annotated cochlear hair-cell datasets, labeled with commonly used hair-cell markers and imaged using various fluorescence microscopy techniques. The collection includes samples from mouse, human, pig and guinea pig cochlear tissue, from normal conditions and following in-vivo and in-vitro ototoxic drug application. The dataset includes over 90'000 hair cells, all of which have been manually identified and annotated as one of two cell types: inner hair cells and outer hair cells. This dataset is the result of a collaborative effort from multiple laboratories and has been carefully curated to represent a variety of imaging techniques. With suggested usage parameters and a well-described annotation procedure, this collection can facilitate the development of generalizable cochlear hair cell detection models or serve as a starting point for fine-tuning models for other analysis tasks. By providing this dataset, we aim to supply other groups within the hearing research community with the opportunity to develop their own tools with which to analyze cochlear imaging data more fully, accurately, and with greater ease.
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Affiliation(s)
- Christopher J Buswinka
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
- Speech and Hearing Biosciences and Technology graduate program, Harvard University, Cambridge, MA, 02138, USA
| | - David B Rosenberg
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
| | - Rubina G Simikyan
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
| | - Richard T Osgood
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Katharine Fernandez
- Section on Sensory Cell Biology, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Hidetomi Nitta
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
| | - Yushi Hayashi
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
| | - Leslie W Liberman
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
| | - Emily Nguyen
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
| | - Erdem Yildiz
- Department of Otolaryngology, Head and Neck Surgery, Vienna General Hospital and Medical University of Vienna, 1090 Vienna, Austria
| | - Jinkyung Kim
- Department of Otolaryngology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
- Department of Otolaryngology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Justine Renauld
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Ella Wesson
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
| | - Punam Thapa
- The University of Mississippi Medical Center, Dept. of Otolaryngology - Head and Neck Surgery, Jackson, MS, USA
| | - Pierrick Bordiga
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
| | - Noah McMurtry
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Juan Llamas
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, 90033, USA
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery, University of Southern California, Los Angeles, CA, 90033, USA
| | - Siân R Kitcher
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Ana I López-Porras
- Department of Physiology, University of Kentucky, Lexington, KY, 40536, USA
| | - Runjia Cui
- Section on Sensory Physiology and Biophysics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Ghazaleh Behnammanesh
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, 32610, USA; Myology Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Jonathan E Bird
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, 32610, USA; Myology Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Angela Ballesteros
- Section on Sensory Physiology and Biophysics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20814, USA
| | | | - Albert Sb Edge
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
| | - Michael R Deans
- Department of Neurobiology, Spencer Fox Eccles School of Medicine at the University of Utah, Salt Lake City, UT 84112, USA
- Department of Otolaryngology - Head & Neck Surgery, Spencer Fox Eccles School of Medicine at the University of Utah, Salt Lake City, UT, 84132, USA
| | - Ksenia Gnedeva
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA, 90033, USA
- Tina and Rick Caruso Department of Otolaryngology-Head and Neck Surgery, University of Southern California, Los Angeles, CA, 90033, USA
| | - Brikha R Shrestha
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
| | - Uri Manor
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
- Department of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, 92093
| | - Bo Zhao
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Anthony J Ricci
- Department of Otolaryngology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Basile Tarchini
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA
- Department of Medicine, Tufts University, Boston, 02111, MA, USA
- Graduate School of Biomedical Science and Engineering (GSBSE), University of Maine, Orono, ME, 04469, USA
| | - Martin Basch
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Ruben S Stepanyan
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Department of Neurosciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Lukas D Landegger
- Department of Otolaryngology, Head and Neck Surgery, Vienna General Hospital and Medical University of Vienna, 1090 Vienna, Austria
