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Guo H, Urban AE, Wong WH. Prioritizing disease-related rare variants by integrating gene expression data. RESEARCH SQUARE 2024:rs.3.rs-4355589. [PMID: 38766095 PMCID: PMC11100897 DOI: 10.21203/rs.3.rs-4355589/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Rare variants, comprising a vast majority of human genetic variations, are likely to have more deleterious impact on human diseases compared to common variants. Here we present carrier statistic, a statistical framework to prioritize disease-related rare variants by integrating gene expression data. By quantifying the impact of rare variants on gene expression, carrier statistic can prioritize those rare variants that have large functional consequence in the diseased patients. Through simulation studies and analyzing real multi-omics dataset, we demonstrated that carrier statistic is applicable in studies with limited sample size (a few hundreds) and achieves substantially higher sensitivity than existing rare variants association methods. Application to Alzheimer's disease reveals 16 rare variants within 15 genes with extreme carrier statistics. We also found strong excess of rare variants among the top prioritized genes in diseased patients compared to that in healthy individuals. The carrier statistic method can be applied to various rare variant types and is adaptable to other omics data modalities, offering a powerful tool for investigating the molecular mechanisms underlying complex diseases.
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Guo H, Urban AE, Wong WH. Prioritizing disease-related rare variants by integrating gene expression data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585836. [PMID: 38562756 PMCID: PMC10983955 DOI: 10.1101/2024.03.19.585836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Rare variants, comprising a vast majority of human genetic variations, are likely to have more deleterious impact on human diseases compared to common variants. Here we present carrier statistic, a statistical framework to prioritize disease-related rare variants by integrating gene expression data. By quantifying the impact of rare variants on gene expression, carrier statistic can prioritize those rare variants that have large functional consequence in the diseased patients. Through simulation studies and analyzing real multi-omics dataset, we demonstrated that carrier statistic is applicable in studies with limited sample size (a few hundreds) and achieves substantially higher sensitivity than existing rare variants association methods. Application to Alzheimer's disease reveals 16 rare variants within 15 genes with extreme carrier statistics. The carrier statistic method can be applied to various rare variant types and is adaptable to other omics data modalities, offering a powerful tool for investigating the molecular mechanisms underlying complex diseases.
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Affiliation(s)
- Hanmin Guo
- Department of Statistics, Stanford University, Stanford, California 94305, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alexander Eckehart Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, Stanford, California 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California 94305, USA
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3
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Geerardyn A, Zhu M, Klabbers T, Huinck W, Mylanus E, Nadol JB, Verhaert N, Quesnel AM. Human Histology after Structure Preservation Cochlear Implantation via Round Window Insertion. Laryngoscope 2024; 134:945-953. [PMID: 37493203 DOI: 10.1002/lary.30900] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/22/2023] [Accepted: 07/05/2023] [Indexed: 07/27/2023]
Abstract
OBJECTIVES Current surgical techniques aim to preserve intracochlear structures during cochlear implant (CI) insertion to maintain residual cochlear function. The optimal technique to minimize damage, however, is still under debate. The aim of this study is to histologically compare insertional trauma and intracochlear tissue formation in humans with a CI implanted via different insertion techniques. METHODS One recent temporal bone from a donor who underwent implantation of a full-length CI (576°) via round window (RW) insertion was compared with nine cases implanted via cochleostomy (CO) or extended round window (ERW) approach. Insertional trauma was assessed on H&E-stained histological sections. 3D reconstructions were generated and virtually re-sectioned to measure intracochlear volumes of fibrosis and neo-ossification. RESULTS The RW insertion case showed electrode translocation via the spiral ligament. 2/9 CO/ERW cases showed no insertional trauma. The total volume of the cochlea occupied by fibro-osseous tissue was 10.8% in the RW case compared with a mean of 30.6% (range 8.7%-44.8%, N = 9) in the CO/ERW cases. The difference in tissue formation in the basal 5 mm of scala tympani, however, was even more pronounced when the RW case (12.3%) was compared with the cases with a CO/ERW approach (mean of 93.8%, range 81% to 100%, N = 9). CONCLUSIONS Full-length CI insertions via the RW can be minimally traumatic at the cochlear base without inducing extensive fibro-osseous tissue formation locally. The current study further supports the hypothesis that drilling of the cochleostomy with damage to the endosteum incites a local tissue reaction. LEVEL OF EVIDENCE 4: Case-control study Laryngoscope, 134:945-953, 2024.
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Affiliation(s)
- Alexander Geerardyn
- Department of Otolaryngology-Head & Neck Surgery, Harvard Medical School, Boston, Massachusetts, U.S.A
- Otopathology Laboratory, Massachusetts Eye and Ear, Boston, Massachusetts, U.S.A
- ExpORL, Department of Neurosciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | - MengYu Zhu
- Otopathology Laboratory, Massachusetts Eye and Ear, Boston, Massachusetts, U.S.A
| | - Tim Klabbers
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Wendy Huinck
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Emmanuel Mylanus
- Department of Otorhinolaryngology, Radboudumc, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Joseph B Nadol
- Department of Otolaryngology-Head & Neck Surgery, Harvard Medical School, Boston, Massachusetts, U.S.A
- Otopathology Laboratory, Massachusetts Eye and Ear, Boston, Massachusetts, U.S.A
| | - Nicolas Verhaert
- ExpORL, Department of Neurosciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Alicia M Quesnel
- Department of Otolaryngology-Head & Neck Surgery, Harvard Medical School, Boston, Massachusetts, U.S.A
- Otopathology Laboratory, Massachusetts Eye and Ear, Boston, Massachusetts, U.S.A
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4
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Moyaert J, Gilles A, Mertens G, Lammers MJW, Gommeren H, Janssens de Varebeke S, Fransen E, Verhaert N, Denys S, van de Berg R, Pennings R, Vanderveken O, Van Rompaey V. Interaural and sex differences in the natural evolution of hearing levels in pre-symptomatic and symptomatic carriers of the p.Pro51Ser variant in the COCH gene. Sci Rep 2024; 14:184. [PMID: 38167558 PMCID: PMC10762206 DOI: 10.1038/s41598-023-50583-6] [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: 06/15/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
Hearing impairment constitutes a significant health problem in developed countries. If hearing loss is slowly progressive, the first signs may not be noticed in time, or remain untreated until the moment the auditory dysfunction becomes more apparent. The present study will focus on DFNA9, an autosomal dominant disorder caused by pathogenic variants in the COCH gene. Although several cross-sectional studies on this topic have been conducted, a crucial need for longitudinal research has been reported by many authors. Longitudinal trajectories of individual hearing thresholds were established as function of age and superimposed lowess curves were generated for 101 female and male carriers of the p.Pro51Ser variant. The average number of times patients have been tested was 2.49 years with a minimum of 1 year and a maximum of 4 years. In addition, interaural and sex differences were studied, as they could modify the natural evolution of the hearing function. The current study demonstrates that, both in female carriers and male carriers, the first signs of hearing decline, i.e. hearing thresholds of 20 dB HL, become apparent as early as the 3rd decade in the highest frequencies. In addition, a rapid progression of SNHL occurs between 40 and 50 years of age. Differences between male and female carriers in the progression of hearing loss are most obvious between the age of 50 and 65 years. Furthermore, interaural discrepancies also manifest from the age of 50 years onwards. High-quality prospective data on the long-term natural evolution of hearing levels offer the opportunity to identify different disease stages in each cochlea and different types of evolution. This will provide more insights in the window of opportunity for future therapeutic intervention trials.
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Affiliation(s)
- Julie Moyaert
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.
- Department of Otorhinolaryngology and Head and Neck Surgery, Antwerp University Hospital, Edegem, Belgium.
| | - Annick Gilles
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Department of Otorhinolaryngology and Head and Neck Surgery, Antwerp University Hospital, Edegem, Belgium
| | - Griet Mertens
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Department of Otorhinolaryngology and Head and Neck Surgery, Antwerp University Hospital, Edegem, Belgium
| | - Marc J W Lammers
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Department of Otorhinolaryngology and Head and Neck Surgery, Antwerp University Hospital, Edegem, Belgium
| | - Hanne Gommeren
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Department of Otorhinolaryngology and Head and Neck Surgery, Antwerp University Hospital, Edegem, Belgium
| | | | - Erik Fransen
- Centre of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Nicolas Verhaert
- Department of Neurosciences, Research Group Experimental Otorhinolaryngology (ExpORL), KU Leuven, Leuven, Belgium
- Department of Otorhinolaryngology and Head and Neck Surgery, University Hospitals of Leuven, Leuven, Belgium
| | - Sam Denys
- Department of Neurosciences, Research Group Experimental Otorhinolaryngology (ExpORL), KU Leuven, Leuven, Belgium
- Department of Otorhinolaryngology and Head and Neck Surgery, University Hospitals of Leuven, Leuven, Belgium
| | - Raymond van de Berg
- Division of Balance Disorders, Department of Otorhinolaryngology and Head and Neck Surgery, Faculty of Health Medicine and Life Sciences, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Ronald Pennings
- Department of Otorhinolaryngology and Head and Neck Surgery, Radboud UMC, Nijmegen, The Netherlands
| | - Olivier Vanderveken
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Department of Otorhinolaryngology and Head and Neck Surgery, Antwerp University Hospital, Edegem, Belgium
| | - Vincent Van Rompaey
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Department of Otorhinolaryngology and Head and Neck Surgery, Antwerp University Hospital, Edegem, Belgium
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Honda T, Kawasaki N, Yanagihara R, Tamura R, Murakami K, Ichimiya T, Matsumoto N, Nishihara S, Yamamoto K. Involvement of cochlin binding to sulfated heparan sulfate/heparin in the pathophysiology of autosomal dominant late-onset hearing loss (DFNA9). PLoS One 2022; 17:e0268485. [PMID: 35901072 PMCID: PMC9333281 DOI: 10.1371/journal.pone.0268485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/01/2022] [Indexed: 11/30/2022] Open
Abstract
Late-onset non-syndromic autosomal dominant hearing loss 9 (DFNA9) is a hearing impairment caused by mutations in the coagulation factor C homology gene (COCH). COCH encodes for cochlin, a major component of the cochlear extracellular matrix. Though biochemical and genetic studies have characterized the properties of wild-type and mutated cochlins derived from DFNA9, little is known about the underlying pathogenic mechanism. In this study, we established a cochlin reporter cell, which allowed us to monitor the interaction of cochlin with its ligand(s) by means of a β-galactosidase assay. We found a class of highly sulfated glycosaminoglycans (GAGs), heparin, that were selectively bound to cochlin. The interaction was distinctly abrogated by N-desulfation, but not by 2-O- or 6-O-desulfation. The binding of cochlin to GAG was diminished by all of the point mutations found in DFNA9 patients. Through GAG composition analysis and immunostaining using mouse cochlin/immunoglobulin-Fc fusion protein, we identified moderately sulfated GAGs in mouse cochlea tissue; this implies that cochlin binds to such sulfated GAGs in the cochlea. Since GAGs play an important role in cell growth and survival as co-receptors of signal transduction mechanisms, the interaction of cochlin with GAGs in the extracellular matrix could aid the pathological research of autosomal dominant late-onset hearing loss in DFNA9.