| | - Mark Rutherford
- Department of Otolaryngology, Washington University, 660 S. Euclid Avenue, Campus Box 8115, St. Louis, MO, 63110, USA
| | - M Charles Liberman
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
- Speech and Hearing Biosciences and Technology graduate program, Harvard University, Cambridge, MA, 02138, USA
| | - Bradley J Walters
- The University of Mississippi Medical Center, Dept. of Otolaryngology - Head and Neck Surgery, Jackson, MS, USA
| | - Corné J Kros
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Guy P Richardson
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Lisa L Cunningham
- Section on Sensory Cell Biology, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Artur A Indzhykulian
- Eaton Peabody Laboratories, Mass Eye and Ear, Boston, MA, 02114, USA
- Department of Otolaryngology, Head and Neck Surgery, Harvard Medical School, Boston, MA, 02114, USA
- Speech and Hearing Biosciences and Technology graduate program, Harvard University, Cambridge, MA, 02138, USA
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5
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Buswinka CJ, Osgood RT, Simikyan RG, Rosenberg DB, Indzhykulian AA. The hair cell analysis toolbox is a precise and fully automated pipeline for whole cochlea hair cell quantification. PLoS Biol 2023; 21:e3002041. [PMID: 36947567 PMCID: PMC10069775 DOI: 10.1371/journal.pbio.3002041] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/03/2023] [Accepted: 02/17/2023] [Indexed: 03/23/2023] Open
Abstract
Our sense of hearing is mediated by sensory hair cells, precisely arranged and highly specialized cells subdivided into outer hair cells (OHCs) and inner hair cells (IHCs). Light microscopy tools allow for imaging of auditory hair cells along the full length of the cochlea, often yielding more data than feasible to manually analyze. Currently, there are no widely applicable tools for fast, unsupervised, unbiased, and comprehensive image analysis of auditory hair cells that work well either with imaging datasets containing an entire cochlea or smaller sampled regions. Here, we present a highly accurate machine learning-based hair cell analysis toolbox (HCAT) for the comprehensive analysis of whole cochleae (or smaller regions of interest) across light microscopy imaging modalities and species. The HCAT is a software that automates common image analysis tasks such as counting hair cells, classifying them by subtype (IHCs versus OHCs), determining their best frequency based on their location along the cochlea, and generating cochleograms. These automated tools remove a considerable barrier in cochlear image analysis, allowing for faster, unbiased, and more comprehensive data analysis practices. Furthermore, HCAT can serve as a template for deep learning-based detection tasks in other types of biological tissue: With some training data, HCAT's core codebase can be trained to develop a custom deep learning detection model for any object on an image.
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Affiliation(s)
- Christopher J Buswinka
- Mass Eye and Ear, Harvard Medical School, Boston, Massachusetts, United States of America
- Speech and Hearing Bioscience and Technology Program, Harvard University, Cambridge, Massachusetts, United States of America
| | - Richard T Osgood
- Mass Eye and Ear, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rubina G Simikyan
- Mass Eye and Ear, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David B Rosenberg
- Mass Eye and Ear, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Artur A Indzhykulian
- Mass Eye and Ear, Harvard Medical School, Boston, Massachusetts, United States of America
- Speech and Hearing Bioscience and Technology Program, Harvard University, Cambridge, Massachusetts, United States of America
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Akturk A, Day M, Tarchini B. RGS12 polarizes the GPSM2-GNAI complex to organize and elongate stereocilia in sensory hair cells. SCIENCE ADVANCES 2022; 8:eabq2826. [PMID: 36260679 PMCID: PMC9581478 DOI: 10.1126/sciadv.abq2826] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/31/2022] [Indexed: 06/10/2023]
Abstract
Inhibitory G proteins (GNAI/Gαi) bind to the scaffold G protein signaling modulator 2 (GPSM2) to form a conserved polarity complex that regulates cytoskeleton organization. GPSM2 keeps GNAI in a guanosine diphosphate (GDP)-bound state, but how GPSM2-GNAI is generated or relates to heterotrimeric G protein signaling remains unclear. We find that RGS12, a GTPase-activating protein (GAP), is required to polarize GPSM2-GNAI at the hair cell apical membrane and to organize mechanosensory stereocilia in rows of graded heights. Accordingly, RGS12 and the guanine nucleotide exchange factor (GEF) DAPLE are asymmetrically co-enriched at the hair cell apical junction, and Rgs12 mouse mutants are deaf. GPSM2 and RGS12 share GoLoco motifs that stabilize GNAI(GDP), and GPSM2 outcompetes RGS12 to bind GNAI. Our results suggest that polarized GEF/GAP junctional activity might dissociate heterotrimeric G proteins, generating free GNAI(GDP) for GPSM2 at the adjacent apical membrane. GPSM2-GNAI(GDP), in turn, imparts asymmetry to the forming stereocilia to enable sensory function in hair cells.