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Affiliation(s)
- Tomoko Honda
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Norihito Kawasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Rei Yanagihara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Ryo Tamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Karin Murakami
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Tomomi Ichimiya
- Department of Bioinformatics, Graduate School of Engineering, Soka University, Hachioji, Tokyo, Japan
| | - Naoki Matsumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Shoko Nishihara
- Department of Bioinformatics, Graduate School of Engineering, Soka University, Hachioji, Tokyo, Japan
- Glycan & Life System Integration Center (GaLSIC), Soka University, Hachioji, Tokyo, Japan
| | - Kazuo Yamamoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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6
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Keithley EM. Inner ear immunity. Hear Res 2022; 419:108518. [DOI: 10.1016/j.heares.2022.108518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/26/2022]
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Xiang J, Zhang H, Sun X, Zhang J, Xu Z, Sun J, Peng Z. Utility of Whole Genome Sequencing for Population Screening of Deafness-Related Genetic Variants and Cytomegalovirus Infection in Newborns. Front Genet 2022; 13:883617. [PMID: 35571039 PMCID: PMC9099144 DOI: 10.3389/fgene.2022.883617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Hearing loss affects approximately two out of every 1,000 newborns. Genetic factors and congenital cytomegalovirus (CMV) infections account for around 90% of the etiology. The purpose of this study was to develop and test a whole genome sequencing (WGS) approach to detect deafness-related genetic variants and CMV infections simultaneously in newborns.Method: Deafness-related genes causing congenital or childhood hearing loss were curated and selected for newborn screening. Nine dried blood spots from newborns with known genetic variants (n = 6) or CMV infections (n = 3) were employed to develop and validate the WGS testing and analytic pipeline. We then pilot tested the WGS analysis on 51 de-identified clinical samples.Results: 92 gene-disease pairs were selected for screening hearing loss in newborns. In the validation test, WGS accurately detected all types of genetic variants, including single nucleotide variations, insertions/deletions, and copy number variations in the nuclear or mitochondrial genome. Sequence reads mapping to the CMV reference genome were discovered in CMV infected samples. In the pilot test, WGS identified nine out of 51 (18%) newborns carrying pathogenic variants associated with deafness.Conclusion: WGS can simultaneously detect genetic variants and CMV infections in dried blood spot specimens from newborns. Our study provides proof of principle that genome sequencing can be a promising alternative for newborn screening of hearing loss.
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Affiliation(s)
- Jiale Xiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | | | - Junqing Zhang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Zhenpeng Xu
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Zhiyu Peng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- *Correspondence: Zhiyu Peng,
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8
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Ko KI, Merlet JJ, DerGarabedian BP, Zhen H, Suzuki-Horiuchi Y, Hedberg ML, Hu E, Nguyen AT, Prouty S, Alawi F, Walsh MC, Choi Y, Millar SE, Cliff A, Romero J, Garvin MR, Seykora JT, Jacobson D, Graves DT. NF-κB perturbation reveals unique immunomodulatory functions in Prx1 + fibroblasts that promote development of atopic dermatitis. Sci Transl Med 2022; 14:eabj0324. [PMID: 35108061 DOI: 10.1126/scitranslmed.abj0324] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Skin is composed of diverse cell populations that cooperatively maintain homeostasis. Up-regulation of the nuclear factor κB (NF-κB) pathway may lead to the development of chronic inflammatory disorders of the skin, but its role during the early events remains unclear. Through analysis of single-cell RNA sequencing data via iterative random forest leave one out prediction, an explainable artificial intelligence method, we identified an immunoregulatory role for a unique paired related homeobox-1 (Prx1)+ fibroblast subpopulation. Disruption of Ikkb-NF-κB under homeostatic conditions in these fibroblasts paradoxically induced skin inflammation due to the overexpression of C-C motif chemokine ligand 11 (CCL11; or eotaxin-1) characterized by eosinophil infiltration and a subsequent TH2 immune response. Because the inflammatory phenotype resembled that seen in human atopic dermatitis (AD), we examined human AD skin samples and found that human AD fibroblasts also overexpressed CCL11 and that perturbation of Ikkb-NF-κB in primary human dermal fibroblasts up-regulated CCL11. Monoclonal antibody treatment against CCL11 was effective in reducing the eosinophilia and TH2 inflammation in a mouse model. Together, the murine model and human AD specimens point to dysregulated Prx1+ fibroblasts as a previously unrecognized etiologic factor that may contribute to the pathogenesis of AD and suggest that targeting CCL11 may be a way to treat AD-like skin lesions.
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Affiliation(s)
- Kang I Ko
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jean J Merlet
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Brett P DerGarabedian
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Huang Zhen
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Periodontology, Peking University School and Hospital of Stomatology, Haidian District, Beijing 100081, China
| | - Yoko Suzuki-Horiuchi
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew L Hedberg
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eileen Hu
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anh T Nguyen
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephen Prouty
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Faizan Alawi
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew C Walsh
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yongwon Choi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sarah E Millar
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ashley Cliff
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Jonathon Romero
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Michael R Garvin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - John T Seykora
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Dana T Graves
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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9
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Bally JF, Zhang M, Dwosh E, Sato C, Rutka J, Lang AE, Rogaeva E. Genomic study of a large family with complex neurological phenotype including hearing loss, imbalance and action tremor. Neurobiol Aging 2021; 113:137-142. [DOI: 10.1016/j.neurobiolaging.2021.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/15/2021] [Accepted: 12/17/2021] [Indexed: 11/30/2022]
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10
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Verdoodt D, Peeleman N, Szewczyk K, Van Camp G, Ponsaerts P, Van Rompaey V. Cochlin Deficiency Protects Aged Mice from Noise-Induced Hearing Loss. Int J Mol Sci 2021; 22:ijms222111549. [PMID: 34768980 PMCID: PMC8584124 DOI: 10.3390/ijms222111549] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/19/2021] [Accepted: 10/23/2021] [Indexed: 12/18/2022] Open
Abstract
Several studies have shown that type IV fibrocytes, located in the spiral ligament, degenerate first after noise exposure. Interestingly, this is the region where Coch expression is most abundant. As it is suggested that cochlin plays a role in our innate immune system, our goal is to investigate hearing thresholds and inner ear inflammation after noise exposure in Coch knockout (Coch−/−) mice compared to Coch wildtype (Coch+/+) mice. Animals were randomly allocated to a noise exposure group and a control group. Vestibular and auditory testing was performed at 48 h and one week after noise exposure. Whole mount staining and cryosectioning of the cochlea was performed in order to investigate hair cells, spiral ganglion neurons, inner ear inflammation, Coch expression and fibrocyte degeneration. Hearing assessment revealed that Coch+/+ mice had significantly larger threshold shifts than Coch−/− mice after noise exposure. We were unable to identify any differences in hair cells, neurons, fibrocytes and influx of macrophages in the inner ear between both groups. Interestingly, Coch expression was significantly lower in the group exposed to noise. Our results indicate that the absence of Coch has a protective influence on hearing thresholds after noise exposure, but this is not related to reduced inner ear inflammation in the knockout.
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Affiliation(s)
- Dorien Verdoodt
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (N.P.); (K.S.); (V.V.R.)
- Laboratory of Experimental Hematology, Faculty of Medicine and Health Sciences, Vaccine and Infectious Disease Institute (Vaxinfectio), University of Antwerp, 2610 Wilrijk, Belgium;
- Correspondence: ; Tel.: +32-477-89-98-92
| | - Noa Peeleman
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (N.P.); (K.S.); (V.V.R.)
| | - Krystyna Szewczyk
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (N.P.); (K.S.); (V.V.R.)
| | - Guy Van Camp
- Centre of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp, 2650 Edegem, Belgium;
| | - Peter Ponsaerts
- Laboratory of Experimental Hematology, Faculty of Medicine and Health Sciences, Vaccine and Infectious Disease Institute (Vaxinfectio), University of Antwerp, 2610 Wilrijk, Belgium;
| | - Vincent Van Rompaey
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Wilrijk, Belgium; (N.P.); (K.S.); (V.V.R.)
- Department of Otorhinolaryngology and Head & Neck Surgery, Antwerp University Hospital, 2650 Edegem, Belgium
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11
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Mackowetzky K, Yoon KH, Mackowetzky EJ, Waskiewicz AJ. Development and evolution of the vestibular apparatuses of the inner ear. J Anat 2021; 239:801-828. [PMID: 34047378 PMCID: PMC8450482 DOI: 10.1111/joa.13459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/07/2021] [Accepted: 05/06/2021] [Indexed: 12/16/2022] Open
Abstract
The vertebrate inner ear is a labyrinthine sensory organ responsible for perceiving sound and body motion. While a great deal of research has been invested in understanding the auditory system, a growing body of work has begun to delineate the complex developmental program behind the apparatuses of the inner ear involved with vestibular function. These animal studies have helped identify genes involved in inner ear development and model syndromes known to include vestibular dysfunction, paving the way for generating treatments for people suffering from these disorders. This review will provide an overview of known inner ear anatomy and function and summarize the exciting discoveries behind inner ear development and the evolution of its vestibular apparatuses.
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Affiliation(s)
- Kacey Mackowetzky
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Kevin H. Yoon
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | | | - Andrew J. Waskiewicz
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Women & Children’s Health Research InstituteUniversity of AlbertaEdmontonAlbertaCanada
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12
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Seist R, Landegger LD, Robertson NG, Vasilijic S, Morton CC, Stankovic KM. Cochlin Deficiency Protects Against Noise-Induced Hearing Loss. Front Mol Neurosci 2021; 14:670013. [PMID: 34108864 PMCID: PMC8180578 DOI: 10.3389/fnmol.2021.670013] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/16/2021] [Indexed: 12/20/2022] Open
Abstract
Cochlin is the most abundant protein in the inner ear. To study its function in response to noise trauma, we exposed adolescent wild-type (Coch +/+ ) and cochlin knock-out (Coch -/-) mice to noise (8-16 kHz, 103 dB SPL, 2 h) that causes a permanent threshold shift and hair cell loss. Two weeks after noise exposure, Coch-/- mice had substantially less elevation in noise-induced auditory thresholds and hair cell loss than Coch + / + mice, consistent with cochlin deficiency providing protection from noise trauma. Comparison of pre-noise exposure thresholds of auditory brain stem responses (ABRs) and distortion product otoacoustic emissions (DPOAEs) in Coch-/- mice and Coch + / + littermates revealed a small and significant elevation in thresholds of Coch-/- mice, overall consistent with a small conductive hearing loss in Coch-/- mice. We show quantitatively that the pro-inflammatory component of cochlin, LCCL, is upregulated after noise exposure in perilymph of wild-type mice compared to unexposed mice, as is the enzyme catalyzing LCCL release, aggrecanase1, encoded by Adamts4. We further show that upregulation of pro-inflammatory cytokines in perilymph and cochlear soft-tissue after noise exposure is lower in cochlin knock-out than wild-type mice. Taken together, our data demonstrate for the first time that cochlin deficiency results in conductive hearing loss that protects against physiologic and molecular effects of noise trauma.
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Affiliation(s)
- Richard Seist
- Eaton-Peabody Laboratories and Department of Otolaryngology – Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, United States
- Department of Otolaryngology – Head and Neck Surgery, Harvard Medical School, Boston, MA, United States
- Department of Otorhinolaryngology – Head and Neck Surgery, Paracelsus Medical University, Salzburg, Austria
| | - Lukas D. Landegger
- Eaton-Peabody Laboratories and Department of Otolaryngology – Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, United States
- Department of Otolaryngology – Head and Neck Surgery, Harvard Medical School, Boston, MA, United States
- Department of Otorhinolaryngology – Head and Neck Surgery, Medical University of Vienna, Vienna, Austria
| | - Nahid G. Robertson
- Department of Obstetrics and Gynecology and of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Sasa Vasilijic
- Eaton-Peabody Laboratories and Department of Otolaryngology – Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, United States
- Department of Otolaryngology – Head and Neck Surgery, Harvard Medical School, Boston, MA, United States
| | - Cynthia C. Morton
- Department of Obstetrics and Gynecology and of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Manchester Centre for Audiology and Deafness, School of Health Sciences, University of Manchester, Manchester, United Kingdom
- Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA, United States
| | - Konstantina M. Stankovic
- Eaton-Peabody Laboratories and Department of Otolaryngology – Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, United States
- Department of Otolaryngology – Head and Neck Surgery, Harvard Medical School, Boston, MA, United States
- Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA, United States
- Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, United States
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de Vrieze E, Cañas Martín J, Peijnenborg J, Martens A, Oostrik J, van den Heuvel S, Neveling K, Pennings R, Kremer H, van Wijk E. AON-based degradation of c.151C>T mutant COCH transcripts associated with dominantly inherited hearing impairment DFNA9. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 24:274-283. [PMID: 33815940 PMCID: PMC7985667 DOI: 10.1016/j.omtn.2021.02.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/24/2021] [Indexed: 01/22/2023]
Abstract
The c.151C>T founder mutation in COCH is a frequent cause of late-onset, dominantly inherited hearing impairment and vestibular dysfunction (DFNA9) in the Dutch/Belgian population. The initial clinical symptoms only manifest between the 3rd and 5th decade of life, which leaves ample time for therapeutic intervention. The dominant inheritance pattern and established non-haploinsufficiency disease mechanism indicate that suppressing translation of mutant COCH transcripts has high therapeutic potential. Single-molecule real-time (SMRT) sequencing resulted in the identification of 11 variants with a low population frequency (<10%) that are specific to the c.151C>T mutant COCH allele. Proof of concept was obtained that gapmer antisense oligonucleotides (AONs), directed against the c.151C>T mutation or mutant allele-specific intronic variants, are able to induce mutant COCH transcript degradation when delivered to transgenic cells expressing COCH minigenes. The most potent AON, directed against the c.151C>T mutation, was able to induce a 60% decrease in mutant COCH transcripts without affecting wild-type COCH transcript levels. Allele specificity decreased when increasing concentrations of AON were delivered to the cells. With the proven safety of AONs in humans, and rapid advancements in inner ear drug delivery, our in vitro studies indicate that AONs offer a promising treatment modality for DFNA9.
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Affiliation(s)
- Erik de Vrieze
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Corresponding author: Erik de Vrieze, Department of Otorhinolaryngology, Radboud University Medical Center, P.O. Box 9101, 6525 GA Nijmegen (Route 855), the Netherlands.
| | - Jorge Cañas Martín
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Jolien Peijnenborg
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Aniek Martens
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Jaap Oostrik
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Simone van den Heuvel
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Radboud Institute for Health Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Ronald Pennings
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Hannie Kremer
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
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14
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Mei C, Dong H, Nisenbaum E, Thielhelm T, Nourbakhsh A, Yan D, Smeal M, Lundberg Y, Hoffer ME, Angeli S, Telischi F, Nie G, Blanton SH, Liu X. Genetics and the Individualized Therapy of Vestibular Disorders. Front Neurol 2021; 12:633207. [PMID: 33613440 PMCID: PMC7892966 DOI: 10.3389/fneur.2021.633207] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/13/2021] [Indexed: 02/06/2023] Open
Abstract
Background: Vestibular disorders (VDs) are a clinically divergent group of conditions that stem from pathology at the level of the inner ear, vestibulocochlear nerve, or central vestibular pathway. No etiology can be identified in the majority of patients with VDs. Relatively few families have been reported with VD, and so far, no causative genes have been identified despite the fact that more than 100 genes have been identified for inherited hearing loss. Inherited VDs, similar to deafness, are genetically heterogeneous and follow Mendelian inheritance patterns with all modes of transmission, as well as multifactorial inheritance. With advances in genetic sequencing, evidence of familial clustering in VD has begun to highlight the genetic causes of these disorders, potentially opening up new avenues of treatment, particularly in Meniere's disease and disorders with comorbid hearing loss, such as Usher syndrome. In this review, we aim to present recent findings on the genetics of VDs, review the role of genetic sequencing tools, and explore the potential for individualized medicine in the treatment of these disorders. Methods: A search of the PubMed database was performed for English language studies relevant to the genetic basis of and therapies for vestibular disorders, using search terms including but not limited to: “genetics,” “genomics,” “vestibular disorders,” “hearing loss with vestibular dysfunction,” “individualized medicine,” “genome-wide association studies,” “precision medicine,” and “Meniere's syndrome.” Results: Increasing numbers of studies on vestibular disorder genetics have been published in recent years. Next-generation sequencing and new genetic tools are being utilized to unearth the significance of the genomic findings in terms of understanding disease etiology and clinical utility, with growing research interest being shown for individualized gene therapy for some disorders. Conclusions: The genetic knowledge base for vestibular disorders is still in its infancy. Identifying the genetic causes of balance problems is imperative in our understanding of the biology of normal function of the vestibule and the disease etiology and process. There is an increasing effort to use new and efficient genetic sequencing tools to discover the genetic causes for these diseases, leading to the hope for precise and personalized treatment for these patients.
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Affiliation(s)
- Christine Mei
- Department of Otolaryngology, University of Miami, Coral Gables, FL, United States
| | - Hongsong Dong
- Department of Otolaryngology, University of Miami, Coral Gables, FL, United States.,Shenzhen Second People's Hospital, Shenzhen, China
| | - Eric Nisenbaum
- Department of Otolaryngology, University of Miami, Coral Gables, FL, United States
| | - Torin Thielhelm
- Department of Otolaryngology, University of Miami, Coral Gables, FL, United States
| | - Aida Nourbakhsh
- Department of Otolaryngology, University of Miami, Coral Gables, FL, United States
| | - Denise Yan
- Department of Otolaryngology, University of Miami, Coral Gables, FL, United States
| | - Molly Smeal
- Department of Otolaryngology, University of Miami, Coral Gables, FL, United States
| | - Yesha Lundberg
- Department of Otolaryngology, Boys Town National Research Hospital, Omaha, NE, United States
| | - Michael E Hoffer
- Department of Otolaryngology, University of Miami, Coral Gables, FL, United States
| | - Simon Angeli
- Department of Otolaryngology, University of Miami, Coral Gables, FL, United States
| | - Fred Telischi
- Department of Otolaryngology, University of Miami, Coral Gables, FL, United States
| | - Guohui Nie
- Shenzhen Second People's Hospital, Shenzhen, China
| | - Susan H Blanton
- Department of Otolaryngology, University of Miami, Coral Gables, FL, United States
| | - Xuezhong Liu
- Department of Otolaryngology, University of Miami, Coral Gables, FL, United States
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15
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Nisenbaum E, Prentiss S, Yan D, Nourbakhsh A, Smeal M, Holcomb M, Cejas I, Telischi F, Liu XZ. Screening Strategies for Deafness Genes and Functional Outcomes in Cochlear Implant Patients. Otol Neurotol 2021; 42:180-187. [PMID: 33885265 PMCID: PMC9237809 DOI: 10.1097/mao.0000000000002969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVES To review the current state of knowledge about the influence of specific genetic mutations that cause sensorineural hearing loss (SNHL) on cochlear implant (CI) functional outcomes, and how this knowledge may be integrated into clinical practice. A multistep and sequential population-based genetic algorithm suitable for the identification of congenital SNHL mutations before CI placement is also examined. DATA SOURCES, STUDY SELECTION A review was performed of the English literature from 2000 to 2019 using PubMed regarding the influence of specific mutations on CI outcomes and the use of next-generation sequencing for genetic screening of CI patients. CONCLUSION CI is an effective habilitation option for patients with severe-profound congenital SNHL. However, it is well known that CI outcomes show substantial inter-patient variation. Recent advances in genetic studies have improved our understanding of genotype-phenotype relationships for many of the mutations underlying congenital SNHL, and have explored how these relationships may account for some of the variance seen in CI performance outcomes. A sequential genetic screening strategy utilizing next-generation sequencing-based population-specific gene panels may allow for more efficient mutation identification before CI placement. Understanding the relationships between specific mutations and CI outcomes along with integrating routine comprehensive genetic testing into pre-CI evaluations will allow for more effective patient counseling and open the door for the development of mutation-specific treatment strategies.
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Affiliation(s)
- Eric Nisenbaum
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Sandra Prentiss
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Aida Nourbakhsh
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Molly Smeal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Meredith Holcomb
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Ivette Cejas
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Fred Telischi
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
- Dr. John T. Macdonald Foundation Department of Human Genetics, and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
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16
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Verdoodt D, Van Camp G, Ponsaerts P, Van Rompaey V. On the pathophysiology of DFNA9: Effect of pathogenic variants in the COCH gene on inner ear functioning in human and transgenic mice. Hear Res 2020; 401:108162. [PMID: 33421658 DOI: 10.1016/j.heares.2020.108162] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/27/2020] [Accepted: 12/27/2020] [Indexed: 12/20/2022]
Abstract
DeaFNess Autosomal Dominant 9 (DFNA9) is a dominant hereditary non-syndromic form of progressive sensorineural hearing loss often associated with vestibular dysfunction. DFNA9 is caused by pathogenic variants in the COCH gene. This gene encodes for cochlin, a protein that is abundantly expressed in the spiral ligament and spiral limbus of the inner ear but the function of cochlin is still not fully understood. There are 22 known pathogenic variants located in different domains of the COCH gene that can cause DFNA9, all expressing slightly different phenotypes. It is believed that COCH mutations affect the intracellular trafficking of cochlin which could explain the characteristic pathology seen in temporal bones of DFNA9 patients. This pathology involves a widespread accumulation of acellular eosinophilic deposits throughout the labyrinth. To gain a better understanding of the pathology underlying DFNA9, different mouse models were developed. The objective of this review is to describe the different pathogenic variants in the COCH gene and their effect on intracellular trafficking, associated phenotypes and histopathological findings in both patients and mouse models.
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Affiliation(s)
- Dorien Verdoodt
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Belgium; Laboratory of Experimental Hematology, Faculty of Medicine and Health Sciences, Vaccine and Infectious Disease Institute (Vaxinfectio), University of Antwerp, Belgium.
| | - Guy Van Camp
- Centre of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp, Belgium
| | - Peter Ponsaerts
- Laboratory of Experimental Hematology, Faculty of Medicine and Health Sciences, Vaccine and Infectious Disease Institute (Vaxinfectio), University of Antwerp, Belgium
| | - Vincent Van Rompaey
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Belgium; Department of Otorhinolaryngology and Head & Neck surgery, Antwerp University Hospital, Belgium
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17
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Escalera-Balsera A, Roman-Naranjo P, Lopez-Escamez JA. Systematic Review of Sequencing Studies and Gene Expression Profiling in Familial Meniere Disease. Genes (Basel) 2020; 11:E1414. [PMID: 33260921 PMCID: PMC7761472 DOI: 10.3390/genes11121414] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/21/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023] Open
Abstract
Familial Meniere Disease (FMD) is a rare inner ear disorder characterized by episodic vertigo associated with sensorineural hearing loss, tinnitus and/or aural fullness. We conducted a systematic review to find sequencing studies segregating rare variants in FMD to obtain evidence to support candidate genes for MD. After evaluating the quality of the retrieved records, eight studies were selected to carry out a quantitative synthesis. These articles described 20 single nucleotide variants (SNVs) in 11 genes (FAM136A, DTNA, PRKCB, COCH, DPT, SEMA3D, STRC, HMX2, TMEM55B, OTOG and LSAMP), most of them in singular families-the exception being the OTOG gene. Furthermore, we analyzed the pathogenicity of each SNV and compared its allelic frequency with reference datasets to evaluate its role in the pathogenesis of FMD. By retrieving gene expression data in these genes from different databases, we could classify them according to their gene expression in neural or inner ear tissues. Finally, we evaluated the pattern of inheritance to conclude which genes show an autosomal dominant (AD) or autosomal recessive (AR) inheritance in FMD.
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Affiliation(s)
- Alba Escalera-Balsera
- Otology & Neurotology Group CTS 495, Department of Genomic Medicine, Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, 18016 Granada, Spain; (A.E.-B.); (P.R.-N.)
| | - Pablo Roman-Naranjo
- Otology & Neurotology Group CTS 495, Department of Genomic Medicine, Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, 18016 Granada, Spain; (A.E.-B.); (P.R.-N.)
| | - Jose Antonio Lopez-Escamez
- Otology & Neurotology Group CTS 495, Department of Genomic Medicine, Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, 18016 Granada, Spain; (A.E.-B.); (P.R.-N.)