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Affiliation(s)
- Anil Akturk
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Matthew Day
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Basile Tarchini
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- School of Medicine, Tufts University, Boston, MA 02111, USA
- Graduate School of Biomedical Science and Engineering (GSBSE), University of Maine, Orono, ME 04469, USA
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Zhao LJ, Zhang ZL, Fu Y. Novel m.4268T>C mutation in the mitochondrial tRNA Ile gene is associated with hearing loss in two Chinese families. World J Clin Cases 2022; 10:205-216. [PMID: 35071519 PMCID: PMC8727281 DOI: 10.12998/wjcc.v10.i1.205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/23/2021] [Accepted: 11/29/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Herein, we report the genetic, clinical, molecular and biochemical features of two Han Chinese pedigrees with suggested maternally transmitted non-syndromic hearing loss.
AIM To investigate the pathophysiology of hearing loss associated with mitochondrial tRNA mutations.
METHODS Sixteen subjects from two Chinese families with hearing loss underwent clinical, genetic, molecular, and biochemical evaluations. Biochemical characterizations included the measurements of tRNA levels using lymphoblastoid cell lines derived from five affected matrilineal relatives of these families and three control subjects.
RESULTS Three of the 16 matrilineal relatives in these families exhibited a variable seriousness and age-at-onset (8 years) of deafness. Analysis of mtDNA mutation identified the novel homoplasmic tRNAIle 4268T>C mutation in two families both belonging to haplogroup D4j. The 4268T>C mutation is located in a highly conserved base pairing (6U–67A) of tRNAIle. The elimination of 6U–67A base-pairing may change the tRNAIle metabolism. Functional mutation was supported by an approximately 64.6% reduction in the level of tRNAIle observed in the lymphoblastoid cell lines with the 4268T>C mutation, in contrast to the wild-type cell lines. The reduced level of tRNA was below the proposed threshold for normal respiration in lymphoblastoid cells. However, genotyping analysis did not detect any mutations in the prominent deafness-causing gene GJB2 in any members of the family.
CONCLUSION These data show that the novel tRNAIle 4268T>C mutation was involved in maternally transmitted deafness. However, epigenetic, other genetic, or environmental factors may be attributed to the phenotypic variability. These findings will be useful for understanding families with maternally inherited deafness.