- Department of Otolaryngology, Instituto de Investigación Biosanitaria, ibs.GRANADA, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
- Department of Surgery, Division of Otolaryngology, Universidad de Granada, 18016 Granada, Spain
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18
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Gallego-Martinez A, Lopez-Escamez JA. Genetic architecture of Meniere’s disease. Hear Res 2020; 397:107872. [DOI: 10.1016/j.heares.2019.107872] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/12/2019] [Accepted: 12/09/2019] [Indexed: 01/26/2023]
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19
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Maamari D, El-Khoury H, Saifi O, Muwakkit SA, Zgheib NK. Implementation of Pharmacogenetics to Individualize Treatment Regimens for Children with Acute Lymphoblastic Leukemia. Pharmgenomics Pers Med 2020; 13:295-317. [PMID: 32848445 PMCID: PMC7429230 DOI: 10.2147/pgpm.s239602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/20/2020] [Indexed: 12/28/2022] Open
Abstract
Despite major advances in the management and high cure rates of childhood acute lymphoblastic leukemia (ALL), patients still suffer from many drug-induced toxicities, sometimes necessitating dose reduction, or halting of cytotoxic drugs with a secondary risk of disease relapse. In addition, investigators have noted significant inter-individual variability in drug toxicities and disease outcomes, hence the role of pharmacogenetics (PGx) in elucidating genetic polymorphisms in candidate genes for the optimization of disease management. In this review, we present the PGx data in association with main toxicities seen in children treated for ALL in addition to efficacy, with a focus on the most plausible germline PGx variants. We then follow with a summary of the highest evidence drug-gene annotations with suggestions to move forward in implementing preemptive PGx for the individualization of treatment regimens for children with ALL.
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Affiliation(s)
- Dimitri Maamari
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Habib El-Khoury
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Omran Saifi
- Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Samar A Muwakkit
- Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Nathalie K Zgheib
- Department of Pharmacology and Toxicology, American University of Beirut, Faculty of Medicine, Beirut, Lebanon
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20
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Abstract
OBJECTIVE In this review the authors discuss evidence from the literature concerning vitamin D and temporal bone diseases (benign paroxysmal positional vertigo [BPPV], Menière's disease [MD], vestibular neuritis, idiopathic facial paralysis, idiopathic acute hearing loss). Common features shared by Menière's disease, glaucoma, and the possible influence by vitamin D are briefly discussed. DATA SOURCES, STUDY SELECTION Publications from 1970 until recent times have been reviewed according to a keyword search (see above) in PubMed. CONCLUSIONS MD, BPPV, vestibular neuritis, idiopathic facial paralysis, idiopathic acute hearing loss may all have several etiological factors, but a common feature of the current theories is that an initial viral infection and a subsequent autoimmune/autoinflammatory reaction might be involved. Additionally, in some of these entities varying degrees of demyelination have been documented. Given the immunomodulatory effect of vitamin D, we postulate that it may play a role in suppressing an eventual postviral autoimmune reaction. This beneficial effect may be enhanced by the antioxidative activity of vitamin D and its potential in stabilizing endothelial cells. The association of vitamin D deficiency with demyelination has already been established in other entities such as multiple sclerosis and experimental autoimmune encephalitis. Mice without vitamin D receptor show degenerative features in inner ear ganglia, hair cells, as well as otoconia. The authors suggest further studies concerning the role of vitamin D deficiency in diseases of the temporal bone. Additionally, the possible presence and degree of demyelination in these entities will have to be elucidated more systematically in the future.
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21
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Bommakanti K, Iyer JS, Stankovic KM. Cochlear histopathology in human genetic hearing loss: State of the science and future prospects. Hear Res 2019; 382:107785. [PMID: 31493568 PMCID: PMC6778517 DOI: 10.1016/j.heares.2019.107785] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/30/2019] [Accepted: 08/15/2019] [Indexed: 12/22/2022]
Abstract
Sensorineural hearing loss (SNHL) is an extraordinarily common disability, affecting 466 million people across the globe. Half of these incidents are attributed to genetic mutations that disrupt the structure and function of the cochlea. The human cochlea's interior cannot be imaged or biopsied without damaging hearing; thus, everything known about the morphologic correlates of hereditary human deafness comes from histopathologic studies conducted in either cadaveric human temporal bone specimens or animal models of genetic deafness. The purpose of the present review is to a) summarize the findings from all published histopathologic studies conducted in human temporal bones with known SNHL-causing genetic mutations, and b) compare the reported phenotypes of human vs. mouse SNHL caused by the same genetic mutation. The fact that human temporal bone histopathologic analysis has been reported for only 22 of the nearly 200 identified deafness-causing genes suggests a great need for alternative and improved techniques for studying human hereditary deafness; in light of this, the present review concludes with a summary of promising future directions, specifically in the fields of high resolution cochlear imaging, intracochlear fluid biopsy, and gene therapy.
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Affiliation(s)
- Krishna Bommakanti
- Department of Otolaryngology, Harvard Medical School, Boston, MA, USA; Eaton Peabody Laboratories and Department of Otolaryngology, Massachusetts Eye and Ear, Boston, MA, USA; University of California San Diego School of Medicine, San Diego, CA, USA
| | - Janani S Iyer
- Department of Otolaryngology, Harvard Medical School, Boston, MA, USA; Eaton Peabody Laboratories and Department of Otolaryngology, Massachusetts Eye and Ear, Boston, MA, USA; Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA, USA; Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
| | - Konstantina M Stankovic
- Department of Otolaryngology, Harvard Medical School, Boston, MA, USA; Eaton Peabody Laboratories and Department of Otolaryngology, Massachusetts Eye and Ear, Boston, MA, USA; Program in Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA, USA; Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.
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22
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Basu A, Boczek NJ, Robertson NG, Nasr SH, Jethanamest D, McPhail ED, Kurtin PJ, Dasari S, Butz M, Morton CC, Highsmith WE, Zhou F. First Report of Bilateral External Auditory Canal Cochlin Aggregates ("Cochlinomas") with Multifocal Amyloid-Like Deposits, Associated with Sensorineural Hearing Loss and a Novel Genetic Variant in COCH Encoding Cochlin. Head Neck Pathol 2019; 14:808-816. [PMID: 31493294 PMCID: PMC7413963 DOI: 10.1007/s12105-019-01073-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 08/30/2019] [Indexed: 01/22/2023]
Abstract
Pathogenic variants in COCH, encoding cochlin, cause DFNA9 deafness disorder with characteristic histopathologic findings of cochlin deposits in the inner and middle ears. Here, we present the first case of deafness associated with bilateral external auditory canal (EAC) cochlin deposits, previously unreported evidence suggestive of cochlin-derived amyloid formation, and a novel COCH variant. A 54-year-old woman presented with progressive sensorineural hearing loss and bilateral EAC narrowing by subcutaneous thickening. Excision and histologic evaluation of tissue from both EACs showed paucicellular eosinophilic aggregates containing multiple Congo red-positive foci with yellow and green birefringence under crossed polarization light microscopy. Mass spectrometry performed on both the Congo red-positive and Congo red-negative areas identified cochlin as the most abundant protein, as well as a low abundance of universal amyloid signature peptides only in the Congo red-positive areas. Peptides indicative of a canonical amyloid type were not detected. Electron microscopy showed haphazard, branched microfibrils (3-7 nm in diameter) consistent with cochlin, as well as swirling fibrils (10-24 nm in diameter) reminiscent of amyloid fibrils. Cochlin immunohistochemical staining showed positivity throughout the aggregates. Sequencing of the entire COCH gene coding region from the patient's blood revealed a novel variant resulting in a non-conservative amino acid substitution of isoleucine to phenylalanine (c.1621A>T, p.I541F) in the vWFA2 domain at the protein's C-terminus. Our findings reveal a new pathologic manifestation of cochlin, raise the possibility of previously undescribed cochlin-derived amyloid formation, and highlight the importance of thoroughly investigating all aggregative tissue findings in the practice of diagnostic pathology.
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Affiliation(s)
- Atreyee Basu
- Department of Pathology, New York University School of Medicine, New York, NY USA
| | - Nicole J. Boczek
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Nahid G. Robertson
- Department of Obstetrics and Gynecology, Brigham and Women’s Hospital, Boston, MA USA
| | - Samih H. Nasr
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Daniel Jethanamest
- Department of Otolaryngology-Head and Neck Surgery, New York University School of Medicine, New York, NY USA
| | - Ellen D. McPhail
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Paul J. Kurtin
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Surendra Dasari
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN USA
| | - Malinda Butz
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Cynthia C. Morton
- Departments of Obstetrics and Gynecology and of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA USA
- Broad Institute of MIT and Harvard, Cambridge, MA USA
- University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - W. Edward Highsmith
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN USA
| | - Fang Zhou
- Department of Pathology, New York University School of Medicine, New York, NY USA
- Department of Pathology, New York University Langone Health, Tisch Hospital, 550 First Avenue, New York, NY 10016 USA
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23
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Oza AM, DiStefano MT, Hemphill SE, Cushman BJ, Grant AR, Siegert RK, Shen J, Chapin A, Boczek NJ, Schimmenti LA, Murry JB, Hasadsri L, Nara K, Kenna M, Booth KT, Azaiez H, Griffith A, Avraham KB, Kremer H, Rehm HL, Amr SS, Abou Tayoun AN. Expert specification of the ACMG/AMP variant interpretation guidelines for genetic hearing loss. Hum Mutat 2019; 39:1593-1613. [PMID: 30311386 DOI: 10.1002/humu.23630] [Citation(s) in RCA: 285] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/23/2018] [Accepted: 08/25/2018] [Indexed: 12/23/2022]
Abstract
Due to the high genetic heterogeneity of hearing loss (HL), current clinical testing includes sequencing large numbers of genes, which often yields a significant number of novel variants. Therefore, the standardization of variant interpretation is crucial to provide consistent and accurate diagnoses. The Hearing Loss Variant Curation Expert Panel was created within the Clinical Genome Resource to provide expert guidance for standardized genomic interpretation in the context of HL. As one of its major tasks, our Expert Panel has adapted the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines for the interpretation of sequence variants in HL genes. Here, we provide a comprehensive illustration of the newly specified ACMG/AMP HL rules. Three rules remained unchanged, four rules were removed, and the remaining 21 rules were specified. These rules were further validated and refined using a pilot set of 51 variants assessed by curators and disease experts. Of the 51 variants evaluated in the pilot, 37% (19/51) changed category based upon application of the expert panel specified rules and/or aggregation of evidence across laboratories. These HL-specific ACMG/AMP rules will help standardize variant interpretation, ultimately leading to better care for individuals with HL.
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Affiliation(s)
- Andrea M Oza
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts
| | - Marina T DiStefano
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Sarah E Hemphill
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Brandon J Cushman
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Andrew R Grant
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Rebecca K Siegert
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Jun Shen
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham & Women's Hospital, Boston, Massachusetts
| | | | - Nicole J Boczek
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Lisa A Schimmenti
- Department of Otorhinolaryngology, Clinical Genomics and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota
| | - Jaclyn B Murry
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Kiyomitsu Nara
- Division of Hearing and Balance Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Margaret Kenna
- Department of Otolaryngology and Communication Enhancement, Boston Children's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Kevin T Booth
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospital and Clinics, Iowa City, Iowa.,The Interdisciplinary Graduate Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa Hospital and Clinics, Iowa City, Iowa
| | - Andrew Griffith
- Audiology Unit, National Institute on Deafness and Other Communication Disorders (NIDCD), NIH, Bethesda, Maryland
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Hannie Kremer
- Department of Otorhinolaryngology and Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sami S Amr
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham & Women's Hospital, Boston, Massachusetts
| | - Ahmad N Abou Tayoun
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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24
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Conte G, Lo Russo F, Caschera L, Zanetti D, Castorina P, Sina C, Triulzi F, Di Berardino F. Audiovestibular Phenotypes and Advanced Magnetic Resonance Imaging Features of Cochlin Gene Mutation Carriers. Audiol Neurootol 2019; 24:166-173. [PMID: 31390618 DOI: 10.1159/000501292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 06/03/2019] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE To describe clinical and imaging findings in a group of patients affected by nonsyndromic deafness A9 (DFNA9), using advanced magnetic resonance imaging (MRI) with 3-dimensional (3D) fluid-attenuated inversion recovery (FLAIR) sequence. METHOD A retrospective case review was conducted in a tertiary referral center in Italy. Four sequential adult DFNA9-affected patients, who had undergone MRI at our Department between January 2017 and June 2018, were enrolled (male = 2, female = 2; median age: 65.6 years; 8 diseased ears analyzed). Three patients were relatives; the fourth was unrelated. The main outcome measures - age, sex, records of audiological and vestibular testing, genetic assessment, MRI findings - were analyzed. RESULTS All subjects suffered from bilateral progressive sensorineural hearing loss, more severely at the high frequencies and with a typical clinical pattern of bilateral chronic degenerative cochleovestibular deficit. Aural fullness was reported at the onset of the disease. All patients revealed a pathogenic heterozygous mutation in the Limulus factor C, Coch-5b2 and Lgl1 domain of cochlin. None of the patients showed a significant vestibular and cochlear endolymphatic hydrops at MRI, while high bilateral contrast enhancement on 4-h delayed postcontrast 3D FLAIR sequence was observed in all ears. CONCLUSIONS Increased perilymph enhancement on 4-h delayed postcontrast 3D FLAIR sequence is the common imaging feature of DFNA9 ears, suggesting that blood-labyrinthine barrier breakdown may play the main role in the pathophysiology of this disease. Significant hydrops has been excluded by MRI. This finding might be clinically useful in differentiating DFNA9 disease from other pathologies with similar clinical findings like Ménière's disease.
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Affiliation(s)
- Giorgio Conte
- Department of Neuroradiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Francesco Lo Russo
- Postgraduation School of Radiodiagnostics, Università degli Studi di Milano, Milan, Italy,
| | - Luca Caschera
- Postgraduation School of Radiodiagnostics, Università degli Studi di Milano, Milan, Italy
| | - Diego Zanetti
- Audiology Unit, Department of Clinical Sciences and Community, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Pierangela Castorina
- Audiology Unit, Department of Clinical Sciences and Community, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Clara Sina
- Department of Neuroradiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Fabio Triulzi
- Department of Neuroradiology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Federica Di Berardino
- Audiology Unit, Department of Clinical Sciences and Community, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
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25
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Tucci DL, Doherty JK. Contributions of Contemporary Human Temporal Bone Histopathology to Clinical Otology. Otolaryngol Head Neck Surg 2019; 161:725-733. [PMID: 31359831 DOI: 10.1177/0194599819863368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Contemporary techniques have greatly enhanced the contributions of human temporal bone (HTB) histopathology to our understanding of the mechanisms of human otologic disease and disease treatment. Herein, we review some of the most salient contributions of this research to disease management. The field of HTB histopathology is challenged by limited resources as applies to trained investigators, infrastructure, and well-equipped laboratories. This research provides insights into clinical otology that cannot be obtained by any other means. Measures should be taken to preserve and extend the contributions of HTB research.
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Affiliation(s)
- Debara L Tucci
- Department of Head and Neck Surgery & Communication Sciences, Duke University School of Medicine, Durham, North Carolina, USA
| | - Joni K Doherty
- Rick and Tina Caruso Department of Otolaryngology-Head & Neck Surgery, Keck Medicine of University of Southern California, Los Angeles, California, USA
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26
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What if? Mouse proteomics after gene inactivation. J Proteomics 2019; 199:102-122. [DOI: 10.1016/j.jprot.2019.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 03/09/2019] [Accepted: 03/10/2019] [Indexed: 12/17/2022]
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27
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Pavlovic S, Kotur N, Stankovic B, Zukic B, Gasic V, Dokmanovic L. Pharmacogenomic and Pharmacotranscriptomic Profiling of Childhood Acute Lymphoblastic Leukemia: Paving the Way to Personalized Treatment. Genes (Basel) 2019; 10:E191. [PMID: 30832275 PMCID: PMC6471971 DOI: 10.3390/genes10030191] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 02/07/2023] Open
Abstract
Personalized medicine is focused on research disciplines which contribute to the individualization of therapy, like pharmacogenomics and pharmacotranscriptomics. Acute lymphoblastic leukemia (ALL) is the most common malignancy of childhood. It is one of the pediatric malignancies with the highest cure rate, but still a lethal outcome due to therapy accounts for 1%⁻3% of deaths. Further improvement of treatment protocols is needed through the implementation of pharmacogenomics and pharmacotranscriptomics. Emerging high-throughput technologies, including microarrays and next-generation sequencing, have provided an enormous amount of molecular data with the potential to be implemented in childhood ALL treatment protocols. In the current review, we summarized the contribution of these novel technologies to the pharmacogenomics and pharmacotranscriptomics of childhood ALL. We have presented data on molecular markers responsible for the efficacy, side effects, and toxicity of the drugs commonly used for childhood ALL treatment, i.e., glucocorticoids, vincristine, asparaginase, anthracyclines, thiopurines, and methotrexate. Big data was generated using high-throughput technologies, but their implementation in clinical practice is poor. Research efforts should be focused on data analysis and designing prediction models using machine learning algorithms. Bioinformatics tools and the implementation of artificial i Lack of association of the CEP72 rs924607 TT genotype with intelligence are expected to open the door wide for personalized medicine in the clinical practice of childhood ALL.
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Affiliation(s)
- Sonja Pavlovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Nikola Kotur
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Biljana Stankovic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Branka Zukic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Vladimir Gasic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11000 Belgrade, Serbia.
| | - Lidija Dokmanovic
- University Children's Hospital, 11000 Belgrade, Serbia.
- University of Belgrade, Faculty of Medicine, 11000 Belgrade, Serbia.
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28
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A systematic review of hearing and vestibular function in carriers of the Pro51Ser mutation in the COCH gene. Eur Arch Otorhinolaryngol 2019; 276:1251-1262. [DOI: 10.1007/s00405-019-05322-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/30/2019] [Indexed: 01/08/2023]
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29
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Li L, Sajdyk T, Smith EML, Chang CW, Li C, Ho RH, Hutchinson R, Wells E, Skiles JL, Winick N, Martin PL, Renbarger JL. Genetic Variants Associated With Vincristine-Induced Peripheral Neuropathy in Two Populations of Children With Acute Lymphoblastic Leukemia. Clin Pharmacol Ther 2019; 105:1421-1428. [PMID: 30506673 DOI: 10.1002/cpt.1324] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/25/2018] [Indexed: 01/29/2023]
Abstract
Vincristine is one of the core chemotherapy agents used in the treatment of pediatric acute lymphoblastic leukemia (ALL). However, one of the major toxicities resulting from vincristine exposure is vincristine-induced peripheral neuropathy (VIPN). When VIPN results in significant morbidity, the vincristine dose may need to be reduced, thus potentially decreasing the effectiveness of treatment. To date, there are no robust biomarkers used clinically to determine which patients will be at risk for worse neuropathy. The current study included genomewide association study (GWAS) in two independent cohorts: Pediatric Oncology Group (POG) ALL trials and a multicenter study based at Indiana University in children with ALL. A meta-analysis of the cohorts identified two single-nucleotide polymorphisms (SNPs), rs1045644 and rs7963521, as being significantly (P value threshold 0.05/4749 = 1.05E-05) associated with neuropathy. Subsequently these SNPs may be effective biomarkers of VIPN in children with ALL.
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Affiliation(s)
- Lang Li
- Ohio State University, Columbus, Ohio, USA
| | - Tammy Sajdyk
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | | | | | - Claire Li
- Merck, Upper Gwynedd, Pennsylvania, USA
| | - Richard H Ho
- Vanderbilt University, Nashville, Tennessee, USA
| | | | - Elizabeth Wells
- Children's Children Research Institute, Washington, District of Columbia, USA
| | - Jodi L Skiles
- Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Naomi Winick
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Paul L Martin
- Duke University Medical Center, Durham, North Carolina, USA
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30
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Gene expression dataset for whole cochlea of Macaca fascicularis. Sci Rep 2018; 8:15554. [PMID: 30349143 PMCID: PMC6197234 DOI: 10.1038/s41598-018-33985-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/09/2018] [Indexed: 11/17/2022] Open
Abstract
Macaca fascicularis is a highly advantageous model in which to study human cochlea with regard to both evolutionary proximity and physiological similarity of the auditory system. To better understand the properties of primate cochlear function, we analyzed the genes predominantly expressed in M. fascicularis cochlea. We compared the cochlear transcripts obtained from an adult male M. fascicularis by macaque and human GeneChip microarrays with those in multiple macaque and human tissues or cells and identified 344 genes with expression levels more than 2-fold greater than in the other tissues. These “cochlear signature genes” included 35 genes responsible for syndromic or nonsyndromic hereditary hearing loss. Gene set enrichment analysis revealed groups of genes categorized as “ear development” and “ear morphogenesis” in the top 20 gene ontology categories in the macaque and human arrays, respectively. This dataset will facilitate both the study of genes that contribute to primate cochlear function and provide insight to discover novel genes associated with hereditary hearing loss that have yet to be established using animal models.
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31
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Hosokawa K, Hosokawa S, Ishiyama G, Ishiyama A, Lopez IA. Immunohistochemical localization of Nrf2 in the human cochlea. Brain Res 2018; 1700:1-8. [PMID: 29981724 DOI: 10.1016/j.brainres.2018.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 07/02/2018] [Accepted: 07/04/2018] [Indexed: 02/08/2023]
Abstract
Oxidative stress plays an important role in several inner ear diseases and normal aging. Nuclear (erythroid-derived 2)-like 2, also known as Nrf2, is a transcription factor encoded by the NFE2L2 gene that controls the expression of genes necessary to reduce oxidative stress. There are no studies to the date on the localization of Nrf2 in the human inner ear in normal or pathological conditions. Therefore, we investigated the immunohistochemical localization of Nrf2 in the human cochlea and vestibule using formalin-fixed celloidin-embedded human temporal bone sections. Nrf2 immunoreactivity (IR) was found in the inner and outer hair cells and supporting cells of the organ of Corti throughout the cochlea. Nfr2-IR was also found in hair cells and supporting cells of the maculae and cristae vestibular sensory epithelia. Nrf2-IR was decreased in the organ of Corti of older age individuals. The immunolocalization of Nrf2 in both auditory and vestibular sensory epithelia suggest that this transcription factor may play a relevant role in protecting sensory hair cells from oxidative stress.
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Affiliation(s)
- Kumiko Hosokawa
- Department of Head and Neck Surgery, David Geffen School of Medicine, University of California, Los Angeles, USA; Department of Otorhinolaryngology/ Head & Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Seiji Hosokawa
- Department of Head and Neck Surgery, David Geffen School of Medicine, University of California, Los Angeles, USA; Department of Otorhinolaryngology/ Head & Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Gail Ishiyama
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Akira Ishiyama
- Department of Head and Neck Surgery, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Ivan A Lopez
- Department of Head and Neck Surgery, David Geffen School of Medicine, University of California, Los Angeles, USA.
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32
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Medendorp WP, Alberts BBGT, Verhagen WIM, Koppen M, Selen LPJ. Psychophysical Evaluation of Sensory Reweighting in Bilateral Vestibulopathy. Front Neurol 2018; 9:377. [PMID: 29910766 PMCID: PMC5992424 DOI: 10.3389/fneur.2018.00377] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/08/2018] [Indexed: 11/13/2022] Open
Abstract
Perception of spatial orientation is thought to rely on the brain's integration of visual, vestibular, proprioceptive, and somatosensory signals, as well as internal beliefs. When one of these signals breaks down, such as the vestibular signal in bilateral vestibulopathy, patients start compensating by relying more on the remaining cues. How these signals are reweighted in this integration process is difficult to establish, since they cannot be measured in isolation during natural tasks, are inherently noisy, and can be ambiguous or in conflict. Here, we review our recent work, combining experimental psychophysics with a reverse engineering approach, based on Bayesian inference principles, to quantify sensory noise levels and optimal (re)weighting at the individual subject level, in both patients with bilateral vestibular deficits and healthy controls. We show that these patients reweight the remaining sensory information, relying more on visual and other nonvestibular information than healthy controls in the perception of spatial orientation. This quantification approach could improve diagnostics and prognostics of multisensory integration deficits in vestibular patients, and contribute to an evaluation of rehabilitation therapies directed toward specific training programs.