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Affiliation(s)
- Li-Jing Zhao
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang Province, China
| | - Zhi-Li Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang Province, China
| | - Yong Fu
- Department of Otorhinolaryngology Head and Neck Surgery, The Children’s Hospital, Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang Province, China
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Saleem IB, Masoud MS, Qasim M, Ali M, Ahmed ZM. Identification and Computational Analysis of Rare Variants of Known Hearing Loss Genes Present in Five Deaf Members of a Pakistani Kindred. Genes (Basel) 2021; 12:genes12121940. [PMID: 34946889 PMCID: PMC8702217 DOI: 10.3390/genes12121940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 12/12/2022] Open
Abstract
Hearing loss (HL) is the most common neurosensory defect in humans that affects the normal communication. Disease is clinically and genetically heterogeneous, rendering challenges for the molecular diagnosis of affected subjects. This study highlights the phenotypic and genetic complexity of inherited HL in a large consanguineous Pakistan kindred. Audiological evaluation of all affected individuals revealed varying degree of mild to profound sensorineural HL. Whole exome (WES) of four family members followed by Sanger sequencing revealed candidate disease-associated variants in five known deafness genes: GJB2 (c.231G>A; p.(Trp77 *)), SLC26A4 (c.1337A>G; p.(Gln446Arg)), CDH23 (c.2789C>T; p.(Pro930Leu)), KCNQ4 (c.1672G>A; p.(Val558Met)) and MPDZ (c.4124T>C; p.(Val1375Ala)). All identified variants replaced evolutionary conserved residues, were either absent or had low frequencies in the control databases. Our in silico and 3-Dimensional (3D) protein topology analyses support the damaging impact of identified variants on the encoded proteins. However, except for the previously established “pathogenic” and “likely pathogenic” categories for the c.231G>A (p.(Trp77 *)) allele of GJB2 and c.1377A>G (p.(Gln446Arg)) of SLC26A4, respectively, all the remaining identified variants were classified as “uncertain significance” based on the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) variant pathogenicity guidelines. Our study highlights the complexity of genetic traits in consanguineous families, and the need of combining the functional studies even with the comprehensive profiling of multiple family members to improve the genetic diagnosis in complex inbred families.
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Affiliation(s)
- Irum Badshah Saleem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan; (I.B.S.); (M.Q.)
| | - Muhammad Shareef Masoud
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan; (I.B.S.); (M.Q.)
- Correspondence: (M.S.M.); (Z.M.A.)
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan; (I.B.S.); (M.Q.)
| | - Muhammad Ali
- Department of Animal Sciences, Quaid-e-Azam University, Islamabad 46000, Pakistan;
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Correspondence: (M.S.M.); (Z.M.A.)
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Deans MR. Conserved and Divergent Principles of Planar Polarity Revealed by Hair Cell Development and Function. Front Neurosci 2021; 15:742391. [PMID: 34733133 PMCID: PMC8558554 DOI: 10.3389/fnins.2021.742391] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/28/2021] [Indexed: 11/13/2022] Open
Abstract
Planar polarity describes the organization and orientation of polarized cells or cellular structures within the plane of an epithelium. The sensory receptor hair cells of the vertebrate inner ear have been recognized as a preeminent vertebrate model system for studying planar polarity and its development. This is principally because planar polarity in the inner ear is structurally and molecularly apparent and therefore easy to visualize. Inner ear planar polarity is also functionally significant because hair cells are mechanosensors stimulated by sound or motion and planar polarity underlies the mechanosensory mechanism, thereby facilitating the auditory and vestibular functions of the ear. Structurally, hair cell planar polarity is evident in the organization of a polarized bundle of actin-based protrusions from the apical surface called stereocilia that is necessary for mechanosensation and when stereociliary bundle is disrupted auditory and vestibular behavioral deficits emerge. Hair cells are distributed between six sensory epithelia within the inner ear that have evolved unique patterns of planar polarity that facilitate auditory or vestibular function. Thus, specialized adaptations of planar polarity have occurred that distinguish auditory and vestibular hair cells and will be described throughout this review. There are also three levels of planar polarity organization that can be visualized within the vertebrate inner ear. These are the intrinsic polarity of individual hair cells, the planar cell polarity or coordinated orientation of cells within the epithelia, and planar bipolarity; an organization unique to a subset of vestibular hair cells in which the stereociliary bundles are oriented in opposite directions but remain aligned along a common polarity axis. The inner ear with its complement of auditory and vestibular sensory epithelia allows these levels, and the inter-relationships between them, to be studied using a single model organism. The purpose of this review is to introduce the functional significance of planar polarity in the auditory and vestibular systems and our contemporary understanding of the developmental mechanisms associated with organizing planar polarity at these three cellular levels.
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Affiliation(s)
- Michael R Deans
- Department of Surgery, Division of Otolaryngology, University of Utah School of Medicine, Salt Lake City, UT, United States.,Department of Neurobiology, University of Utah School of Medicine, Salt Lake City, UT, United States
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