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Affiliation(s)
- W. Pieter Medendorp
- Radboud University Nijmegen, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, Netherlands
| | - Bart B. G. T. Alberts
- Radboud University Nijmegen, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, Netherlands
| | - Wim I. M. Verhagen
- Department of Neurology, Canisius Wilhelmina Hospital, Nijmegen, Netherlands
| | - Mathieu Koppen
- Radboud University Nijmegen, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, Netherlands
| | - Luc P. J. Selen
- Radboud University Nijmegen, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, Netherlands
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33
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Mielczarek M, Olszewski J, Pietkiewicz P. Sequencing of exons 4, 5, 12 of COCH gene in patients with postlingual sensorineural hearing loss accompanied by vestibular lesion. Arch Med Sci 2018; 14:625-628. [PMID: 29765451 PMCID: PMC5949911 DOI: 10.5114/aoms.2016.60094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/07/2016] [Indexed: 12/03/2022] Open
Abstract
INTRODUCTION Mutations at the DFNA9 locus on chromosome 14q12 are the third most common form of DFNA hearing loss, which is clinically characterized by late onset (in adulthood) progressive sensorineural hearing loss accompanied by vestibular dysfunction. The aim of the study was to search for COCH gene mutations (P51S, V66G, G87W, G88E, V104del, I109N, W117R, A119T, M512T, C542Y) in patients with severe or profound sensorineural hearing loss accompanied by a vestibular lesion. MATERIAL AND METHODS The study was based on a group of 30 patients. Qualification criteria comprised the presence of progressive postlingual, severe to profound sensorineural hearing loss with tinnitus, early age of sensorineural hearing loss onset, before the 40th year of life, and a positive family history of early onset hearing loss. All patients were diagnosed with peripheral vestibular lesions. RESULTS The authors did not find P51S, V66G, G87W, G88E, V104del, I109N, W117R, A119T, M512T, or C542Y mutations in the COCH gene in the tested group (no differences were found in the nucleotide sequences of exomes 4, 5 and 12 when compared to the published cDNA sequence of the COCH gene). CONCLUSIONS No cochlin mutations were found in the group of patients with severe to profound sensorineural hearing impairment accompanied by a vestibular lesion. The COCH gene needs further exploration and analysis of genotype-phenotype correlations.
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Affiliation(s)
- Marzena Mielczarek
- Department of Otolaryngology, Laryngological Oncology, Audiology and Phoniatrics, Medical University of Lodz, Lodz, Poland
| | - Jurek Olszewski
- Department of Otolaryngology, Laryngological Oncology, Audiology and Phoniatrics, Medical University of Lodz, Lodz, Poland
| | - Piotr Pietkiewicz
- Department of Otolaryngology, Laryngological Oncology, Audiology and Phoniatrics, Medical University of Lodz, Lodz, Poland
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34
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Gallego-Martinez A, Espinosa-Sanchez JM, Lopez-Escamez JA. Genetic contribution to vestibular diseases. J Neurol 2018; 265:29-34. [PMID: 29582143 DOI: 10.1007/s00415-018-8842-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 03/18/2018] [Accepted: 03/20/2018] [Indexed: 12/22/2022]
Abstract
Growing evidence supports the contribution of allelic variation to vestibular disorders. Heritability attributed to rare allelic variants is found in familial vestibular syndromes such as enlarged vestibular aqueduct syndrome or familial Meniere disease. However, the involvement of common allelic variants as key regulators of physiological processes in common and rare vestibular diseases is starting to be deciphered, including motion sickness or sporadic Meniere disease. The genetic contribution to most of the vestibular disorders is still largely unknown. This review will outline the role of common and rare variants in human genome to episodic vestibular syndromes, progressive vestibular syndrome, and hereditary sensorineural hearing loss associated with vestibular phenotype. Future genomic studies and network analyses of omic data will clarify the pathway towards a personalized stratification of treatments.
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Affiliation(s)
- Alvaro Gallego-Martinez
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, Centre for Genomics and Oncological Research-Pfizer/University of Granada/Andalusian Regional Government (GENYO), Avda de la Ilustración, 114, 18016, Granada, Spain
| | - Juan Manuel Espinosa-Sanchez
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, Centre for Genomics and Oncological Research-Pfizer/University of Granada/Andalusian Regional Government (GENYO), Avda de la Ilustración, 114, 18016, Granada, Spain
- Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Universitario Virgen de las Nieves, Granada, Spain
| | - Jose Antonio Lopez-Escamez
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, Centre for Genomics and Oncological Research-Pfizer/University of Granada/Andalusian Regional Government (GENYO), Avda de la Ilustración, 114, 18016, Granada, Spain.
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.
- Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Universitario Virgen de las Nieves, Granada, Spain.
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35
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De Belder J, Matthysen S, Claes AJ, Mertens G, Van de Heyning P, Van Rompaey V. Does Otovestibular Loss in the Autosomal Dominant Disorder DFNA9 Have an Impact of on Cognition? A Systematic Review. Front Neurosci 2018; 11:735. [PMID: 29375286 PMCID: PMC5767272 DOI: 10.3389/fnins.2017.00735] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 12/18/2017] [Indexed: 12/21/2022] Open
Abstract
Background and Purpose: Cognitive impairment has been observed in patients with bilateral vestibular loss (BVL) and in patients with sensorineural hearing loss (SNHL). DFNA9 is an autosomal dominant disorder that causes a combination of both sensory deficits by the 3rd to 5th decade. We therefore hypothesize a combined detrimental effect on cognition. The aim of this systematic review was to identify studies related to DFNA9 in general and its relationship with cognitive impairment more specifically. Materials and Methods: Several databases including Medline, Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials, ISI Web of Knowledge, and Web of Science were searched to accumulate information about DFNA9-mutations, including phenotype, genotype, pathophysiology, quality of life (QOL), and imaging in general and cognitive function more specifically. A qualitative analysis was performed on the 55 articles that qualified. Results: The clinical features of DFNA9 are different along the 24 COCH mutations, described up to now. Vestibular symptoms generally present themselves a few years after SNHL onset in mutations associated with the vWFA-domain although they can precede SNHL onset in other mutations associated with the LCCL-domain. QoL has not been studied extensively in DFNA9, although scarce work is available on the positive impact of cochlear implantation to rehabilitate hearing. No studies were found evaluating cognition in DFNA9 patients. Conclusion: Although cognitive impairment has been demonstrated in patients with hearing loss as well as in patients with BVL, no studies have been reported on the combination of both sensory deficits, such as in DFNA9. Further research is warranted to correlate otovestibular status with cognition.
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Affiliation(s)
- Jonas De Belder
- Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Stijn Matthysen
- Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Annes J Claes
- Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Department of Otorhinolaryngology and Head and Neck Surgery, Antwerp University Hospital, Edegem, Belgium
| | - Griet Mertens
- Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Department of Otorhinolaryngology and Head and Neck Surgery, Antwerp University Hospital, Edegem, Belgium
| | - Paul Van de Heyning
- Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Department of Otorhinolaryngology and Head and Neck Surgery, Antwerp University Hospital, Edegem, Belgium
| | - Vincent Van Rompaey
- Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Department of Otorhinolaryngology and Head and Neck Surgery, Antwerp University Hospital, Edegem, Belgium
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Alberts BBGT, Selen LPJ, Verhagen WIM, Pennings RJE, Medendorp WP. Bayesian quantification of sensory reweighting in a familial bilateral vestibular disorder (DFNA9). J Neurophysiol 2017; 119:1209-1221. [PMID: 29357473 DOI: 10.1152/jn.00082.2017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
DFNA9 is a rare progressive autosomal dominantly inherited vestibulo-cochlear disorder, resulting in a homogeneous group of patients with hearing impairment and bilateral vestibular function loss. These patients suffer from a deteriorated sense of spatial orientation, leading to balance problems in darkness, especially on irregular surfaces. Both behavioral and functional imaging studies suggest that the remaining sensory cues could compensate for the loss of vestibular information. A thorough model-based quantification of this reweighting in individual patients is, however, missing. Here we psychometrically examined the individual patient's sensory reweighting of these cues after complete vestibular loss. We asked a group of DFNA9 patients and healthy control subjects to judge the orientation (clockwise or counterclockwise relative to gravity) of a rod presented within an oriented square frame (rod-in-frame task) in three different head-on-body tilt conditions. Our results show a cyclical frame-induced bias in perceived gravity direction across a 90° range of frame orientations. The magnitude of this bias was significantly increased in the patients compared with the healthy control subjects. Response variability, which increased with head-on-body tilt, was also larger for the patients. Reverse engineering of the underlying signal properties, using Bayesian inference principles, suggests a reweighting of sensory signals, with an increase in visual weight of 20-40% in the patients. Our approach of combining psychophysics and Bayesian reverse engineering is the first to quantify the weights associated with the different sensory modalities at an individual patient level, which could make it possible to develop personal rehabilitation programs based on the patient's sensory weight distribution. NEW & NOTEWORTHY It has been suggested that patients with vestibular deficits can compensate for this loss by increasing reliance on other sensory cues, although an actual quantification of this reweighting is lacking. We combine experimental psychophysics with a reverse engineering approach based on Bayesian inference principles to quantify sensory reweighting in individual vestibular patients. We discuss the suitability of this approach for developing personal rehabilitation programs based on the patient's sensory weight distribution.
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Affiliation(s)
- Bart B G T Alberts
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen , Nijmegen , The Netherlands
| | - Luc P J Selen
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen , Nijmegen , The Netherlands
| | - Wim I M Verhagen
- Neurology, Canisius Wilhelmina Hospital , Nijmegen , The Netherlands
| | - Ronald J E Pennings
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen , Nijmegen , The Netherlands.,Department of Otorhinolaryngology, Radboud University Medical Centre , Nijmegen , The Netherlands
| | - W Pieter Medendorp
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen , Nijmegen , The Netherlands
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Parzefall T, Frohne A, Koenighofer M, Kirchnawy A, Streubel B, Schoefer C, Gstoettner W, Frei K, Lucas T. Identification of a rare COCH mutation by whole-exome sequencing : Implications for personalized therapeutic rehabilitation in an Austrian family with non-syndromic autosomal dominant late-onset hearing loss. Wien Klin Wochenschr 2017; 130:299-306. [PMID: 28733840 PMCID: PMC5966484 DOI: 10.1007/s00508-017-1230-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 06/26/2017] [Indexed: 12/24/2022]
Abstract
Background Non-syndromic autosomal dominant hearing impairment is characteristically postlingual in onset. Genetic diagnostics are essential for genetic counselling, disease prognosis and understanding of the molecular mechanisms of disease. To date, 36 causative genes have been identified, many in only individual families. Gene selection for genetic screening by traditional methods and genetic diagnosis in autosomal dominant patients has therefore been fraught with difficulty. Whole-exome sequencing provides a powerful tool to analyze all protein-coding genomic regions in parallel, thus allowing the comprehensive screening of all known genes and associated alterations. Methods In this study, a previously undiagnosed late-onset progressive autosomal dominant hearing loss in an Austrian family was investigated by means of whole-exome sequencing. Results were confirmed by Sanger sequencing. Results A previously described c.151C>T missense (p.Pro51Ser) mutation in the LCCL (limulus factor C, cochlin, late gestation lung protein Lgl1) domain of the cochlin gene (COCH) was identified as causative and segregated with disease in five members of the family. Molecular diagnostics led to the decision to perform cochlear implantation in an index patient who subsequently showed excellent postoperative auditory performance. The c.151C>T mutation was not found in 18 screened Austrian families with autosomal dominant hearing loss but was represented alongside other known pathogenic mutant COCH alleles in the Genome Aggregation Database (gnomAD) in European populations. A combined allele frequency of 0.000128 implies an orphan disease frequency for COCH-induced hearing loss of 1:3900 in Europe. Conclusions Exome sequencing successfully resolved the genetic diagnosis in a family suffering from autosomal dominant hearing impairment and allowed prediction of purported auditory outcome after cochlear implantation in an index patient. Personalized treatment approaches based on the molecular mechanisms of disease may become increasingly important in the future.
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Affiliation(s)
- Thomas Parzefall
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Alexandra Frohne
- Department for Cell and Developmental Biology, Orphan disease genetics group, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Martin Koenighofer
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Andreas Kirchnawy
- Department for Cell and Developmental Biology, Orphan disease genetics group, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Berthold Streubel
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Christian Schoefer
- Department for Cell and Developmental Biology, Orphan disease genetics group, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Gstoettner
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Klemens Frei
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.
| | - Trevor Lucas
- Department for Cell and Developmental Biology, Orphan disease genetics group, Center for Anatomy and Cell Biology, Medical University of Vienna, Vienna, Austria
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Laser-capture micro dissection combined with next-generation sequencing analysis of cell type-specific deafness gene expression in the mouse cochlea. Hear Res 2017; 348:87-97. [PMID: 28263850 DOI: 10.1016/j.heares.2017.02.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 12/25/2016] [Accepted: 02/28/2017] [Indexed: 12/13/2022]
Abstract
Cochlear implantation (CI), which directly stimulates the cochlear nerves, is the most effective and widely used medical intervention for patients with severe to profound sensorineural hearing loss. The etiology of the hearing loss is speculated to have a major influence of CI outcomes, particularly in cases resulting from mutations in genes preferentially expressed in the spiral ganglion region. To elucidate precise gene expression levels in each part of the cochlea, we performed laser-capture micro dissection in combination with next-generation sequencing analysis and determined the expression levels of all known deafness-associated genes in the organ of Corti, spiral ganglion, lateral wall, and spiral limbs. The results were generally consistent with previous reports based on immunocytochemistry or in situ hybridization. As a notable result, the genes associated with many kinds of syndromic hearing loss (such as Clpp, Hars2, Hsd17b4, Lars2 for Perrault syndrome, Polr1c and Polr1d for Treacher Collins syndrome, Ndp for Norrie Disease, Kal for Kallmann syndrome, Edn3 and Snai2 for Waardenburg Syndrome, Col4a3 for Alport syndrome, Sema3e for CHARGE syndrome, Col9a1 for Sticker syndrome, Cdh23, Cib2, Clrn1, Pcdh15, Ush1c, Ush2a, Whrn for Usher syndrome and Wfs1 for Wolfram syndrome) showed higher levels of expression in the spiral ganglion than in other parts of the cochlea. This dataset will provide a base for more detailed analysis in order to clarify gene functions in the cochlea as well as predict CI outcomes based on gene expression data.
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Massively Parallel Sequencing of a Chinese Family with DFNA9 Identified a Novel Missense Mutation in the LCCL Domain of COCH. Neural Plast 2016; 2016:5310192. [PMID: 28116169 PMCID: PMC5223038 DOI: 10.1155/2016/5310192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/16/2016] [Accepted: 11/23/2016] [Indexed: 11/25/2022] Open
Abstract
DFNA9 is a late-onset, progressive, autosomal dominantly inherited sensorineural hearing loss with vestibular dysfunction, which is caused by mutations in the COCH (coagulation factor C homology) gene. In this study, we investigated a Chinese family segregating autosomal dominant nonsyndromic sensorineural hearing loss. We identified a missense mutation c.T275A p.V92D in the LCCL domain of COCH cosegregating with the disease and absent in 100 normal hearing controls. This mutation leads to substitution of the hydrophobic valine to an acidic amino acid aspartic acid. Our data enriched the mutation spectrum of DFNA9 and implied the importance for mutation screening of COCH in age related hearing loss with vestibular dysfunctions.
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40
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Abstract
In this review, we provide a description of the recent methods used for immunohistochemical staining of the human inner ear using formalin-fixed frozen, paraffin and celloidin-embedded sections. We also show the application of these immunohistochemical methods in auditory and vestibular endorgans microdissected from the human temporal bone. We compare the advantages and disadvantages of immunohistochemistry (IHC) in the different types of embedding media. IHC in frozen and paraffin-embedded sections yields a robust immunoreactive signal. Both frozen and paraffin sections would be the best alternative in the case where celloidin-embedding technique is not available. IHC in whole endorgans yields excellent results and can be used when desiring to detect regional variations of protein expression in the sensory epithelia. One advantage of microdissection is that the tissue is processed immediately and IHC can be made within 1 week of temporal bone collection. A second advantage of microdissection is the excellent preservation of both morphology and antigenicity. Using celloidin-embedded inner ear sections, we were able to detect several antigens by IHC and immunofluorescence using antigen retrieval methods. These techniques, previously applied only in animal models, allow for the study of numerous important proteins expressed in the human temporal bone potentially opening up a new field for future human inner ear research.
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41
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Pauw RJ, Huygen PLM, Collin RWJ, Cruysberg JRM, Hoefsloot LH, Kremer H, Cremers CWRJ. Phenotype Description of a Novel DFNA9/COCH Mutation, I109T. Ann Otol Rhinol Laryngol 2016; 116:349-57. [PMID: 17561763 DOI: 10.1177/000348940711600506] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objectives: This is a report of the audiological and vestibular characteristics of a Dutch DFNA9 family with a novel mutation, I109T, in the LCCL domain of COCH. Methods: From the family with the novel I109T COCH mutation, audiometric data were collected and analyzed longitudinally. Results were compared to those obtained in previously identified P51S, G88E, and G87W COCH mutation carriers. Special attention was also given to a comparison of age-related features such as progressive hearing loss and vestibular impairment. Results: A novel mutation (I109T) in COCH segregates with hearing impairment and vestibular dysfunction in the present family. Pure tone thresholds, phoneme recognition scores, and vestibular responses of the I109T mutation carriers were essentially similar to those previously established in P51S, G87W, and G88E mutation carriers. Deterioration of hearing in the I109T mutation carriers started at 43 years of age, and vestibular function deteriorated at least 7 years later. Conclusions: The phenotype associated with the novel COCH (I109T) mutation is largely similar to that associated with P51S and G88E mutation carriers. However, subtle differences in terms of onset age and rate of progression seem to exist.
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Affiliation(s)
- Robert J Pauw
- Department of Otorhinolaryngology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
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42
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Genetics of vestibular disorders: pathophysiological insights. J Neurol 2016; 263 Suppl 1:S45-53. [PMID: 27083884 PMCID: PMC4833787 DOI: 10.1007/s00415-015-7988-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 11/01/2015] [Accepted: 11/29/2015] [Indexed: 01/09/2023]
Abstract
The two most common vestibular disorders are motion sickness and vestibular migraine, affecting 30 and 1–2 % of the population respectively. Both are related to migraine and show a familial trend. Bilateral vestibular hypofunction is a rare condition, and some of patients also present cerebellar ataxia and neuropathy. We present recent advances in the genetics of vestibular disorders with familial aggregation. The clinical heterogeneity observed in different relatives of the same families suggests a variable penetrance and the interaction of several genes in each family. Some Mendelian sensorineural hearing loss also exhibits vestibular dysfunction, including DFNA9, DFNA11, DFNA15 and DFNA28. However, the most relevant finding during the past years is the familial clustering observed in Meniere’s disease. By using whole exome sequencing and combining bioinformatics tools, novel variants in DTNA and FAM136A genes have been identified in familial Meniere’s disease, and this genomic strategy will facilitate the discovery of the genetic basis of familial vestibular disorders.
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Burgess BJ, O'Malley JT, Kamakura T, Kristiansen K, Robertson NG, Morton CC, Nadol JB. Histopathology of the Human Inner Ear in the p.L114P COCH Mutation (DFNA9). Audiol Neurootol 2016; 21:88-97. [PMID: 27023102 DOI: 10.1159/000443822] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/04/2016] [Indexed: 01/05/2023] Open
Abstract
The histopathology of the inner ear in a patient with hearing loss caused by the p.L114P COCH mutation and its correlation with the clinical phenotype are presented. To date, 23 COCH mutations causative of DFNA9 autosomal dominant sensorineural hearing loss and vestibular disorder have been reported, and the histopathology of the human inner ear has been described in 4 of these. The p.L114P COCH mutation was first described in a Korean family. We have identified the same mutation in a family of non-Asian ancestry in the USA, and the temporal bone histopathology and clinical findings are presented herein. The histopathology found in the inner ear was similar to that shown in the 4 other COCH mutations and included degeneration of the spiral ligament with deposition of an eosinophilic acellular material, which was also found in the distal osseous spiral lamina, at the base of the spiral limbus, and in mesenchymal tissue at the base of the vestibular neuroepithelium. This is the first description of human otopathology of the COCH p.L114P mutation. In addition, it is the only case with otopathology characterization in an individual with any COCH mutation and residual hearing, thus allowing assessment of primary histopathological events in DFNA9, before progression to more profound hearing loss. A quantitative cytologic analysis of atrophy in this specimen and immunostaining using anti-neurofilament and anti-myelin protein zero antibodies confirmed that the principal histopathologic correlate of hearing loss was degeneration of the dendritic fibers of spiral ganglion cells in the osseous spiral lamina. The implications for cochlear implantation in this disorder are discussed.
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Affiliation(s)
- Barbara J Burgess
- Human Otopathology Laboratory, Department of Otolaryngology, Massachusetts Eye and Ear Infirmary, Boston, Mass., USA
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Distinct vestibular phenotypes in DFNA9 families with COCH variants. Eur Arch Otorhinolaryngol 2016; 273:2993-3002. [PMID: 26758463 DOI: 10.1007/s00405-015-3885-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/26/2015] [Indexed: 10/22/2022]
Abstract
Mutations of COCH can cause hearing loss and less frequently vestibular symptoms. However, vestibular phenotypes, especially in terms of the location of specific variants are not well documented yet. In this study, a retrospective and prospective cohort survey was performed in two tertiary referral hospitals to demonstrate vestibular phenotypes of DFNA9 subjects with a focus on the relationship with the location of COCH mutations. Two DFNA9 subjects were recruited from the previously collected cohort, each segregating p.G38D and p.C162Y of the COCH gene. Another two DFNA9 families were newly detected by targeted resequencing of known 129 deafness genes (TRS-129). These two families segregated the p.G38D variant of the COCH gene as the causative mutation, making p.G38D the most frequent COCH mutation in our Korean cohorts. Regarding the detailed clinical phenotype of the four DFNA9 families with documented vestibular phenotypes, we were able to classify them into two groups: one (p.C162Y variant) with a Meniere's disease (MD)-like phenotype and the other three (p.G38D variant) with significant bilateral vestibular loss without any definite MD symptoms. Distinct vestibular phenotypes depending on the location of COCH mutations were demonstrated, and this study correlates a genotype of p.G38D in COCH to the phenotype of bilateral total vestibular loss, therefore expanding the vestibular phenotypic spectrum of DFNA9 to range from bilateral vestibular loss without episodic vertigo to MD-like features with devastating episodic vertigo. In addition, the p.G38D variant of the COCH gene is suggested to be a frequent cause of progressive audiovestibular dysfunction in Koreans eventually requiring cochlear implantation.
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Alawieh A, Mondello S, Kobeissy F, Shibbani K, Bassim M. Proteomics studies in inner ear disorders: pathophysiology and biomarkers. Expert Rev Proteomics 2015; 12:185-96. [PMID: 25795149 DOI: 10.1586/14789450.2015.1024228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Although proteomics has been exploited in a wide range of diseases for identification of biomarkers and pathophysiological mechanisms, there are still biomedical disciplines such as otology where proteomics platforms are underused due to technical challenges and/or complex features of the disease. Thus, in the past few years, healthcare and scientific agencies have advocated the development and adoption of proteomic technologies in otological research. However, few studies have been conducted and limited literature is available in this area. Here, we present the state of the art of proteomics in otology, discussing the substantial evidence from recent experimental models and clinical studies in inner-ear conditions. We also delineate a series of critical issues including minute size of the inner ear, delicacy and poor accessibility of tissue that researchers face while undertaking otology proteomics research. Furthermore, we provide perspective to enhance the impact and lead to the clinical implementation of these proteomics-based strategies.
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Affiliation(s)
- Ali Alawieh
- Department of Neurosciences, Medical University of South Carolina, Charleston, SC 29425, USA
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Masuda M, Mutai H, Arimoto Y, Nakano A, Matsunaga T. A novel frameshift variant of COCH supports the hypothesis that haploinsufficiency is not a cause of autosomal dominant nonsyndromic deafness 9. Biochem Biophys Res Commun 2015; 469:270-4. [PMID: 26631968 DOI: 10.1016/j.bbrc.2015.11.106] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 11/23/2015] [Indexed: 11/25/2022]
Abstract
COCH (coagulation factor C homology) encodes cochlin, and certain mutations of COCH cause autosomal dominant nonsyndromic deafness 9 (DFNA9). Hearing loss due to COCH mutation begins in adulthood, and 17 missense mutations and two in-frame mutations have been reported. Studies with animal and cellular models have suggested that the underlying biological mechanism of DFNA9 is the dominant-negative effect of mutated COCH and not haploinsufficiency. However, no human cases of DFNA9 that support this hypothesis have been reported. The proband of the present case was an 18-year-old male with congenital or infantile hearing loss. Targeted next-generation sequencing analysis detected a heterozygous novel frameshift mutation of COCH (c.146dupT, p.C50LfsX8) in the proband, whose hearing loss began earlier than what is typical for DFNA9. His mother also carried the mutation but had normal hearing. Consequently, the mutation was not considered to be the cause of the proband's hearing loss. This family is the first case of a truncating COCH variant and supports the hypothesis that COCH haploinsufficiency is not the cause of hearing loss in humans.
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Affiliation(s)
- Masatsugu Masuda
- Laboratory of Auditory Disorders, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka Meguro-ku, Tokyo 152-8902, Japan; Department of Otolaryngology, School of Medicine, Kyorin University, 6-20-2 Shinkawa, Mitaka-shi, Tokyo 181-8611, Japan.
| | - Hideki Mutai
- Laboratory of Auditory Disorders, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka Meguro-ku, Tokyo 152-8902, Japan.
| | - Yukiko Arimoto
- Department of Otolaryngology, Chiba Children's Hospital, 579-1 Hetacho, Midori-ku, Chiba-shi, Chiba 266-0007, Japan.
| | - Atsuko Nakano
- Department of Otolaryngology, Chiba Children's Hospital, 579-1 Hetacho, Midori-ku, Chiba-shi, Chiba 266-0007, Japan.
| | - Tatsuo Matsunaga
- Laboratory of Auditory Disorders, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka Meguro-ku, Tokyo 152-8902, Japan; Medical Genetics Center, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka Meguro-ku, Tokyo 152-8902, Japan.
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47
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Bae SH, Robertson NG, Cho HJ, Morton CC, Jung DJ, Baek JI, Choi SY, Lee J, Lee KY, Kim UK. Identification of pathogenic mechanisms of COCH mutations, abolished cochlin secretion, and intracellular aggregate formation: genotype-phenotype correlations in DFNA9 deafness and vestibular disorder. Hum Mutat 2015; 35:1506-1513. [PMID: 25230692 DOI: 10.1002/humu.22701] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 09/08/2014] [Indexed: 11/06/2022]
Abstract
Mutations in COCH (coagulation factor C homology) cause autosomal-dominant nonsyndromic hearing loss with variable degrees of clinical onset and vestibular malfunction. We selected eight uncharacterized mutations and performed immunocytochemical and Western blot analyses to track cochlin through the secretory pathway. We then performed a comprehensive analysis of clinical information from DFNA9 patients with all 21 known COCH mutations in conjunction with cellular and molecular findings to identify genotype-phenotype correlations. Our studies revealed that five mutants were not secreted into the media: two von Willebrand factor A (vWFA) domain mutants, which were not transported from the endoplasmic reticulum to Golgi complex and formed high-molecular-weight aggregates in cell lysates, and three LCCL domain mutants, which were detected as intracellular dimeric cochlins. Mutant cochlins that were not secreted and accumulated in cells result in earlier age of onset of hearing defects. In addition, individuals with LCCL domain mutations show accompanying vestibular dysfunction, whereas those with vWFA domain mutations exhibit predominantly hearing loss. This is the first report showing failure of mutant cochlin transport through the secretory pathway, abolishment of cochlin secretion, and formation and retention of dimers and large multimeric intracellular aggregates, and high correlation with earlier onset and progression of hearing loss in individuals with these DFNA9-causing mutations.
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Affiliation(s)
- Seung-Hyun Bae
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea.,School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program), Kyungpook National University
| | - Nahid G Robertson
- Department of Obstetrics & Gynecology, Brigham & Women's Hospital, Boston, MA, USA
| | - Hyun-Ju Cho
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea
| | - Cynthia C Morton
- Departments of Obstetrics & Gynecology and Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, Broad Institute, Cambridge, MA, USA
| | - Da Jung Jung
- Department of Otolaryngology, College of Medicine, Kyungpook National University, Daegu, South Korea
| | - Jeong-In Baek
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Soo-Young Choi
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jaetae Lee
- Department of Nuclear Medicine, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Kyu-Yup Lee
- Department of Otolaryngology, College of Medicine, Kyungpook National University, Daegu, South Korea
| | - Un-Kyung Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea.,School of Life Sciences, KNU Creative BioResearch Group (BK21 plus program), Kyungpook National University
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48
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Alberts BBGT, Selen LPJ, Verhagen WIM, Medendorp WP. Sensory substitution in bilateral vestibular a-reflexic patients. Physiol Rep 2015; 3:3/5/e12385. [PMID: 25975644 PMCID: PMC4463819 DOI: 10.14814/phy2.12385] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Patients with bilateral vestibular loss have balance problems in darkness, but maintain spatial orientation rather effectively in the light. It has been suggested that these patients compensate for vestibular cues by relying on extravestibular signals, including visual and somatosensory cues, and integrating them with internal beliefs. How this integration comes about is unknown, but recent literature suggests the healthy brain remaps the various signals into a task-dependent reference frame, thereby weighting them according to their reliability. In this paper, we examined this account in six patients with bilateral vestibular a-reflexia, and compared them to six age-matched healthy controls. Subjects had to report the orientation of their body relative to a reference orientation or the orientation of a flashed luminous line relative to the gravitational vertical, by means of a two-alternative-forced-choice response. We tested both groups psychometrically in upright position (0°) and 90° sideways roll tilt. Perception of body tilt was unbiased in both patients and controls. Response variability, which was larger for 90° tilt, did not differ between groups, indicating that body somatosensory cues have tilt-dependent uncertainty. Perception of the visual vertical was unbiased when upright, but showed systematic undercompensation at 90° tilt. Variability, which was larger for 90° tilt than upright, did not differ between patients and controls. Our results suggest that extravestibular signals substitute for vestibular input in patients’ perception of spatial orientation. This is in line with the current status of rehabilitation programs in acute vestibular patients, targeting at recognizing body somatosensory signals as a reliable replacement for vestibular loss.
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Affiliation(s)
- Bart B G T Alberts
- Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour, Montessorilaan 3, 6525HR, Nijmegen, the Netherlands
| | - Luc P J Selen
- Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour, Montessorilaan 3, 6525HR, Nijmegen, the Netherlands
| | - Wim I M Verhagen
- Neurology, Canisius Wilhelmina Hospital, Weg Door Jonkerbos 100, 6532 SZ, Nijmegen, the Netherlands
| | - W Pieter Medendorp
- Radboud University Nijmegen Donders Institute for Brain, Cognition and Behaviour, Montessorilaan 3, 6525HR, Nijmegen, the Netherlands
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Nishio SY, Hattori M, Moteki H, Tsukada K, Miyagawa M, Naito T, Yoshimura H, Iwasa YI, Mori K, Shima Y, Sakuma N, Usami SI. Gene expression profiles of the cochlea and vestibular endorgans: localization and function of genes causing deafness. Ann Otol Rhinol Laryngol 2015; 124 Suppl 1:6S-48S. [PMID: 25814645 DOI: 10.1177/0003489415575549] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
OBJECTIVES We sought to elucidate the gene expression profiles of the causative genes as well as the localization of the encoded proteins involved in hereditary hearing loss. METHODS Relevant articles (as of September 2014) were searched in PubMed databases, and the gene symbols of the genes reported to be associated with deafness were located on the Hereditary Hearing Loss Homepage using localization, expression, and distribution as keywords. RESULTS Our review of the literature allowed us to systematize the gene expression profiles for genetic deafness in the inner ear, clarifying the unique functions and specific expression patterns of these genes in the cochlea and vestibular endorgans. CONCLUSIONS The coordinated actions of various encoded molecules are essential for the normal development and maintenance of auditory and vestibular function.
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Affiliation(s)
- Shin-Ya Nishio
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
| | - Mitsuru Hattori
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hideaki Moteki
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Keita Tsukada
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Maiko Miyagawa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
| | - Takehiko Naito
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hidekane Yoshimura
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yoh-Ichiro Iwasa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kentaro Mori
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yutaka Shima
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Naoko Sakuma
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Otorhinolaryngology and Head and Neck Surgery, Yokohama City University School of Medicine, Yokohama, Japan
| | - Shin-Ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
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Tsukada K, Ichinose A, Miyagawa M, Mori K, Hattori M, Nishio SY, Naito Y, Kitajiri SI, Usami SI. Detailed hearing and vestibular profiles in the patients with COCH mutations. Ann Otol Rhinol Laryngol 2015; 124 Suppl 1:100S-10S. [PMID: 25780252 DOI: 10.1177/0003489415573074] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
OBJECTIVES To evaluate the clinical features of Japanese DFNA9 families with mutations of the COCH gene. METHODS Mutation screening was performed using targeted next-generation sequencing (NGS) for 63 previously reported deafness genes. The progression of hearing loss and vestibular dysfunction were evaluated by pure-tone audiometry, caloric testing, cVEMP, and computed dynamic posturography. RESULTS We detected 1 reported mutation of p.G88E and 2 novel mutations of p.I372T and p.C542R. The patients with the novel mutations of p.I372T and p.C542R within the vWFA2 domain showed early onset progressive hearing loss, and the patients with the p.G88E mutation showed late onset hearing loss and acute hearing deterioration over a short period. Vestibular symptoms were reported in the patients with p.G88E and p.C542R. Vestibular testing was performed for the family with the p.G88E mutation. Severe vestibular dysfunction was observed in the proband, and the proband's son showed unilateral semicircular canal dysfunction with mild hearing loss. CONCLUSIONS Targeted exon resequencing of selected genes using NGS successfully identified mutations in the relatively rare deafness gene, COCH, in the Japanese population. The phenotype is compatible with that described in previous reports. Additional supporting evidence concerning progressive hearing loss and deterioration of vestibular function was obtained from our study.
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Affiliation(s)
- Keita Tsukada
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Aya Ichinose
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Maiko Miyagawa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kentaro Mori
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Mitsuru Hattori
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Shin-Ya Nishio
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yasushi Naito
- Department of Otorhinolaryngology, Kobe City Medical Center General Hospital, Hyogo, Japan
| | - Shin-Ichiro Kitajiri
- Department of Otolaryngology, Head and Neck Surgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Shin-Ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
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